Archive for the ‘Chimpanzee’ Category

The Hybrid-Driven Evolution of Hominids

November 27, 2011 5 comments

The acceptance of hybridization processes in the origin of species already came much closer with fossil DNA analyses and more detailed comparisons with extant organisms. For humans the strong suggestion of genetic ‘admixtures’, already claimed in various genetic studies dealing with Neanderthal and Denisova hominines, is reinforced by new investigations that now even start to penetrate the holiest of Out of Africa strongholds, that is Africa. This is no longer about a select set of single genes whose implications for origin and whereabouts could be happily reduced, but about entire sequences of diverging genome ‘regions with unusual patterns of genetic variation’: new results reveal the survival in African genes of ‘an archaic population that split from the ancestors of anatomically modern humans ~700 kya.’ (Hammer et al., 2011). Being much more than a mere warning against obsolete paradigms, this should already give us a valuable insight in what happened within the human species at a supra-regional level.

Improved distribution map of Denisova alleles, at SNPs where Denisova is different from chimpanzee and Neandertal. There is an appreciable match with A*1101 HLA alleles

In Africa the introgression event of ‘archaic’ humans was claimed to have happened about 35kya, recent enough for not spoiling the Recent Out of Africa theory altogether. So now we are required to believe that homo sapiens interbred first in Eurasia (and the north of Africa) and only afterwards with their closest African neighbors? A patched “Recent Out of Africa” scenario would now ‘predicate’ that Homo Sapiens quickly replaced much older hominines anywhere but in Sub-Saharan Africa. However, mere reluctance to believe otherwise may eventually prove futile:

I bet that a few years from now, we will look with amazement at the naivete of the passing Out of Africa orthodoxy that bundled all Africans into an amorphous category of “our ancestors in Africa”. It is also becoming clearer that increased African genetic variation is, at least in part, due to the continent being home to multiple deeply divergent populations that persisted, in various admixtures down to the present. (Dienekes’ blog, 2011-9-16)

The amount of new scientific publications able to shed more light on the issue is already dazzling and for sure preludes an inevitable change of paradigm:

We are only now beginning to harness the power of full human genomes for evolutionary inferences, but it is inevitable that a new theory of human origins will appear that will reconcile the different and conflicting lines of evidence. That theory must take into account latent admixture as a cause of African genetic diversity, and it must also harmonize with the paleoanthropological record. (Dienekes’ blog, 2011-9-19)

Scientists already speak out openly on how the ‘vast amount of recombination information in the human genome has long been ignored or deliberately avoided in studies on human population genetic relationships’ (Xu et al., 2011). The latter now introduced a method of ‘chromosome-wide haplotype sharing’ (CHS) to reconstruct reliable phylogenies of human populations and state that instead of variation being an unbiased measure of population age, ‘the majority of the variation in CHS matrix can be attributed to recombination.’
Unfortunately, time and origin of the admixtures remain hard to quantify. Sampled fossil hominines so far didn’t correspond to much closer modern matches in the wider geographic region. Denisova admixtures have top levels in SE Asia and Australia while traces are virtually absent in South Siberia, where of both Denisova fossils were found. Likewise, Neanderthal admixtures have top levels in East Asia and the Americas, far removed from the known European habitats of Neanderthal, where 1000 Genome Project results are at most comparable, and sowehat lower in northern Europe. In his blog John Hawks suggests population history and natural selection may have caused this distorted picture, while much of the purported evidence for local continuity of Denisova genes may be of a quite different magnitude. Certain HLA genes, part of the modern human immune system also found in the genomes of Denisova and Neanderthal hominines, would have been straightforward evidence for introgression and local continuity – if only those genes didn’t derive from much older primate genes. Balanced natural selection could have been an alternative to account for the survival of ancient genes, supplying false positives for the survival of a select set of Denisova genes. Still, the current geographical distribution of the HLA-A*11 variety found in Denisova, by Parham, concurred remarkably with that of other derived Denisova alleles, published afterwards:

[…] we found that East Asian populations, particularly Southeast Asian populations, had, on average, a greater frequency of the derived Denisova allele compared with other populations (except for Oceanians) […]. (Skoglund & Jakobsson, 2011)

Since this particular HLA-A*11 variety is mostly found in Asians and never in Africans this indeed suggests introgression by interbreeding outside of Africa. True, such alleles existed already at the same position in the genomes of apes, but now with supporting evidence this detail should supply an entirely new dimension to the issue: introgression of DNA previously conserved merely on evolutionary sidelines should imply temporal extinction of the gene on the main hominine lineage!
At least, extinction is exactly what happened at a much larger scale with primate ABO blood group genes: chimpanzees so far attested for blood type A and some O, but not for B, and gorillas attested for blood type B and some O, but not for A. The ABO blood type is controlled by a single ‘ABO’ gene, for humans on the long arm of the ninth chromosome (9q34).

In the case of human ABO blood group genes, three alleles (i.e., A, B, and O alleles) have been observed, but it is known that chimpanzees have two alleles (i.e., A and O alleles). (Kitano et al., 2000)

Blood groups are inherited from both parents, that may be homozygous for one or heterozygous for two classes. This means that despite being ancient, any of the groups could become extinct once an epidemic demands a strong response that involves unbalanced selection of another allele. Eg., blood group O was observed to have an advantage against malaria, leading to the hypothesis that ‘selective pressure imposed by malaria may contribute to the variable global distribution of ABO blood groups in the human population.’ (Rowe et al., 2007). Since malaria is strongly related to warm wetland habitats, this may be an example of an ancient immune system whose usefulness and survival may be a matter of habitat. If so, then speciation – that implies a formative stage of isolation within a new habitat – also implies an increased risk. Among the great apes only orangutan attested all three types, suggesting that extinction of immune system-related alleles may indeed have happened more often. Reintroduction of ancient genes that became lost may be an almost impossible affair without subsequent introgression by hybridization. Nowadays such potential hybridization partners may be hard to find for chimps or gorillas, probably characterizing the evolutionary costs of their speciation. However, for the human lineage hybridization remained a possibility with species or subspecies that co-evolved within a wide range of different habitats, where different survival patterns and demands had their unique effect on local adaptations, ie. including the immune system! In summary, balancing selection may play a trick on us here, but the evidence is highly suggestive of the deep time depths involved for the genetic divergence achieved before introgression.
Equally remarkable was the absence of Denisova genes being confirmed for Central and South Asia, closer to the fossil origin. The route of Denisova genes to SE Asia must have led through East Asia, but the replacement in Central Asia by other rare varieties of HLA raises even more questions. Such as the origin of the Central Asiatic allele HLA-B*73, not attested in Denisovans, but in modern humans always associated with the ‘Denisovan’ HLA-C*15 antigen, thus suggesting either an hitherto unknown presence in other Denisovans, or a hybrid neighbor.
A recently deciphered genome “from a 100-year-old lock of hair donated by an Aboriginal man” confirmed that despite long time isolation, their proportion of Neanderthal segments match that observed in European and Asian sequences. This Neanderthal component may have been available when the ‘aboriginal Australians split from the ancestral Eurasian population 62,000 to 75,000 years B.P.’ (Rasmussen et al., 2011). However, even though according to the latest insights East Asians are considered significantly closer to Denisova relative to Neandertal, the morphology of aboriginals is rather related to archaic populations and fossils in the wider region of South and South East Asia:

This study has shown that Southeast Asia was settled by modern humans in multiple waves: One wave contributed the ancestors of present-day Onge [Andaman Islands], Jehai [Malaysia], Mamanwa [Philippines], New Guineans, and Australians (some of whom admixed with Denisovans)
we considered the possibility that the secondary gene-flow event into the ancestors of Australians and New Guineans came from relatives of Chinese (CHB) rather than western Negritos such as the Onge. (Reich et al., 2011)

Indeed the Denisova admixtures follow a rather geographic pattern, being present in eastern Indonesia and among the Mamanwa ‘Negritos’, but virtually absent in the ‘Negritos’ of Malaysia and the Andaman Islands. Most probably the aboriginals, where tests revealed ‘slightly less allele sharing than observed for Papuans’ – got the component from their closest geographic neighbors, thus flouting the Out of Africa model and increasing the mystery of the timing and origin of Denisova intrusion.

