OVER SEX RATIO en EVOLUTIE


EVOLUTIEBIOLOGIE      evolutie en natuurlijke selectie    //  evolutie  en   sex 

(Mijn (met marge  notas voorziene )  bewerkte  , uitgebreide ,  en  becommentarieerde vertalings- poging naar het Nederlands 

van Jerry Coyne blogpost   en enkele comments  op dat artikel  ( aldaar na te lezen  samen met  de naam vermelding van de reaguurders ) als bron =

Another case of individual selection trumping group selection

http://whyevolutionistrue.wordpress.com/2013/02/27/another-case-of-individual-selection-trumping-group-selection/

)

SEX RATIO en
Natuurlijke selectie
(heterosis, enz.),
in

Doug Futuyma’s Evolution (Sinauer). op pagina 319: en onder
“frequentie-afhankelijke selectie:”

valt te lezen :

” …..Waarom is de sex-ratio in vele diersoorten ongeveer fifty/fifty ? (1:1 ) (1 A )
Dit is een nogal ingewikkelde puzzel, want uit een groep-selectionistisch perspectief, kunnen we verwachten dat een overheersende vrouwelijk- sex ratio (dat wil zeggen,
= de productie van meer vrouwen dan mannen)voordelig zou zijn omdat een dergelijke populatie sneller zou kunnen groeien.
[ dergelijke overwegend vrouwelijke sex-ratio- groep zou dan andere groepen met andere ratio’s , in de plaatselijk opeenvolgende generaties van de populatie ,gaan overheersen
en of uiteindelijk de anderen kunnen wegconcurreren ].

Als de sex ratio echter evolueert door individuele selectie, en als alle vrouwen ongeveer hetzelfde aantal nakomelingen kunnen produceren tijdens hun levensloop ,
Zou dan zulk een genotype een sex ratio kunnen produceren dat geen evolutionair voordeel oplevert ten opzichte van andere sexratio’s ? ….”
(Why is the sex ratio about even (1:1) in many species of animals? This is quite a puzzle, because from a group-selectionist perspective, we might expect that a female-biased sex ratio
(i.e., production of more females than males) would be advantagesous because such a population could grow more rapidly. [JAC: such a sex-ratio-biased group would then outcompete other groups and predominate].
If sex ratio evolves by individual selection, however, and if all females have the same number of progeny, why should a genotype producing an even sex ratio have an advantage over any other? ) 
Het prille antwoord op dit vraagstuk kwam in 1930 van Ronald Fisher .
nml :
Het de  aan het individu gebonden “frequentie-afhankelijke ‘selectie die de geslachtsverhouding afdwingt.
GEDACHTENEXPERIMENT

Denk bijvoorbeeld aan een populatie waarbij vrouwen de overhand hebben , en mannen zeldzaam zijn .In die bevolking, zou een vrouw die meer mannetjes heeft geproduceert , meer kleinkinderen hebben dan andere vrouwen…M.a.w het gemiddelde voortplantingssucces van haar nakomelingen zal hoger zijn.(Stel je voor dat er slechts een mannetje is op miljoenen vrouwtjes in een populatie.

Elk mannetje zou dan grote aantallen kleinkinderen hebben : dat geld trouwens ook ook voor de mutante (?) moeder(s) die meer mannetjes produceren dan de andere vrouwtjes ,want haar “zonen ” zouden het merendeel van de  beschikbare vrouwtjes
bevruchten .

Evolutionair kan men in dit geval , verwachten dat de genen voor de mannelijke geslachts-ratio gaan toenemen in de populatie.)

Het omgekeerde zou het geval zijn als mannen overheersten in de bevolking:
maar elke “mutante” individuele productie van meer vrouwen zou echter ook meer kleinkinderen opleveren .

In beide gevallen gevallen heeft dus de zeldzamere(mutante ) sex-ratio variant wel altijd een reproductief voordeel
= elke individuele producent en drager van de zeldzamere sex-ratio variant zou een evolutionair voordeel hebben en zijn aandeel kunnen vergroten in de volgende generaties van de lokale populatie .De uitkomst (? ) is dat in de opeenvolgende generaties van een lokale (1) populatie , uiteindelijk in het sex-ratio een evenwicht (dat wil zeggen, evenveel mannen als vrouwen = 1:1 = bij veel diersoorten waargenomen als controleerbaar feit )zal moeten worden bereikt ….(2) .

Deze gedachtengang   is experimenteel getest door het variëren van geslachtsverhoudingen in soorten met drie geslachtschromosomen : de populatie ging in opeenvolgende generaties zich altijd uiteindelijk vestigen rond een 50/50 sex-ratio.

Hoewel er uitzonderingen ( zoals altijd in de biologie ) zijn op een 50/50 sex-ratio bij dieren, voldoen de meeste soorten aan de 50/50 waarde.
Dit is precies wat is te verwachten als het sex-ratio is een gevolg is van selectie op individueel niveau .
Ergo, als de twee varianten zijn in evolutionaire conflict, wat hier het geval is , wint de individuele selectie altijd .
Het is ook het antwoord op een vraag die men zich zelden stelt : waarom zijn er ongeveer evenveel vrouwen als mannen?

Ik weet van geen aanpassingen in de natuur, dat een aannemlelijker verklaring suggereert dan deze door individuele en/of kin selectie,
Maar
er zijn echter tal van aanpassingen,( zoals seks-ratio,)die gemakkelijk te verklaren zijn door individuele- en/ of kin-selectie.

Het is tijd om te stoppen met het hameren op “groep selectie ” … Althans totdat we degelijk bewijs en aanwijzingen vinden dat dit mechanisme heeft gewerkt in de natuur.
We hebben geen tijd te verliezen door te blijven hangen in discussies rond theoretisch plausibele maar hooguit zelden optredende mechanismen (indien ze al optreden ) en waarvoor er vooral (nog)geen voldoende bewijs
aanwezig is ….

_______________________________________________________________
OPMERKINGEN EN NOTEN

°” er zijn zoals altijd in de biologie vele uitzonderingen ;”

°¨°
Dit maakt misschien hermafrodieten begrijpelijker. ?  :  

( uit een recent artikel op de BBC website over zeeslakken -.
http://www.bbc.co.uk/news/science-environment-21431678

Een expert zei
” zeeslakken zijn solitair en niet in grote aantallen aanwezig in hun habitat ,
in die omstandigheden hermafrodiet zijn , is zinvol want het zorgt ervoor dat elke ontmoeting met een andere zeeslak kan leiden tot paring.

“Wat zijn echter de stadia die van hermafrodieten leiden tot het hebben van twee verschillende geslachten? ”
—-> (speculatief antwoorden )

°(Genetisch gedreven ) hormonale veranderingen tijdens de ontwikkeling (veranderingen in de deels genetisch geprogrammmeerde/gestuurde ontwikkelings-stadia ? ) zouden wel eens kunnen de oorzaak zijn …
Een embryo kan door veranderingen in hormonale evenwichten en invloeden trouwens in tweeslachtige organismen in een (anatomisch en gevoelsmatige ) vrouwelijke of mannelijke richting gezet worden
(terwijl er genetisch niets is veranderd aan de meegekregen geslachtschromosomen constellatie van de zygote )

°-de uiteindelijke differentiatie van hermafrodieten in twee geslachten, is meestal niet gunstig (zoals reeds boven aanghaald ) : maar mogelijk ook omdat “vrouwelijk zijn” (dikwijls) met zich meebrengt om extra middelen te vereisen
bij de specifieke taak die ze krijgt te vervullen in het daadwerkelijk produceren van de startlichamen ( eerste larven ) van levensvatbaar nageslacht die duidelijk meer voedselverwerven , opeisen ….
Wisseling van geslacht tijdens de levensloop( zowel vader als moeder tijdens verschillende levensfasen ) komt ook voor
¨°°
Wohlbachia bacterieen zijn dikwijls de oorzaak van verstoorde sex ratio’s bij arthropoden
Wanneer de effekten van wolhkbachia bacterieen door de evolutie geneutraliseerd worden dan stijgen opnieuw de sex ratio’s naar normalere waarden …

http://www.kennislink.nl/publicaties/vlinders-houden-van-mannen

Mannelijk exemplaar van de vlindersoort Hyoplimnas bolina; in het juiste licht gloeien lichtblauwe plekken op de vleugels op.
bron: Sylvain Charlat / Science.

A male Hypolimnas bolina, or blue moon, butterfly

The bacteria selectively kills male “blue moons” before they can hatch

Wohlbachia infections neutralised
http://news.bbc.co.uk/2/hi/science/nature/6896753.stm

Leo Beukeboom ; evolutie van geslachtsbepalingsystemen bij insekten
http://edepot.wur.nl/51651
(1A) frequentie afhankelijkheid argument gaat als een 1:1 sex ratio voorpelling slechts op , voor het moment van de gemiddeld meest optimale periode van de voortplanting in de levensloop stadia van de specimen van een soort
en niet de verhouding op het moment van de “geboorte” …..uiteraard is dat altijd het geval bij geslachtsdieren (imago= bij bijvoorbeeld de insekten )die men kan beschouwen als pas geborenen terwijl de larven de
embryonalee volvreet-stadia vertegenwoordigen ….. Sommige imago”s eten zelf niet meer …..
Dergelijke ratio gaat natuurlijk ook niet op wanneer men een telling doet NA het paarseizoen in cannabalistische soorten (bidsprinkhanen , spinnen )
° Het opvreten van mannetjes na de paring levert bovendien de wijfjes extra bonus -voeding
___en later op het seizoen ook minder voedselconcurentie ….

°
(1)
°Alle ” fitness criteria ” zijn lokaal
( in andere omstandigheden/omgevingen kan een “voordeel” een “nadeel “worden en vice versa )

 °
(2)
en dat zou nog worden vergemakkelijkt als er uiteindelijk geen zeldzamere sex varianten meer zouden worden geproduceerd (wat niet zo meteen voor de hand liggend is want mutaties zijn produkten een oncontroleerbaar toeval- proces )
Wat echter wel kan is dat die varianten ( door bijvoorbeeld sociohormonen= denk aan mieren ) worden onderdrukt of geelimineerd ) en/of de vrouwelijke voortplantingsfuncties slechts toegelaten worden tot ontwikkeling te komen in enkele individuen
( de uitzwermende jonge “maagdelijke ” koninginnen en kortlevende mannetjes die sterven na de bruidsvlucht ) ___ wat de kans op mutanten alweer verlaagt omdat er minder geslachtsdieren zijn dan steriel gehouden vrouwtjes in een kolonie
( waarschijnlijk zal de regerende koningin chemische boodschappers produceren die dat verwezenlijken ) ____
ofwel
dat ” een nieuw opduikend ” mutant sexratio dragend individu ” geen reproductief voordeel meer heeft (bijvoorbeeld niet meer aan bod komt of tijdig wordt geelimineerd of gefnuikt ( chemisch en/of fysisch gesteriliseert ) voordat het
zich voortplant )
Maar dat is een ander verhaal

http://en.wikipedia.org/wiki/Sex_ratio#Sex_ratio_theory

Evolution of sex ratio
http://www.tb.ethz.ch/education/model/sexratio
•Download the reader describing the model.
•Download and run the R script for the model.

°

Lethal combat and sex ratio evolution in a paristoid wasp
http://www.zoo.ox.ac.uk/group/west/pdf/Innocent_etal_07.pdf

°

VERVROUWELIJKING VAN MANNETJES   VAN  RIVIER ORGANISMEN  

Verstoringen in de sex ratio’s  van  riviervissen (o.a. vervrouwelijking van mannelijke dieren  )door (vermoedelijke )   loozing (via rioolwater )van hormonen (o.a.   oestrogenen ….) gebruikt in de “pil” waarvan restanten  in de  urine van  vrouwen de eerste oorzaak zijn    ?

http://www.stowa.nl/Upload/publicaties/2009-38_webversie.pdf

 
°
2007
( De Standaard )
 
 
 
…….Mannelijke vissen in Vlaanderen vertonen tekenen van vervrouwelijking. Dat blijkt uit een onderzoek in opdracht van de Vlaamse Milieumaatschappij (VMM) bij blankvoorns op 36 meetplaatsen verspreid over Vlaanderen. De VMM voerde van begin 2006 tot medio 2007 onderzoek naar de ecologische effecten van hormoonverstoring.
 
blankvoorn.jpg
 
 
Mannelijke vissen vertonen tekenen van vervrouwelijking
 
 
blankvoorn                Rutilus rutilus
De kleur van de blankvoorn is afhankelijk van de omgeving waarin hij leeft 
 
 
 
 
 
 
Bij gevangen mannelijke blankvoorns werd vitellogenine (VTG) gemeten in het bloed, een dooiereiwit dat normaal alleen door vrouwelijke blankvoorns wordt aangemaakt’, weet de VMM. Ongeveer de helft van de blankvoorns bleken in hun mannelijke geslachtsorganen ook eicellen aan te maken.‘Het is opmerkelijk, maar het is wel de eerste maal dat we dergelijke cijfers in Vlaanderen vaststellen’, legt Mie Van den Kerchove, woordvoerster bij VMM, uit.
 
‘Iets, een bepaalde stof of cocktail van stoffen in ons oppervlaktewater moet die effecten veroorzaken, ook al weten we op dit moment nog niet precies hoe het in mekaar zit’, aldus de woordvoerster.Toch is het resultaat geen echte verrassing
. ‘In onze buurlanden is dit soort onderzoek al gevoerd, met vergelijkbare resultaten’, zegt Van den Kerchove. Onderzoek toont daar aan dat er meer hormoonverstoring optreedt op plaatsen waar ruw huishoudelijk afvalwater geloosd wordt in oppervlaktewater.In het onderzoek bleek de verhoogde oestrogene activiteit op alle meetplaatsen voor te komen.
De vervrouwelijkte blankvoorns zijn vermoedelijk steriel ( ze zijn dus  individueel  uitgeschakeld als deelnemers aan  de genenpoel-verzameling   van  de toekomstige generaties van hun populatie(s ) 
 
 
De vervrouwelijking   van een aantal vis– en kikkersoorten staat intussen wel onomstotelijk vast.
 
 
___________________________________________________________________________________________________
 
 
 
*Zie ook over group selection :
 
 
 
_______________________________________________________________________________________________________
APPENDIX 
 
°
_andere citaten  uit Doug Futuyma’s Evolution (Sinauer)
 Cover Image
 
 
Doug Futuyma’s Evolution (second edition, Sinauer).
 
 

Chapter 1 Summary

  1. Evolution is the unifying theory of the biological sciences. Evolutionary biology aims to discover the history of life and the causes of the diversity and characteristics of organisms.
  2. Darwin’s evolutionary theory, published in The Origin of Species in 1859, consisted of two major hypotheses: first, that all organisms have descended, with modification, from common ancestral forms of life, and second, that a chief agent of modification is natural selection.
  3. Darwin’s hypothesis that all species have descended with modification from common ancestors is supported by so much evidence that it has become as well established a fact as any in biology. His theory of natural selection as the chief cause of evolution was not broadly supported until the “evolutionary synthesis” that occurred in the 1930s and 1940s.
  4. The evolutionary theory developed during and since the evolutionary synthesis consists of a body of principles that explain evolutionary change. Among these principles are (a) that genetic variation in phenotypic characters arises by random mutation and recombination; (b) that changes in the proportions of alleles and genotypes within a population may result in replacement of genotypes over generations; (c) that such changes in the proportions of genotypes may occur either by random fluctuations (genetic drift) or by nonrandom, consistent differences among genotypes in survival or reproduction rates (natural selection); and (d) that as a result of different histories of genetic drift and natural selection, populations of a species may diverge and become reproductively isolated species.
  5. Evolutionary biology makes important contributions to other biological disciplines and to social concerns in areas such as medicine, agriculture, computer science, and our understanding of ourselves.
  6. The implications of Darwin’s theory, which revolutionized Western thought, include the ideas that change rather than stasis is the natural order; that biological phenomena, including those seemingly designed, can be explained by purely material causes rather than by divine creation; and that no evidence for purpose or goals can be found in the living world, other than in human actions.
  7. Like other sciences, evolutionary biology cannot be used to justify beliefs about ethics or morality. Nor can it prove or disprove theological issues such as the existence of a deity. Many people hold that, although evolution is incompatible with a literal interpretation of some passages in the Bible, it is compatible with religious belief.

