speciation

The Milwaukee Journal-Sentinel prints a nice article about the work of my UW colleague, Jenny Boughman. Boughman studies adaptation and mating behavior in sticklebacks -- a model species for much current research on speciation.

Either form of cuckoldry undermines female choice, she said, and works against females’ central role in controlling reproduction in the species. It can also undermine the entire speciation process.

“The female had selected a male to mate with, but in fact the father of her offspring was not the male that she picked.”

Although the thieving and sneaking Boughman saw was between males of the same species, if habitat conditions change, it could just as easily happen between species, she noted.

All her research is pointing to one overall conclusion: the speciation process is much more fragile than scientists had once thought.

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Lizard dimorphism, ecology, and hominids

You know I like the lizard analogies for human evolution -- I wrote about limb length and predation last time around -- and now we have another paper from Jonathan Losos' group looking at ecological differentiation and sexual dimorphism:

Sexual dimorphism is widespread and substantial throughout the animal world (1, 2). It is surprising, then, that such a pervasive source of biological diversity has not been integrated into studies of adaptive radiation, despite extensive and growing attention to both phenomena (1, 3, 4, 5, 6, 7). Rather, most studies of adaptive radiation either group individuals without regard to sex or focus solely on one sex. Here we show that sexual differences contribute substantially to the ecomorphological diversity produced by the adaptive radiations of West Indian Anolis lizards: within anole species, males and females occupy mostly non-overlapping parts of morphological space; the overall extent of sexual variation is large relative to interspecific variation; and the degree of variation depends on ecological type. Thus, when sexual dimorphism in ecologically relevant traits is substantial, ignoring its contribution may significantly underestimate the adaptive component of evolutionary radiation. Conversely, if sexual dimorphism and interspecific divergence are alternative means of ecological diversification, then the degree of sexual dimorphism may be negatively related to the extent of adaptive radiation.

These anoles have evolved into four different ecomorphs repeatedly on different islands of the Greater Antilles, and the sexes differentiate not only in their morphology but also their habitat use and diet.

Primates are generally group foragers, and because they forage together, males and females eat the same foods a lot of the time. The major components of sexual dimorphism across primates have mostly been considered in relation to body size and canine dimorphism, both of which have a strong social import, but less obvious ecological import. That is an apparent contrast to the anoles, whose dimorphism allows males and females to specialize to slightly different niches.

But even though body size and canine size are the main elements of dimorphism that can be compared across all primates, both these features and others may take on ecological importance within primate species. For one thing, sexual dimorphism leads to ecological differentiation even within foraging groups -- not necessarily because different sized individuals can exploit different foods, but because large individuals have preferential access. This has clear dietary and behavioral import -- for example, hunting is a social activity in chimpanzees; males hunt and females don't, and if a female did hunt (with males around), the males would probably take away the kill. That's not entirely because males are larger, but sexual dimorphism helps to determine the social ecology.

What about hominids? In the Plio-Pleistocene, there were at least three sympatric species of hominids in East Africa (and possibly more) and at least two in South Africa (and possibly more). These species were differentiated by body size, relative brain size, and masticatory adaptations. In other words, they occupied different ecologies involving different foods, and natural selection reinforced their ecological differences (even if the average diet involved much overlap, as I reviewed earlier).

The robust species in East Africa (A. boisei) appears to have had substantial body size dimorphism. The habiline species (H. habilis) was either substantially dimorphic, or was actually composed of two species. The large-bodied Homo may have had reduced dimorphism comparable to that in recent humans. Yet, many people have suggested that this least dimorphic species should have been the one where males and females had the greatest ecological differentiation. This is based on analogy with recent hunter-gatherers, assuming that the introduction of meat in substantial quantities requires a sexual division of labor.

Male and female lions have substantial body size dimorphism, and they are ecologically differentiated by prey size. Just thinking out loud...

References:

Butler MA, Sawyer SA, Losos JB. 2007. Sexual dimorphism and adaptive radiation in Anolis lizards. Nature 447:202-205. doi:10.1038/nature05774

Dingo difficulties

From the discussion of L. C. Birch's paper, "Evolutionary opportunity for insects and mammals in Australia", in the edited volume The Genetics of Colonizing Species, edited by H. G. Baker and G. L. Stebbins, p. 212:

Waddington: At what date was the ordinary dog introduced into Australia? Dingoes were there before white men?
Birch: Dingoes probably came to Australia with the aborigines some millenia [sic] ago. The domesticated dog of the white man has been in Australia less than 2 centuries.
Mayr: Well, the dingo is a dog. If you go to the mountains of New Guinea you will see dogs which cannot be distinguished from dingoes. They do not bark. These dingo-like dogs are associated with the native villages and I would say that the dog or dingo came to Australia with one of the early waves of aborigines, whether this was 6000 or 12,000 B.C. or earlier.
Waddington: It is not a feral European dog?
Birch: It would be awfully hard to study this.
Mayr: You would need to wear chain mail.

Minireview

I found that exchange very entertaining, but if I'm posting it I figured I'd better provide some pointers to recent work on dingo evolution. Tim Flannery (2003) attributed the arrival of the dingo in Australia to contacts with Lapita people between 4000 and 3500 years ago. It has been suggested that ancient Polynesian dogs were also of this type, represented archaeologically by the "Pukapuka dog" (Shigehara et al. 1993). Flannery also mentions the work of Gordon Corbett, who proposed that Australian lice had been transferred back to Asia on one or more dingoes at some point. This transfer occurred in ancient times, and requires that some people landed on Australia, picked up some dingoes, and schlepped them back to Indonesia.

Peter Savolainen and colleagues (2004) studied the mitochondrial DNA variation in dingoes and compared their sequences to dogs from populations throughout the world. They find that dingoes have a very circumscribed degree of mtDNA variation, with one major haplotype (A29) and several minor haplotypes that are one- or two- mutation variants of this one. The haplotype A29 is otherwise found only in Asian, Polynesian and Arctic dogs. Their conclusion has this:

Among domestic dogs, A29 was found only among East Asian, Island Southeast Asian, and American dogs, and the mtDNA types radiating from A29 in the minimum-spanning network were found almost exclusively in East Asia (11), strongly indicating an East Asian rather than Indian origin for the dingo ancestor. The estimated time for the founding of the dingo population, 5,000 yr ago, fits relatively well with the archaeological record of the region, with the oldest finds of dingo being 3,500 years old and the earliest finds of dogs on nearby islands being 3,500-year-old remains on Timor (7). An East Asian ancestry 5,000 yr ago suggests that the dingoes may have arrived in connection with the expansion from south China into Island Southeast Asia of the Austronesian culture, which involved domestic dogs, pigs, and chicken. According to the current theories, the expansion started 6,000 yr ago from Taiwan via the Philippines to Indonesia, where it was split into a westward and an eastward direction and had by 4,000 yr ago reached Timor (7, 21).
In conclusion, this study of mtDNA sequence variation among dingoes provides a number of clues from which a detailed picture of the origin and history of the Australian dingo can be derived. The dingo originated from a population of East Asian dogs. Type A29 was one of several domestic dog mtDNA types brought into Island Southeast Asia, but only A29 reached Australia. The dingo population was probably founded from a small number of animals, as the last trickle of domestic dogs through a series of bottlenecks, or even by a single chance event and has since remained effectively isolated from other dog populations. The dingoes may have arrived in connection with the expansion, starting 6,000 yr ago, from south China into Island Southeast Asia of the Austronesian culture. By this time, domestic dogs had existed for several thousand years (4, 11), and the present semidomestic state of the dingo can probably be attributed to a long existence as a feral animal. After >3,500 years of isolation, the dingoes represent a unique isolate of early undifferentiated dogs.

They also note that the A29 haplotype is found in the New Guinea "singing" dogs -- the feral dogs that Mayr mentions. The New Guinea dogs were reviewed by Janice Koler-Matznick and colleagues (2003). They can be distinguished from dingoes, both in terms of their behaviors and in their size -- the New Guinea dogs average smaller than the smallest dingoes. The two are apparently related to each other, and Balinese street dogs also include the dingo-like mtDNA sequence, although their variation is much higher than found in dingoes (Irion et al. 2005). Other "pariah" dogs with similar phenotypes (e.g., light tan coloration) exist in India, Phillipines, and Southeast Asia, but these may have evolved convergently with the dingo.

That's my quick dingo mini-review. I don't claim it's complete, but it gives some directions for further looking for those interested.