[…] it is becoming increasingly difficult to imagine a structure model that can fully explain the complex pattern of archaic ancestry in non-Africans without invoking any restricted admixture events with archaic humans. Instead, we suggest that direct gene flow from archaic populations is the most likely explanation for the shared genetic ancestry between East Asian populations and the Denisova genome (Skoglund & Jakobsson, 2011)

Likewise, somewhat lower averages of the Neanderthal component in their previous (esp. north-) European heartlands and unpublished reports of unrelated archaic admixtures both in Europe and South Asia should make us weary about the significance of current geography for the origin question at all. If dislocation of genetic affinity with fossil samples defines a tendency, we can’t even be sure the African archaic admixtures mentioned above indeed derive from an African core region. However, Wall et al. (HGV2011) reported that part of the genetic regions on the human genome ‘were found in the genomes of both sub-Saharan African and non-African populations’. At least some of the archaic admixture became international, not unlike we already known of the V and M haplotypes of gene ASAH1, coalescent-time depth 2.4 million years ago, that ended up evenly dispersed around the world. The mere age of the African archaic introgressive DNA currently under investigation vastly exceeds the age of Neanderthal and Denisova, even that of their (and our) common ancestor Homo heidelbergensis, an extinct species of the genus Homo that lived between 600 and 400 thousand years ago. This seems to be ever less in agreement with the traditional biological species concept (BSC) that tends to relate speciation with highly effective reproductive isolation, and questions the very nature of the human speciation process over time.
Actually, current biology textbooks don’t hesitate anymore to supply ‘prohibitive’ answers, that simply urge to be applied to the human species:

Typically, gene flow occurs between the different populations of a species. This ongoing exchange of alleles tend to hold the population together genetically. (Campbell Biology, ninth edition, 2011)

Speciation still occurs by the evolution of reproductive isolation, but ‘there are many pairs of species that are morphologically and ecologically distinct, and yet gene flow occurs between them.’ An example is the grizzly bear and the polar bear, that despite occasional natural hybridization remain distinct. ‘This observation has led some researchers to argue that the biological species concept overemphasizes gene flow and downplays the role of natural selection.’ (Campbell Biology, 2011). Some other species appear to be actually fully hybrid, like the Tiger Swallowtail Butterfly (appalachiensis): ‘Inter-specific hybridization is widespread in nature and may have important consequences in evolution, from the transfer of adaptive alleles between species to the formation of hybrid species’ (Kunte et al., 2011). According to the investigators the ‘evolution and persistence of appalachiensis in contact with its parental species suggests that hybridization among animals may result in selectively favored hybrid species that contribute to biodiversity.’ Hence, this example exposes a ‘potential role for natural selection in the origin and maintenance of hybrid species.’
Indeed, ‘hybridization is not always a dead end, as the BSC might suggest, but a potential source of new array of hybrids (hybrid swarms) that may establish themselves, eventually in new ecotone habitats, and evolve as new species. One common feature of the process that accompanies hybridization is the rapidity of genome repatterning which is hardly explained by the conventional mutation and recombination rates. Rather, transposition bursts ensuing hybridization suggest their involvement in these rapid genome reorganizations.’ (Fontdevila, 2005)
The risk of speciation may be genetic isolation and inbreeding, the risk of illimited hybridization of subspecies is the potential loss of local environmental adaptations, like the white color of polar bears following the example above. Over time, reproductive barriers may be either reinforced or weakened. In the latter case, hybridization may eventually lead to ‘the fusion of the parent species’ gene pool and a loss of species.’ (Campbell Biology, ninth edition, 2011)
As such, there is no specific reason why mere biology wouldn’t supply answers for the apparently torturous evolution of the human species, or for the sudden appearance of African apes:

In a punctuated pattern, new species change most as they branch from a parent species and then change little for the rest of their existence. (Campbell Biology, 2011)

Both patterns of how species evolve have been observed for the radiation of the mammals over the last 165-million-year. The majority of mammal species, including even the most speciose orders (Rodentia and Chiroptera), experienced an explosive 10-52 fold increase in the rate of evolution only during their initial formation up to the common ancestor. Stable rates of evolution of species, however diverse, were recorded almost everywhere else.

These results necessarily decouple morphological diversification from speciation and suggest that the processes that give rise to the morphological diversity of a class of animals are far more free to vary than previously considered. Niches do not seem to fill up, and diversity seems to arise whenever, wherever and at whatever rate it is advantageous. (Venditti et al., 2011)

The sudden appearance of chimps and also gorilla in the fossil record may indicate their speciation occurred relatively rapidly, when they occupied and then filled their ecological niches. Over the wider humanoid lineage things may be different:

For species whose fossils changed more gradually […] it is likely that speciation in such groups occurred relatively slowly, perhaps taking millions of years. (Campbell Biology, 2011)

How literally we could take these ‘millions of years’ for the lineage leading to great apes and modern man? Decades of behavioral studies resulted in the insight that apes are far more hominized than was once believed. According to Krützen et al. (2011) this already applies to the cultural plasticity of orangutan. Since this tendency to share particular behaviors in a group was also demonstrated in wild populations of chimpanzees this suggests evolutionary roots in the ancestors that all great apes share with humans. How realistic this would be for the biological species concept, assuming orangutan diverged from our common ancestor 15 mya, or more? Many hominizing tendencies, like the slowing down of juvenile growth, could develop for all humanoid lineages well after such divergence dates. Or would hominized behavior invoke exactly the opposite of BSC with the first onset of organizing a beneficial habitat to the temporarily impaired, like hybrids? Hominized groups could offer better opportunities to overcome some hybrid-related barriers such as lower fitness and fertility. Better survival opportunities would enhance the possibility that hybrid-related genome repatterning could stabilize recombination by endogenous purifying selection over a longer period, maybe several generations, to the effect that both fitness and fertility could be restored over time by the natural resilience of genetic processes. Indeed, if hybridization may explain parallel developments among humans and great apes, we could postulate genetic exchange between diverging ape lineages spanning millions of years.
The laboratory or Reich in Boston has a record in the study of hybrid-driven evolution, and substantiated hybridization already in 2006 for the hominine lineage. What the team called a ‘realistic upper bound of < 17 Mya for human-orangutan genome divergence' resulted in a common ancestor with chimpanzee less than 5.4 mya, including a considerable period of mutual hybridization:

Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently. (Patterson et al., 2006)

The study concluded that introgression of chimp-like DNA in the human lineage, or the other way round, happened after about 1,2 million years of divergence. This year’s ICHG meeting a team of accredited scientists led by J. X. Sun presented a tight refinement of previous date estimates:

Human-chimpanzee speciation is estimated to be 3.92-5.91 Mya, challenging views of the Toumaï fossil [Sahelanthropus] as dating to >6.8 Mya and being on the hominin lineage since the final separation of humans and chimpanzees. (Sun et al., 2011)

Indeed, despite initial efforts to link this transitional period of hybridization with older hominines, the time span of Ardipithecus would make a much better match, and more so due to the immediate succession of Australopithecus: this hominine ancestor complied even less to the more chimpanzee-like anatomy commonly expected with the genetic similarity of humans and chimps:

In an assessment of fossils from Kanapoi (3.9-4.2 Myr ago), the anagenetic series Ar. ramidus, Au. anamensis and Au. afarensis has been hypothesized. The evidence reported here from the Afar Rift constitutes a strong test from a single stratigraphic succession that fails to falsify this hypothesis (White et al., 2006)

The cited evidence of introgression revolted against traditional phylogeny, but the proposal adhered to the established view: one single lineage up to a common ancestor of humans and chimps. Supportive molecular evidence and dating is commonly cited, but the devil is in the details:

Although chimpanzees are our closest relatives, there are many loci at which humans and gorillas (or chimpanzees and gorillas) are the most closely related; we estimate that this is the case over about 18–29% of the genome (Patterson et all, 2006 Supp.)