Chapter 2 Summary

  1. A phylogeny is the history by which species or other taxa have successively originated from common ancestors. It may be depicted by a phylogenetic tree, in which each branch point represents the division of an ancestral species into two lineages. Closely related species have more recent common ancestors than distantly related species. A group of species descended from a particular common ancestor is a monophyletic group; a phylogenetic tree portrays nested sets of monophyletic groups. Phylogenetic trees, estimated from the characteristics of the taxa, represent evolutionary relationships and provide a framework for analyzing many aspects of evolution.
  2. Overall similarity among organisms is not the best indicator of phylogenetic relationships. Two species may be more similar to each other than to a third because they retain ancestral character states (whereas the third has diverged), because they independently evolved similar character states (homoplasy), or because they share derived character states that evolved in their common ancestor. Only unique shared derived character states are evidence of phylogenetic relationship. Thus a monophyletic group is marked by uniquely derived character states shared by the group’s members.
  3. Phylogenetic relationships can be obscured by different rates of evolution among lineages and by homoplasy. Several methods are used to estimate phylogenies in the face of these misleading features. The method of maximum parsimony is frequently used, according to which the best estimate of the phylogeny is the tree that requires one to postulate the smallest number of evolutionary changes to account for the differences among species. Some other methods are sometimes more reliable.
  4. A phylogenetic tree is a statement about evolutionary relationships, and like all scientific statements, it is a hypothesis. We gain confidence in the validity of the hypothesis when new data, such as different characters, support it. Uncertainties remain about the phylogenetic relationships among many taxa, but there are also many well-supported phylogenies.
  5. Molecular data are increasingly used to infer phylogenies. The rate of evolution of DNA sequences can be shown in some cases to be fairly constant (providing a “molecular clock”), such that sequences in different lineages diverge at a roughly constant rate. The absolute rate of sequence evolution can sometimes be calibrated if fossils of some lineages are known. This rate, in turn, can be used to estimate the absolute age of some evolutionary events, such as the origin of other taxa.
  6. Evolutionary processes may make it difficult to infer phylogenetic relationships. For example, shared derived character states may be erased by subsequent evolution, as when successive base pair substitutions occur at the same site in a DNA sequence. If multiple lineages originate from a common ancestor within a short time, the relationships among them may be unresolved because there was not enough time for derived character states to evolve between successive branching events. An accurately estimated phylogeny of genes (DNA sequences) from different species may differ from the phylogeny of the species themselves. With enough data, these difficulties can usually be surmounted.
  7. A phylogeny must consider more than just the branching pattern if some species have originated by hybridization between different ancestral species, or if there has been horizontal (lateral) transfer of some genes among different lineages. Such phenomena may be suspected if different genes imply different branching phylogenies.

Chapter 3 Summary

  1. Most traditional classifications of organisms have been devised to reflect both branching (phylogeny) and phenotypic divergence. Many contemporary systematists adopt the “cladistic position” that classification should explicitly reflect phylogenetic relationships, and that all higher taxa should be monophyletic.
  2. Phylogenetic analyses have many uses in addition to describing the branching history of life. An important one is inferring the history of evolution of interesting characteristics by parsimoniously “mapping” changes in character states onto a phylogeny that has been derived from other data. Such systematic studies have yielded information on common patterns and principles of character evolution.
  3. New features almost always evolve from pre-existing characters.
  4. Homoplasy, which is common in evolution, is often a result of similar adaptations in different lineages. It includes convergent evolution, parallel evolution, and reversal.
  5. For the most part, different characters evolve piecemeal, at different rates. Conservative characters are those that are retained with little or no change over long time periods; other characters may evolve rapidly and vary widely across a single lineage. This phenomenon is called mosaic evolution.
  6. Differences among related species illustrate that large differences often evolve gradually, by small steps. Although this pattern is common, it may not be universal.
  7. Changes in structure are often associated with change in a character’s function. Different structures may be modified to serve similar functions in different lineages.
  8. The evolution of morphological features involves changes in their development. Such evolutionary changes include individualization of repeated structures, alterations in the timing (heterochrony) or site (heterotopy) of developmental events, and increases and decreases in structural complexity. Heterochrony can result in changes in the shape of features, often because of allometric growth.
  9. Trends in the evolution of a character may be documented by phylogenetic analysis. Evolutionary trends may occur within a single lineage or repeatedly among different lineages.
  10. In an adaptive radiation, numerous related lineages arise in a relatively short time and evolve in many different directions as they adapt to different habitats or ways of life. Radiation is perhaps the most common pattern of long-term evolution.
  11. Phylogenetic and comparative studies also reveal many aspects of the evolution of genes and genomes, such as changes in the amount of DNA, the number of genes, and the origin of new genes by gene duplication.

Chapter 4 Summary

  1. Although many evolutionary histories are well known, the fossil record of most lineages of organisms is very incomplete.
  2. Unusually detailed records of change within individual species show that although characters commonly remain relatively unchanged for long periods, when changes do occur they are rapid and may pass gradually through intermediate steps.
  3. The origins of many higher taxa, such as tetrapods, birds, mammals, cetaceans, and the genus Homo, have been documented in the fossil record. These examples show mosaic evolution and gradual change in individual features. The decision of whether to classify intermediate fossils in one taxon or another is often arbitrary.
  4. Changes in the form of characters are sometimes associated with major changes in their function.
  5. The relative times of origin of taxa, as inferred from phylogenetic analysis, often correspond to their relative times of appearance in the fossil record.
  6. Evolutionary trends, which can often be attributed to natural selection, are evident in the fossil record, but such trends may be reversed in related lineages.
  7. Species may display very little change for long periods (stasis), and then shift rapidly to new phenotypes. The term “punctuated equilibria” refers both to this pattern and to the hypothesis, not widely accepted, that most changes in morphology occur in association with the evolution of new species (i.e., splitting of lineages).

Chapter 5 Summary

  1. Evidence from living organisms indicates that all living things are descended from a single common ancestor. Some progress has been made in understanding the origin of life, but a great deal remains unknown.
  2. The first fossil evidence of life dates from about 3.5 billion years ago, about a billion years after the formation of the Earth. The earliest life forms of which we have evidence were prokaryotes.
  3. Eukaryotes evolved about 1.5 billion years ago. Their mitochondria and chloroplasts evolved from endosymbiotic bacteria.
  4. The fossil record displays an explosive diversification of the animal phyla near the beginning of the Cambrian period, about 542 Mya. The causes of this rapid diversification are debated, but may include a combination of genetic and ecological events.
  5. Terrestrial plants evolved in the Ordovician, and terrestrial arthropods in the late Silurian; amphibians evolved in the late Devonian from lobe-finned fishes.
  6. The most devastating mass extinction of all time occurred at the end of the Permian (about 252 Mya). It profoundly altered the taxonomic composition of the Earth’s biota.
  7. Seed plants and amniotes (“reptiles”) became diverse and ecologically dominant during the Mesozoic era (251–65.5 Mya). Flowering plants and plant-associated insects diversified greatly from the middle of the Cretaceous onward. A mass extinction (the “K/T extinction”) at the end of the Mesozoic included the extinction of the last nonavian dinosaurs.
  8. Most orders of placental mammals probably originated in the late Cretaceous, but underwent adaptive radiation in the early Tertiary (about 65.5–50 Mya). It is possible that the extinction of nonavian dinosaurs permitted them to diversify.
  9. The climate became drier during the Cenozoic era, favoring the development of grasslands and the evolution of herbaceous plants and grassland-adapted animals.
  10. A series of glacial and interglacial episodes occurred during the Pleistocene (the last 1.8 Myr), during which some extinctions occurred and the distributions of species were greatly altered.
  11. With the passage of time, the composition of the Earth’s biota has become increasingly similar to its composition today.

Chapter 6 Summary

  1. The geographic distributions of organisms provided Darwin and Wallace with some of their strongest evidence for the reality of evolution.
  2. Biogeography, the study of organisms’ geographic distributions, has both historical and ecological components. Certain distributions are the consequence of long-term evolutionary history; others are the result of contemporary ecological factors.
  3. The historical processes that affect the distribution of a higher taxon include extinction, dispersal, and vicariance (fragmentation of a continuous distribution by the emergence of a barrier). These processes may be affected or accompanied by environmental change, adaptation, and speciation.
  4. Histories of dispersal or vicariance can often be inferred from phylogenetic data. When a pattern of phylogenetic relationships among species in different areas is repeated for many taxa, a common history of vicariance is likely.
  5. Disjunct distributions are attributable in some instances to vicariance and in others to dispersal.
  6. Genetic patterns within species, especially phylogenetic relationships among genes that characterize different geographic populations, can provide information on historical changes in a species’ distribution. Studies of this kind are illuminating the origin and spread of human populations.
  7. The local distribution of species is affected by ecological factors, including both abiotic aspects of the environment and biotic features such as competitors and predators. Why species do not enlarge their range indefinitely, by incrementally adapting to conditions farther and farther away, is a major question in evolutionary ecology.
  8. In some cases, sets of species have independently evolved to partition resources in similar ways, suggesting that competition may limit species diversity and may result in different communities with a similar structure. However, convergence of community structure is usually incomplete, suggesting that evolutionary history has had an important impact on ecological assemblages.
  9. Geographic patterns in the number and diversity of species may stem partly from current ecological factors, but they probably cannot be understood without recourse to long-term evolutionary history.

Chapter 7 Summary

  1. Analyses of diversity in the fossil record require procedures to correct for biases caused by the incompleteness of the record.
  2. The diversity of skeletonized marine animals has increased during the Phanerozoic, but some aspects are uncertain. By direct count of numbers of taxa at each geological stage, diversity appears to have increased in the Cambrian to an approximate equilibrium that lasted for almost two-thirds of the Paleozoic; then, after a mass extinction at the end of the Permian, it appears to have increased (with interruptions) since the beginning of the Mesozoic, accelerating in the Cenozoic. Terrestrial plants and vertebrates show a similar pattern, except that their diversity was relatively stable for much of the Mesozoic. By the Pliocene, the diversity of families and lower taxa was apparently higher than ever before in the history of life. However, recent analyses that account for biases suggest considerably lower post-Permian increases.
  3. The “background” rate of extinction (in between mass extinctions) declined during the Phanerozoic, perhaps because higher taxa that were particularly prone to extinction became extinct early.
  4. Five major mass extinctions (at the ends of the Ordovician, Devonian, Permian, Triassic, and Cretaceous), as well as several less pronounced episodes of heightened extinction rates, are recognized. Although the cause of the incomparably devastating end-Permian extinction is unknown, it may have been the result of a rapid episode of major environmental changes initiated by the volcanic release of vast quantities of lava. The impact of a large extraterrestrial body at the end of the Cretaceous may have caused the extinction of many taxa, including the last of the nonavian dinosaurs.
  5. Broad geographic and ecological distributions, rather than adaptation to “normal” conditions, enhanced the likelihood that taxa would survive mass extinctions. The diversification of many of the surviving lineages was probably released by extinction of other taxa that had occupied similar adaptive zones. Newly diversifying groups have sometimes displaced other taxa by direct competitive exclusion, but more often they have replaced incumbent taxa after these became extinct.
  6. The increase in diversity over time appears to have been caused mostly by adaptation to vacant or underused ecological niches (“ecological space”), often as a consequence of the evolution of key adaptations, and by increasing provinciality (differentiation of the biota in different geographic regions) owing to the separation of land masses in the Mesozoic and Cenozoic and the consequent development of greater latitudinal variation in climate.
  7. The rates of both extinction and origination of taxa have been diversity-dependent. Such observations imply that diversity tends toward an equilibrium. However, an equilibrium can change over geological time because of changes in climates and the configuration of continents, and because organisms evolve new ways of using habitats and resources.
  8. Differences among taxa in contemporary species richness are attributable to different rates of diversification in some cases, and simply to differences in clade age in others.

Chapter 8 Summary

  1. Mutations of chromosomes or genes are alterations that are subsequently replicated. They ordinarily do not constitute new species, but instead are variant chromosomes or genes (alleles, haplotypes) within a species.
  2. At the molecular level, mutations of genes include base pair substitutions, frameshifts, changes caused by insertion of various kinds of transposable elements, and duplications and deletions that can range from single base pairs to long segments of chromosome. New DNA sequences also arise by intragenic recombination.
  3. Mutations that result in amino acid substitution in a protein (nonsynonymous mutations) and mutations in regulatory sequences may affect the phenotype and perhaps fitness. Synonymous mutations, those that do not alter the amino acid sequence, may not affect the phenotype or fitness, and so may be selectively neutral. The extent to which mutations in noncoding DNA, which dominates eukaryotic genomes, affect fitness is largely unknown.
  4. The rate at which any particular mutation arises is quite low: on average, about 10–6 to 10–5 per gamete for mutations detected by their phenotypic effects, and about 10–9 per base pair. The mutation rate, by itself, is too low to cause substantial changes of allele frequencies. However, the total input of genetic variation by mutation, for the genome as a whole or for individual polygenic characters, is appreciable.
  5. The magnitude of change in morphological or physiological features caused by a mutation can range from none to drastic. In part because most mutations have pleiotropic effects, the average effect of mutations on fitness is deleterious, but some mutations are advantageous.
  6. Mutations alter pre-existing biochemical or developmental pathways, so not all conceivable mutational changes are possible. Some adaptive changes may not be possible without just the right mutation of just the right gene. For these reasons, the rate and direction of evolution may in some instances be affected by the availability of mutations.
  7. Mutations appear to be random, in the sense that their probability of occurrence is not directed by the environment in favorable directions, and in the sense that specific mutations cannot be predicted. The likelihood that a mutation will occur does not depend on whether or not it would be advantageous.
  8. Mutations of the karyotype (chromosome complement) include polyploidy and structural rearrangements (e.g., inversions, translocations, fissions, fusions). Many such rearrangements reduce fertility in the heterozygous condition.

Chapter 9 Summary

  1. Evolution occurs by the replacement of some genotypes by others. Hence evolution requires genetic variation.
  2. The all-important concepts of allele frequency and genotype frequency are central to the Hardy-Weinberg principle, which states that in the absence of perturbing factors, allele and genotype frequencies remain constant over generations. For two alleles with frequencies p and q at an autosomal locus, the Hardy-Weinberg genotype frequencies are in the ratio p2:2pq:q2.
  3. The potential causes of allele frequency changes at a single locus are those factors that can cause deviations from the Hardy-Weinberg equilibrium. These factors are (a) nonrandom mating; (b) finite population size, resulting in random changes in allele frequencies (genetic drift); (c) incursion of genes from other populations (gene flow); (d) mutation; and (e) consistent differences among genes or genotypes in reproductive success (natural selection).
  4. Inbreeding occurs when related individuals mate and have offspring. Inbreeding increases the frequency of homozygous genotypes and decreases the frequency of heterozygotes. Most diploid populations contain rare recessive deleterious alleles at many loci, so inbreeding causes a decline in components of fitness (inbreeding depression).
  5. Populations of most species contain a great deal of genetic variation. This variation includes rare alleles at many loci, which usually appear to be deleterious. But it also includes many common alleles, so that many loci—perhaps up to a third of them—are polymorphic, as revealed by enzyme electrophoresis. Most genes are variable when analyzed at the level of DNA sequence.
  6. Many phenotypic traits, including morphological, physiological, and behavioral features, exhibit polygenic variation.
  7. Alleles at different loci, affecting the same or different traits, sometimes are nonrandomly associated within a population, a condition called linkage disequilibrium, or LD.
  8. Variation in most phenotypic traits includes both a genetic component and a nongenetic (“environmental”) component. Variation in some traits may also include components caused by nongenetic maternal effects and epigenetic inheritance. The proportion of the phenotypic variance that is due to genetic variation (genetic variance) is the heritability of the trait. Genetic variance and heritability can be estimated by breeding experiments and by artificial selection. Many characters appear to be so genetically variable that we should expect them to be able to evolve quite rapidly.
  9. Genetic differences among different populations of a species take the form of differences in the frequencies of alleles that may also be polymorphic within populations. Unless countered by natural selection or genetic drift, gene flow among populations will cause them to become homogeneous.
  10. Patterns of allele frequency differences and the phylogeny of alleles or haplotypes can shed light on the history that gave rise to geographic variation.