References:

Birch LC. 1965. Evolutionary opportunity for insects and mammals in Australia. Pp. 197-214 in The Genetics of Colonizing Species, edited by Baker HG, Stebbins GL. Academic Press, New York.

Flannery TF. 2003. The Future Eaters: An Ecological History of the Australian Lands and People. Grove Press, New York.

Irion DN, Schaffer AL, Grant S, Wilton AN, Pedersen NC. 2005. Genetic variation analysis of the Bali street dog using microsatellites. BMC Genet 6:6. doi:10.1186/1471-2156-6-6

Koler-Matznick J, Brisbin IL, Jr, Geinstein M, Bulmer S. 2003. An updated description of the New Guinea singing dog (Canis hallstromi, Troughton 1957). J Zool Lond 261:109-118. doi:10.1017/S0952836903004060

Savolainen P, Leitner T, Wilton AN, Matisoo-Smith E, Lundeberg J. 2004. A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc Nat Acad Sci USA 101:12387-12390. doi:10.1073/pnas.0401814101

Shigehara N, Matsu'Ura S, Nakamura T, Kondo M. 1993. First discovery of the ancient dingo-type dog in Polynesia (Pukapuka, Cook Islands). Int J Osteoarcheol 3:315-320. doi:10.1002/oa.1390030410

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Invasive species

The story of colonizing species encompasses a wide range of "colonizing ability". From attempts at deliberate introductions, we know that some species just don't have a great potential to colonizing new territory; others succeed for a while and then explode.

We don't know the number of failed accidental introductions, but we do know a lot about one extreme -- the accidental introductions of alien species that become invasive problems. Such species have such a high colonizing potential (at least in certain contexts) that their populations explode beyond the numbers in their native ranges.

Brown (1957), discussing the colonizing ability of populations at the center of population ranges, brings in a number of examples of such invasive species, whose spread is often apparent within the span of decades or even years. One of these is the invasion and spread of the fire ant into North America.

Fire ants were inadvertently imported to the U.S. from South America sometime around 1918. Wilson (1953) gave an account of the early population history of these ants. It was clear in these early years that there were two forms of the ants, a dark-colored form and a red form. Of these, the red form was the more invasive, but it appeared that the real invasive character of the population might be attibutable to hybridization between the two. Brown (1957:259) quoted Wilson (1953):

For about ten years [the Mobile population] remained both genetically homogeneous, corresponding to the dark southern race richteri Forel of the South American parental population, and relatively unsuccessful in its new surroundings. In the period following 1930 a smaller reddish form rose to abundance, interbred extensively with the original dark form, and apparently precipitated the species' explosive increase to pest proportions. By 1949 the reddish form had largely replaced the dark form, which had become limited principally to the southern strip of the main population and part of its eastern and western periphery and to two outlying, isolated populations in Mississippi.

To this, Brown (1957:260) added:

The dark-phase colonies are now limited to certain separated peripheral areas of the range and a few minor enclaves within the main area of infestation, and even where they occur, they are often in the minority. All degrees of intergration [sic] link dark and red phases. As the red forms press outward, the dark forms apparently suffer both genetic swamping and competition-aggression, and consequently tend to extinction in most habitats. In spite of these forces at work against it, the dark form persists, genetically embedded, so to speak, in the dense and expanding matrix of red populations. This case is very instructive in showing how, regardless of its origin in this particular case, a genetic change actually spreads from a central point of introduction and tends in this way to cause a central-peripheral differential.

For Brown, the entire case of fire ant invasion is an evidence for central species having a greater colonizing potential than peripheral ones, because the tropical Solenopsis species were displacing congeneric S. geminata and S. xyloni, which had been common throughout the Caribbean and Gulf of Mexico coastal areas. The entire New World, from the point of view of Solenopsis is a zone with a tropical center and subtropical and temperate peripheries. In this case, Brown proposed that the displacement of fire ants from a central area (southern Brazil or Argentina) to the northern periphery had enabled the invasive character of the spread, although with probable adaptive changes in the new colonizing population.

The other element of this argument is that populations face more competition from similar competitor species and more natural disease and predation in the central parts of their ranges. Where a species can exist at higher densities, it can support more parasites, pathogens, and predators. For fire ants, these predators and parasites include a number of species that have been deliberately introduced as part of efforts to control their spread in the U.S.

Fire ant initial invasion area from 1928-1949

Fire ant dispersal in southern U.S. from ca. 1939 to 1995. Figure from Brown 1957 p. 260. Brown took the plot from Wilson (1951).

I looked at that figure and gasped -- imagine living in one of the outlying counties in 1949 and knowing that pattern of spread.

Of course, from there the dispersal simply exploded. A good review of the history of fire ant spread was given by Anne-Marie Callcott and Homer Collins (1996). Their maps of infested counties over time say it all:

Fire ant dispersal map, 1939-1995

Fire ant dispersal in southern U.S. from ca. 1939 to 1995. Figures from Callcott and Collins 1996, pp. 244-246, recompiled for web format.

By the 1970's it was understood that the two forms of invasive fire ants had been two species (the dark form, Solenopsis richteri and the red Solenopsis invicta). The differentiation between the two at the colonizing edges of the fire ant wave is a genuine hybrid zone. Shoemaker and colleagues (1996) sampled the genetics of ants in this hybrid zone, finding that genetic markers and morphological characters introgressed at different rates, and that there appeared to be selection against hybrids in contact with one or the other parental type.

Later, Ross and Shoemaker (2005) studied the genetics of these South American species (S. richteri and S. invicta) in their native ranges. They found that the species were fully reproductively isolated at study sites where both were found. Additionally, the extent of genetic differentiation between different populations of each, and the presence of a third closely related species (S. quinquecuspis) led them to suggest that the group "is actively radiating species". This would be a confirmation of Brown's (1957) argument for the high speciation potential of the central populations in the range of this genus. It remains to be seen whether these central populations have actively generated new colonizing species to displace more peripheral populations by natural movement.

In the case of fire ants, the rapid colonization of the North American invaders has been aided by some unique social changes, described by Kenneth Ross and colleagues (1996). Probably most people think of ant colonies as having a single queen and many workers and soldier ants. But some kinds of ants form colonies with multiple queens. Imported fire ants have both single-queen and multiple-queen colonies, but the size and proportion of multiple-queen colonies has greatly increased relative to their South American range. This reduces intercolony competition and facilitates their spread compared to native species.

Later work has shown that S. invicta has a genetic switch that determines whether queens will form their own colonies or whether they will remain in their natal colony or attempt to join a new one. The system is described by Tsutsui and Suarez (2003):

Queens from the two social forms typically possess different genotypes at the general protein-9 (Gp-9) allozyme locus (Ross 1997; Ross & Keller 1998; Krieger & Ross 2002 ). Monogyne colonies contain queens that are BB at Gp-9 and produce new BB queens that disperse and found colonies independently (Shoemaker & Ross 1996). Conversely, the queens in polygyne colonies are almost exclusively Bb and can produce BB, Bb, and bb queens. New Bb queens either join their natal colony or attempt to join other polygyne colonies (DeHeer et al. 1999). Any BB queens that attempt to join polygyne colonies or reproduce within them are killed by the Bb workers present in polygyne colonies (Ross & Keller 1998). Studies of queen dispersal have shown that newly produced polygyne queens with the BB genotype, who are doomed to execution if they remain in their natal colony or attempt to join other colonies, may attempt to found colonies independently, but with limited success (DeHeer et al. 1999). The bb genotype appears to be lethal in workers, and fertile bb queens are extremely rare (Ross 1997; but see DeHeer et al. 1999; Goodisman et al. 2000. Interestingly, polygyne colonies in the native range can possess reproductive queens that are either BB or Bb (Keller & Ross 1999). This difference between native and introduced populations could indicate the presence of other undiscovered genes or alleles that affect queen number or could be the result of a genetic bottleneck on variation at the loci involved in this process (Keller & Ross 1999; Krieger & Ross 2002).

This is an interesting case with several elements. A simple genetic strategy is held polymorphic because the homozygotes for the multiple-queen strategy are completely nonviable. In the new founder populations, this allele might be lost completely. Also, possible modifier loci may lose alleles that restrain the formation of supercolonies in their native range.