Likewise, ‘data based on morphological analyses and with the data based on mitochondrial ribosomal genes […] suggest a closer relationship between gorilla and chimpanzee’ (Rasheed et al., 1991).
A much longer history of shared ‘hominizing’ evolution that encompass all great apes may be implied, and more so by additional inconsistencies in the order African apes are supposed to have diverged from the lineage leading to modern humans:

The late-divergence hypothesis […] specifically focuses on the divergence between humans and the ape, emphasizing that there were two different divergence points in the evolution of recent hominoids. (Wolpoff, 1982)

Thin enamel, knuckle walking and specialized feet for grasping are just a few shared features of African apes that are difficult to reconcile with two separate speciation events from an otherwise more hominine fossil record. For instance, despite Begun’s certainty on the knuckle-walking habits of our earliest common hominid ancestors, this remains utterly hypothetical – and utterly unsuported by more complete and recent fossils like A. sediba, and even Ardipithecus had not evolved the hands and wrists of a knuckle-walker. Homoplasty among different African apes that feature knuckle-walking is equally unsupported:

[This study] does not support the hypothesis of a knuckle-walking complex, nor does it support the contention that knuckle-walking could have been easily evolved independently in chimpanzees and gorillas. (Williams, 2010)

Instead, Grehan and Schwartz (2010) make a case for grouping ‘the monophyly of hominids and various Miocene–Pliocene fossil apes and orangutans into a ‘dental-hominoid clade’, with the African apes as a sister clade along with the putative [hominines] Ardipithecus and Sahelanthropus.’ In this view only the early hominine Orrorin could link the ‘dental-hominoid-clade’ to humans, thus suggesting a smooth transition along this lineage to hominids, but leaving the close family relationship with African apes unresolved.

Orrorin is […] already quite distinct morphologically from the African Great Apes (Gorillidae). This indicates a divergence between Hominidae and Gorillidae that dates back to a substantial period prior to 6 Ma, and we estimate about 8-7 Ma for this event. If so, then the discovery of Orrorin refutes all hypotheses in which humans diverged from apes later than 7 Ma, including most of the recent estimates by molecular biologists who tend to think of the divergence as having taken place later than 5 Ma, and even as recently as 2.5 Ma. (Martin Pickford, 2001)

Molecular evidence favors a close relation with African apes, but a much tighter morphological affiliation of the human lineage with orangutan can be observed:

[…] in addition to the development of low-cusped cheek teeth and thick molar enamel, humans shared a significant number of derived features uniquely with the orangutan (e.g. in reproductive physiology (gestation length, estriol levels, absence of estrus), degree of cerebral asymmetries, fetal adrenal zone size, lack of keratinized ischial callosities, mammary gland separation, hair length, incisive foramen number] (Schultz, 2004)

Indeed, the duration of the menstrual cycle varies with species; about 29 days in orangutans, about 30 days in gorillas and about 37 days in chimpanzees. Only the genus Hoolock (previously Bunopithecus), probably the most basal member of the lesser apes (gibbons), match human females ‘precisely’ – except for a considerable variability – in having an average menstrual cycle of 28 days (Geissmann et al., 2009). Cytogenetic evidence pleads for a shared development that considerably exceeds a basal relationship with great apes but unfortunately, so far gibbons are generally dismissed as even more distant from humans than orangutan.
Grehan (2006) expanded on this paradox by noting that ‘the orangutan relationship is supported by about 28 well-supported characters, and it is also corroborated by the presence of orangutan-related features in early hominids’ such as a thickened posterior palate and anterior zygomatic roots. We could add characteristics of their close fossil relatives such as dental structure, thick enamel, shoulder blade structure, thick posterior palate, single incisive foramen.

Comparative morphology supports a unique common ancestry for humans and orangutans as the only phylogenetic theory with substantial corroborated evidence. Even supporters of a unique common ancestry for humans and chimpanzees collectively support more (26) orangutan-related human characters than they do for chimpanzee-related human characters (Grehan, 2006)

Despite the impressive list of unique correlations shared between the human lineage and orangutans, the vast overall genetic distance between the species is often cited as evidence to a deep and rather straightforward phylogenetic affiliation. Genetic isolation of the orangutan lineage – according to molecular evidence between 14-17 mya (million years ago)- doesn’t help in understanding the last recorded interspecies hybridization event between ancestral humans and chimps from the ‘dental-hominoid’ point of view. In the words of Schwartz such an extended period of geneflow between widely divergent ape lineages certainly “pushes the limits of credulity” regarding the hybridization hypothesis.
For the moment I could suffice to notice that morphological and molecular evidence, that challenges the joint divergence of hominines and chimp ancestors from the ancestors of gorilla, may be explained by introgression: as in the example of hybrid polar bears, hybridization doesn’t necessarily imply the fusion of divergent evolutionary adaptive lineages. But hybridization could have complicated the hominid phylogeny beyond limits over a very long time, and even more so as the common source of adaptive radiation events towards speciation was rooted in a common ancestry that started long ago as a balanced process between evolving species.
Actually, human curiosity supplied comparable results for other species, suggesting relative time depths that correspond to what could be expected for the hybridization of diverging ape lineages:

Recent interspecific hybridizations have been well documented for the Bos and Bison species […] : zebu and ox in several tropical regions; zebu and banteng in Indonesia; taurine cattle and yak in China, Mongolia and Siberia, etc. Ox-zebu hybrids are completely fertile, while male progeny of other hybridizations are sterile. Earlier introgression events may be indicated by the anomalies in the mitochondrial phylogeny […] that are incongruent with trees of nuclear genes, AFLP fingerprints (these studies) and Y chromosomal sequence variation
Since exchange of genetic material depends on the geographical overlap of the regions inhabited by the species and their ancestors, this is consistent with the hypothesis that reticulation influenced the phylogeny of the Bovini. (Buntjer et al., 2001)

Cross-breeding of ox (genus Bos) and bison yielded fertile females and (mostly) infertile males. The same was implied by Reich, Pattison and colleges for hominine interbreeding with chimps. The fossil record already distinguishes bison in the range late Pliocene-Early Pleistocene up to 2 million years ago, while the origin of Bos (ie. cows) is contested. Their divergence is unlikely to be less than 2 million years, and possibly considerably longer:

The oldest clear evidence of Bos is the skull fragment ASB-198-1 from the middle Pleistocene (~ 0.6 – 0.8 Ma) site of Asbole (Lower Awash Valley, Ethiopia).
Although the origin of Bos has traditionally been connected with Leptobos and Bison […] we propose here a different origin, connecting the middle Pleistocene Eurasian forms of B. primigenius with the African Late Pliocene and early Pleistocene large size member of the tribe Bovini Pelorovis sensu stricto.
The Bison lineage […], based on skull anatomy, can be interpreted as resulting from anagenetic evolution of the Late Pliocene forms of Leptobos across the Plio-Pleistocene transition (~2.0 – 1.7 Ma)
The cranial anatomy of Bos, however, is highly derived as to be considered the result of a direct anagenetic evolution from any form of Leptobos. Martinez-Navarro et al., 2007)

Bison cows ordinarily conceive for the first time at 2 years of age while chimps reach their reproductive age only at 13.5 years, almost 7 times later. Accordingly, this translates to the feasibility of an extended period of geneflow for the ape lineage that may even exceed the lapse of 10 million years to bridge all genetic divergence between the common ancestor of all great apes and the reported chimp-hominine hybridization event.
As a caveat it should be noticed that fertile first generation (F-1) half-bison bulls are also registered (Wyoming Thunder being one example). This possibility increases when the bull parent already had some cattle blood, though in some cases this could not be confirmed. This observation typifies hybrid infertility as an essentially temporal evolutionary problem.

The grolar bear is a natural hybrid of grizzly bear and the polar bear. To the right the beefalo, fertile offspring of bison and cattle. Below Wyoming Thunder, a F-1 fertile bull from a male bison.