Chapter 10 Summary

  1. The frequencies of alleles that differ little or not at all in their effect on organisms’ fitness (neutral alleles) fluctuate at random. This process, called random genetic drift, reduces genetic variation and leads eventually to the random fixation of one allele and the loss of others, unless it is countered by other processes, such as gene flow or mutation.
  2. Different alleles are fixed by chance in different populations.
  3. The probability, at any time, that a particular allele will be fixed in the future equals the frequency of the allele at that time. For example, if a newly arisen mutation is represented by one copy in a diploid population of N individuals, the probability that it will increase to fixation is 1/(2N).
  4. The smaller the effective size of a population, the more rapidly random genetic drift operates. The effective size is often much smaller than the apparent population size.
  5. Patterns of allele frequencies at some loci in both experimental and natural populations conform to predictions from the theory of genetic drift.
  6. The theory of genetic drift has been applied especially to variation at the molecular level. The neutral theory of molecular evolution holds that, although many mutations are deleterious, and a few are advantageous, most molecular variation within and among species is selectively neutral. The fraction of mutations that are neutral varies: it is high for proteins that lack strong functional constraints and for sequences that are not transcribed. Likewise, it is higher for synonymous than for nonsynonymous (amino acid–replacing) nucleotide substitutions.
  7. As the neutral theory predicts, synonymous mutations and mutations in less constrained genes are fixed more rapidly than those that are more likely to affect function. The neutral theory also predicts that over long spans of time, substitutions will occur at an approximately constant rate for a given gene (providing a basis for the “molecular clock”). The rate of molecular evolution, as measured by differences among species, appears to be more nearly constant for synonymous than for nonsynonymous substitutions.
  8. For neutrally evolving loci, the number of nucleotide differences among sequences increases over time as a result of new mutations, but genetic drift, leading to the loss of gene lineages, reduces genetic variation. When these factors balance, the level of sequence variation reaches equilibrium. Thus, given an estimate of the mutation rate, the level of sequence variation provides a basis for estimating the historical effective size (Ne) of a population.
  9. Applying the above principles to human genes supports the hypothesis that the human population has descended from an African population of about 10,000 breeding members, from which colonists migrated into Europe and Asia perhaps only 40 Kya.

Chapter 11 Summary

  1. A feature is an adaptation for a particular function if it has evolved by natural selection for that function by enhancing the relative rate of increase—the fitness—of biological entities with that feature.
  2. Natural selection is a consistent difference in fitness among phenotypically different biological entities, and is the antithesis of chance. Natural selection may occur at different levels, such as genes, individual organisms, populations, and species.
  3. Selection at the level of genes or organisms is likely to be the most important because the numbers and turnover rates of these entities are greater than those of populations or species. Therefore, most features are unlikely to have evolved by group selection, the one form of selection that could in theory promote the evolution of features that benefit the species even though they are disadvantageous to the individual organism.
  4. Not all features are adaptations. Methods for identifying and elucidating adaptations include studies of function and design, experimental studies of the correspondence between fitness and variation within species, and correlations between the traits of species and environmental or other features (the comparative method). Phylogenetic information may be necessary for proper use of the comparative method.
  5. Natural selection does not necessarily produce anything that we can justly call evolutionary progress. It need not promote harmony or balance in nature, and, utterly lacking any moral content, it provides no foundation for morality or ethics in human behavior.

Chapter 12 Summary

  1. Even at a single locus, the diverse genetic effects of natural selection cannot be summarized by the slogan “survival of the fittest.” Selection may indeed fix the fittest genotype, or it may maintain a population in a state of stable polymorphism, in which inferior genotypes may persist.
  2. The absolute fitness of a genotype is measured by its rate of increase, the major components of which are survival, female and male mating success, and fecundity. In sexual species, differences among gametic (haploid) genotypes may also contribute to selection among alleles.
  3. Rates of change in the frequencies of alleles and genotypes are determined by differences in their relative fitness, and are also affected by genotype frequencies and the degree of dominance at a locus.
  4. Much of adaptive evolution by natural selection consists of replacement of previously prevalent genotypes by a superior homozygote (directional selection). However, genetic variation at a locus often persists in a stable equilibrium condition, owing to a balance between selection and recurrent mutation, between selection and gene flow, or because of any of several forms of balancing selection.
  5. The kinds of balancing selection that maintain polymorphism include heterozygote advantage, inverse frequency-dependent selection, and variable selection arising from variation in the environment.
  6. Often the final equilibrium state to which selection brings a population depends on its initial genetic constitution: there may be multiple possible outcomes, even under the same environmental conditions. This is especially likely if the genotypes’ fitnesses depend on their frequencies, or if two homozygotes both have higher fitness than the heterozygote.
  7. When genotypes differ in fitness, selection determines the outcome of evolution if the population is large; in a sufficiently small population, however, genetic drift is more powerful than selection. When the heterozygote is less fit than either homozygote, genetic drift is necessary to initiate a shift from one homozygous equilibrium state to the other.
  8. Studies of variable loci in natural populations show that the strength of natural selection varies greatly, but that selection is often strong, and is thus a powerful force of evolution.
  9. Variation in DNA sequences can provide evidence of natural selection. Compared with the level of variation expected under neutral mutation and genetic drift alone, positive selection (of an advantageous mutation) causes “selective sweeps” that reduce the level of neutral variation at closely linked sites. It can also create linkage disequilibrium among neutral variants in the region of the advantageous mutation. Purifying (background) selection against deleterious mutations also reduced linked neutral variation. Balancing selection results in higher levels of linked variation than under the neutral theory. Studies of DNA sequence variation in humans and other species have provided evidence of extensive recent directional selection.
  10. Selection can also be inferred from DNA sequence comparisons among different species, as indicated by the incidence of nonsynonymous versus synonymous nucleotide substitutions.

Chapter 13 Summary

  1. Quantitative trait loci (QTL) can be mapped using molecular or other markers. The variation in many traits is caused by variation at several or many loci, some with large and others with small effects. For certain characters, some of the genes have been identified and their function is known.
  2. Variation (variance) in a phenotypic trait (VP) may include genetic variance (VG) and variance due to the environment (VE). Genetic variance may include both additive genetic variance (VA) due to the additive effects of alleles and nonadditive genetic variance due to dominance and epistasis. Only the additive variance creates a correlation between parents and offspring (and it can be measured by this correlation). Thus only VA enables response to selection.
  3. If alleles that contribute to variation in a polygenic trait are selectively neutral and change in frequency by genetic drift, the short-term rate of evolution depends on the effective population size, but the long-term rate is proportional to the rate of polygenic neutral mutation. Evolutionary rates are often lower than the neutral model predicts, implying that stabilizing selection or purifying selection has acted.
  4. The ratio VA/VP is the heritability (h2N, or simply h2) of a trait. Heritability is not fixed, but depends on allele frequencies and on the amount of phenotypic variation induced by environmental variation. The short-term effect of selection (“response” to selection) on a character can be predicted from the heritability and the strength of selection.
  5. Most, although not all, characters show substantial genetic variance in natural populations and may therefore evolve rapidly if selection pressures change. Many examples of rapid evolution, within a century or less, have been described.
  6. Artificial selection experiments show that traits can often be made to evolve far beyond the initial range of variation. The response to selection is based on both genetic variation in the original population and new mutations that occur during the experiments.
  7. Stabilizing selection is common in natural populations, either because the character is nearly at its optimum or because conflicting selection pressures or negative pleiotropic effects prevent further change.
  8. The causes of high levels of genetic variation (high VA and h2N) in natural populations are uncertain, but input by mutation may balance losses due to selection and genetic drift.
  9. Linkage disequilibrium and especially pleiotropy cause genetic correlations among characters, which, together with correlations caused by environmental factors, give rise to phenotypic correlations. The evolution of a trait is governed both by selection on that trait and by selection on other traits with which it is genetically correlated. The effect of a genetic correlation depends on its strength and degree of permanence. Genetic correlations can enhance the rate of adaptation (if functionally interdependent features show adaptive correlation), can cause a trait to evolve in a maladaptive direction (if selection on a correlated trait is strong enough), or may reduce the rate at which characters evolve toward their optimal states. It is not certain whether genetic correlations are especially strong among characters that are functionally integrated (the hypothesis of phenotypic integration).
  10. The norm of reaction—the expression of the phenotype under different environmental conditions—can evolve if genotypes vary in the degree to which the phenotype is altered by the environment in which an individual develops. Some characters exhibit adaptive phenotypic plasticity, whereas selection in other cases favors constancy of phenotype despite differences in environment.
  11. Canalization is the buffering of development against alteration by environmental or genetic variation. Canalized characters include threshold characters, in which underlying polygenic variation is not phenotypically expressed unless a drastic mutation or environmental perturbation breaks down canalization. Canalization can evolve under some circumstances. The evolution of canalization may explain the constancy of some characters over vast periods of evolutionary time.
  12. Although many characters are genetically variable and can evolve rapidly, evolution appears often to be constrained, partly because of limitations on genetic variation, some of which may be due to the origin of variation by mutation. Genetic variation appears to be rare or lacking in some traits, but more often, pleiotropic genetic correlations may be antagonistic to the direction of selection on multiple characters. Understanding genetic constraints is the key to understanding phenomena that range from phylogenetically conservative characters to extinction, both in the past and in the near future.

Chapter 14 Summary

  1. Life history features such as reproductive rates and longevity do not evolve to perpetuate the species. They can best be understood from the perspective of individual selection. Life history traits are components of the fitness of individual genotypes, the basis for natural selection.
  2. Models of the evolution of adaptive characteristics include both population genetic models and optimal models, which attempt to determine which character states might be expected to evolve under specified conditions, and under specified constraints. Optimal models include those that find the ESS (evolutionarily stable strategy) when fitness depends on the frequencies of different phenotypes among interacting individuals.
  3. The major components of fitness (the per capita rate of increase of a genotype, r) are the age-specific values of survival, female fecundity, and male mating success. Natural selection on morphological and other phenotypic characters results chiefly from the effects of the characters on these life history traits.
  4. Constraints, especially trade-offs between reproduction and survival and among the several components of reproduction such as the number and size of offspring, prevent organisms from evolving indefinitely long life spans and infinite fecundity.
  5. The effect of changes in survival (lx) or fecundity (mx) on fitness depends on the age at which such changes are expressed and declines with age. Hence selection for reproduction and survival at advanced ages is weak.
  6. Consequently, senescence (physiological aging) evolves. Senescence appears to be a result, in part, of the negative pleiotropic effects on later age classes of genes that have advantageous effects on earlier age classes.
  7. If reproduction is very costly (in terms of growth or survival), repeated (iteroparous) and/or delayed reproduction may evolve, provided that reproductive success at later ages more than compensates for the loss of fitness incurred by not reproducing earlier. Otherwise a semelparous life history, in which all of the organism’s resources are allocated to a single reproductive effort, is optimal. Iteroparity is especially likely to evolve if juvenile mortality is high relative to adult mortality and if population density is stable.
  8. Because lower fecundity and delayed reproduction can evolve, the intrinsic rate of population increase, the maximal rate of increase that is expressed at low population density, may evolve to be lower. In such populations, however, the rate of population growth is often close to zero because of density-dependent limitations.

Chapter 15 Summary

  1. Alleles that increase mutation rates are generally selected against because they are associated with the deleterious mutations they cause. Therefore, we would expect mutation rates to evolve to the minimal achievable level, even if this should reduce genetic variation and increase the possibility of a species’ extinction.
  2. Asexual populations have a high extinction rate, so sex has a group-level advantage in the long term. But this is unlikely to offset the short-term advantage of asexual reproduction.
  3. In a constant environment, alleles that decrease the recombination rate are advantageous because they lower the proportion of offspring with unfit recombinant genotypes. In addition, asexual reproduction has approximately a twofold advantage over sexual reproduction because only half of the offspring of sexuals (i.e., the females) contribute to population growth, whereas all of the (all-female) offspring of asexuals do so. Therefore, the prevalence of recombination and sex requires explanation.
  4. Among the several hypotheses for the short-term advantage of sex are: (a) in asexual populations, fitness declines because genotypes with few deleterious mutations, if lost by genetic drift, cannot be reconstituted, as they are in populations with recombination (Muller’s ratchet); (b) deleterious mutations can be more effectively purged by natural selection in sexual than in asexual populations, thus maintaining higher mean fitness; (c) recombination enables the mean of a polygenic character to evolve to new, changing optima in a fluctuating environment; (d) the rate of adaptation, by fixing combinations of advantageous mutations, may be higher in sexual than asexual populations, if the populations are large.
  5. In large, randomly mating populations, a 1:1 sex ratio is an evolutionarily stable strategy, because if the population sex ratio deviates from 1:1, a genotype that produces a greater proportion of the minority sex has higher fitness. If, however, populations are characteristically subdivided into small local groups whose offspring then colonize patches of habitat anew, a female-biased sex ratio can evolve because female-biased groups contribute a greater proportion of offspring to the population as a whole.
  6. The evolution of hermaphroditism versus dioecy (separate sexes) depends on how reproductive success via female or male function is related to the allocation of an individual’s energy or resources. Dioecy is advantageous if the reproductive “payoff” from one or the other sexual function increases disproportionately with allocation to that function.
  7. Outcrossing can be advantageous because it prevents inbreeding depression in an individual’s progeny. Conversely, self-fertilization may evolve if fewer resources need to be expended on reproduction, if an allele for selfing becomes associated with advantageous homozygous genotypes, or if selfing ensures reproduction despite low population density or scarcity of pollinators.
  8. Differences between the sexes in the size and number of gametes give rise to conflicts of reproductive interest and to sexual selection, in which individuals of one sex compete for mates (or for opportunities to fertilize eggs). The several forms of sexual selection include direct competition between males, or between their sperm, and female choice among male phenotypes.
  9. Females may prefer certain male phenotypes because of sensory bias, direct contributions of the male to the fitness of the female or her offspring, or indirect contributions to female or offspring fitness. Indirect benefits may include fathering offspring that are genetically superior with respect to mating success (“runaway sexual selection”) or with respect to components of viability (“good genes models”). Sexually selected male features may also evolve by antagonistic coevolution: selection on females to resist mating, and on males to overcome female resistance with irresistible stimuli.
  10. The evolution of reproductive effort by males is governed by similar principles as in females. Delayed maturation may evolve if larger males are more successful in attracting or competing for mates. Similar principles explain phenomena such as sequential hermaphroditism (sex change with age) and alternative mating strategies.
  11. The evolution of features of genetic systems, such as rates of mutation and recombination, sexual versus asexual reproduction, and rates of inbreeding, can usually be understood best as consequences of selection at the level of genes and individual organisms, rather than group selection.