Still, when it comes to social changes of invasive ants, nothing compares to the case of the Argentine ant (Linepithema humile). Like fire ants, the Argentine ant invaded the American South, becoming common early in the 1900's. They have also invaded California and the Southwest as well as five of the other six continents (sparing Antarctica...). In Argentine ants, the genetic uniformity of new colonizing populations is so great that the ants form supercolonies stretching across large areas. Here's a passage from a review paper by Neil Tsutsui and Andrew Suarez (2003):

Throughout their introduced range Argentine ants are highly unicolonial ( Newell & Barber 1913; Markin 1970; Keller & Passera 1989; Way et al. 1997; Suarez et al. 1999; Tsutsui et al. 2000; Giraud et al. 2002) and can attain remarkably high densities. For example, in an early attempt to eradicate Argentine ants from a 19-acre ( 7.7-ha) orange grove in Louisiana, Horton (1918 )reported trapping an astounding 1.3 million queens in artificial nest boxes over the course of 1 year. Including workers and brood, the total volume of Argentine ants collected was over 1000 gallons (Horton 1918). Although a single "supercolony" occupies virtually the entire Californian range ( Tsutsui et al. 2000), close examination has revealed several smaller "secondary" colonies (Holway et al. 1998; Tsutsui & Case 2001). The secondary colonies are spatially restricted, aggressive toward one another and toward the large supercolony, genetically distinct from one another and the large supercolony, and may be the result of separate introductions or genetic drift (Suarez et al. 1999; Tsutsui et al. 2001).

Yuck! Looking at the 20 inches of snow lining my yard is a whole lot easier when I consider how few invasive ant species have come from Siberia.

The invading Argentine ants have an even more substantial reduction in genetic diversity than fire ants, with heterozygosity being reduced to a third of its value in the native range of the ants. Not only founder effects, but also unique patterns of social behavior and selection maintain this low diversity. There is selection against genetically different colonies, who are outcompeted by supercolonies of genetically similar lineages. Also, a phenomenon called "queen execution" tends to increase the relatedness of individuals within colonies by eliminating a proportion of reproductives.

Tsutsui and Suarez (2003) present a good argument for understanding the genetics of this transformation to highly invasive phenotypes:

Finally, there are dozens of introduced ant species about which virtually nothing is known (McGlynn 1999). Many of these species may have the potential to become invasive, and prevention may be possible only if we are aware of their dispersal capabilities (both natural and human-mediated) and the factors that could facilitate their successful establishment and spread.

Invasive fire ants have recently reached California and are busily displacing the Argentine ants there. After reading through a number of articles, the final message of many of them has been that invasive species will ultimately be controlled only by the arrival of new invasive competitors.

Yippee.

References:

Brown WL, Jr. 1957. Centrifugal speciation. Q Rev Biol 32:247-277.

Callcott A-M, Collins HL. 1996. Invasion and range expansion of imported fire ants (Hymenoptera: Formicidae) in North America from 1918-1995. The Florida Entomologist 79:240-251.

Ross KG, Vargo EL, Keller L. 1996. Social evolution in a new environment: the case of introduced fire ants. Proc Nat Acad Sci USA 93:3021-3025. Abstract

Shoemaker DD, Ross KG, Arnold ML. 1996. Genetic structure and evolution of a fire ant hybrid zone. Evolution 50:1958-1976.

Tsutsui ND, Suarez AV. 2003. The colony structure and population biology of invasive ants. Conservation Biol 17:48-58. doi:10.1046/j.1523-1739.2003.02018.x

Wilson EO. 1953. Origin of the variation in the imported fire ant. Evolution 7:262-263.

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Center and edge

Fifty years ago in science:

Various ideas and data more or less closely related to the present hypothesis are apparently widespread in the literature (e.g., Matthew, 1915; Lutz, 1916; Timoféeff-Ressovsky, 1940, among others), and it would be interesting but difficult to trace the historical continuity of thoughts along this line. For instance, there is the venerable notion that variation in the genus Homo has proceeded prevailingly outward from more central continental areas into peripheral Europe, riding on successive population waves. There seem to be no serious objections to this point of view. It may well be that speciation in early man depended on central-peripheral processes as outlined in the present hypothesis. In fact, I predict that good evidence for this will be available in a very short time (Brown 1957:265).

Well, maybe not a short time, but one or another variant of this idea have certainly dominated both before and after that paper.

A problem is that there are at least two different evolutionary patterns that can lead to the outcome of variable center and less variable periphery populations. One is the repeated proliferation of colonizing species at the center and their partial or complete replacement of populations at the periphery. This is the "centrifugal speciation" model. The other is radial gene flow directed from the center to the periphery.

The difference between these two alternatives is really a matter of degree. Both scenarios depend on a common source-sink population dynamic. The peripheral populations absorb more migrants from the center than they produce; the center populations produce more new genetic variants. Possibly the center population includes distinct morphs with different colonizing potential, and the peripheral populations ultimately receive only the best colonizers. The difference between the "centrifugal speciation" model and simple radial gene flow is a matter of clumpiness -- do genes tend to move together with each other in discrete migrations (with possible population replacements) or individually with continuous genetic exchanges?

Another way to put this distinction is to consider the behavior of clines of variation over time. With recurrent colonization from a central population, clines of variation tend to move in synchrony with each other as multiple genetic systems (possibly coadapted gene complexes) disperse with new colonists into the peripheral populations. At the extreme of speciation, all genes move together, establishing new clines entirely (although some genes may introgress from the original peripheral populations). In contrast, under long-term radial gene flow, geographic clines may evolve nearly independently from each other for different genes (depending on linkage and interactions among them).

There are two scenarios in which the two patterns can be differentiated. If one of the peripheral populations expands in size and itself becomes a colonizer (possibly impinging or displacing a central population), the overall pattern of variation may be noticeably different from the simple centrifugal pattern. Or, as Thorne and Wolpoff (1981) suggest, recurrent gene flow from the central populations may be opposed by selection in the peripheries, leading to long-term stable clines.

Which pattern characterized human evolution? Almost certainly, it was different at different times and in different places -- sometimes major dispersals, other times long-term gene flow.

References:

Brown WL, Jr. 1957. Centrifugal speciation. Q Rev Biol 32:247-277.

Thorne AG, Wolpoff MH. 1981. Regional continuity in Australasian Pleistocene hominid evolution. Am J Phys Anthropol 55:337-349. doi:10.1002/ajpa.1330550308

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Genetic discord

I ran across this paper from a few years ago by John Avise and DeEtte Walker, which considers the implication of reticulation-based species concepts for mtDNA-generated phylogenies.

After quoting Dobzhansky on natural categories, they point to the central problem with using mtDNA phylogenies to define species: a clonally inherited gene does not easily lend itself to testing horizontal gene transfer:

In this same spirit, we ask here whether biotic discontinuities as seen through the eyes of laboratory-based mitochondrial geneticists tend to bear resemblance in number and composition to the biological units currently recognized as taxonomic species. There are additional reasons for interest in the outcome. First, discontinuities might be evident in local biotas (the nondimensional species perception) but may blur when geographic variation is taken into account. Molecular phylogeographic studies address this issue, because they explicitly analyze spatial variation (6, 7). Second, under the biological species concept (BSC), a sexual species usually is perceived as a reproductive community whose gene pool retains coherency primarily via the bonds of interbreeding and genetic exchange (1, 8); however, mtDNA molecules are transmitted asexually, and matrilines are nonreticulate. Thus, any genuine unities within (and discontinuities between) groups of organisms in mtDNA genotype cannot be attributed to "horizontal" patterns of contemporary lineage anastomosis via mating per se. Instead, they must be caused by "vertical" connections (and partitions) in matrilineal phylogenies. However, vertical connections themselves are functions of the demographic histories of population units demarcated by temporally extended patterns of interbreeding and gene flow.

I think this passage puts the situation more direly than deserved -- after all, every gene is vertically inherited. Mitochondrial DNA is no exception. It can be transferred by gene flow just as surely as any autosomal gene.

No, the key difference is that clonal inheritance leaves mtDNA with a greatly reduced effective size compared to autosomal (or X-linked) genes. This means that a given amount of gene flow is vastly less effective at dispersing mtDNA variants. Hence mtDNA (and Y chromosomes) have much higher FST (at equilibrium) than other genetic markers.