A strict phylogenetic model appears to be insufficient to reconcile genetic evidence with the origin of the human lineage from any ape clade in particular. Common biological insights on speciation suggest we should get rid of the thought that divergence, even irreversible speciation is the most natural thing to happen over time. Adaptive radiation may not be synonymous with isolation, especially in the initial period when the new phenotypes are still evolving. A re-evaluation of the entire fossil evidence would be necessary before we could even try to clarify the most controversial issues in human evolution today.
New paleontological evidence and analysis can often be relied on for correcting the phylogeny, even if molecular and morphological data turn out to be contradictory or are giving false positives. This was true respectively for whales, whose fossil ancestors confirmed their genetic affiliation with even-toed ungulates, and the Laotian rock-rat Laonastes whose genetic missing link status for New World Caviomorpha and ‘African’ Hystricognathi didn’t survive renewed scrutiny due to new fossils that revealed it as a Lazarus species of the extinct -essentially Asiatic- diatomyid taxon. Instead, so far paleontological data didn’t resolve contradictory evidence for hominids. There is an ever stronger tendency among scientists to reject the reliability of fossil evidence, and to recur to the possibilities of ‘extraordinary plasticity’.
True, mosaic evolution is considered rampant among primates, from the earliest prosimians up to modern humans, and the list of abortive evolutionary lineages towards modern primates and humans is getting ever more awesome. The ancestors of hominines must have been generalists that had still much in common with the very first anthropoids, or apes maybe as early as late Oligocene, irrespective of the evolutionary changes that were attested in the fossil record of Eurasiatic apes commonly identified as members of two clades, Dryopithecus and Sivapithecus. Unlimited plasticidity of species would open up the possibility of a thorough rejection of all current fossil evidence. Any primitive African ape could have remained in stasis for millions of years, in the middle of countless abortive lineages each well on its way to evolve into the same direction, until one ancestral species followed in their footsteps and plunged itself into an accelerated evolution towards the surviving modern African apes and hominines? and assumes African apes and humans developed from another common ancestor. In a Popperian sense this scenario can´t be falsified, since no fossils are required to meet this standard, what renders this scenario remarkably unscientific. But, could it be?
Only recently molecular evidence forced scientists to the abandon their reliance on morphological and anatomic arguments for equids, whose fossil record was once considered a textbook example of gradual, straight-line evolution. The North American evolutionary sequence from ‘Eohippus’ (Hyracotherium) to ‘Equus’, that eventually became an immigrant to the Old World, was exploited as an argument by Thomas Huxley in his defense of Darwins evolution theory. For a long time this remained one of the most widely-known examples of simple evolutionary progression, notwithstanding the few decades we already knew this ‘straight line’ was rather a bush, where even gradual transformation didn’t always apply. Regarding the once flourishing bush of species, modern equines – like humans! – were still considered a single twig. However, the scientific community was utterly unprepared for the blow this concept would receive of molecular evidence extracted from fossils. Nowadays we have compelling evidence that at least once this twig became intertwined with another.

Cladistic analysis of dental, cranial, and postcranial characters separate Hippidion and Equus into two different clades, which share the North American late Miocene Pliohippus as a common ancestor around 10 MA (Prado and Alberdi 1996).
Alternatively, MacFadden (1997) has suggested that Equus is derived from Dinohippus, and Hippidion from Pliohippus sensu lato (including Astrohippus), implying that the divergence between Dinohippus and Pliohippus occurred prior to 10 MA.
(Orlando et al., 2007)

Molecular evidence proved that the Hippidion, an extinct south american horse with some Pliohippus characteristics, was most similar with moders equids.

Hippidion is considered to be a descendant of the pliohippines, a primitive group of Miocene horses that diverged from the ancestral lineage of equines (a category including all living and extinct members of the genus Equus, such as caballine horses, hemiones, asses, and zebras) prior to 10 Ma ago […]. A recent study presented genetic data from three southern Patagonian specimens morphologically identified as Hippidion. Unexpectedly, the sequences clustered inside the genus Equus (Weinstock et al., 2005)

Hippidion differed less from caballine equids than all extant non-caballine equids (including donkeys, zebras etc.). This result inspired the team to question the deep morphological split:

The close phylogenetic relationship between Hippidion and caballine horses is in direct contrast to current paleontological models of hippidiform origins. Nevertheless, we are confident that these sequences are those of Hippidion rather than the South American caballine form E. (Amerhippus), which dispersed into South America about 1 to 1.5 Ma later than Hippidion. (Weinstock et al., 2005)

On morphological grounds, the phylogenetic separation between the lineages of Pliohippus/Hippidion and Dinohippus/Equus (modern equines) was previously estimated at 10 mya, and tentatively associated with the merychippine radiation of 15 mya. but the close genetic relationship now attested for Hippidion and caballine equids shatters such deep divergence. Equine evolution now faces the same dilemma as the human origin question, where morphology and molecular evidence are equally at odds. History repeated itself and like what happened before in paleoanthropology in the face of molecular evidence, scientific consensus rather conformed to the biological species concept and concluded that morphology was deceiving:

These data suggest that temporal and regional variation in body size and morphological and anatomic features should be considered a sign of extraordinary plasticity within each of these lineages. Such environment-driven adaptative changes would explain why the taxonomic diversity of equids has been overestimated on morphoanatomical grounds. (Orlando et al., 2007)

Another phylogeny isn’t hard to make, but even the divergence date of extant equines becomes questionable now the DNA of all three extinct American horse species was revealed to cluster specifically with cabelline horses. Genetically, the most recent common ancestor of all modern equids should have lived ‘merely’ ~5.6 mya, and still this appears inconsistent with proposals towards a single Out of America exodus event through Beringia during the glacials, at most 3 mya. Perhaps the easiest way to deal with evolutionary inconsistencies is to just forget about the need of a strict phylogenetic tree at all. For being a viable alternative to morphological continuity, hybridization processes must have been an important element in equine evolution for millions of years. Naturally, divergence dates would easily be overestimated with a last common hybrid ancestor, and easily underestimated for the species – or subspecies – that were the constituent components of the hybridization. For sure this would urge for another evolutionary model, and perhaps the identification of very different genetic signals.
It is suggested that among mammals, equines exhibit the highest rate of chromosomal evolution. Commonly considered Old World immigrants from North America, they feature a progressive ‘decrease’ of their chromosome count moving further away from Beringia: Prezewalski still has 66 chromosomes, 2 more than the domestic horse that is commonly believed to belong to the same species. Of their closest neighbors, the Asian asses, the count ‘drops’ to 56, while the African ass could preserve 62 chromosomes. Extant zebras count 46 chromosomes for the northern Grévy-zebra, 44 chromosomes for the common plains zebra and 32 for the southernmost mountain zebra. Before, maybe inspired by equivocal ideas concerning equine evolution, scientists were inclined to assume the primacy of chromosome fusion in karyotypic evolution, but:

Recent advances in cell-cycle regulation, chromosome behavior, fossil record, and phylogenetic inferences dispute that the primary direction of karyotypic evolution by sequential fusion of chromosomes is toward an arbitrary reduction in diploid number. (Kolnicki et al., 2000)

Lower chromosome counts of equids the further away from the American origin of Equus may now be attributed to conservatism, and the higher counts to ongoing change and evolution.

A key postulate of Todd’s karyotypic fission theory is the idea that in a postfissioned karyotype with a high number of acrocentric chromosomes, a trend for acrocentrics to revert to smaller mediocentrics by pericentric inversion (or centric fusion) repotentiates the karyotype for further fissions correlated with episodes of adaptive radiation directly inferable in the fossil record (Fontdevila, 2005)

For instance, the reduction-argument has been ‘turned on its phylogenetic head’ with investigations on cycads – often mistaken for palms or ferns, but only distantly related to either. The cycad fossil record dates to the early Permian, 280 mya.