Chapter 16 Summary

  1. Many biological phenomena result from conflict or cooperation among organisms or among genes. The evolution of most interactions can be explained best by selection at the level of individual organisms or genes.
  2. Characteristics that contribute to conflict and cooperation often evolve by frequency-dependent selection. Such features can sometimes be modeled by calculating the evolutionarily stable strategy (ESS): the phenotype that, once established, cannot be replaced by mutant phenotypes. In animals, interactions are often mediated by signals that may or may not honestly indicate the individual’s strength, potential parental caregiving, or other relevant variable.
  3. Altruism benefits other individuals and reduces the fitness of the cooperative individual, whereas cooperative behavior need not reduce the actor’s fitness. Cooperation can evolve because it is directly beneficial to the actor, although the benefit may be delayed, or by reciprocity, based on repeated interactions between individuals or on long-lasting associations in which the fitness interests of the associates are aligned. Altruism generally evolves by kin selection, based on differences among alleles or genotypes in inclusive fitness: the combination of an allele’s direct effects (on its carrier’s fitness) and its indirect effects (on other copies of the allele, borne by the carrier’s kin). Hamilton’s rule describes the condition for increase of an allele for an altruistic trait in terms of the coefficient of relationship, the benefit to the beneficiary, and the cost to the donor. Under multilevel selection, short-lived groups containing altruistic genotypes may contribute disproportionately to the entire population, but these groups generally consist of kin. Thus this form of group selection is generally the same as kin selection.
  4. Cooperative interactions, both within and between species, are often maintained in part by “policing,” or punishment of cheaters.
  5. Conflict and kin selection together affect the evolution of many interactions among family members. The genetic benefit of caring for offspring is an increase in the number of current offspring that survive. The genetic cost is the number of additional offspring that the parent could expect to have if she/he abandoned the offspring and reproduced again. Parental care is expected to evolve only if its genetic benefit exceeds its genetic cost. Whether or not one or both parents evolve to provide care can depend on the male’s confidence of paternity and on the relative cost/benefit ratio for each parent.
  6. Conflicts between parents and offspring may arise because a parent’s fitness may be increased by allocating some resources to its own survival and future reproduction, thus providing fewer resources to current offspring than would be optimal from the offspring’s point of view. This principle may be one of several reasons why in many species, parents may reduce their brood size by aborting some embryos, killing some offspring, or allowing siblicide among their offspring.
  7. Conflicts may exist among different genes in a species’ genome. For example, a gene may spread at a faster rate than other parts of the genome, engendering selection for other genes to prevent it from doing so. At loci that are transmitted through only one sex, gene-level selection favors alleles that alter the sex ratio in favor of that sex. Such alteration creates selection at other loci for suppressors that restore the 1:1 sex ratio.
  8. Other phenomena explained by genetic conflicts include genomic imprinting, which affects the expression of maternally and paternally derived alleles in mammalian embryos, and the evolution of integration among cells—the very essence of multicellular organisms.
  9. The most extreme examples of cooperation and altruism are in eusocial insects and humans. In eusocial insects, in which unmated workers rear other workers and reproductive individuals (queens and males), many interactions are governed by kin selection and by policing.
  10. The extent to which human behaviors, including social behaviors, have an evolved genetic foundation is highly controversial. It is most readily addressed in studies of traits that vary within populations. Variation in some behavioral traits, such as sexual orientation, appears to have a heritable component, but unknown environmental factors also contribute to variation. Behavioral differences among human populations appear to be attributable to nongenetic factors, including culture.
  11. Human traits that are claimed to be universal, although usually variable in expression (e.g., language, body adornment), are likely to have some genetic foundation that has evolved since our common ancestor with other apes. How trait-specific the genetic bases may be is unknown. Evolutionary psychologists propose that the brain includes many rather problem-specific psychological “modules.” Another view is that we have broad genetic predispositions, some of which are held in common with other apes (e.g., altruism toward close kin) and others of which evolved more recently by natural selection stemming from cultural environments (e.g., capacity for empathy with strangers in large societies). Cultures evolve nongenetically by processes that are partly analogous to genetic evolution, and cultural and genetic changes may influence each other. Such genetic predispositions as may constitute so-called human nature, however, do not evidently constrain or limit any groups of people more than others.

Chapter 17 Summary

  1. Many definitions of “species” have been proposed. The biological species concept (or variants of it) is the one most widely used by evolutionary biologists. It defines species by reproductive discontinuity based on differences between populations, not by phenotypic differences (although phenotypic differences may be indicators of reproductive discontinuity). Among other species concepts, the most widely adopted is the phylogenetic species concept, according to which species are sets of populations with character states that distinguish them.
  2. The biological species concept (BSC) has a restricted domain; moreover, some populations cannot be readily classified as species because the evolution of reproductive discontinuity is a gradual process. Although the BSC applies validly to allopatric populations, it is often difficult to determine whether or not such populations are distinct species.
  3. The biological differences that constitute barriers to gene exchange are many in kind, the chief distinction being between prezygotic barriers (e.g., ecological or sexual isolation) and postzygotic barriers (hybrid inviability or sterility). Some species are also isolated by postmating, prezygotic barriers (e.g., gametic isolation).
  4. Among prezygotic barriers to gene exchange, sexual (ethological) isolation is important in animals. It entails a breakdown in communication between the courting and the courted sexes, and therefore, usually, genetic divergence in both the signal and the response. The differences in male and female components are usually genetically independent.
  5. Postzygotic isolation is usually caused by differences in nuclear genes and/or structural differences in chromosomes. Genic differences that yield hybrid sterility or inviability consist of differences at two or more (usually considerably more) loci that interact disharmoniously in the hybrid. The role of chromosome differences in hybrid sterility is not well understood.
  6. Reproductive barriers evolve gradually. Hybrid sterility or inviability of the heterogametic sex (often male) usually evolves before its manifestation in the homogametic sex (often female); this is known as Haldane’s rule.
  7. Levels of molecular divergence between closely related species vary greatly, and some recently formed species cannot be distinguished by molecular markers. Some species share ancestral molecular polymorphisms. In some cases, some gene copies in one species are more closely related to gene copies in another species than to other gene copies in the same species. In such cases, the phylogeny of genes may not match the phylogeny of the species that carry the genes.
  8. Species (or semispecies) sometimes hybridize, often in hybrid zones, which in many cases are regions of contact between formerly allopatric populations. Alleles at some loci, but not others, may be introduced between hybridizing populations by gene flow, forming allele frequency clines of varying steepness. The steepness of such a cline depends on the rate of dispersal, the strength of selection, and linkage to selected loci.

Chapter 18 Summary

  1. Probably the most common mode of speciation is allopatric speciation, in which gene flow between populations is reduced by geographic or habitat barriers, allowing genetic divergence by natural selection and/or genetic drift.
  2. In vicariant allopatric speciation, a widespread species becomes sundered by a geographic barrier, and one or both populations diverge from the ancestral state.
  3. In a simple model of the evolution of reproductive isolation, complementary allele substitutions that do not reduce the fitness of heterozygotes occur at several loci in one or both populations. Epistatic interactions between alleles fixed in the two populations reduce the fitness of hybrids (postzygotic isolation). Likewise, genetic divergence may result in prezygotic isolation.
  4. Reproductive isolation in allopatric populations appears to evolve as a side effect of divergent ecological or sexual selection. Both processes require further study before their relative importance can be assessed.
  5. Prezygotic isolation evolves mostly while populations are allopatric, but may be reinforced when the populations become parapatric or sympatric.
  6. Peripatric speciation, or founder effect speciation, is a hypothetical form of allopatric speciation in which genetic drift in a small peripheral population initiates rapid evolution, and reproductive isolation is a by-product. The likelihood of this form of speciation differs greatly depending on the mathematical model used. Although the geographic pattern of speciation predicted by this hypothesis may be common, there is little evidence for the process of drift-induced speciation.
  7. Sympatric speciation, the origin of reproductive isolation within an initially randomly mating population, can occur as a result of disruptive selection. However, the sympatric evolution of sexual isolation is unlikely, due to recombination among loci affecting mating and loci affecting the disruptively selected character. Sympatric speciation may occur, however, if recombination does not oppose selection. For example, if disruptive selection favors preference for different habitats and if mating occurs within those habitats, prezygotic isolation may result. How often this occurs is debated.
  8. Instantaneous speciation by polyploidy is common in plants. Allopolyploid species arise from hybrids between genetically divergent populations. Establishment of a polyploid population probably requires ecological or spatial segregation from the diploid ancestors because backcross offspring have low reproductive success. Polyploid species can have multiple origins.
  9. In recombinational (hybrid) speciation, some genotypes of diploid hybrids are fertile and are reproductively isolated from the parent species, and so give rise to new species. This process appears to be uncommon, and has been documented more often in plants than in animals.
  10. The time required for speciation to proceed to completion is highly variable. It is shorter for some modes of speciation (polyploidy, recombinational speciation) than others (especially speciation by mutation and drift of neutral alleles that confer incompatibility). The process of speciation may require 2 to 3 Myr, on average, for some groups of organisms; it is much longer in some cases and very much shorter in others.
  11. Speciation is the source of the diversity of sexually reproducing organisms, and it is the event responsible for every branch in their phylogeny. It probably does not stimulate evolutionary change in morphological characters, as suggested by the hypothesis of punctuated equilibria, but rates of evolutionary change may nevertheless be correlated with speciation. This is probably because speciation prevents interbreeding between populations from undoing the changes wrought by natural selection or genetic drift.

Chapter 19 Summary

  1. Coevolution is reciprocal evolutionary change in two or more species resulting from the interaction among them. Species also display many adaptations to interspecific interactions that appear one-sided rather than reciprocal.
  2. Phylogenetic studies can provide information on the age of associations among species and on whether or not they have codiversified or acquired adaptations to each other. The phylogenies of certain symbionts and parasites are congruent with the phylogenies of their hosts, implying cospeciation, but in other cases such phylogenies are incongruent and imply shifts between host lineages.
  3. Coevolution in predator-prey and parasite-host interactions can theoretically result in an ongoing evolutionary arms race, a stable genetic equilibrium, indefinite fluctuations in genetic composition, or even extinction.
  4. Parasites (including pathogenic microorganisms) may evolve to be more or less virulent, depending on the correlation between virulence and the parasite’s reproductive rate, vertical versus horizontal transmission between hosts, infection of hosts by single versus multiple parasite genotypes, and other factors. Parasites do not necessarily evolve to be benign.
  5. Mutualism is best viewed as reciprocal exploitation. Selection favors genotypes that provide benefits to another species if this action yields benefits to the individual in return. Thus the conditions that favor low virulence in parasites, such as vertical transmission, can also favor the evolution of mutualisms. Mutualisms may be unstable if “cheating” is advantageous, or stable if it is individually advantageous for each partner to provide a benefit to the other.
  6. Evolutionary responses to competition among species may lead to divergence in resource use and sometimes in morphology (character displacement). Competition has caused ecological diversification, whereas alleviation of competition can enhance the rate of increase in the number of species.
  7. Character displacement between species that are subjected to a common predator may occur, but not many examples have as yet been reported. Convergence of prey species, as illustrated by defensive mimicry, occurs if it reduces predation.
  8. The structure of ecological communities is affected by evolutionary adjustment of coexisting species to each other and by ecological sorting of species on the basis of characteristics that affect the likelihood of coexistence. Convergence of the structure of independently formed ecological communities can occur by both processes, but differences among communities may exceed similarities.

Chapter 20 Summary

  1. New technologies that drive forward the field of genomics enable biologists to study genomes on hitherto unprecedented scales, and have revealed several new elements of genomes, such as diverse classes of untranslated RNA sequences. The structures of thousands of genes and entire genomes can be compared with one another to search for patterns of ancestry and evolution.
  2. A true “theory of genomes” is still in its infancy. A major hypothesis that has emerged in recent years is that apparently deleterious trends, such as the accumulation of transposable elements, have been driven by genetic drift in lineages with small population size. Although not a universal explanation for genome characteristics, this idea makes specific predictions that can be tested with further data.
  3. Proteins are composed of a diversity of building blocks called domains and exhibit widely varying rates of evolution. Level of gene expression (a proxy measure of protein abundance) seems to correlate negatively with a protein’s evolutionary rate. This implies that highly expressed proteins may be under strong purifying selection to maximize translational robustness, that is, to minimize the occurrence of missense mutations that could alter a protein’s folded three-dimensional structure.
  4. Genome size varies by several orders of magnitude across life forms. The C-value paradox refers to the discrepancy between genome size and organismal complexity in eukaryotes. It was resolved by noting that the coding portion of genomes may increase with organismal complexity, whereas the noncoding portion, comprising highly repetitive DNA, transposable elements, and other types of “selfish DNA,” varies with features other than complexity, such as population size.
  5. New genes arise in genomes through a variety of mechanisms. Lateral gene transfer occurs when a gene is transferred between completely unrelated genomes, presumably by viruses or other genomic vehicles. New genes can also arise from pre-existing genes by exon shuffling of domains. Such shuffling can create chimeric genes with novel functions.
  6. Genes can also arise by retrotransposition, a process that can generate new intronless genes and often produces processed pseudogenes. Such retrotransposed genes can sometimes produce new exons and regulatory regions up- and downstream, thereby gaining functions and expression patterns that differ from those of the progenitor gene.
  7. Genes can duplicate individually or as parts of large chromosomal regions and sometimes as part of whole-genome duplications. Gene duplication is frequent in eukaryotic and prokaryotic genomes and provides an opportunity for the generation of novel genes with derived functions. Gene duplication is the major mode of growth of multigene families, which are the most complex expression of coding region diversity in genomes. Variation in the copy number of chromosomal segments is also a major source of genomic variation in species.
  8. Duplicate genes sometimes undergo concerted evolution, wherein all or part of the DNA sequences of a gene are transferred unidirectionally to other members of the multigene family. Like gene duplication, concerted evolution has important consequences for the phylogenetic relationships of genes in gene families and can be inferred by phylogenetic analysis of orthologs and paralogs from multiple species.
  9. Multigene families have been responsible for enabling some of the major transitions of life, such as the origin of multicellularity and immunity. Multigene families diversify through gene duplication, and the acquisition of new functions is sometimes accompanied by strong signatures of positive selection, such as high values of ω = dn/ds.
  10. Neofunctionalization is the process whereby a newly duplicated gene acquires a new function relative to its ancestral gene. In subfunctionalization, by contrast, new gene duplicates undergo complementary degenerative mutations that knock out one of several functions present in the ancestral gene; thus both duplicates retain one of the ancestral gene’s functions and are preserved. Subfunctionalization is thought to be common among duplicated genes.

Chapter 21 Summary

  1. Evolutionary developmental biology (EDB) seeks to integrate data from comparative embryology and developmental genetics with theory and data on morphological evolution and population genetics.
  2. Phylogenetic homology can differ from biological homology, a concept based on the realization that homology must take into account information on the developmental genetics of morphological traits.
  3. Many of the genes and developmental pathways underlying morphogenesis in multicellular organisms are conserved across wide phyletic ranges, showing that the vast diversity of multicellular eukaryotes is largely due to diverse uses of a highly conserved “toolkit” of genes and developmental pathways.
  4. Modularity among body parts is achieved by segment-specific patterning mechanisms that result from modularity in gene regulation, allowing genes to be independently regulated in different parts of the body and at different developmental stages. Modularity has been important in enabling different parts of the body to develop divergent morphologies. Differences in morphology among segments of bilaterian animals, regulated by Hox proteins, provide many classic examples of mosaic evolution enabled by modular developmental pathways that can be deployed differently in each segment.
  5. Noncoding DNA sequences called enhancers or cis-regulatory elements independently control expression of each gene by binding different sets of transcription factors that are present in different areas of the developing body. The evolution of differences in gene expression is largely due to evolution of these enhancers.
  6. The genes responsible for developmental pathways include those that encode signaling proteins, transcription factors, and structural genes. Evolutionary change in the regulatory connections among signaling pathways and transcription factors, and between transcription factors and their targets, is believed to underlie much of the phenotypic diversity seen in nature. Evolution of protein-coding sequences has also given rise to many novel adaptive traits. Morphological variation within and among species has been found to be caused by both regulatory changes and changes in protein coding sequences. The relative importance of these two fundamental types of genetic changes to phenotypic evolution is currently under debate.
  7. During evolution, genes and developmental pathways have often been co-opted, or recruited, for new functions that probably are responsible for the evolution of many novel morphological traits. This process results from evolutionary changes in gene regulation and diversification in the function and expression patterns of duplicated genes.
  8. Many differences among species are due to heterochronic or allometric changes in the relative developmental rates of different body parts or in the rates or durations of different life history stages. The modularity of morphogenesis in different body parts and in different developmental stages facilitates such changes.
  9. Several kinds of constraints on evolution may determine that certain evolutionary trajectories are followed and not others. Some correlations of traits in natural populations can be easily broken using artificial selection, whereas others cannot. This suggests that some pairs of traits are constrained to vary in limited ways due to limitations in the function and regulation of the underlying genes.
  10. Some genes may be involved in phenotypic evolution more often than others in the same pathway (e.g., yellow in Drosophila species and Mc1r in vertebrates), suggesting that not all components of developmental genetic pathways are readily available for natural selection to act upon. This could be because of differential pleiotropy among genes.
  11. “Loss-of-function” alleles of genes involved in the development of morphological traits can segregate at appreciable frequencies in natural populations and be key components of morphological evolution when environmental changes occur or when small subpopulations colonize new habitats, as seen in stickleback fish.