In other words, longstanding populations within a species will tend to look more divergent considering only their mitochondrial DNA than considering their autosomal genes. We can see this pattern when considering differences among subspecies of chimpanzees and other hominoids. The subspecies are highly distinct from each other considering only their mtDNA, with long divergence times ranging higher than a million years. The other uniparentally inherited genetic system, the nonrecombining portion of the Y chromosome (NRY) shows a similar pattern -- subspecies of chimpanzees are highly distinct, sharing no NRY lineages (Stone et al. 2001). In contrast, there is substantially more sharing of variants at autosomal sites (Fischer et al. 2004). Chimpanzee subspecies share many fewer autosomal variants than are shared among human groups, but they share many more autosomal than mtDNA or Y chromosome variants. Gorilla genes follow a similar pattern: mtDNA indicates very strong divergence between western and eastern gorillas, while autosomal genes show evidence for recurrent gene flow between them up to 150,000 years ago (Thalmann et al. 2007).
Avise and Walker compared mtDNA phylogenies for vertebrates with commonly accepted taxonomic species, finding roughly twice as many deep mtDNA phylogroups as taxonomic species. They consider that these generally represent historical patterns of demography and constrained gene flow within species.

Coalescent patterns in gene trees are related intimately to historical patterns in population demography (7, 21, 22). In particular, tight connections among nonanastomose [nonreticulating] genotypes suggest recent lineage coalescence to a shared ancestor, likely because of relatively small evolutionary effective population sizes that cause extant lineages to have shallow temporal depth. Conversely, large genetic gaps between gene-tree branches suggest long-standing historical population separations. In support of this likelihood, nearly all of the deep phylogenetic disjunctions registered in the intraspecific mtDNA gene trees in this review involved regionally separate populations.

This is basically saying that regional differentiation within species is an important source of genetic variability. They mention that male-mediated dispersal would create patterns not easily tested with mtDNA; this is one factor but broadly, any single gene will create a phylogeny that is potentially discordant with others in various ways.

References:

Avise JC, Walker D. 1999. Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome. Proc Nat Acad Sci USA 96:992-995. Abstract

Fischer A, Wiebe V, Pääbo S, Przeworski M. 2004. Evidence for a complex demographic history of chimpanzees. Mol Biol Evol 21:799-808. doi:10.1093/molbev/msh083

Stone AC, Griffiths RC, Zegura SL, Hammer MF. 2002. High levels of Y-chromosome nucleotide diversity in the genus Pan. Proc Nat Acad Sci USA 99:43-48. doi:10.1073/pnas.012364999

Thalmann O, Fischer A, Lankester F, Pääbo S, Vigilant L. 2007. The complex evolutionary history of gorillas: insights from genomic data. Mol Biol Evol 24:146-158. doi:10.1093/molbev/msl160

Sweeping away differences

Thinking about those wolves and their population structure a bit more, I was leafing through a back issue of New Phytologist, and found an article by Loren Rieseberg and colleagues. From a theoretical perspective, strong population differentiation is no problem, since there is always recourse to natural selection as a mechanism to make local populations different -- exactly the solution proposed for the wolves.

Rieseberg and colleagues have a section that considers the opposite problem: what is it that keeps species with low gene flow cohesive?

Students of speciation have primarily focused on the conservative role of gene flow, in which high levels of gene flow (Nem > 4, where Nem is the effective number of migrants per generation) serve to homogenize populations at neutral loci (Hartl & Clark, 1997). It was recognized more than three decades ago, however, that levels of gene flow in many species are not nearly this high (Ehrlich & Raven, 1969). Indeed, for many plant and animal species, estimates of Nem fall well below one (Fig. 1), the level of gene flow required to prevent divergence at neutral loci (Wright, 1931).

Humans today have Nem > 1, but a lot of large mammal species don't (as a yardstick, Nem > 1 predicts FST < 0.2).

Consideration of the creative role of gene flow as a mechanism for the spread of advantageous alleles offers a potential solution to this problem (Rieseberg & Burke, 2001). Only very low levels of gene flow are required for the spread of advantageous alleles and fixation times are much less than for their neutral counterparts (Slatkin, 1976). Thus, it is conceivable that species' populations could remain connected through repeated selective sweeps of favored mutations and associated hitchhiking events or 'genetic draft' (Gillespie, 2001).
Is this scenario likely? In low gene flow species, population subdivision greatly reduces the rate of allelic spread, particularly for weakly selected or neutral alleles (Slatkin, 1976; Whitlock, 2003). Thus, one concern is whether a favored allele will spread to fixation before it goes extinct. A second concern is whether selective sweeps are frequent enough to produce cohesion. If they are rare or restricted to a handful of loci, the level of connectedness might not be sufficient to account for the apparent cohesiveness observed for many species in nature.

They discuss modeling results that quantify the possible dispersal rates of favorable mutations with low gene flow, concluding:

In sum, the effects of population subdivision are to greatly increase fixation times relative to panmictic populations with a slight positive effect on fixation probabilities. More importantly, however, population subdivision magnifies the differences in time to fixation for strongly and weakly selected alleles. Thus, weakly selected alleles that spread to fixation in panmictic populations are less likely to do so in subdivided populations, possibly biasing fixed interspecific differences toward major genes.

Next comes an empirical question: are beneficial mutations typically selected strongly enough to disperse through such metapopulations? They conclude that they often are, so much so that repeated sweeps may be the major reason that the genomes of widespread species remain connected instead of fragmenting into local, isolated variants.

The theme of the paper as a whole is to discuss the ways that natural selection may lead to speciation, focusing on peripatric and sympatric contexts. Thus, several "sterility loci", and other genes promoting and maintaining differentiation of populations, are described.

References:

Rieseberg LH, Church SA, Morjan CL. 2004. Integration of populations and differentiation of species. New Phytologist 161:59--70. DOI link

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Duck species collapsing in face of mallard onslaught

Earlier this year, I discussed a paper about the collapse of stickleback species due to increasing hybridization. In a similar vein, I ran across this 2004 paper by Judith Mank reviewing the apparent breakdown of the distinction between American black ducks and mallards:

American black ducks (Anas rubripes) and mallards (A. platyrhynchos) are morphologically and behaviorally similar species that were primarily allopatric prior to European colonization of North America. Subsequent sympatry has resulted in hybridization, and recent molecular analyses of mallards and black ducks failed to identify two distinct taxa, either due to horizontal gene flow, homoplasy, or shared ancestry. We analyzed microsatellite markers in modern and museum specimens to determine if the inter-relatedness of mallards and black ducks was an ancestral or recent character. Gst, a measure of genetic differentiation, decreased from 0.146 for mallards and black ducks living before 1940, to 0.008 for birds taken in 1998. This is a significant reduction in genetic differentiation, and represents a breakdown in species integrity most likely due to hybridization. Using modern specimens, we observed that despite a lower incidence of sympatry, northern black ducks are now no more distinct from mallards than their southern conspecifics.

Turns out that this outcome was predicted a long time ago, as reflected in a 1967 paper by Paul Johnsgard:

Owing to its much smaller gene pool, the Black Duck is vulnerable to eventual swamping through hybridization and introgression, although the present hybridization rate is sufficiently low as to make this unlikely in the foreseeable future (Johnsgard 1967:51).

Hybridization of introduced mallards with endemic species is a problem all over the world. For instance, New Zealand grey ducks:

Small numbers of Mallard (Anas platyrhynchos) were introduced into New Zealand from Great Britain and North America over 100 years ago. Both sexes have undergone differentiation in size and plumage characters as a consequence of hybridization with the indigenous Grey Duck (A. superciliosa). Pure forms of both species, as documented by early descriptions, appear to be disappearing, particularly the Grey Duck. As a consequence of hybridization, two morphologically distinct hybrid populations have been produced: one resembles the Grey Duck and the other the Mallard. By 1981-1982 levels of hybridization, based on plumage analysis, had reached 51%, and the proportion of pure Grey Ducks had dropped to 4.5%, which is below the level suggested for the maintenance of a species. In the absence of reproductive isolation or antihybridization mechanisms between these two species, the Mallard and hybrid populations represent a potential threat to the conservation of the New Zealand Grey Duck (Gillespie 1985:459).

And a review entitled "Extinction by hybridization and introgression" by Rhymer and Simberloff, there is this passage:

Hybridization with introduced mallards has contributed to the decline of the endangered, endemic Hawaiian duck (A. wyvilliana) and has hampered attempts to reintroduce this species to Oahu and Hawaii. Domesticated nonmigratory mallards that escaped or were released for hunting breed with the endemic Florida mottled duck (A. fulvigula fulvigula), and the resultant introgression threatens the existence of the latter subspecies. Introgression also occurs between domesticated introduced mallards and the native Australian (Pasific) black duck, A. superciliosa rogersi (Rhymer and Simberloff 1996:86)

Mallards are not alone, apparently ruddy ducks of North American origin now threaten the endangered population of European white-headed ducks (Oxyura leucocephala).