Zamia is unique among cycads in that both inter- and intraspecific chromosome numbers range from 16 to 28, excluding 20 […], with varied karyotype composition
The large size of chromosomes in all cycad taxa excluding Zamiaceae […] indicates that chromosomal fission has been rare or absent in these taxa.
Molecular analysis has generated limited evidence for any chromosomal rearrangements, including chromosomal fission and pericentric inversion, as the main mechanism driving karyotypic evolution in Zamia.
(Olspon et al., 2011)

In chromosomal fission the total number of chromosome arms remains the same, ‘whereas pericentric inversion and/or hybridization of different karyotypes may either add or subtract from the total arm count’:

Pericentric inversions of the different combinations of telocentric chromosomes and/or hybridization were almost certainly involved in generating the chromosome arm numbers observed, a conclusion based on the size and number of chromosomes. Chromosome arm counts for all [Zamia] taxa in this study […] suggest that chromosomal fission, pericentric inversion, hybridization of different karyotypes and a combination of these mechanisms occurred in the evolutionary history of this genus (Olspon et al., 2011)

All corroborate to the notion that – under certain circumstances – adaptive radiation and speciation are symptomatic to chromosomal change.
The significance is obvious: ‘Chromosomal fission decreases genetic hitchhiking by severing transcentromeric linkages, allowing for direct selection on newly unlinked genes’ (Olspon). However, there must also be a drawback since in the course of evolution the number of chromosomes didn’t increase without limit. As for cycads in general, and most zamia in particular, the preferred count seems to stabilize at a low number chromosomes: ‘most early diverging cycad taxa have 2n= 16 or 18, with mostly metacentric and submetacentric chromosomes’.
Despite the exceptional features of some members of the clade, chromosomal stability and equilibrium is suggested for most cycad species. A straightforward correlation with morphological variability and stressful or widely variable habitats, that would require high levels of genetic adaptation, is falsified by the stable habitat, primitive morphology and high chromosome number found at the species Z. roezlii that inhabits the Colombian rainforest. The high age of the clade may be important evidence that fission may also be reminiscent of adaptive radiation events in the past. Over time this may be compensated by a corresponding reversal of the chromosome count by fusion. At least this is indicated in basal vertebrates, where ‘some ancestral segments were fused prior to the divergence of salamanders and anurans’ (Voss et al, 2011).
A pattern of chromosomal equilibrium may be observed in cichlid fishes:

Perciformes represents the largest order of vertebrates with approximately 9.300 species. It includes more than 3.000 species of the family Cichlidae [1,2] that is one of the most species-rich families of vertebrates
Phylogenetic reconstructions are consistent with cichlid origins prior to Gondwanan landmass fragmentation 121-165 MYA
The karyotype formula 2n = 48 st/a [subtelo/acrocentric] elements is characteristic of Perciformes
Although there is extensive variation in the karyotypes of cichlid fishes (from 2n = 32 to 2n = 60 chromosomes), the modal chromosome number for South American species was 2n = 48 and the modal number for the African ones was 2n = 44.
Pericentric inversions are thought to be the main mechanism contributing to changes in the basal chromosome arm size of Perciformes. Other mechanisms of
chromosomal rearrangement and translocation probably have contributed to the karyotypic diversification of South American cichlids. The chromosome number variation observed in some species suggests that events of chromosomal translocation followed by chromosome fission and fusion were also involved.
(Poletto et al., 2010)

Like already observed with horses, increased chromosome counts rather represent an evolutionary stage of change rather than a new equilibrium. Kolnicki’s karyotypic fission theory that ‘ posits that all mediocentric chromosomes simultaneously fission’ is just a variation of the theme:

That chromosomal diversity of such distinct taxa is explicable by fission implies this mode of animal evolution is important.
Increases up to nearly doubling of smaller derivative chromosomes throughout the Cenozoic underlie adaptive radiations, at least in artiodactyls, carnivores, lemurs, Old World monkeys, and apes. (Kolnicki, 2000)

This is not the place to discuss the general applicability of Kolnicki-type processes, except that Müller’s hypothesized ancestor of the lesser apes (Hylobatidae or gibbons) may now be attributed too lightly to an amazing diploid chromosome number of 2n = 64. For clarity I simply discard any existing intention to derive great ape chromosomes from a similar hypothetic ancestor, confident that in the same effort nobody would try seriously to derive monkeys from great apes. All gibbons share the same three chromosomal fission events with other apes that compare with macaque chromosome numbers 2, 7 and 13 and the corresponding fissioned pairs: for humans chromosomes 7 and 21, 14 and 15, 20 and 22 respectively. This detail strongly pleads for an ultimate derivation of gibbon chromosomes from the same macaque-like ancestor having a reduced set of chromosomes (2n = 42), as well as from the same ancestral ape having 2n = 48 chromosomes like great apes. Then subsequent changes should have reduced the count for Hoolock genus to 2n = 38, an even lower diploid chromosome number than macaques, while for other gibbon genera the number is higher: 44 (Hylobates), 50 (Symphalangus) and 52 (Nomascus), respectively. This implies that all additional ape-related fusion events on chromosomal level, as observed for humans and gibbons, were preceded by these three fission events that are shared by all apes.
Fission is one way to trigger accelerated recombination, and to increase plasticity. Hybrid-driven recombination is another, whether or not in combination with the mechanism of fission. Reversely, biological justification of chromosome fusion may rather be found among the advantages of synteny, ie. the physical co-localization of genetic loci on the same chromosome. It is suggested that genetic change by hybridization is not an overnight process, and may create instability on chromosome level for at least a few generations. Hybridization of chromosomes and homogenization processes, per definition occurring after considerable divergence, opens up a whole new array of possible combinations, but also new risks of meiotic nondisposition. Natural selection could become a cumbersome, even impossible strain to reproduction if also the whole array of possible deleterious combinations would eventually result in low-fitness birth. Reproductive consequence would be less for miscarriages, or just lower rates of viable gametes. Still, even the fecundity of plants would be harmed by the possibility of unlimited recombination, not in the least for the reproductory investments of cycads that also have the record for the world’s largest sperm. Encapsulation of heterozygous content in fused chromosomes could reduce this risk to future generations. It goes without saying that fusion of chromosomes also offers a better protection against cytogenetic instability of hybrids. As such, fusion of chromosomes emerges as a potential strategy towards endogenous purifying selection and increased fitness of the hybrid lineage.
An example of chromosomal instability is trisomy, that typically results in miscarriage, or low-fitness offspring. Human low-fitness births related to trisomy are the Patau syndrome (trisomy 13), that affects somewhere between 1 in 10,000 and 1 in 21,700 live births, the Edwards syndrome (trisomy 18) that occurs in approximately 1 in 3,000 conceptions and half this rate for live births, with a median lifespan of 5–15 days, and the Down syndrome, whose incidence is due to trisomy 21 for 95% of the cases, and estimated at one per 800 – 1000 births.

Trisomies of all chromosomes with the exception of chromosome 1 have been reported in spontaneous abortions in humans; however, the only numerical autosomal anomalies surviving to birth are trisomies 13, 18, and 21. There are only six reported cases of autosomal trisomies in live horses ([…] 23, 26, 27, 28, 30, and 31) […]. Similar to that observed in humans, trisomies in horses predominantly involve small chromosomes. (Brito et al., 2008)

Human trisomy indeed involves chromosomes that are either small (18, 21), or with low gene density (13), apparently important preconditions against a spontaneous abortion. Despite the deleterious nature of the three trisomy-ridden human chromosomes mentioned above, these already existed before the lesser apes split off from great ape ancestors. Chromosomes 13 and 18 must have been present even in the common ancestor of apes and macaques. Only different gibbon genera managed to neutralize these potential dangers by fusion: in Hylobates the equivalents of human chromosomes 13, 18 and 21 are all fused (respectively with chromosomes equivalent to 3, fissioned remnants of 1 and 15).