Chapter 22 Summary

  1. The average rate of evolution of most characters is very low because long periods of little change (stasis) are averaged with short periods of rapid evolution, or the character mean fluctuates without long-term directional change. The highest rates of character evolution in the fossil record are comparable to rates observed in contemporary populations and can readily be explained by known processes such as mutation, genetic drift, natural selection, and speciation. The duration of speciation is short enough to account for the observed rates of increase in species diversity.
  2. The fossil record provides examples of both gradual change and the pattern called punctuated equilibrium: a rapid shift from one static phenotype to another. The hypothesis that such shifts require the occurrence of peripatric speciation is not widely accepted because responses to selection do not depend on speciation.
  3. Stasis can be explained by genetic constraints, stabilizing selection (owing largely to habitat tracking), or the erasure of divergence by episodic massive gene flow among populations with ancestral and derived character states.
  4. Higher taxa arise not in single steps, by macromutational jumps (saltation), but by multiple changes in genetically independent characters (mosaic evolution). Most such characters evolve gradually, through intermediate stages, but some characters evolve discontinuously as a result of mutations with moderately large effects.
  5. Characters may be phylogenetically conservative because of limits on the origin of variation (genetic and developmental constraints) or because of niche conservatism (resulting in stabilizing selection).
  6. New features often are advantageous even at their inception. They often evolve by modification of pre-existing characters to serve accentuated or new functions, or sometimes as by-products of the development of other structures. Evolutionary novelties often result when two or more functions of a structure are decoupled, or when structures are duplicated and diverge in structure and function.
  7. Complex structures such as eyes evolve by rather small, individually advantageous steps. They may acquire functional integration with other structures so that they become indispensable.
  8. Some fundamental characteristics of developmental processes and organismal integration, such as modularity, may enhance “evolvability,” the capacity of a genome to produce variants that are potentially adaptive. In theory, some aspects of evolvability can evolve by natural selection, but whether or not this has commonly occurred is not known.
  9. Long-term trends may result from individual selection, species selection, or species hitchhiking, the phylogenetic association of a character with other characters that affect speciation or extinction rates. Active trends, whereby the entire frequency distribution of a character among species in a clade shifts in a consistent direction over time, are less common than passive trends, in which variation among species (and therefore the mean of the clade) expands from an ancestral state that is located near a boundary (e.g., the clade may begin near a minimal body size).
  10. Probably no feature exhibits a trend common to all living things. Features such as genome size and structural complexity display passive trends, in that the maximum has increased since very early in evolutionary history, but such changes have been inconsistent among lineages. There is no clear evidence of trends in measures of adaptedness such as the longevity of species or higher taxa in geological time. The most conspicuous directional change in evolutionary history is an increase (with setbacks due to major extinctions) in the species diversity and the phenotypic and ecological disparity of organisms taken as a whole.
  11. If “progress” implies a goal, then there can be no progress in evolution. If it implies betterment or improvement, we still cannot identify objective criteria by which the history of evolution can be shown to be one of “improvement.” Characters improve in their capacity to serve certain functions, but these functions are specific to the ecological context of each species.

Chapter 23 Summary

Creationists and Other Skeptics
Science, Belief, and Education
The Evidence for Evolution

  • The fossil record
  • Phylogenetic and comparative studies
  • Genes and genomes
  • Biogeography
  • Failures of the argument from design
  • Evolution and its mechanisms, observed

Refuting Creationist Arguments

  • On arguing for evolution

Why Should We Teach Evolution?

  • Health and medicine
  • Agriculture and natural resources
  • Environment and conservation
  • Human behavior
  • Understanding nature and humanity
  1. Evolution is a fact—a hypothesis that is so thoroughly supported that it is extremely unlikely to be false. The theory of evolution is not a speculation, but rather a complex set of well-supported hypotheses that explain how evolution happens.
  2. Although many people do not think there is any necessary incompatibility between evolution and religion, many others reject evolution and instead accept divine creation, because they think evolution conflicts with their religious beliefs. The positions taken by creationists on issues such as the age of the Earth and of life vary.
  3. Science is tentative, it accepts hypotheses provisionally and changes in the face of convincing new evidence, and it is concerned only with testable hypotheses; it depends on empirical studies that are subject to peer scrutiny and that can be verified and repeated by others. Supernatural hypotheses, in contrast, cannot be tested. Creationism has none of the features of science, so it has no claim to be taught in science classes.
  4. The evidence for evolution comes from all realms of biology and geology, including comparative studies of morphology, development, life histories, and other features, molecular biology, genomics, paleontology, and biogeography. Evolutionary principles can explain features of organisms that would not be expected of a beneficent intelligent designer, such as imperfect adaptation, useless or vestigial features, extinction, selfish DNA, sexually selected characteristics, conflicts among genes within the genome, and infanticide. Furthermore, all the proposed mechanisms of evolution have been thoroughly documented, and evolution has been observed.
  5. The arguments used by creationists are all logically refutable in scientific terms and are contradicted by data.
  6. It is important to understand evolution because it has broad implications for how we think about nature and humanity, and because it has many practical ramifications. Evolutionary science contributes to many aspects of medicine and public health, agriculture and natural-resource management, pest management, and conservation.
  7. One of the most difficult and controversial challenges is to join biological and social science in order to understand how the distinctively human cognitive and behavioral characteristics evolved, the extent to which human behaviors have an evolved genetic foundation, how that foundation interacts with cultural and other environmental factors to shape individual behavior, and how genes and culture have coevolved.
 

Glossary

Click on a letter below to jump to it in the glossary. Letters that are not linked have no terms starting with that letter.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

absolute fitness
The per capita growth rate of a genotype.
adaptation
A process of genetic change in a population whereby, as a result of natural selection, the average state of a character becomes improved with reference to a specific function, or whereby a population is thought to have become better suited to some feature of its environment. Also, an adaptation: a feature that has become prevalent in a population because of a selective advantage conveyed by that feature in the improvement in some function. A complex concept; see Chapter 11.
adaptive landscape
A plot of mean fitness against allele frequency, representing a “surface” or “hillside.”
adaptive peak
That allele frequency, or combination of allele frequencies at two or more loci, at which the mean fitness of a population has a (local) maximum. Also, the mean phenotype (for one or more characters) that maximizes mean fitness. An adaptive valley is a set of allele frequencies at which mean fitness has a minimum.
adaptive radiation
Evolutionary divergence of members of a single phylogenetic lineage into a variety of different adaptive forms; usually the taxa differ in the use of resources or habitats, and have diverged over a relatively short interval of geological time. The term evolutionary radiation describes a pattern of rapid diversification without assuming that the differences are adaptive.
adaptive zone
A set of similar ecological niches occupied by a group of (usually) related species, often constituting a higher taxon.
additive effect
The magnitude of the effect of an allele on a character, measured as half the phenotypic difference between homozygotes for that allele compared with homozygotes for a different allele.
additive genetic variance
That component of the genetic variance in a character that is attributable to additive effects of alleles.
additive inheritance
Inheritance in which the heterozygote’s phenotype is precisely intermediate between those of the homozygotes.
allele
One of several forms of the same gene, presumably differing by mutation of the DNA sequence. Alleles are usually recognized by their phenotypic effects; DNA sequence variants, which may differ at several or many sites, are usually called haplotypes.
allele frequency
The proportion of gene copies in a population that are a given allele; i.e., the probability of finding this allele when a gene is taken randomly from the population; also called gene frequency.
allochthonous
In reference to a taxon of a geographical region, meaning it originated elsewhere. Cf. autochthonous.
allometric growth
Growth of a feature during ontogeny at a rate different from that of another feature with which it is compared.
allopatric speciation
The evolution of reproductive barriers in populations that are prevented by a geographic barrier from exchanging genes at more than a negligible rate.
allopatric
Of a population or species, occupying a geographic region different from that of another population or species. Cf. parapatric, sympatric.
allopolyploid
A polyploid in which the several chromosome sets are derived from more than one species.
allozyme
One of several forms of an enzyme encoded by different alleles at a locus.
alternative splicing
Splicing of different sets of exons from mRNA to form mature transcripts that are translated into different proteins (thus allowing the same gene to encode different proteins).
altruism
Conferral of a benefit on other individuals at an apparent cost to the donor.
anagenesis
Evolution of a feature within a lineage over an arbitrary period of time.
ancestral character state
The character state originally present in the ancestor of a given lineage. It may be retained or changed in descendants of that ancestor.
aneuploid
Of a cell or organism, possessing too many or too few of one or more chromosomes.
antagonistic selection
A source of natural selection that opposes another source of selection on a trait.
apomixis
Parthenogenetic reproduction in which an individual develops from one or more mitotically produced cells that have not experienced recombination or syngamy.
apomorphic
Having a derived character or state, with reference to another character or state. See synapomorphy.
aposematic
Coloration or other features that advertise noxious properties; warning coloration.
arithmetic mean
See mean.
artificial selection
Selection by humans of a deliberately chosen trait or combination of traits in a (usually captive) population; differing from natural selection in that the criterion for survival and reproduction is the trait chosen, rather than fitness as determined by the entire genotype.
asexual
Pertaining to reproduction that does not entail meiosis and syngamy.
associative overdominance
The apparent but erroneous superiority of a heterozygote at an observed locus resulting from masking of a recessive deleterious allele. See overdominance.
assortative mating
Nonrandom mating on the basis of phenotype; usually refers to positive assortative mating, the propensity to mate with others of like phenotype.
autapomorphy
A derived character that is restricted to a single lineage.
autochthonous
In reference to the taxon of a geographical region, meaning it originated within the region. Cf. allochthonous.
autopolyploid
A polyploid in which the several chromosome sets are derived from the same species.
autosome
A chromosome other than a sex chromosome.

B

back mutation
Mutation of a “mutant” allele back to the allele (usually the wild type) from which it arose. Usually detected by its phenotypic effect.
background extinction
A long-prevailing rate at which taxa become extinct, in contrast to the highly elevated rates that characterize mass extinction.
background selection
Elimination of deleterious mutations in a region of the genome; may explain low levels of neutral sequence variation.
balancing selection
A form of natural selection that maintains polymorphism at a locus within a population.
base pair substitution
See substitution (base pair or amino acid).
base pairs (bp)
In nucleic acids, the pairs of purines (adenine, A, or guanine, G) and pyrimidines (thymine, T, or cytosine, C) that make up a genome’s genetic material.
Bauplan (pl., Baupläne)
The body plan of an animal.
behavioral isolation
Reduction in the frequency of successful matings between individuals in separate populations of a species as a result of behavioral differences. Also called sexual isolation or ethological isolation.
benthic
Inhabiting the bottom, or substrate, of a body of water. Cf. planktonic.
biodiversity
Biological diversity, typically measured by species richness, or the number of species found in a given area.
biogeographic realm
One of several defined, continental-scale regions of Earth, each of which has a biota distinct from that of the others.
biogeography
The study of the geographic distribution of organisms.
biological homology concept
An evolutionary concept based on the realization that homology must take into account information on the developmental genetics of morphological traits.
biological species
A population or group of populations within which genes are actually or potentially exchanged by interbreeding, and which are reproductively isolated from other such groups.
bottleneck
A severe, temporary reduction in population size.

C

Cambrian explosion
The rapid diversification of animal phyla that took place during the Cambrian period.
canalization
The evolution of internal factors during development that reduce the effect of perturbing environmental and genetic influences, thereby constraining variation and consistently producing a particular (usually wild-type) phenotype.
candidate gene
A gene thought to be involved in the evolution of a particular trait based on its mutant phenotype or the function of the protein it encodes.
carrying capacity
The population density that can be sustained by limiting resources.
category
In taxonomy, one of the ranks of classification (e.g., genus, family). Cf. taxon.
character
A feature, or trait. Cf. character state.
character displacement
Usually refers to a pattern of geographic variation in which a character differs more greatly between sympatric than between allopatric populations of two species; sometimes used for the evolutionary process of accentuation of differences between sympatric populations of two species as a result of the reproductive or ecological interactions between them.
character state
One of the variant conditions of a character (e.g., yellow versus brown as state of the character “color of snail shell”).
chimeric gene
A gene that consists of pieces derived from two or more different ancestral genes.
chronospecies
A segment of an evolving lineage preserved in the fossil record that differs enough from earlier or later members of the lineage to be given a different binomial (name). Not equivalent to biological species.
cis-regulatory element
A noncoding DNA sequence in or near a gene required for proper spatiotemporal expression of that gene, often containing binding sites for transcription factors. Often used interchangeably with enhancer.
clade
The set of species descended from a particular ancestral species.
cladistic
Pertaining to branching patterns; a cladistic classification classifies organisms on the basis of the historical sequences by which they have diverged from common ancestors.
cladogenesis
Branching of lineages during phylogeny.
cladogram
A branching diagram depicting relationships among taxa; i.e., an estimated history of the relative sequence in which they have evolved from common ancestors. Used by some authors to mean a branching diagram that displays the hierarchical distribution of derived character states among taxa.
cline
A gradual change in an allele frequency or in the mean of a character over a geographic transect.
clone
A lineage of individuals reproduced asexually, by mitotic division.
coadapted gene pool
A population or set of populations in which prevalent genotypes are composed of alleles at two or more loci that confer high fitness in combination with each other, but not with alleles that are prevalent in other such populations.
coalescence
Derivation of the gene copies in one or more populations from a single ancestral copy, viewed retrospectively (from the present back into the past).
codon
A triplet of nucleotides in mRNA that direct the placement of a particular amino acid into a polypeptide chain.
codon bias
Non-random usage of alternative codons that encode the same amino acid.
coefficient of relationship
In altruism, the fraction of the donor’s genes that are identical by descent to any of the recipient’s genes.
coefficient of selection
The amount by which the fitness of a genotype differs from that of a reference genotype.
coevolution
Strictly, the joint evolution of two (or more) ecologically interacting species, each of which evolves in response to selection imposed by the other. Sometimes used loosely to refer to evolution of one species caused by its interaction with another, or simply to a history of joint divergence of ecologically associated species.
commensalism
An ecological relationship between species in which one is benefited but the other is little affected.
common ancestor
An ancestor shared by two or more descendants or groups of descendants.
common garden
A place in which (usually conspecific) organisms, perhaps from different geographic populations, are reared together, enabling the investigator to ascribe variation among them to genetic rather than environmental differences. Originally applied to plants, but now more generally used to describe any experiment of this design.
comparative genomics
The comparative study of whole genomes.
comparative method
A procedure for inferring the adaptive function of a character by correlating its states in various taxa with one or more variables, such as ecological factors hypothesized to affect its evolution.
compartment
A contiguous group of cells, descended from the same progenitor cell, that form a spatially discrete part of a developing organ or structure and often act as a discrete developmental unit. Cells from one compartment typically do not intermix with cells from other compartments.
competition
An interaction between individuals of the same species or different species whereby resources used by one are made unavailable to others.
competitive exclusion
Extinction of a population due to competition with another species.
components of fitness
Any of the factors that contribute to a genotype’s fitness.
concealed genetic variation
Genetic variation not revealed in an organism’s phenotype; for example, genetic variation represented by a rare recessive allele.
concerted evolution
Maintenance of a homogeneous nucleotide sequence among the members of a gene family, which evolves over time.
condition-dependent indicator
A trait correlated with genetic quality and dependent on an organism’s overall vigor or condition.
conservative characters
Characters retained with little or no change over long periods among the many descendants of an ancestor; for example, the pentadactyl limb, which first evolved in early amphibians and is retained in humans.
conspecific
Belonging to the same species.
constraints
Factors that limit evolution; they may be physical, functional, genetic, or developmental.
control regions (enhancers and repressors)
Areas on a protein-encoding gene that regulate transcription of one strand of the gene into RNA.
cooperation
Activity that benefits both the actor and other individuals.
convergent evolution (convergence)
Evolution of similar features independently in different evolutionary lineages, usually from different antecedent features or by different developmental pathways.
co-option
The evolution of a function for a gene, tissue, or structure other than the one it was originally adapted for. At the gene level, used interchangeably with recruitment and, occasionally, exaptation.
Cope’s rule
The tendency observed in some taxa (e.g., horses) for body size to increase over evolutionary time.
copy number variants
Variations in the copy number of chromosomal segments.
correlated selection
Selection that favors some combination of genetically independent character states over others, usually because the characters are functionally related.
correlation
A statistical relationship that quantifies the degree to which two variables are associated. For phenotypic correlation, genetic correlation, environmental correlation as applied to the relationship between two traits, see Chapter 13.
cost
A reduction in fitness caused by a correlated effect of a feature that provides an increment in fitness (i.e., a benefit).
cost of reproduction
A reduction in fitness (e.g., decreased survival or growth) caused by reproductive effort.
cost of sex
A reference to the fact that, all else being equal, the rate of increase of an asexual genotype is approximately twice as great as that of a sexual genotype.
creationism
The doctrine that each species (or perhaps higher taxon) was created separately, essentially in its present form, by a supernatural Creator.
creationist movement
A movement in the United States and a few other countries that opposes the teaching of evolution in public schools, or at least demands equal time for teaching creationism.
creationists
Those who believe in creationism.
crown group
A group of species with distinctive derived characters that is descended from a stem group; for example, the class Aves, or birds.
C-value paradox
The lack of correlation between the DNA content of eukaryotic genomes and a given organism’s phenotypic complexity (i.e., the genome of a less complex eukaryotic organism, such as a plant, may contain far more DNA than that of a more complex organism, such as a human being). The paradox is explained by the amount of noncoding repetitive DNA sequences in a genome.