References:

Gillespie GD. 1985. Hybridization, introgression, and morphometric differentiation between mallard (Anas platyrhynchos ) and grey duck (Anas superciliosa ) in Otago, New Zealand. Auk 102:459-469.

Johnsgard PA. 1967. Sympatry changes and hybridization incidence in mallards and black ducks. American Midland Naturalist 77:1:51-65. DOI link

Mank JE, Carlson JE, Brittingham MC. 2004. A century of hybridization: decreasing genetic distance between American black ducks and mallards. Conservation Genetics 5:395-403. DOI link

Rhymer JM, Simberloff D. 1996. Extinction by hybridization and introgression. Ann Rev Ecol Syst 27:83-109.

Half-grizzly half-polar bear hybrid

Here's the story:

Officials seized the creature after noticing its white fur was scattered with brown patches and that it had the long claws and humped back of a grizzly. Now a DNA test has confirmed that it is indeed a hybrid -- possibly the first documented in the wild.
"We've known it's possible, but actually most of us never thought it would happen," said Ian Stirling, a polar bear biologist with the Canadian Wildlife Service in Edmonton.
Polar bears and grizzlies have been successfully paired in zoos before -- Stirling could not speculate why -- and their offspring are fertile.

It seems to me it would be a lot more useful for all the Bigfoot-hunting types to go looking for rare hybrids. We would certainly learn a lot more from it.

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If hybrid zones are transient, what are the likely outcomes? One possibility is that hybrid zones represent secondary contact and neutral diffusion, that the differentiated populations will fuse, yielding a single, possibly polymorphic, species. Alternatively, hybrid zones might represent the "wave of advance" of a superior competitor, resulting in the eventual extinction of one of the two hybridizing taxa. In fact, fusion and extinction are not mutually exclusive outcomes because the fusion of two taxa might involve either selective or random extinction of alleles from each of the parental types (Harrison, 1990).

In this sense, "extinction" means the disappearance of one of the parental types, not necessarily the disappearance of its alleles from the subsequent population.

(continued) If certain recombinate genotypes produced by hybridization and backcrossing persist as local "hybrid swarms" or "stabilized introgressants," the product of fusion may be considered a distinct species.
One of the most controversial issues surrounding hybrid zones is whether they are sites of "reinforcement" -- the evolution of prezygotic barriers to gene exchange in response to selection against hybrids. A mode of speciation originally championed by Dobzhansky (1940, 1941), the "reinforcement model" has met with considerable criticism in recent years (Patterson 1978, 1982; Butlin, 1987, 1989)....

This strain is picked up in the third chapter of the volume by Howard (1993).

(continued) Finally, selection within hybrid zones can lead to the weakening (rather than the strengthening) of barriers to gene exchange. Selection may favor those variants that show the least reduction in viability and fertility when crossed with either of the parental types.

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Hybridization among Darwin's finches

This is an old paper by Peter and Rosemary Grant, from 2002:

Unpredictable Evolution in a 30-Year Study of Darwin's Finches
Peter R. Grant and B. Rosemary Grant
Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galápagos island of Daphne Major. From 1972 to 2001, Geospiza fortis (medium ground finch) and Geospiza scandens (cactus finch) changed several times in body size and two beak traits. Natural selection occurred frequently in both species and varied from unidirectional to oscillating, episodic to gradual. Hybridization occurred repeatedly though rarely, resulting in elevated phenotypic variances in G. scandens and a change in beak shape. The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.

It seems like the purpose of the paper is to demonstrate the fluctuating evolution of the finches in response to environmental change. But I was drawn to it by the demonstration of biased gene flow from one species to the other:

The proportionally greater gene flow from G. fortis to G. scandens than vice versa has an ecological explanation. Adult sex ratios of G. scandens became male biased after 1983 (Fig. 4C) as a result of heavy mortality of the socially subordinate females. High mortality was caused by the decline of their principal dry-season food, Opuntia cactus seeds and flowers; rampantly growing vines smothered the bushes (16). G. fortis, more dependent on small seeds of several other plant species, retained a sex ratio close to 1:1 (Fig. 4C). Thus, when breeding resumed in 1987 after 2 years of drought, competition among females for mates was greater in G. fortis than in G. scandens. All 23 G. scandens females paired with G. scandens males, but two of 115 G. fortis females paired interspecifically. All their F1 offspring later bred with G. scandens (43) because choice of mates is largely determined by a sexual imprinting-like process on paternal song (42).

They conclude that this hybridization had an introgressive effect, acting in the same direction as selection for beak shape during the early 1990's, but continuing throughout the decade while there was little evidence for selection. There was little or no fitness loss to interspecific hybrids.

The case is distinctive because the effects of introgression on the characters of beak size and shape are consistently large enough to be measured each generation. This despite the fact that the proportion of F1 hybrids and first-generation backcrosses in the G. scandens population was never greater than 20 percent.

References:

Grant PR, Grant BR. 2002. Unpredictable evolution in a 30-year study of Darwin's finches. Science 296:707-711. Full text (subscription)

Why are hybrids usually bad?

Two hypotheses, discussed by Burke and Arnold (2001):

The role of epistasis in adaptive evolution has been a controversial issue ever since Sewall Wright and R.A. Fisher first formalized their views in the early 1930s. According to Wright (113, 114), natural selection retains favorably interacting gene combinations. Therefore, as a result of the highly integrated nature of the genome, selection may lead to the production of what Dobzhansky (43) has termed "coadapted" gene complexes. In contrast, Fisher (48) argued that natural selection acts primarily on single genes, rather than on gene complexes. In Fisher's view, therefore, selection favors alleles that elevate fitness, on average, across all possible genetic backgrounds within a lineage. Such alleles have been termed "good mixers" (75). Regardless of the role of epistasis within lineages, however, negative epistasis in a hybrid genetic background, or hybrid incompatibility, is fully consistent with both the Wrightian and Fisherian worldviews. This is because allelic fixation occurs in any one lineage without regard to the compatibility (or lack thereof) of new alleles with those in any other lineage. Hybridization then produces a vast array of recombinant genotypes that have never before been subjected to selection. On average, these genotypes will be less well adapted than their parents, giving rise to some level of selection against hybrids.
Hybrid breakdown, or the reduction in fitness of segregating hybrid progeny that often results from intercrossing genetically divergent populations or taxa, has long been taken as evidence of unfavorable interactions between the genomes of the parental individuals (e.g., 39, 42, 43, 75, 80). The most widely accepted genetic model for the occurrence of such incompatibilities was first described by Bateson (15, as cited in 83), and later by Dobzhansky (39) and Muller (79, 80). In short, the Bateson-Dobzhansky-Muller (BDM) model assumes that an ancestral population consisting solely of individuals of the genotype aa/bb is broken into two parts that are temporarily isolated from each other. In one subpopulation, a new allele (A) is then assumed to arise at the first locus. Meanwhile, a new allele (B) is assumed to arise in the other subpopulation. Because individuals of the genotype aa/bb, Aa/bb, and AA/bb can interbreed freely, the A allele can then spread to fixation in the first subpopulation; likewise, individuals of the genotype aa/bb, aa/Bb, and aa/BB can interbreed freely, and the B allele spreads to fixation in the second subpopulation. However, although A is compatible with b, and B is compatible with a, the interaction of A with B is assumed to produce some sort of developmental or physiological breakdown, such that hybridization between the two subpopulations leads to the production of offspring with decreased levels of viability and/or fertility. Although this model focuses on negative interactions between differentiated regions of the nuclear genome, similar interactions between one or more regions of the nuclear genome and some component of the cytoplasm (e.g., the chloroplast or mitochondrial genome) could also play an important role in hybrid incompatibility. Unfortunately, the BDM model does not provide any mechanistic explanation as to how mutations that are neutral (or beneficial) within a given lineage will produce strongly disadvantageous incompatibilities when combined in a hybrid background (Burke and Arnold 2001, emphasis added).

References:

Burke JM, Arnold ML. 2001. Genetics and the fitness of hybrids. Annu Rev Genet 35:31-52. DOI link

Hybrid swarms

I found this paper by E. B. Taylor and colleagues from a link on evolgen. The paper is titled "Speciation in reverse", and it is about the loss of distinction between two stickleback morphs in Enos Lake, British Columbia.

From the abstract:

Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of 'hybrids'; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm.