Even though Hominoidea chromosomes 13, 14, 15, 18, 20, 21, and 22 constitute a single, uninterrupted chromosomal block in the lar gibbon, most of them are part of larger chromosomes and/or show internal rearrangements. (Misceo et al., 2008)

Such evidence may indicate that chromosome fusion is neither coincidental nor imperative per definition. This is especially interesting for the unique fusion of two ancestral great ape chromosomes into human chromosome 2.

The human chromosome number 2 is a fusion of two great ape chromosomes. Displayed are respectively the versions of humans, chimps, gorillas and orangutan. The banding pattern of chimps equals the human version most.

This fusion was evidenced by similarities in chromosome banding patterns as well as homologies in DNA sequences, where chimps make the best match. Normally, the extreme ends of chromosomes (telomeres) form a dynamic buffer against loss of internal sequences and prevent chromosomes from fusing, but apparently here telomeric DNA was involved in the fusion, to the extend that some telomeric DNA was preserved at location 2q13 near the new centromere.

Comparative cytogenetic studies in mammalian species indicate that Robertsonian changes have played a major role in karyotype evolution [..]. This study demonstrates that telomere-telomere fusion, rather than translocation after chromosome breakage, is responsible for the evolution of human chromosome 2 from ancestral ape chromosomes. (IJdo et al., 1991)

Somehow this event set us apart from great apes. As the assigned number indicates, chromosome 2 is our second largest chromosome. Commonly described as important for cognitive capacities, this particular fusion implies the importance of synteny for imposing genetic stability on cytogenetic level, that exceeds protection against semi-viable trisomy.
Evolving species may be expected to rely on an evolutionary boost to give them an edge. Since non-deleterious point mutations are rare, much depends on a quick and adequate mechanism to experiment with new complex DNA combinations. Species having low effective population sizes may have a problem if biological divergence is insufficient for regular recombination to produce successful genetic results. At major adaptive radiation events a species could recur to fission as a strategy to compensate for an initially low biological divergence. Next, increased divergence by the process of adaptive radiation may be expected to eventually reduce the need for fission – unless effective population sizes remain too low for harboring major biological variety. Lesser apes may have continued on the strategy of fission where great apes didn’t, implying their divergence probably occurred right here. Instead the lineage of great apes, including hominines, could take advantage of hybridization to incorporate successful mutations in the genome, no matter where these originated. This mechanism must have been a possibility within a certain time window, somewhere between population divergence and irreversible speciation. An extended continuation of this process may have relied on sub-species cross-breeding and hybridization – ie. contrasting with recurrent vicariance events as cited in the case of the gibbon genera, where low effective population sizes urged for continuous cytogenetic change in order to cope with the needs of environmental adaptation. Either way such periods of adaptive radiation should have left traces in the human chromosomes, not in the least if true hybridization was involved:

Contrary to the view that hybrids are lineages devoid of evolutionary value, a number of case studies are given that show how hybrids are responsible for reticulate evolution that may lead to the origin of new species. Hybrid evolution is mediated by extensive genome repatterning followed by rapid stabilization and fixation of highly adapted genotypes. Some well-documented cases demonstrate that bursts of transposition follow hybridization and may contribute to the genetic instability observed after hybridization. The mechanism that triggers transposition in hybrids is largely unknown. (Fontdevila, 2005)

Geneflow within the genetic continuum of a species happens all along, but let’s ‘[…] define hybridization as gene flow between two populations after an isolation barrier has formed between them.’ (Patterson et al., 2006 Supp.). The latter is most likely a major element in evolution, still waiting for recognition. And a potential cul de sac since, contrary to equids, zamia and gibbons, chromosomal changes in great apes and humans are far from impressive. No chromosomal fission event postdated the divergence from lesser apes, not even in hominin-specific evolution. Genetic recombination was significant enough for rapid change and plasticity, but apparently without the need for massive reorganization on chromosomal level, or even significant mutational activity on genetic level. Segmental duplications make a remarkable exception:

Although [the genomes of] terminal hominid lineages show an excess of [segmental] duplications, the most significant burst of activity (4–10-fold […]) occurs in the common ancestor of human/chimpanzee and gorilla and after divergence of gorilla from the human–chimpanzee lineage […] We note that this burst of duplication activity corresponds to a time when other mutational processes, such as point substitutions and retrotransposon activity, were slowing along the hominoid lineage. (Marques-Bonet et al., 2009)

Duplication indeed contributes to diversity, though indicative of actual genetic activity rather than anything else:

Gene models associated with signal transduction, neuronal activities (for example, neurotransmitter release, synaptic transmission) and muscle contraction are significantly enriched in human, chimpanzee and orang-utan lineage-specific duplications […]. Human and great-ape shared duplications or those shared with macaque are, in contrast, enriched for biological processes associated with amino acid metabolism […] or oncogenesis (Marques-Bonet et al., 2009)

Some sort of genomic destabilization is implied ‘at a period before and perhaps during hominid speciation’. But why and how this process could have been so different for humans, compared with an evolutionary strategy towards increased chromosomal change for lesser apes?
Exchange of alelles between hominine subspecies is nowadays sufficiently attested in modern genome research, but cross-breeding of diverging subspecies – or species! – should suggest chromosomal change of a higher order. Indeed, at least something has happened on chromosome level since the human divergence from apes, most notably the reduction of the chromosome count from 48 to 46, or the unique X-transposed region of the human Y-chromosome, dated right after chimp divergence and a virtually unprecedented event all by itself.

A third sequence class in the human MSY euchromatin — the X-transposed sequences — has no counterpart in the chimpanzee MSY. The presence of these sequences in the human MSY is the result of an X-to-Y transposition that occurred in the human lineage after its divergence from the chimpanzee lineage (Hughes et al., 2011)

Also chromosomal changes in chromosome 7, one of the new ape chromosomes that originated by fission, could be mentioned: the chromosome was subject to a pericentric inversion (including the centromere) after the divergence of orangutan, followed by a paracentric inversion after the divergence of gorilla. Another translocation of genetic information from chromosome 15 to chromosome 4 has been documented only for African apes: gorilla suffered deletions that preclude proper interpretation, but all derived basepairs of the 4q copy in chimps indicate this to be the result of hybrid recombination that happened before the divergence of gorilla:

If the duplication was followed by speciation and independent accrual of mutations, we would expect to find the human 15q and chimpanzee 15q copies to show higher identity to each other than either does to the copy found on chimpanzee 4q. Instead, the two chimpanzee copies are the most closely related pair of this trio.
By comparing ~19.1 kb of hand-curated, well-aligned block-5 sequences, we find that the chimpanzee 4q and 15q copies are only 1.43% diverged (Jukes-Cantor adjusted). They also share 43 derived mutations, including a 4-bp deletion that disrupts the ORF of gene H, not seen in the macaque or human 15q copies.
In contrast, the human 15q and chimpanzee 15q copies are 1.65% diverged and share 22 derived mutations not seen in chimpanzee 4q; and the human 15q and chimpanzee 4q copies are 1.64% diverged and share 13 derived mutations not seen in chimpanzee 15q.
(Rudd et al., 2008)

Such macro genetic events may be of an entirely different category than the published evidence that involve autosomal admixture of genetic regions from different hominine subspecies (Neanderthal, Denisova), or even of genetic harmonizing on the X-chromosome, already quoted as valid evidence for true cross-species genetic exchange with chimpanzee ancestors. Still, they are only in modest agreement with the prospected results of radical hybridization.
Notwithstanding an extended period of great ape evolution, lasting millions of years since the divergence of lesser apes, it has all appearance that over time hybridization remained a gradual process and rarely exceeded the level of subspecies crossbreeding.
Ever since this last major hybridization event(s) between chimp and human ancestors the hominine lineage apparently entered an extended period of rapid development. A full discussion is not the context of this article, but we can be sure nature did its utmost to exploit all available intra-species diversity to experiment with genetic recombination. There is an increasing awareness of natural interbreeding and admixture on subspecies level, whose impact on human evolution genetic science only started to disentangle. Another challenge still awaits us in the preposition that hominines could be essentially more related to orangutan than chimpanzees. Genetically this doesn’t seem right, but a successful hybrid is also a collation of DNA and morphology that rather define a new composition than an average of parental features. Current evidence corroborates to the implication that the genetic result of hybridization isn’t even random:

[…] endogenous selection is acting against intermediate hybrid individuals, that is, those that contain the highest number of alien genetic elements (Arnold, 1997). In a similar way, Rieseberg et al. (1996), working with H. anomalus, found that similar linkage groups of genes exist in several artificial hybrid lines with high fertility. (Fontdevila et al., 2005)

All we could propose is a complicated pattern of cross-breeding events to close the evolutionary gap of up to 16 million years since common Griphopiths precursors of great apes started to diverge.