D

deme
A local population; usually, a small, panmictic population.
demographic
Pertaining to processes that change the size of a population (i.e., birth, death, dispersal).
density-dependent
Affected by population density.
derived character (state)
A character (or character state) that has evolved from an antecedent (ancestral) character or state.
descent with modification
The Darwinian theory that all species, living and extinct, have descended, without interruption, from one or a few original forms of life. One of the two major theses of Darwin’s Origin of Species.
deterministic
Causing a fixed outcome, given initial conditions. Cf. stochastic.
developmental circuits (= developmental pathways)
The hierarchies, or networks, in which genes that regulate morphogenesis function.
differential gene expression
Differences in the time, location, and/or quantitative level at which a gene expresses the protein it encodes. Differential gene expression involves differences between species, developmental stages, or physiological states in the specific cells, tissues, structures, or body segments that express a given gene; it is believed to be a significant agent of morphological change over evolutionary time.
dioecious
Referring to organisms in which eggs and sperm are not produced in the same individuals.
diploid
Of a cell or organism, possessing two chromosome complements. See also haploid, polyploid.
direct development
A life history in which the intermediate larval stage is omitted and development proceeds directly from an embryonic form to an adult-like form. Cf. indirect development.
directional selection
Selection for a value of a character that is higher or lower than its current mean value.
disjunct distribution
A geographical distribution that has a gap in it.
disparity
Phenotypic diversity, as in a taxon or clade.
dispersal
In population biology, movement of individual organisms to different localities; in biogeography, extension of the geographic range of a species by movement of individuals.
disruptive selection
Selection in favor of two or more modal phenotypes and against those intermediate between them; also called diversifying selection.
divergence
The evolution of increasing difference between lineages in one or more characters.
diversification
An evolutionary increase in the number of species in a clade, usually accompanied by divergence in phenotypic characters.
diversification rate
In mathematical modeling of the rate of change in taxonomic diversity, the number of new taxa that originate minus the number of taxa that become extinct during a given interval.
diversifying selection
See disruptive selection.
diversity-dependent factor
A factor that affects changes in the number of species or higher taxa by reducing origination rates or increasing extinction rates as the number of species increases.
Dobzhansky-Muller incompatibility
Epistatic incompatibility between loci.
domain
A relatively small protein segment or module (100 amino acids or less) that can fold into a specific three-dimensional structure independently of other domains.
domain accretion
The production of new genes by the addition of domains to the beginnings or ends of ancestral genes.
dominance
Of an allele, the extent to which it produces when heterozygous the same phenotype as when homozygous. Of a species, the extent to which it is numerically (or otherwise) predominant in a community.
driven trend (= active trend)
See trend.
duplication
The production of another copy of a locus (or other sequence) that is inherited as an addition to the genome.

E

ecological biogeography
The study of the geographic distributions of organisms by focusing on ecological factors. Complements historical biogeography.
ecological space
A term roughly equivalent to a set of adaptive zones.
ecological niche
The range of combinations of all relevant environmental variables under which a species or population can persist; often more loosely used to describe the “role” of a species, or the resources it utilizes.
ecological release
The expansion of a population’s niche (e.g., range of habitats or resources used) where competition with other species is alleviated.
ecological speciation
The evolution of barriers to gene flow caused by divergent ecologically based selection.
ecotype
A genetically determined phenotype of a species that is found as a local variant associated with certain ecological conditions.
ectopic expression
Expression of a gene in a part of the body where it is not normally expressed.
effective population size
The effective size of a real population is equal to the number of individuals in an ideal population (i.e., a population in which all individuals reproduce equally) that produces the rate of genetic drift seen in the real population.
electrophoresis
A technique for visualizing proteins on DNA, by separating substances on the basis of their electric charges and molecular weights.
endosymbiont
A species living inside the body (or cells) of another species.
enhancer
A DNA sequence that, when acted on by transcription factors controls transcription of an associated gene. Cf. cis-regulatory element, promoter.
endemic
Of a species, restricted to a specified region or locality.
environment
Usually, the complex of external physical, chemical, and biotic factors that may affect a population, an organism, or the expression of an organism’s genes; more generally, anything external to the object of interest (e.g., a gene, an organism, a population) that may influence its function or activity. Thus, other genes within an organism may be part of a gene’s environment, or other individuals in a population may be part of an organism’s environment.
environmental correlation
The degree to which two features in individuals with the same genotype vary in concert because both are affected by environmental factors (e.g., nutrition).
environmental variance
Variation among individuals in a phenotypic trait that is caused by variation in the environment rather than by genetic differences.
epigenetic inheritance
Transmission of phenotypic differences that are not based on DNA sequence differences among generations of dividing cells in multicellular organisms and sometimes from parents to offspring.
epistasis
An effect of the interaction between two or more gene loci on the phenotype or fitness whereby their joint effect differs from the sum of the loci taken separately.
epoch
A division on the geological time scale during the Cenozoic era; the Cenozoic comprises seven epochs.
equilibrium
An unchanging condition, as of population size or genetic composition. Also, the value (e.g., of population size, allele frequency) at which this condition occurs. An equilibrium need not be stable. See stability, unstable equilibrium.
ESS
See evolutionarily stable strategy.
era
The largest division on the geological time scale; there are five eras on the scale.
escape-and-radiate coevolution
Evolution that occurs when a species evolves a defense against enemies and is thereby enabled to proliferate into a diverse clade.
essentialism
The philosophical view that all members of a class of objects (such as a species) share certain invariant, unchanging properties that distinguish them from other classes.
euploid
Having a balanced complement of chromosomes.
evolution
In a broad sense, the origin of entities possessing different states of one or more characteristics and changes in the proportions of those entities over time. Organic evolution, or biological evolution, is a change over time in the proportions of individual organisms differing genetically in one or more traits. Such changes transpire by the origin and subsequent alteration of the frequencies of genotypes from generation to generation within populations, by alteration of the proportions of genetically differentiated populations within a species, or by changes in the numbers of species with different characteristics, thereby altering the frequency of one or more traits within a higher taxon.
evolutionary developmental biology (EDB)
The field of biology that seeks to understand the mechanisms by which development has evolved, both in terms of developmental processes and evolutionary processes. Often called “evo-devo.”
evolutionarily stable strategy (ESS)
A phenotype such that, if almost all individuals in a population have that phenotype, no alternative phenotype can invade the population or replace it.
evolutionary radiation
See adaptive radiation.
evolutionary reversal
The evolution of a character from a derived state back toward a condition that resembles an earlier state.
evolutionary synthesis
The reconciliation of Darwin’s theory with the findings of modern genetics, which gave rise to a theory that emphasized the coaction of random mutation, selection, genetic drift, and gene flow; also called the modern synthesis.
evolutionary trend
The process of repeated changes of a character in the same direction, either within a single lineage or in many lineages independently.
evolvability
The capacity of a genome to produce variants that are potentially adaptive.
exaptation
The evolution of a function of a gene, tissue, or structure other than the one it was originally adapted for; can also refer to the adaptive use of a previously nonadaptive trait.
exon
That part of a gene that is translated into a polypeptide (protein). Cf. intron.
exon shuffling
The formation of new genes by assembly of exons from two or more preexisting genes. The classical model of exon shuffling generates new combinations of exons mediated via recombination of intervening introns; however, exon shuffling can also come about by retrotransposition of exons into pre-existing genes.
exponential growth
Growth, especially in the number of organisms in a population, that is a geometric function of the size of the growing entity: the larger the entity, the faster it grows.

F

F2 breakdown
The manifestation of hybrid sterility and inviability in F2 hybrids among different geographic populations of the same species.
fact
A hypothesis that has become so well supported by evidence that it is accepted as true.
fecundity
The quantity of gametes (usually eggs) produced by an individual.
fission (of chromosomes)
The process whereby a chromosome splits, resulting in an additional chromosome in the genome. One of the mutational foundations for the evolution of chromosome number. Cf. fusion (of chromosomes).
fitness
The success of an entity in reproducing; hence, the average contribution of an allele or genotype to the next generation or to succeeding generations. See also relative fitness.
fixation
Attainment of a frequency of 1 (i.e., 100 percent) by an allele in a population, which thereby becomes monomorphic for the allele.
founder effect
The principle that the founders of a new population carry only a fraction of the total genetic variation in the source population.
founder effect speciation
See peripatric speciation.
frameshift mutation
An insertion or deletion of base pairs in a translated DNA sequence that alters the reading frame, resulting in multiple downstream changes in the gene product.
frequency
In this book, usually used to mean proportion (e.g., the frequency of an allele is the proportion of gene copies having that allelic state).
frequency-dependent selection
A mode of natural selection in which the fitness of each genotype varies as a function of its frequency in the population.
function
The way in which a character contributes to the fitness of an organism.
functional constraint
In reference to a gene, an interaction that reduces the rate of a protein’s evolution.
fusion (of chromosomes)
The process whereby two chromosome fuse, resulting in one less chromosome in the genome. One of the mutational foundations for the evolution of chromosome number. Cf. fission (of chromosomes).

G

G matrix
A table of values showing additive genetic variance and covariance between characters. Also called the genetic variance-covariance matrix, or simply G.
gene
The functional unit of heredity. A complex concept.
gene complex
A group of two or more genes that are members of the same family and in most cases are located in close proximity to one another in the genome, often in tandem separated by various amounts of intergenic, noncoding DNA.
gene conversion
A process involving the unidirectional transfer of DNA information from one gene to another. In a typical conversion event, a gene or part of a gene acquires the same sequence as the other allele at that locus (intralocus or intra-allelic conversion), or the same sequences as a different, usually paralogous, locus (interlocus conversion). One consequence of gene conversion may be the homogenization of sequences among members of a gene family.
gene dispensability
The relationship between the elimination of a particular gene and its genome’s fitness.
gene duplication
When new genes arise as copies of preexisting gene sequences. The result can be a gene family.
gene family
Two or more loci with similar nucleotide sequences that have been derived from a common ancestral sequence.
gene flow
The incorporation of genes into the gene pool of one population from one or more other populations.
gene-for-gene interactions
A mechanism for resistance to pathogens, in which a host’s resistance is triggered by the interaction of genes in the host and pathogen.
gene frequency
See allele frequency.
gene pool
The totality of the genes of a given sexual population.
genetic assimilation
The process of a character state that initially developed in response to the environment becoming genetically determined.
genetic code
The set of instructions, in the form of nucleotide triplets, that translate a linear sequence of nucleotides in mRNA into a linear sequence of amino acids in a protein.
gene tree
A diagram representing the history by which gene copies have been derived from ancestral gene copies in previous generations.
genetic conflict
Antagonistic fitness relationships between alleles at different loci in a genome.
genetic correlation
Correlated differences among genotypes in two or more phenotypic characters, due to pleiotropy or linkage disequilibrium.
genetic distance
Any of several measures of the degree of genetic difference between populations, based on differences in allele frequencies.
genetic drift
Random changes in the frequencies of two or more alleles or genotypes within a population.
genetic load
Any reduction of the mean fitness of a population resulting from the existence of genotypes with a fitness lower than that of the most fit genotype.
genetic variance
Variation in a trait within a population, as measured by the variance that is due to genetic differences among individuals.
genic selection
A form of selection in which the single gene is the unit of selection, such that the outcome is determined by fitness values assigned to different alleles. See individual selection, kin selection, natural selection.
geological time scale
A chronological model showing the major events of Earth’s history. Times on the scale are approximate, and subject to revision as more information accumulates.
genome
The entire complement of DNA sequences in a cell or organism. A distinction may be made between the nuclear genome and organelle genomes, such as those of mitochondria and plastids.
genotype
The set of genes possessed by an individual organism; often, its genetic composition at a specific locus or set of loci singled out for discussion.
genotype × environment interaction
Phenotypic variation arising from the difference in the effect of the environment on the expression of different genotypes.
genotype frequency
The proportion of a population that has a certain genotype.
geographic variation
Differences among spatially distributed populations of a species.
Gondwana
The Southern Hemisphere supercontinent that separated from Pangaea during the Jurassic. Present-day remnants are South America, Africa, India, Australia, New Zealand, and Antarctica.
grade
A group of species that have evolved the same state in one or more characters and typically constitute a paraphyletic group relative to other species that have evolved further in the same direction.
gradualism
The proposition that large differences in phenotypic characters have evolved through many slightly different intermediate states.
group selection
The differential rate of origination or extinction of whole populations (or species, if the term is used broadly) on the basis of differences among them in one or more characteristics. See also interdemic selection, species selection.
guild coevolution (= diffuse coevolution)
Evolution of several species whose effects on one another are not independent; for example, evolution of a prey species and two or more of its predators.

H

habitat selection
The capacity of an organism (usually an animal) to choose a habitat in which to perform its activities. Habitat selection is not a form of natural selection.
habitat tracking
Shifting of the geographic distribution of a species in concert with the distribution of its typical habitat.
Haldane’s rule
The generalization that when there is reduced fitness of hybrids and only one sex is affected, it is usually the heterogametic sex.
Hamilton’s rule
The principal that an altruistic trait can increase in frequency if the benefit received by the donor’s relatives, weighted by their relationship to the donor, exceeds the cost of the trait to the donor’s fitness.
haploid
Of a cell or organism, possessing a single chromosome complement, hence a single gene copy at each locus.
haplotype
A DNA sequence that differs from homologous sequences at one or more base pair sites.
Hardy-Weinberg
Pertaining to the genotype frequencies expected at a locus under ideal equilibrium conditions in a randomly mating population.
heritability
The proportion of the variance in a trait among individuals that is attributable to differences in genotype. Heritability in the narrow sense is the ratio of additive genetic variance to phenotypic variance.
hermaphroditic
Referring to individuals that can produce both male and female gametes.
heterochrony
An evolutionary change in phenotype caused by an alteration of timing of developmental events.
heterokaryotype
A genome or individual that is heterozygous for a chromosomal rearrangement such as an inversion. Cf. homokaryotype.
heterotopy
Evolutionary change in the position within an organism at which a phenotypic character is expressed.
heterozygosity
In a population, the proportion of loci at which a randomly chosen individual is heterozygous, on average.
heterozygote
An individual organism that possesses different alleles at a locus.
heterozygous advantage
The manifestation of higher fitness by heterozygotes than by homozygotes at a specific locus.
higher taxon
See taxon.
historical biogeography
The study of the geographic distribution of organisms by focusing on historical circumstances. Complements ecological biogeography.
hitchhiking
Change in the frequency of an allele due to linkage with a selected allele at another locus.
homeobox genes
A large family of eukaryotic genes that contain a DNA sequence known as the homeobox. The homeobox sequence encodes a protein homeodomain about 60 amino acids in length that binds DNA. Most homeobox genes are transcriptional regulators. Cf. domain; Hox genes.
homeodomain
See homeobox genes.
homeostasis
Maintenance of an equilibrium state by some self-regulating capacity of an individual.
homeotic mutation
A mutation that causes a transformation of one structure into another of the organism’s structures.
homokaryotype
A genome or individual that is homozygous for a chromosomal rearrangement such as an inversion. Cf. heterokaryotype.
homology
Possession by two or more species of a character state derived, with or without modification, from their common ancestor. Homologous chromosomes are those members of a chromosome complement that bear the same genes.
homonymous
Pertaining to biological structures that occur repeatedly within one segment of the organism, such as teeth or bristles.
homoplasy
Possession by two or more species of a similar or identical character state that has not been derived by both species from their common ancestor; embraces convergence, parallel evolution, and evolutionary reversal.
homozygote
An individual organism that has the same allele at each of its copies of a genetic locus.
horizontal (lateral) gene transfer
See horizontal transmission.
horizontal transmission
Movement of genes or symbionts (such as parasites) between individual organisms other than by transmission from parents to their offspring (which is vertical transmission). Horizontal transmission of genes is also called lateral gene transfer.
Hox genes
A subfamily of homeobox genes, conserved in all metazoan animals, that controls anterior-posterior segment identity by regulating the transcription of many genes during development.
hybrid
An individual formed by mating between unlike forms, usually genetically differentiated populations or species.
hybrid zone
A region in which genetically distinct populations come into contact and produce at least some offspring of mixed ancestry.
hypermorphosis
An evolutionary increase in the duration of ontogenetic development, resulting in features that are exaggerated compared to those of the ancestor.
hypothesis
An informed conjecture or statement of what might be true. A hypothesis may be poorly supported at first but can gain support to the point that it is effectively a fact. Cf. scientific theory.
hypothetico-deductive method
The method of predicting what one will find by deducing it from hypotheses.