I love this paragraph from the introduction:

The persistence of sympatric species that still occasionally hybridize implies that a dynamic balance exists between the occasional production of hybrids and their removal by natural selection. Presumably, there have been cases where completion of speciation in sympatry fails because gene flow overwhelms factors promoting divergence. Perhaps more infrequently, speciation proceeds to completion only to be undone later when environmental conditions change. Such reversals can occur, for instance, if the fitness of hybrids is suddenly improved under the new environmental conditions (e.g. Grant and Grant 2002). Alternatively, environmental cues upon which premating isolation is based may suddenly be altered, leading to a burst of hybridization that selection can no longer overcome (discussed in Coyne and Orr 2004). In either instance, the frail integrity of species that lack complete postzygotic isolation demonstrates the contribution of the environment to their maintenance and, perhaps, provides insight to the identity of factors that initiate speciation.

"The frail integrity of species that lack complete postzygotic isolation."

There is probably a reason why these particular populations have merged. The authors suspect that the introduction of nonnative crayfish may be a factor -- the crayfish eat some of the deep-water sticklebacks and may compete with them for food.

These stickleback populations have postglacial origins -- the age of Enos lake. Elsewhere, the divergence of stickleback populations in postglacial lakes has been found to be independently repeated, in terms of the origin of distinct benthic and limnetic (deep and surface) forms.

The most interesting aspect of this for me is the initial morphological divergence of the populations. They clearly have been adapting to distinct roles in these lakes even with substantial possibility of ongoing gene flow -- even if they were partially isolated by their use of different breeding strategies and water depths.

Highly adaptable. Similar morphological forms repeatedly evolve in similar habitats. Rapid speciation with ongoing genetic exchanges. Rapid collapse of morphological diversity (and genetic distinctiveness) in response to environmental change.

References:

Taylor EB, Boughman JW, Groenenboom M, Sniatynski M, Schluter D, Gow JL. 2006. Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair. Mol Ecol 15:343. DOI link

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Leading me to climate frustration

Science seems to have had a stealth theme going last week on climate change, and it included this perspective by Anna Behrensmeyer on climate change in human evolution.

The central insight is the great difficulty of finding causes among temporally correlated events:

Another challenge is deciding what constitutes a strong case for a causal link between a climate change and an evolutionary event. We can't step into a laboratory to test the impact of climate change on the human genome, but we do have the results of natural experiments--the proxy evidence for environmental changes in continental rock sequences, as well as many fossils of hominins and other organisms that were evolving on different continents during that same time period. There is a rich body of data to draw upon, but hypotheses are often structured around an assumption that "synchronous" events in the geological and paleontological record constitute evidence for cause and effect. These hypotheses, while seductive in their simple explanation of how our species came to be, do not do justice to the complexity of the climate-evolution problem (see the figure) or to the full range of evidence and scientific methodologies that now can be brought to bear on this problem.

I'd say that sums up some frustrating problems very well. There is no climate-altering event during the past seven million years small enough that some paleophile hasn't offered it up as the key factor in human evolution. But how can you prove anything? How can you even test the hypothesis of causation for most of these?

I had to read this sentence a few times, but I think it circumscribes an essential problem:

The related notion that fluctuating lake levels provided environmental stress that drove speciation does not provide a mechanism for how this could have exerted selective pressure on the immediate ancestor of Homo and resulted in the emergence of a new genus and species.

This is the problem with almost any climate-driven hypothesis. How did the change in climate cause anything to happen? Especially considering the huge bias in the sites we have to sample. Sure the Rift Valley paleoenvironment was changing during the Late Pliocene, but how central was that area to the hominid range as a whole? It's like diagnosing the causes of the American Revolution only knowing what happened in Charleston.

What we sorely lack is mechanisms that would link climate change to fitness in hominid populations. So far, there are generally two serious options: "Trees Too Far To Walk Between", and "Volcanic Winter".

The story is especially bad for the origins of Homo in the Late Pliocene. The received wisdom is that the global climate got cooler, and East Africa generally got drier. We know the robust australopithecines appeared, as did stone tool manufacture and presumably Homo. But how are these linked? It would of course help if we knew what robust australopithecines ate! If we link stone tools to meat eating (reasonably), at least we have a mechanism for dietary change in Homo. But what does a drier climate have to do with that? More antelopes?

In that paragraph, Behrensmeyer is discussing the range of climate-change hypotheses for the origin of Homo, it continues:

Other proposals instead have linked human evolution with increasing aridity and climate variability. Finally, other paleoclimatic evidence indicates drier rather than wetter climatic conditions between 2.7 and 2.5 Ma [see the figure, land record (center)], bringing into question the extent of a prolonged high lake phase throughout East Africa. Although the multibasin approach to establishing regional paleoclimate trends is commendable, the proposed causal link between a wet climate phase and the origin of Homo is not yet supported by sufficient evidence to establish its credibility.

Aaarrggh! Are the lake levels a red herring? Are the global climate figures a red herring?

The stinky fish are our only trail. What we've got is the sites we've got and the climate records as they are. Is there a good reason to think they say anything interesting about the human lineage? That depends how much of the lineage we've sampled with those sites. Yuck!

Speciation rates and duration in primates

In the most recent Journal of Evolutionary Biology, Darren Curnoe and colleagues have a paper titled "Timing and tempo of primate evolution". Here's the abstract:

Published molecular clocks for primates are used to estimate typical divergence times for phylogroups (1.6 Ma), species (3.3 Ma), sister species (2.7 Ma), genera (8.9 Ma) and sister genera (8.6 Ma). Significant median differences exist between major groups (infraorders and superfamilies) for various divergence times. These data are employed to estimate typical maximum duration of speciation. Typical primate values (1.1 Ma) suggest this process to be faster than is characteristic of many vertebrates. However, after considering divergence times for hybridizing congeneric and confamilial primates, this value is likely only to estimate the commencement of prezygotic isolating mechanisms, rather than the completion of reproductive isolation. Thus, speciation typically takes around 1.0 Ma to more than 4.0 Ma to occur, depending on whether prezygotic or post-zygotic isolating mechanisms are emphasized. Typical primate genus age is around 5.3 Ma, but we note differences among major groups. In light of these estimates, the classification of humans and chimpanzees is reconsidered using a molecular yardstick approach. Three taxonomic frameworks may flow from molecular analyses, all of them having major implications for understanding the evolution of humans and chimpanzees (Curnoe et al. 2006:59).

You can only go so far with statistics on divergence times in primates (or any other group). Literally any speciation might be unique. The origin of a species might involve very rapid evolution of intersterility with sister species, because of a rapid chromosome change or some other incompatibility.

But of course, the point of statistics is to show what the range of variation of real events actually is. Fossil hominids might or might not look like other primates, but to argue that they necessarily are unlike other primates requires evidence that we don't have.

Here's Table 4 from the paper, which provides a list of known cases of hybridization between species within a genus, and between genera:

GeneraTIS or TIG (Ma)
Congeners
Eulemur 10.43
Saguinus 5.72
Ateles 3.59
Colobus 2.9
Mandrillus 2.7
Papio 1.8
Macaca 5.0
Hylobates 1.31
Pan 2.55
Median2.9
Confamilials
Papio-Theropithecus 4.0
Papio-Macaca 12.05
Cercopithecus-Erythrocebus 8.0
Cercocebus-Mandrillus5.0
Hylobates-Symphalangus6.8
Median6.8

Curnoe et al. (2006) conclude that the median speciation time represents the initiation of prezygotic isolation mechanisms, and that complete reproductive isolation might better be approximated by the median genus divergence time -- 5.3 million years.

Finally, in consideration of the "Homo trodlodytes" taxonomic mini-problem (i.e., some people think the human-chimpanzee common ancestor is too recent to place humans and chimpanzees in different genera, in comparison to other primate genera), they conclude:

An important controversy in primate taxonomy at present is the generic classification of humans and chimpanzees (Goodman et al., 1998; Castresana, 2001; Curnoe & Thorne, 2003). To allow us to consider this question, we have estimated median primate genus ages for samples excluding human-chimpanzee divergence times (Table 5). Overall, typical primate genus ages are unaltered, as are estimates for the hominoids. The estimated age of the last common ancestor (LCA) of humans and chimpanzees derived from the fossil record is presently older than 7.0 Ma (Hailie-Selassie, 2001; Pickford & Senut, 2001; WoldeGabriel et al., 2001; Brunet et al., 2002). Molecular estimates place the divergence time at 7.5 Ma or earlier (data in Appendix 1). Both estimates are older than typical primate, catarrhine and hominoid divergence times presented here, and also older than the genus yardstick of Goodman et al. (1998).
Two of us have previously supported the view that humans and chimpanzees should be classified as congeners on the basis of their estimated divergence time (Curnoe & Thorne, 2003; also see Goodman et al., 1998; Watson et al., 2001). However, we now believe this view requires reconsideration. Two other taxonomic frameworks may flow from the molecular yardstick approach. The second and third hypotheses would see humans and chimpanzees retained in separate genera (Pan and Homo), with the LCA of both classified in a separate and as yet undiscovered genus or classified in a genus that would also comprise the first 2.0-4.0 Ma of both the human and chimpanzee lineages.