Griphopithecins are the first cosmopolitan hominoid taxon, probably as a result of their powerful jaws and teeth that allowed them to exploit a wide variety of resources.
I see the entire region from Germany and Turkey in the north to Kenya in the south as a potential core area in which early hominids could have evolved. But there are major gaps in the record. For example, one species of Kenyapithecus is known from 16–16.5 Ma in Turkey and another from Kenya at about 13.5 Ma […]. It was probably present elsewhere in the intervening interval of time but we have not yet found the fossils. From this core area these stem hominids (not specifically related to either living group of hominids, pongines, or hominines) eventually split, with one segment of the distribution of species dispersing to the north and east and another to the north and west. The causes of this dispersal are unknown, but griphopithecins are the most primitive hominids we know. The later-occurring sivapithecins of Asia and dryopithecins of Europe are more modern, and strong cases can be made that they are related to living orangutans and African apes and humans, respectively. (Begun, 2010)

If both components indeed represent sister lineages of apes rooted in the Miocene, it would be taunting to bolster this almost impossible preposition with genetic evidence.
I suggest the fuss about our purported lack of relatedness with the apparently quite basal gibbon genera might give us an important clue. If both great ape genera acquired their humanizing features by an extended period of hybridization, their common ancestor may indeed remind us to primitive small apes:

[…] Griphopithecus and its relatives retain primitive postcrania. They are more monkey-like than ape-like […] without any indications of the suspensory capabilities of all later fossil and living great apes (Begun, 2010)

Cytogenetic evidence cited above reveals that chromosomes of small apes share the basic pattern that set great apes apart from macaques and thus may derive from an ancestor having eg. orangutan-like chromosomes. From this point onwards small apes can be defined as monophyletic, what may be confirmed by genetic evidence:

Among hominoid primates, gibbons alone contained Alu elements in their EIF1AY gene of the Y chromosome. (Kyung-Won Hong et al., 2007)

There have been different interpretations of the hylobatid evolutionary history regarding the four different gibbon genera, but: ‘Maximum likelihood and Bayesian analyses support Hoolock as the most basal, and both molecular and karyological studies have supported this alternative’ (Israfil et al., 2010).

Of all gibbon genera the genetic distances of Hoolocks (Bunopithecus), the most basal group, are closest to the human and chimp outgroups.

Much of the uncertainty was caused by the implied ‘radiation of the main genera over an interval of less than 1 Ma’, what according to Israfil’s calculations happened between 6.4-8 mya. However, if this radiation event happened completely isolated from other apes then humans and two species of chimps should have an equal genetic distance to all gibbon genera. All the contrary, when distances between taxa were estimated by two measures of sequence divergence, using DNA sequence of the complete mitochondrial control region and adjacent phenylalanine-tRNA, the Hoolock stood out as the gibbon species being closest to all outgroups – especially humans. One way to interpret this results is to consider a much closer relationship between gibbons and great apes than vanity allows us to do, and a radiation event that was less monophylitic than commonly assumed. Instead, genetic evidence would indicate the various gibbon originated by a two-stage isolation from a common source of Miocene apes that were still interconnected by geneflow. The slightly greater distances with chimps in comparison with humans would then be explicable by proceeding geneflow within the clade of great apes, and – notwithstanding an extensive and quite recent history of chimp-human hybridization – a higher degree of (spatial?) isolation for the genetic component of chimps in comparison with humans. Humanizing processes didn’t advance within the gibbon genera as much as within great apes, including orangutan, what should remind us to the primitive stage of development the griphopith ancestors of great apes really had:

[Griphopiths] are more monkey-like than ape-like, as is Proconsul, in having fore and hind limbs of roughly equal length, without any indications of the suspensory capabilities of all later fossil and living great apes (Begun, 2010)

The divergence of the lineage leading to small apes must have happened long before at least two parallel lineages of great apes ‘humanized’ together with hominines. In the fossil record brachiating of great apes seems to develop first within the Dryopith clade, and at this stage one might wonder what could be the involvement here of a gibbon-type introgression event. Contrary to our Griphopith ancestors, modern humans and great apes retain many physical characteristics that suggest a brachiator ancestor, including flexible shoulder joints and fingers well-suited for grasping.

Dryopithecus […] is known from postcranial remains, which are dramatically different from those of the griphopithecins and Proconsul. They show unambiguous indications of the importance of highly mobile limbs and suspensory positional behavior
I interpret this change to be extremely important in the evolution of the African and human clade. It allowed Dryopithecus to remain relatively large and yet retain the capacity to exploit terminal branch resources, by spreading its weight among the branches and by hanging below them to conserve energy […]. It also represents the evolutionary origins of human mobile and highly dexterous upper limbs.
In addition to being relatively primitive compared to later species, the teeth of Dryopithecus differ from those of the griphopithecins in having a thin layer of enamel and less rounded cusps. They more closely resemble the teeth of chimpanzees and have been interpreted as adaptations to a soft fruit diet, as in modern chimpanzees […]. The later occurring dryopithecins Hispanopithecus, Rudapithecus, and Ouranopithecus share even more postcranial derived characters with living great apes (Begun, 2010)

However, again the molecular dates remain difficult to reconcile with the fossil record:

The appearance of Dryopithecus at about 12 Ma parallels the first appearance of Sivapithecus at nearly the same time, suggesting that they diverged from a common ancestor possibly 13 to 16 Ma. (Begun, 2010)

The great ape-gibbon split simply doesn’t concur with the gibbon radiation dates:

Based on a consensus estimate of 15 Ma for the great ape-gibbon split, Chatterjee (2006) undertook molecular clock analyses using cytochrome b gene data and suggests the gibbon radiation dates to approximately 10.5 Ma. (Chatterjee, 2009)

This is still considerably less than the Raaum et al. (2005) estimate of a ‘divergence date of 15.0–18.5 Ma based on the entire mitochondrial genome’ (Chatterjee, 2009), thus apparently contradicting the possible hybridization signal mentioned above.
Molecular clock analysis is often used to estimate the date of speciation events in evolutionary history, but what can be said about its reliability? It didn’t come as a big surprise that paleoanthropologists were reluctant to abandon all the views they still cherished immediately for the sake of biochemistry:

[Wolpoff] admits […] that ramapithecines are also a stem group for the African apes, whose tooth enamel is very thin. This would be a full reverse evolution towards a dentition very similar to that of Dryopythecus. Is this a parsimonious hypothesis? (Bonis, review on Wolpoff, 1982)

Schwartz criticized newly adapted scenarios ‘defending presumed phylogenetic hypotheses rather than rigorous presentations of such hypotheses’, that essentially left the purported ‘reversal’ in dental characteristics of chimps and gorilla back to the primitive conditions of Dryopithecines, unanswered.