I

identical by descent
Of two or more gene copies, being derived from a single gene copy in a specified common ancestor of the organisms that carry the copies.
inbreeding
Mating between relatives that occurs more frequently than if mates were chosen at random from a population.
inbreeding coefficient
The probability that a random pair of gene copies are identical by descent.
inbreeding depression
Reduction, in inbred individuals, of the mean value of a character (usually one correlated with fitness).
inclusive fitness
The fitness of a gene or genotype as measured by its effect on the survival or reproduction of both the organism bearing it and the genes, identical by descent, borne by the organism’s relatives.
incumbent replacement
An evolutionary process whereby the extinction of one taxon allows an ecologically similar taxon to diversity.
indirect development
A life history consisting of a larval stage between embryo and adult stages. Cf. direct development.
individual selection
A form of natural selection consisting of nonrandom differences among different genotypes (or phenotypes) within a population in their contribution to subsequent generations. See also genic selection, natural selection.
individualization
The acquisition of distinct identities by certain modules in the bodies of organisms; for example, the differentiation of teeth into incisors, canines, premolars, and molars during the evolution of mammals. An important basis for mosaic evolution.
ingroup
In phylogenetic analysis, a group of species whose relationship is reconstructed.
inheritance of acquired characteristics
See Lamarckism.
intelligent design (ID)
The doctrine that many biological phenomena are too complicated to have arisen by natural processes, and can only be explained by an intelligent designer (e.g., God).
intensity of selection
Magnitude of fitness differences among genotypes/phyenotypes.
inter-, intra-
Prefixes meaning, respectively, “between” and “within.” For example, “interspecific” differences are differences between species and “intraspecific” differences are differences among individuals within a species.
interaction
Strictly, the dependence of an outcome on a combination of causal factors, such that the outcome is not predictable from the average effects of the factors taken separately. More loosely, an interplay between entities that affects one or more of them (as in interactions between species). See also genotype × environment interaction.
interdemic selection
Group selection of populations within a species.
intragenic recombination
Recombination that takes place within a gene (as opposed to between genes).
intrinsic rate of natural increase
The potential per capita rate of increase of a population with a stable age distribution whose growth is not depressed by the negative effects of density.
introgression
Movement of genes from one species or population into another by hybridization and backcrossing; carries the implication that some genes in a genome undergo such movement, but others do not.
intron
A part of a gene that is not translated into a polypeptide. Cf. exon.
inversion
A 180° reversal of the orientation of a part of a chromosome, relative to some standard chromosome.
isolating barrier, isolating mechanism
A genetically determined difference between populations that restricts or prevents gene flow between them. The term does not include spatial segregation by extrinsic geographic or topographic barriers.
isolation by distance
In population genetics, a model for studying gene flow in a continuously distributed population in which each individual is the center of a “neighborhood” and the probability of mating declines with distance from the center.
iteroparous
Pertaining to a life history in which individuals reproduce more than once. Cf. semelparous.

K

karyotype
The chromosome complement of an individual.
key adaptation
An adaptation that provides the basis for using a new, substantially different habitat or resource.
kin selection
A form of selection whereby alleles differ in their rate of propagation by influencing the impact of their bearers on the reproductive success of individuals (kin) who carry the same alleles by common descent.

L

Lamarckism
The theory that evolution is caused by inheritance of character changes acquired during the life of an individual due to its behavior or to environmental influences.
lateral gene transfer
See horizontal transmission.
Laurasia
The Northern Hemisphere supercontinent that separated from Pangaea during the Jurassic.
lethal allele
An allele (usually recessive) that causes virtually complete mortality, usually early in development.
levels of selection
A reference to the fact that differences in survival and reproduction exist not only among individual organisms but also among genes and among populations and species. Thus, different kinds of biological entities may vary in fitness, resulting in different levels of selection.
life history
The stages an individual goes through during its life.
life history trait
A trait that characterizes an individual’s life history and is a component of fitness; for example, probability of survival, age at which adult size is reached, age at first reproductive event.
lineage
A series of ancestral and descendant populations through time; usually refers to a single evolving species, but may include several species descended from a common ancestor.
lineage sorting
The process by which each of several descendant species, carrying several gene lineages inherited from a common ancestral species, acquires a single gene lineage; hence, the derivation of a monophyletic gene tree, in each species, from the paraphyletic gene tree inherited from their common ancestor.
linkage
Occurrence of two loci on the same chromosome: the loci are functionally linked only if they are so close together that they do not segregate independently in meiosis.
linkage disequilibrium
The association of two alleles at two or more loci more frequently (or less frequently) than predicted by their individual frequencies.
linkage equilibrium
The association of two alleles at two or more loci at the frequency predicted by their individual frequencies.
locus (plural: loci)
A site on a chromosome occupied by a specific gene; more loosely, the gene itself, in all its allelic states.
logistic equation
An equation describing the idealized growth of a population subject to a density-dependent limiting factor. As density increases, the rate of growth gradually declines until population growth stops.

M

macroevolution
A vague term, usually meaning the evolution of substantial phenotypic changes, usually great enough to place the changed lineage and its descendants in a distinct genus or higher taxon. Cf. microevolution.
mass extinction
A highly elevated rate of extinction of species, extending over an interval that is relatively short on a geological time scale (although still very long on a human time scale).
maternal effect
A nongenetic effect of a mother on the phenotype of her offspring, stemming from factors such as cytoplasmic inheritance, transmission of symbionts from mother to offspring, or nutritional conditions.
maximum parsimony
See parsimony.
McDonald-Kreitman test for selection
In molecular evolution, a statistical test used to compare between-species divergence and within-species polymorphism at non-synonymous and synonymous sites.
mean
Usually the arithmetic mean or average; the sum of n values, divided by n. The mean value of x, symbolized as x, equals (x1 + x2 + … + xn)/n.
mean fitness
The arithmetic average fitness of all individuals in a population, usually relative to some standard.
meiotic drive
Used broadly to denote a preponderance (> 50 percent) of one allele among the gametes produced by a heterozygote; results in genic selection.
metapopulation
A set of local populations, among which there may be gene flow and patterns of extinction and recolonization.
microevolution
A vague term, usually referring to slight, short-term evolutionary changes within species. Cf. macroevolution.
microRNAs
Short RNA sequences (about 22 base pairs long) that bind to RNA transcripts and repress their translation into proteins.
microsatellite
A short, highly repeated, untranslated DNA sequence.
migration
Used in theoretical population genetics as a synonym for gene flow among populations; in other contexts, refers to directed large-scale movements of organisms that do not necessarily result in gene flow.
mimicry
Similarity of certain characters in two or more species due to convergent evolution when there is an advantage conferred by the resemblance. Common types include Batesian mimicry, in which a palatable mimic experiences lower predation because of its resemblance to an unpalatable model; and Müllerian mimicry, in which two or more unpalatable species enjoy reduced predation due to their similarity.
modern synthesis
See evolutionary synthesis.
modularity
The ability of individual parts of an organism, such as segments or organs, to develop or evolve independently from one another; the ability of developmental regulatory genes and pathways to be regulated independently in different tissues and developmental stages.
molecular clock
The concept of a steady rate of change in DNA sequences over time, providing a basis for dating the time of divergence of lineages if the rate of change can be estimated.
monomorphic
Having one form; refers to a population in which virtually all individuals have the same genotype at a locus. Cf. polymorphism.
monophyletic
Refers to a taxon, phylogenetic tree, or gene tree whose members are all derived from a common ancestral taxon. In cladistic taxonomy, the term describes a taxon consisting of all the known species descended from a single ancestral species. Cf. paraphyletic, polyphyletic.
mosaic evolution
Evolution of different characters within a lineage or clade at different rates, hence more or less independently of one another.
multigene family
A large group of genes related to one another by clear ancestry and descent, and often having diverse functions that have a common theme.
multilevel selection
Selection at multiple levels, i.e., gene, organism, population.
multiple-niche polymorphism
A phenomenon in which different homozygotes in a single population are best adapted to different microhabitats or resources.
multiple stable equilibria
See equilibrium.
mutation
An error in the replication of a nucleotide sequence, or any other alteration of the genome that is not manifested as reciprocal recombination.
mutational variance
The increment in the genetic variance of a phenotypic character caused by new mutations in each generation.
mutualism
A symbiotic relation in which each of two species benefits by their interaction.

N

naturalistic fallacy
The supposition that what is “natural” is necessarily “good.”
natural laws
Statements that certain patterns of events will always occur if certain conditions hold.
natural selection
The differential survival and/or reproduction of classes of entities that differ in one or more characteristics. To constitute natural selection, the difference in survival and/or reproduction cannot be due to chance, and it must have the potential consequence of altering the proportions of the different entities. Thus natural selection is also definable as a deterministic difference in the contribution of different classes of entities to subsequent generations. Usually the differences are inherited. The entities may be alleles, genotypes or subsets of genotypes, populations, or, in the broadest sense, species. A complex concept; see Chapter 11. See also genic selection, individual selection, kin selection, group selection.
neo-Darwinism
The modern belief that natural selection, acting on randomly generated genetic variation, is a major, but not the sole, cause of evolution.
neofunctionalization
Divergence of duplicate genes whereby one acquires a new function. Cf. subfunctionalization.
neoteny
Heterochronic evolution whereby development of some or all somatic features is retarded relative to sexual maturation, resulting in sexually mature individuals with juvenile features. See also paedomorphosis, progenesis.
neutral alleles
Alleles that do not differ measurably in their effect on fitness.
neutral mutation rate
The mutation rate to alleles that do not affect fitness.
neutral theory of molecular evolution
A view of molecular evolution that postulates that although many mutations are deleterious, and a few are advantageous, most molecular variation within and among species is selectively neutral.
niche conservatism
Long-continued dependence of related species on much the same resources and environmental conditions.
node
On a phylogenetic tree, any point at which the tree “branches.”
nonadaptive evolution
Evolution that does not equip organisms for reproduction and survival.
nonsynonymous mutation
See nonsynonyomous substitution.
nonsynonymous substitution
A base pair substitution in DNA that results in an amino acid substitution in the protein product; also called replacement substitution. Cf. synonymous substitution.
norm of reaction
The set of phenotypic expressions of a genotype under different environmental conditions. See also phenotypic plasticity.
normal distribution
A bell-shaped frequency distribution of a variable; the expected distribution if many factors with independent, small effects determine the value of a variable; the basis for many statistical formulations.
nucleotide substitution
The complete replacement of one nucleotide base pair by another within a lineage over evolutionary time.

O

ontogeny
The development of an individual organism, from fertilized zygote until death.
optimality theory
An approach to understanding particular life history trait adaptations by specifying, often on the basis of mathematical models, which state of some character, among a specified set of plausible states, would maximize individual fitness, subject to specified constraints. Also called optimization theory.
organism
Usually used in this book to refer to an individual member of a species.
orthologous
Refers to corresponding (homologous) members of a gene family in two or more species. Cf. paralogous.
outcrossing
Mating with another genetic individual. Cf. selfing.
outgroup
A taxon that diverged from a group of other taxa before they diverged from one another.
overdominance
The expression by two alleles in heterozygous condition of a phenotypic value for some character that lies outside the range of the two corresponding homozygotes.

P

paedomorphosis
Possession in the adult stage of features typical of the juvenile stage of the organism’s ancestor.
Pangaea
The single land mass formed when all of the continents came together during the Permian period.
panmixia
Random mating among members of a population.
parallel evolution (parallelism)
The evolution of similar or identical features independently in related lineages, thought usually to be based on similar modifications of the same developmental pathways.
paralogous
Refers to the homologous relationship between two different members of a gene family, within a species or in a comparison of different species. Cf. orthologous.
parapatric
Of two species or populations, having contiguous but non-overlapping geographic distributions.
parapatric speciation
The evolution of reproductive barriers in spatially distinct populations between which there is some gene flow.
paraphyletic
Refers to a taxon, phylogenetic tree, or gene tree whose members are all derived from a single ancestor, but which does not include all the descendants of that ancestor. Cf. monophyletic.
parental investment
Parental activities or processes that enhance the survival of existing offspring but whose costs reduce the parent’s subsequent reproductive success.
parent-offspring conflict
The conflict that arises when offspring try to obtain more resources from a parent than it is optimal for the parent to give.
parsimony
Economy in the use of means to an end (Webster’s New Collegiate Dictionary); the principle of accounting for observations by that hypothesis requiring the fewest or simplest assumptions that lack evidence; in systematics, the principle of invoking the minimal number of evolutionary changes to infer phylogenetic relationships.
parthenogenesis
Virgin birth; development from an egg to which there has been no paternal contribution of genes.
passive trend
See trend.
patterns of evolution
Common themes observed in the history of evolutionary changes in the characteristics of organisms.
PCR (polymerase chain reaction)
A laboratory technique by which the number of copies of a DNA sequence is increased by replication in vitro.
peak shift
Change in allele frequencies within a population from one to another local maximum of mean fitness by passage through states of lower mean fitness.
peramorphosis
Evolutionary change that results in delayed maturity and reproduction at a larger size, associated with the extended development of “hyper-adult” features. Cf. paedomorphosis.
period
A division on the geological time scale. Each of the three eras of Phanerozoic time (marked by the first appearance of diverse animals) is divided into periods.
peripatric
Of a population, peripheral to most of the other populations of a species.
peripatric speciation
Speciation by evolution of reproductive isolation in peripatric populations as a consequence of a combination of genetic drift and natural selection.
phenetic
Pertaining to phenotypic similarity, as in a phenetic classification.
phenogram
A diagram portraying the relative genetic difference (or similarity) among populations (or species).
phenotype
The morphological, physiological, biochemical, behavioral, and other properties of an organism manifested throughout its life; or any subset of such properties, especially those affected by a particular allele or other portion of the genotype.
phenotypic correlation
The relationship shown between two phenotypic characters (e.g., body size and fecundity).
phenotypic integration
A hypothesis that functionally related characteristics should be genetically correlated with one another.
phenotypic plasticity
The capacity of an organism to develop any of several phenotypic states, depending on the environment; usually this capacity is assumed to be adaptive.
phenotypic variance
In a phenotypic trait, the sum of genetic variance and environmental variance.
phyletic gradualism
Slow, incremental evolutionary change. Cf. punctuated equilibria.
phylogenetic niche conservatism
A pattern in which related species often have similar ecological requirements, presumably derived from their common ancestor.
phylogenetic species concept
Any of several related concepts of species as sets of populations that are diagnosably different from other populations.
phylogenetic tree
A graphic representation of lines of descent among organisms or their genes.
phylogeny
The history of descent of a group of taxa such as species from their common ancestors, including the order of branching and sometimes the absolute times of divergence; also applied to the genealogy of genes derived from a common ancestral gene.
phylogeography
The description and analysis of the processes that govern the geographic distribution of lineages of genes, especially within species and among closely related species.
planktonic
Living in open water. Cf. benthic.
plate tectonics
The geologic theory that the lithosphere, the solid outer layer of Earth bearing both the continents and the crust below the oceans, consists of eight major and several minor plates that move independently over the denser asthenosphere below.
pleiotropy
A phenotypic effect of a gene on more than one character.
ploidy
The number of chromosome complements in an organism.
point mutation
In classic genetics, a mutation that maps to a single gene locus. In modern usage, often restricted to single base pair substitutions.
polygenic character
A character whose variation is based wholly or in part on allelic variation at more than a few loci.
polymorphism
The existence within a population of two or more genotypes, the rarest of which exceeds some arbitrarily low frequency (say, 1 percent); more rarely, the existence of phenotypic variation within a population, whether or not genetically based. Cf. monomorphic.
polyphenism
The capacity of a species or genotype to develop two or more forms, with the specific form depending on specific environmental conditions or cues, such as temperature or day length. A polyphenism is distinct from a polymorphism in that the former is the property of a single genotype, whereas the latter refers to multiple forms encoded by two or more different genotypes.
polyphyletic
Refers to a taxon, phylogenetic tree, or gene tree composed of members derived by evolution from ancestors in more than one ancestral taxon; hence, composed of members that do not share a unique common ancestor. Cf. monophyletic.
polyploid
Of a cell or organism, possessing more than two chromosome complements.
population
A group of conspecific organisms that occupy a more or less well defined geographic region and exhibit reproductive continuity from generation to generation; ecological and reproductive interactions are more frequent among these individuals than with members of other populations of the same species.
positive selection
Selection for an allele that increases fitness. Cf. purifying selection.
postzygotic
Occurring after union of the nuclei of uniting gametes; usually refers to inviability or sterility that confers reproductive isolation.
postzygotic barriers
Barriers to gene flow that occur after the union of the nuclei of uniting gametes; for example, reduced survival or reproductive rates.
preadaptation
Possession of the necessary properties to permit a shift to a new niche, habitat, or function. A structure is preadapted for a new function if it can assume that function without evolutionary modification.
Precambrian time
The geological time period that includes both the Archean (prior to 2.5 billion years ago) and Proterozoic (2.5 billion–542 million years ago) eras.
premating barriers
Barriers to gene flow that prevent (or reduce the likelihood of) transfer of gametes to members of other species.
prezygotic
Occurring before union of the nuclei of uniting gametes; usually refers to events in the reproductive process that cause reproductive isolation.
prezygotic barriers
Barriers to gene flow that occur before the union of the nuclei of uniting gametes; for example, the failure of gametes of different species to unite.
primordium
A group of embryonic or larval cells destined to give rise to a particular adult structure.
processed pseudogene
A pseudogene that has arisen via the retrotransposition of mRNA into cDNA.
progenesis
A decrease during evolution of the duration of ontogenetic development, resulting in retention of juvenile features in the sexually mature adult. See also neoteny, paedomorphosis.
progress
A word that usually implies movement toward a goal, improvement, and betterment. In this sense, there can be no “progress” in evolution. Characters improve in their capacity to serve certain functions, but these functions are specific to the ecological context of each species.
promoter
Usually refers to the DNA sequences immediately 5′ to (upstream of) a gene that are bound by the RNA polymerase and its cofactors and/or are required in order to transcribe the gene. Sometimes used interchangeably with enhancer.
provinciality
The degree to which the taxonomic composition of a biota is differentiated among major geographic regions.
pseudogene
A nonfunctional member of a gene family that has been derived from a functional gene. Cf. processed pseudogene.
pull of the Recent
In paleobiology, the appearance that species diversity seems to increase as we approach the present. This bias arises because the more recently a taxon arose, the more likely it is to still be extant.
punctuated equilibria
A pattern of rapid evolutionary change in the phenotype of a lineage separated by long periods of little change; also, a hypothesis intended to explain such a pattern, whereby phenotypic change transpires rapidly in small populations, in concert with the evolution of reproductive isolation.
punctuated anagenesis
Evolution of characters occurring between long-stable states in populations that do not undergo speciation.
punctuated gradualism
See punctuated anagenesis.
purifying selection
Elimination of deleterious alleles from a population. Cf. positive selection.
pyrosequencing
A new method of DNA sequencing that isolates each molecule in an individual picoliter well.