An interesting suggestion, since the latter case would place the human-chimpanzee LCA in Australopithecus.

References:

Curnoe D, Thorne A, Coate JA. 2006. Timing and tempo of primate speciation. J Evol Biol 19:59-65. Full text (subscription)

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Speciation

Speciation is the cessation of interbreeding between one animal population and all other populations with which it formerly exchanged genes. When interbreeding between two populations is interrupted, they will become genetically differentiated because the force of gene flow can no longer maintain their similarity. The other evolutionary forces then combine to make the populations diverge:

  1. Genetic drift causes each population to lose alleles. Because drift is a random process, it is likely that each population will lose different alleles, making them steadily more different.
  2. Natural selection will cause the populations to adapt to their environments. When these environments are different, the adaptations of the populations will be different as well.
  3. Unique mutations that occur in individuals in each population cannot move to the other, and as these mutations grow in number, the populations become more genetically different.

If interbreeding is not restored between the populations, the accumulated amount of genetic and phenotypic changes between them eventually will make interbreeding impossible. When one population ceases to interbreed with all other populations, its evolutionary history diverges because genetic changes cannot cross the reproductive barrier. Simply put, the population resulting from a speciation is a species.

Patterns of speciation

Reproductive isolation can occur because populations become physically separated from each other. In primate evolutionary history, this scenario has occurred many times, for example, when anthropoid monkeys first arrived in South America some 50 million years ago. At that time, South America was an island continent separated by ocean from both North America, with which it is presently connected, and Africa, with which it had been connected before about 80 million years ago. The leading hypothesis for this original dispersal of monkeys to South America is that a small number of individuals crossed the then-smaller South Atlantic Ocean on storm-swept "rafts" of logs and other vegetation. Such a dispersal may have depended on the presence of volcanic islands between the continents which no longer exist, or patterns of ocean currents that were stronger when the two continents were closer together (Flynn and Wyss 1998). Like primates, rodents also apparently reached South America by this mechanism. However, the survival of such colonists and their establishment on the South American shore was a rare, unlikely event, and upon their arrival these early anthropoids were stranded with a formidable isolating barrier, the Atlantic Ocean, preventing subsequent mate exchange with their African relatives. Many similar colonizations, usually less spectacular in scope, have occurred throughout primate evolution, including dispersals at different times from Asia to Africa, Africa to Eurasia, and North America to Eurasia.

Populations need not cross oceans or move among continents to become isolated from each other. Isolating barriers may arise for many reasons, including when high water levels separate islands from the mainland, when a drier climate spreads grasslands and divides areas of forest, and when an area in the midst of a population's range undergoes geologic uplift, forming hills or mountains. Isolation caused by physical separation between populations leads to allopatric speciation, meaning that the populations live in different geographic areas from each other.

Peripatric speciation, on the other hand, occurs between populations that are not physically isolated from each other. A large population may be spread across a wide range of local environments that slightly differ from each other. On the edge of such a range, small local groups may be strongly affected by natural selection, tending to adapt them to their distinct environments. If survival at the edge of the range is difficult, such groups may not persist for very long, or may be mostly composed of migrants from the main population from the center. Such a population structure leads to the "center-and-edge effect," in which variation is greater at the center of the species range and limited by genetic drift at the peripheries of the range.

But if new adaptations in the edge subpopulations allow them to survive and proliferate, and the amount of gene flow from the rest of the population is small, then the force of natural selection may overcome the tendency of gene flow to limit divergence. As a subpopulation at the edge of the range becomes more adapted to its local conditions, reproductive contacts with the rest of the population may become less important. Individuals with genes from the center may be at a selective disadvantage, or reproductive contact may be lost entirely. This process can result in speciation, if the edge subpopulation succeeds.

Allopatric vs. peripatric speciation

Reproductive isolation

The process of speciation involves an interplay of all the evolutionary forces that affect populations. The key factor is the cessation of gene flow between the populations involved. Speciation requires more than simply isolation, however. If two subpopulations once separated by geography are brought back into contact, without any other evolutionary changes to impose continued reproductive isolation, they will resume interbreeding with each other. In such a case, no speciation has occurred.

Such circumstances have continually happened to human populations. Often when a human population colonizes a new area, it becomes isolated from other populations for a period of time, sometimes hundreds of generations or more. For example, the initial colonization of the Americas across the Bering land bridge, at least 12,000 years ago, was followed by the isolation of peoples on these continents from the rest of the world after the post-glacial rise in sea levels cut off any further land access. But when the invention of ocean travel reestablished transoceanic contact, people resumed interbreeding, as attested by the large numbers of their common descendants today. This kind of isolation affected other areas, including Australia, where only intermittent immigration from Southeast Asia occurred after the initial habitation of the continent over 50,000 years ago. Even over such long periods of time, these populations experienced no changes in their reproductive functions, and therefore no speciation occurred.


Isolation is initiated by a physical fact: the loss of gene flow between populations. But it is made permanent by the subsequent evolution of reproductive functions in one or both populations. Such reproductive changes occur either (1) as a side effect of adaptive changes in other biological aspects of the population or (2) as part of a process of continual reproductive change that causes populations to diverge after physical or geographic isolation is established.

Processes of continual reproductive change are expressions of sexual selection. In many groups of animals, mating involves a complicated interplay of physical traits and behaviors that animals use to advertise their qualities to potential mates. In every group, the ability of an animal to recognize potential mates depends on the presence of these signals, called the "mate recognition system". In some groups, the mate recognition system depends on the presence and form of specialized anatomical features, such as the antlers of elk or the special facial coloration of mandrills. In other groups, an animal must perform special behaviors for mate recognition to occur. Like any other phenotypic characteristic, these features may evolve over time, either because of changes in the selective balance between these reproductive features and other features leading to reproductive success or because new behaviors become associated with mate desirability. Many of the more complex mating behaviors may be mostly transmitted by learning or observation, only weakly heritable, allowing mate recognition systems to change easily over short periods of time. Two populations that lose genetic contact will be very unlikely to evolve in the same way. If separated for any period of time, members of one population will not recognize the members of the other as potential mates, resulting in speciation.

The ability to reproduce may also be lost for other reasons. Many times, evolutionary change in chromosomal structure or genetic function may occur that makes reproduction impossible even if mating occurs between members of two populations. The chromosomal rearrangement during human evolution that gave us 46 chromosomes instead of the 48 in chimpanzees would by itself make chimpanzee-human hybrids impossible. In other cases, mating and the birth of hybrid offspring between two populations may occur, but genetic changes may make these offspring sterile. This is the case for horses and donkeys, which interbreed with each other, but produce sterile mules as offspring.

Speciation as a hypothesis

It is important to bear in mind that speciation is a concept that must be tested as a hypothesis of population relationships. In particular, when biologists say that a speciation has occurred, they hold the hypothesis that the resulting populations will never again exchange genes in a way that significantly shapes their evolution. The hypothesis of speciation can be tested only by the presence of absence of gene flow.


Often, reproductive isolation is maintained primarily by the continued geographic isolation of the populations involved, even if other substantial evolutionary changes have occurred. Prominent examples are found among zoo animals. Sometimes animals that never have the opportunity to encounter each other in nature are found to interbreed freely when placed in close proximity to each other in zoos. For example, common chimpanzees and bonobos are separated by geographic barriers in the wild: bonobos live only south of the Congo River and common chimps only to the north. These two groups practice distinctive mating behaviors and have some anatomical differences. However, when given the opportunity in captivity, they do interbreed and produce hybrid offspring. Likewise, Sumatran and Bornean orangutans are presently isolated in the wild, and their genetic differences indicate that gene flow between the populations was very limited or nonexistent even during periods when these islands were connected to each other, either because their forested habitat did not extend across the now-submerged land bridge or because intermediate populations died out (Warren et al. 2001). However, there are only slight apparent anatomical differences between the two populations, and they interbreed quite freely in captivity.