Q

QTL
quantitative genetics
The field of genetics that studies quantitative (continuously varying) characters.
Quantitative trait locus (or loci); a chromosome region containing at least one gene that contributes to variation in a quantitative trait. QTL mapping is a procedure for determining the map positions of QTL on chromosomes.
quantitative trait
A phenotypic character that varies continuously rather than as discretely different character states.

R

race
A poorly defined term for a set of populations occupying a particular region that differ in one or more characteristics from populations elsewhere; equivalent to subspecies. In some writings, a distinctive phenotype, whether or not allopatric from others.
radiation
See adaptive radiation.
radiometric dating
A process that determines the “absolute” ages of geological events by measuring the decay of certain radioactive elements in minerals that form in igneous rock.
random genetic drift
See genetic drift.
random walk
Random fluctuation in allele frequency.
randomness
In science, the inability to predict a particular outcome, because physical causes can result in any of several outcomes.
realized heritability
Heritability that can be estimated by a response to experimental selection.
recessive
In genetics, an allele associated with a phenotypic effect only when in the homozygous state.
reciprocal translocation
The exchange of segments, by breakage and reunion, between two nonhomologous chromosomes.
reciprocity
Cooperation based on repeated interactions.
recombinational speciation
Speciation that results when the recombinant offspring of F1 hybrids between two species include genotypes that are fertile but reproductively isolated from the parent species. Also called hybrid speciation.
recruitment
(1) In evolutionary genetics, the evolution of a new function for a gene other than the function for which that gene was originally adapted. (2) In population biology, refers to the addition of new adult (breeding) individuals to a population via reproduction (i.e., individuals born into the population that reach reproductive age).
recurrent mutation
Repeated origin of mutations of a particular kind within a species.
refugia
Locations in which species have persisted while becoming extinct elsewhere.
regression
In geology, withdrawal of sea from land, accompanying lowering of sea level; in statistics, a function that best predicts a dependent from an independent variable.
regulatory modularity
See modularity.
reinforcement
Evolution of enhanced reproductive isolation between populations due to natural selection for greater isolation.
relative fitness
The fitness of a genotype relative to (as a proportion of) the fitness of a reference genotype, which is often set at 1.0.
relict
A species that has been “left behind”; for example, the last survivor of an otherwise extinct group. Sometimes, a species or population left in a locality after extinction throughout most of the region.
repeated sequence
The occurrence of repeated base pairs in a gene.
replacement substitution
See nonsynonymous substitution.
reporter construct
A DNA segment in which a putative cis-regulatory sequence is spliced upstream of a gene whose expression can be easily assayed, such as β-galactosidase or green fluorescent protein.
reproductive effort
The proportion of energy or materials that an organism allocates to reproduction rather than to growth and maintenance.
reproductive success
See fitness.
response to selection
The change in the mean value of a character over one or more generations due to selection.
restriction enzyme
An enzyme that cuts double-stranded DNA at specific short nucleotide sequences. Genetic variation within a population results in variation in DNA sequence lengths after treatment with a restriction enzyme, or restriction fragment length polymorphism (RFLP).
reticulate evolution
Union of different lineages of a clade by hybridization.
retrosequence
A cDNA copy of RNA. Most retrosequences are processed pseudogenes.
RFLP
See restriction enzyme.

S

saltation
A jump; a discontinuous mutational change in one or more phenotypic traits, usually of considerable magnitude.
sampling error
Random variation, meaning the likelihood that proportions of different kinds of items (e.g., alleles) in a sample are likely to differ, by chance, from the proportions in the set of items from which the sample is drawn.
scala naturae
The “scale of nature, ” or Great Chain of Being: the pre-evolutionary concept that all living things were created in an orderly series of forms, from lower to higher.
scientific creationism (= creation science)
A body of teaching that consists of attacks on, and supposedly scientific disproofs of, evolution.
scientific theory
A body of interconnected statements, based on reasoning and strongly supported by evidence, that explain some aspect—or often many aspects—of nature. Cf. hypothesis.
secondary contact
Interbreeding of two formerly allopatric populations that have become genetically differentiated.
selection
Nonrandom differential survival or reproduction of classes of phenotypically different entities. See natural selection, artificial selection.
selection coefficient
The difference between the mean relative fitness of individuals of a given genotype and that of a reference genotype.
selection differential
The difference (S) in mean trait between the population and the selected parents of the next generation.
selection gradient
The slope of the relation between phenotype values and the fitnesses of those phenotypes. A measure of the strength of natural selection.
selection plateau
The point at which response to selection (e.g., for a particular trait) ceases. Commonly observed in selection experiments.
selective advantage
The increment in fitness (survival and/or reproduction) provided by an allele or a character state.
selective sweep
Reduction or elimination of DNA sequence variation in the vicinity of a mutation that has been fixed by natural selection relatively recently.
selfing
Self-fertilization; union of female and male gametes produced by the same genetic individual. Cf. outcrossing.
“selfish DNA”
A DNA sequence that has the capacity for its own replication, or replication via other self-replicating elements, but has no immediate function (or is deleterious) for the organism in which it resides.
selfish genetic elements
See “selfish” DNA
semelparous
Pertaining to a life history in which individuals (especially females) reproduce only once. Cf. iteroparous.
semispecies
One of several groups of populations that are partially but not entirely isolated from one another by biological factors (isolating mechanisms).
senescence
Aging; deteriorative changes with aging; the increased probability of dying with increasing age.
sensory bias
The tendency in an organism for certain traits to be intrinsically stimulating and evoke a greater response simply because of the organization of the sensory system.
serial homology
A relationship among repeated, often differentiated, structures of a single organism, defined by their similarity of developmental origin; for example, the several legs and other appendages of an arthropod.
sex
The union of two genomes, usually carried by gametes.
sex-linked
Of a gene, being carried by one of the sex chromosomes; it may be expressed phenotypically in both sexes.
sex ratio
The proportion of males in a population.
sexual reproduction
Production of offspring whose genetic constitution is a mixture of those of two potentially genetically different gametes.
sexual selection
Differential reproduction as a result of variation in the ability to obtain mates.
sibling species
special creation
The doctrine that each species, living and extinct, was created independently by God, essentially in its present form.
Species that are difficult or impossible to distinguish by morphological characters, but may be discerned by differences in ecology, behavior, chromosomes, or other such characters.
silent substitution
See synonymous substitution.
single nucleotide polymorphism (SNP)
Variation in the identity of a nucleotide base pair at a single position in a DNA sequence, within or among populations of a species.
sister taxa
Two species or higher taxa that are derived from an immediate common ancestor, and are therefore each other’s closest relatives.
speciation
Evolution of reproductive isolation within an ancestral species, resulting in two or more descendant species.
species
In the sense of biological species, the members of a group of populations that interbreed or potentially interbreed with one another under natural conditions; a complex concept (see Chapter 15). Also, a fundamental taxonomic category to which individual specimens are assigned, which often but not always corresponds to the biological species. See also biological species, phylogenetic species concept.
species hitchhiking
The phylogenetic association of a character with other characters that affect speciation or extinction rates.
species selection
A form of group selection in which species with different characteristics increase (by speciation) or decrease (by extinction) in number at different rates because of a difference in their characteristics.
specific coevolution
The evolution of two species in response to each other.
specific mate recognition system
Within a species, the signals and responses used by potential mates. One sex (often the female) will not respond to inappropriate signals.
sperm competition
The opportunity for sperm of two or more males to fertilize one female’s eggs.
spliceosomal intron
An intron that requires a complex group of proteins called a spliceosome to be removed from the mRNA.
stability
Often used to mean constancy; more often in this book, the propensity to return to a condition (a stable equilibrium) after displacement from that condition.
stabilizing selection
Selection against phenotypes that deviate in either direction from an optimal value of a character.
standard deviation
The square root of the variance.
stasis
Absence of evolutionary change in one or more characters for some period of evolutionary time.
stem group
An extinct group of species early in evolutionary time; for example, the dinosaur order Theropoda. Cf. crown group.
stochastic
Random. Cf. deterministic.
strata
Layers of sedimentary rock that were deposited at different times.
subfunctionalization
Divergence of duplicate genes whereby each retains only a subset of the several functions of the ancestral gene. Cf. neofunctionalization.
subspecies
A named geographic race; a set of populations of a species that share one or more distinctive features and occupy a different geographic area from other subspecies.
substitution
The complete replacement of one allele by another within a population or species over evolutionary time. Cf. fixation.
substitution (base pair or amino acid)
The replacement of one nucleotide base pair (e.g., A–T) by another (e.g., G–C), or of one amino acid by another, in an entire population or species. Sometimes, but not always, changes the amino acid specified by the genetic code.
superspecies
A group of semispecies.
symbiosis
An intimate, usually physical, association between two or more species.
sympatric
Of two species or populations, occupying the same geographic locality so that the opportunity to interbreed is presented.
sympatric speciation
The evolution of reproductive barriers within a single, initially randomly mating (panmictic) population.
synapomorphy
A derived character state that is shared by two or more taxa and is postulated to have evolved in their common ancestor.
synonymous substitution
Fixation of a base pair change that does not alter the amino acid in the protein product of a gene; also called silent substitution. Cf. nonsynonymous substitution.

T

tandem repeat
In DNA, a pattern of repeated sequences of base pairs (e.g., ABBC).
target gene
In developmental genetics, a gene regulated by a transcription factor of interest. This regulation may be direct or indirect.
taxon (plural: taxa)
The named taxonomic unit (e.g., Homo sapiens, Hominidae, or Mammalia) to which individuals, or sets of species, are assigned. Higher taxa are those above the species level. Cf. category.
taxonomic category
See category and taxon.
teleology
The belief that natural events and objects have purposes and can be explained by their purposes.
tension zone
A hybrid zone in which the hybrids between populations have low intrinsic fitness, because of heterozygote disadvantage or breakdown of coadapted gene complexes.
territory
An area or volume of habitat defended by an organism or a group of organisms against other individuals, usually of the same species; territorial behavior is the behavior by which the territory is defended.
theistic evolution
The doctrine that God established natural laws (e.g., natural selection) and then let the universe run on its own, without further supernatural intervention.
theory
See scientific theory.
threshold trait
A trait controlled by polygenic variation rather than by single loci.
trade-off
The existence of both a fitness benefit and a fitness cost of a mutation or character state, relative to another.
transcription factor
A protein that interacts with a regulatory DNA sequence and affects the transcription of the associated gene.
transition
A mutation that changes a nucleotide to another nucleotide in the same class (purine or pyrimidine). Cf. transversion.
translational robustness
The ability of an amino acid sequence to maintain proper protein folding in the face of ongoing mutations.
translocation
The transfer of a segment of a chromosome to another, nonhomologous, chromosome; the chromosome formed by the addition of such a segment.
transposable element
A DNA sequence, copies of which become inserted into various sites in the genome.
trans-regulation
Effects on gene expression controlled by factors (often transcription factors) not tightly linked to the gene.
trans-regulatory element
A nucleotide sequence, usually encoding a regulatory protein, that is not closely linked to the structural gene whose expression it regulates. Cf. cis-regulatory element.
transposition
The production of copies of genetic material that become inserted into new positions in the genome.
transversion
A mutation that changes a nucleotide to another nucleotide in the opposite class (purine or pyrimidine). Cf. transition.
trend
A persistent, directional change in the average value of a character or lineage over the course of time. In a passive trend, a character (or lineage) shifts in both directions with equal probability. In a driven (= active) trend, change is more likely in one direction than in the other.

U

underdominance
The manifestation of lower fitness by heterozygotes than by homozygotes.
unequal crossing over
In recombination, the unequal exchange of genetic material. Occurs most commonly when two repeated genes or sequences mispair with their homologues.
uniformitarianism
The principal that the same geological processes that operated in the past operate in the present, and that the observations of geology can therefore be explained by causes we can now observe.
unstable equilibrium
An equilibrium to which a system does not return if disturbed.

V

variability
The ability, or potential, to vary.
variance (σ2, s2, V)
The average squared deviation of an observation from the arithmetic mean; hence, a measure of variation. s2 = [Σ(xix)2]/(n − 1), where x is the mean and n the number of observations.
vegetative propagation
A form of asexual reproduction in which offspring arise from a group of cells, as in plants that spread by runners or stolons.
vertical transmission
See horizontal transmission.
vestigial
Occurring in a rudimentary condition as a result of evolutionary reduction from a more elaborated, functional character state in an ancestor.
viability
Capacity for survival; often refers to the fraction of individuals surviving to a given age, and is contrasted with inviability due to deleterious genes.
vicariance
Separation of a continuously distributed ancestral population or species into separate populations due to the development of a geographic or ecological barrier.
virulence
Usually, the damage inflicted on a host by a pathogen or parasite; sometimes, the capacity of a pathogen or parasite to infect and develop in a host.

W

wild-type
The allele, genotype, or phenotype that is most prevalent (if there is one) in wild populations; with reference to the wild-type allele, other alleles are often termed mutations.

Z

zygote
A single-celled individual formed by the union of gametes. Occasionally used more loosely to refer to an offspring produced by sexual reproduction. 

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