In these instances, it is not obvious whether speciation can be said to have occurred. Clearly the populations involved have been geographically separate for a long time, with no immediate prospect of rejoining each other in their natural ranges. If they were to contact each other in the wild, it is impossible to predict whether gene flow would be reestablished. Future events may or may not reestablish gene flow, so that neither the hypothesis of speciation nor the alternative hypothesis of no speciation can be refuted. Both hypotheses are untestable, because we cannot foretell the future relationships among these organisms.

Sometimes nature permits stronger tests, even when interfertility is possible. For example, lions and tigers are closely related to each other and occurred historically in overlapping geographic ranges in Asia. While the skeletal differences between them are slight, these two kinds of great cats obviously differ in coloration and external anatomy, and in the wild they are successful only in different environments. Tigers are adapted to hunting in densely vegetated areas and lions are adapted to grassy plains. In captivity these two cats can and do produce fertile offspring, called "ligers" or "tigons" (More on hybrid big cats). Even so, apparently mate recognition between these cats does not occur in the wild, even if they are in close contact, which by itself would tend to support the hypothesis of speciation between them. However, a speciation between the two forms is further supported by their reactions to habitat changes that have occurred in their Asian ranges. Lions and tigers remain limited to their environments of greatest adaptation, without moving into each other's ranges, and even under habitat pressure and reduced numbers they do not seek out each other as mates. Thus, gene flow will play no part in their future, even if their human managers allowed it.

In some other cases gene flow extends across a considerable range but does not connect one end of the range to another. It sometimes happens in nature that a long string of interbreeding populations all exchange mates with their immediate neighbors but not over long distances. Genes may flow across the entire length of the chain by continued exchange from one population to the next, and by this mechanism mutation, selection, and genetic drift may cause changes in the entire population. However, when individuals from either end of the chain are brought together, they may be intersterile. Such populations are sometimes called "ring species", especially when they occur around the edge of a large isolating barrier, such as a body of water. Such instances may be difficult to resolve with the concept of speciation, although any large population may contain pairs of individuals who cannot reproduce with each other, but might each reproduce with others. In the case of ring species, speciation may follow quickly if any of the intervening populations lose genetic contact.

Speciation and evolution

The branching process that describes how different kinds of organisms arise is at a different level than the reproduction of organisms within a population. Each speciation is the birth of a new species, and species may disappear by extinction, when none of their members survive. Speciations and extinctions follow a different pattern than the births and deaths of individuals within a population, and although both speciations and extinctions are the result of evolution within populations, their pattern cannot necessarily be predicted from the forces of evolution alone. The study of the factors influencing speciation, extinction, and the resultant diversification of different species of organisms is called macroevolution, while the regular forces of evolution within populations are often called microevolution in contrast.

Macroevolutionary and microevolutionary patterns can reinforce each other during speciation. The initial speciation of a new species may accompanied by strong selection to a new environment. One change may trigger others, and the species may rapidly change in many respects. New anatomical configurations may evolve, along with new behaviors that define a new adaptation with respect to other species in the environment. The new advantages of this species may allow it to spread beyond the range of its parent species, or it may spread back into the parent's range, replacing it. Such broad evolutionary changes might have been impossible without the action of selection and drift in the small isolated population created by speciation.

Because of this possibility of great evolutionary change at the time of speciation, some scientists believe that most evolutionary change happens during these events, and not at other times. This hypothesis is most notably expressed by the model of punctuated equilibrium proposed by paleontologists Niles Eldredge and Stephen Jay Gould (1972). This model predicts that most populations stay mostly the same for long periods of time, a state called evolutionary stasis. Only occasionally, driven by environmental events, do large populations sizes with selective optimizations in a particular environmental niche break down, resulting in the rapid adaptation of small populations to new adaptive niches and new combinations of genetic material. Thus, in punctuated equilibrium, evolution consists of long periods of stasis interrupted by bursts of change that include speciations.

This model may explain the fossil records of different animals that remained relatively unchanged for long periods and then changed greatly in a short time. For example, . Such examples might involve speciations and subsequent rapid adaptations. On the other hand, selection even in the absence of speciation is a rapid evolutionary process, so that the appearance and rapid selection of new variants might lead to the appearance of punctuated evolutionary change within a single species.

Indeed, given the speed of natural selection, slow evolutionary changes may be less common than rapid ones. Nevertheless, there are many examples of slow changes in the fossil record, a pattern called gradualism.

Adaptive radiation

Sometimes, large numbers of speciations in a single group of animals happen at once. The new populations generated by this burst of speciations often are variable in their adaptations to the environmental niches they occupy, as well as in their anatomical and behavioral makeup. Such a burst of speciation is called an adaptive radiation.

Adaptive radiations can happen whenever the reproductive success of a population brings it into contact with new environments in which its members are able to adapt and succeed. For example, the evolution of the four-chambered stomach in the ancestors of antelopes and cattle allowed them to use grasses that were not well used by other herbivores. This adaptation allowed their descendants to radiate into many different niches based on their ability to digest this material, leading to their extensive diversity today, which ranges from tiny Thompson's gazelles to large bison. No one species could occupy all these specialized niches. But in competition with each other, as well as with other species, populations of the original bovid quickly diverged to encompass these adaptations and others. This original adaptive radiation was therefore enabled by the evolution of the digestive system, which provided new energetic and dietary opportunities for bovid species.

Although the great apes today include only a small number of species, apes in the past were much more numerous. One of the reasons underlying this great collapse of ape diversity is the success of the Old World monkeys, which compete with apes for resources in forest environments. The Old World monkeys themselves underwent a substantial adaptive radiation during the Middle Miocene, capitalizing on their great dietary breadth, partly marked by their effective shearing molars, as well as their relatively short birth intervals compared to the apes. As climatic shifts became more rapid and frequent during the Late Miocene, the apes lost further ground to the monkeys, who underwent at least one more adaptive radiation based on the gut specializations toward leaf eating in the colobine monkeys. The evolution of important adaptations--especially those that enable exploitation of new food resources--is an important reason for the success of some lineages.


Sometimes, an adaptive radiation may result from an old adaptation that leads to new opportunities. For example, animals may colonize new areas, exposing many new niches in which they can out-compete other animals. The arrival of monkeys in South America is one such case, in which the combination of placental birth and arboreal adaptation caused these primates to succeed and diversify over many indigenous marsupials and birds. In other cases, an adaptive radiation may occur when an adaptation becomes useful in a broad range of environments. Bipedal locomotion in hominids is an example. Bipedalism may have evolved to allow efficient above-branch walking or walking short distances between groups of trees, but proved very effective in the more open woodlands of the early Pliocene, possibly leading to a radiation of different bipedal species.

Competitive exclusion

One of the patterns of macroevolution is competitive exclusion, which governs the outcome of competition between species for a limiting resource (Hardin 1960). Many natural populations coexist without dire consequences, because they depend on different resources, or are not limited in numbers by the resources that they share. But a limiting resource, the supply of which directly limits the number of individuals that can exist in a population, cannot be shared by two populations without competition. If two populations depend on the same rare food source, or if the activities of one species place the requirements of another in jeopardy, the populations can react in three possible ways:

  1. One of the populations moves away.
  2. One of the populations changes its adaptation to reduce its dependence on the resource.
  3. One of the populations becomes extinct.

The principle of competitive exclusion, described by these three predictions, implies that at most one of the populations can remain unchanged.


Often competitive exclusion occurs when exotic animals move into a new area, competing with native groups. For example, the introduction of dingoes into Australia caused them to come into competition with native marsupial carnivores for prey species. The outcome is a product of the long evolutionary histories of both kinds of mammals, which left the dingo with certain advantages over the native carnivores, leading to their extinction. Such extinctions are a regular pattern of macroevolution.

See also:

Species concepts

Phylogenies

References:

Eldredge N, Gould SJ. 1972. Punctuated equilibria: an alternative to phyletic gradualism. In: Schopf J, editor, Models in paleobiology. San Francisco: Freeman and Cooper. p 82-115.

Flynn JJ, Wyss AR. 1998. Recent advances in South American mammalian paleontology. Trends Ecol Evol 13:449-454.

Hardin G. 1960. The competitive exclusion principle. Science 131:1292-1297.

Warren KS, Verschoor EJ, Langenhuijzen S, Heriyanto, Swan RA, Vigilant L, Heeney JL. 2001. Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus. Mol Biol Evol 18:472-480.

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