I am not swayed by blanket statements of how similar Pan and [hominines] are because most of the similarities appear to be primitive retentions, and I am so far unpersuaded by karyological and biochemical studies for similar reasons as well as others.(Schwartz, review on Wolpoff, 1982)

Even Wolpoff, trying very hard to conciliate paleoanthropology with molecular evidence, couldn’t help to incite Sarich by stating:

Probably the best way to summarize the very disparate points raised is that the “clock” simply should not work […] Consequently, although biochemical evidence seems to support a late Homo-Pan divergence, I believe this is a red herring, and that the molecular “clock”does not support any divergence time (Wolpoff, 1982)

One main issue that remains to be answered is how selective processes may have biased the genetic distances between species, and their biochemistry that, as a matter of fact, directly reflects evolutionary changes of their DNA.
Indeed, the molecular “clock” turned out unreliable because of variation ’caused, in part, by uncertainty or assumptions in key parameters, such as divergence times between species, generation times and ancestral population sizes’ (Conrad et al., 2011). But new results on the very mutation rates themselves indicate that apparently there is more internal logic to mutations on chromosome level than mathematicians were able to assume or deal with. Mutation rate differences exist and already turned out to be essentially individual:

[…] future studies promise to revolutionize our understanding of mutation processes and how they vary between individuals and between families as a result of age, genetic background and environmental exposures (Conrad et al., 2011).

This insight came too late for the immediate resurrection of our theorized ‘dental-hominoid’ ancestor, though in some act of posthumous generosity variable mutation processes should certainly provide for more nuance. How some basal species – humans, chimps and … hoolocks? – could remain genetically more ‘related’ on a molecular level than warranted by their morphological distance? Molecular constraints dictated that African apes and the hominine lineage should share a recent common ancestor, but the underpinning assumptions are still full of inconsistencies. ‘Single recent origin’ may be an interesting null-hypothesis to geneticists, but to paleoanthropology this increasingly reverts into the same unmanageable preposition as before. Molecular evidence is still a pretext to challenge common sense where it may oblige human minds to search for answers about themselves within a limited time window, that in turn implies a limited scope of geography. Adding here the constraints of emotional inquisition and lurking nationalism inherent to any limited region of choice, we could conclude ironically that paleoanthropology still finds itself right in the middle of all the fuss where Darwin’s theory of evolution once started.


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Evolving Chimps are Messing Up Y-DNA Dating

January 28, 2010 5 comments

We are only starting to understand the functionality of Y-DNA. New research on chimpanzees by Hughes et al. (2010) revealed considerable selective pressures that caused the Y-chromosome to evolve more rapidly than anything else. The degree of similarity in orthologous MSY sequences, i.e. of any Y gene found in chimpanzees and humans that can be traced to a common ancestor, amounts to 98.3% nucleotide identity, slightly less than the value reported when comparing the rest of the chimpanzee and human genomes (98.8%). Deletions, insertions and substitutions can be observed and the alignments of nucleotides don’t necessarily imply a direct homology. I think it would be an error to assume these polymorphisms are without meaning and presume no selective differences. However, more strikingly, more than 30% of the MSY sequences is not orthologous. Divergence also involves the so-called X-degenerate region, the realm of genes considered at least 40 million years old, that contains surviving relics of ancient autosomes (non-sex chromosomes) from which the X and Y chromosome co-evolved. The article suggests an extraordinary divergence between humans and chimpanzees:
“The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor.”

Interspecies Handshake for the Blog.

Among other processes, it seems the differences relate to diverging demands that were posed by mating behaviour and sperm production. Obviously the effect of the changes was to enhance functionality. Promiscuous female behaviour caused sperm competition among males that resulted in the chimp ability to produce sperm cells that reach an average speed of 0.7 km/h, against a mere 0.2 km/h to humans.
But how these results interfere with previous assumptions on Y that concern genetic dating? The dating system for Y-DNA haplogroups as proposed by Karafet (2008) heavily builds upon assumptions on the nature of the Y-chromosome that now seem to be rendered obsolete. Karafet defined her dating system on what she thought to be correctly intertwined archeological (paleo-anthropological) and genetic investigation results. She could have been wrong on the validity of both. Then the entire fundament of her reasoning turns out to be circular, and the framework crushes.

To provide estimates of the age of the nodes, we chose to fix the time to the most recent common ancestor of CT (defined by P9.1, M168, and M294) at 70 thousand years ago (Kya), which is consistent with previous estimates from genetic and archaeological data (Lahr and Foley 1998; Hammer and Zegura 2002; Macaulay et al. 2005), and is the chronological approximation given in Jobling et al. (2004) (p250) for the first major human out-of-Africa dispersals.

So far the Y-chromosome was understood thus:
“[…] one-half consists of tandemly repeated SATELLITE DNA and the rest carries few genes, and most of it does not recombine. However, it is because of this disregard for the rules that the Y chromosome is such a superb tool for investigating recent human evolution from a male perspective.” (Jobling et al., 2004)
In a review, The Whitehead Institute for Biomedical Research came up with the following considerations that redefine the human Y-chromosome rather as a hotbed of evolutionary change :

Chimp and human Y chromosomes evolving faster than expected
CAMBRIDGE, Mass. (January 13, 2010) – Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation.
By conducting the first comprehensive interspecies comparison of Y chromosomes, Whitehead Institute researchers have found considerable differences in the genetic sequences of the human and chimpanzee Ys—an indication that these chromosomes have evolved more quickly than the rest of their respective genomes over the 6 million years since they emerged from a common ancestor. The findings are published online this week in the journal Nature.
The region of the Y that is evolving the fastest is the part that plays a role in sperm production,” say Jennifer Hughes, first author on the Nature paper and a postdoctoral researcher in Whitehead Institute Director David Page’s lab. “The rest of the Y is evolving more like the rest of the genome, only a little bit faster.”

Apparently, exact knowledge on Y-DNA and how it works is still lacking:

Wes Warren, Assistant Director of the Washington University Genome Center, agrees. “This work clearly shows that the Y is pretty ingenious at using different tools than the rest of the genome to maintain diversity of genes,” he says. “These findings demonstrate that our knowledge of the Y chromosome is still advancing.”

Still Karafet proposed a system of SNP dating based on freely mutating portions of Y-DNA, whose behaviour could already be assumed sufficiently predicatable. This must be wrong.
As for now, the possibility for a wholesale verification of the (random) Y mutation rate by sequencing has not been fully exploited. We depend on assessments that concern picked microsatelite loci and assume average mutation rates all over Y. Thus, by comparing relatives separated over an increasing amount of documented generations we could retrieve such average values. Comparing all base-pairs is a painstaking exercise that so far has been done only at the euchromatic male-specific region for up to 10Mb out of a total of about 30Mb of Y-chromosome base-pairs, and excluding ‘gaps in the reference sequence, highly repeated sections, and palindromes from our analysis’ (Xue et al., 2009).
“The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 113 or 203, respectively [4]. Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in ~10.15 Mb; eight of these had occurred in vitro and four in vivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 X 10-8 mutations/nucleotide/generation (95% CI: 8.9 X 10-9 – 7.0 X 10-8), consistent with estimates of 2.3 X 10-8 – 6.3 X 10-8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons [5] depending on the generation and split times assumed.”
The human Y-chromosome has 454 genes and 25.121.652 sequenced base pairs (~24 Mb), that is the euchromatic part out of a total of 57,741,652 base pairs. Between 1% and 2% on average of the base pairs are coding, though estimates of the base pairs being expresssed one way or the other run up to 80% of the genome (i.e. the sequenced part). This means that 80% of these 24 Mb base pairs is not ‘junk’ and can’t be considered neutral. Such a huge part simply can’t be permitted to mutate without any restrictions on molecular level, since most mutations are deleterious. The occurrence of mutations at this magnitude is hard to accept for genes that are actually used, one way or the other: we don’t even know to what degree slow mutating STR could be truly included in the junk part of DNA. Coding DNA is fairly immutable since it should be clear that evolution is a slow process that can’t guarantee the survival of successful lineages that are subject to mutations at the same rate as random mutations. At least the occurrence of spontaneous mutations is based on internal processes whose logic doesn’t necessarily depend on mere statistics, but instead of the local availability of structural variability potential as eg. supplied by unevenly distributed palindrome DNA. This little detail alone would already have the potential to decrease the overall mutation count about five times at the assumption of just 20% junk DNA, and thus increase the current SNP dating accordingly by 5 times.
The mutations detected by Xue et al. in only one third of the Y-chromosome indeed seem to approximate the expected values at a normal mutation rate over the whole chromosome, though this result may be biased by their own predefined expectations. Maybe Xue et al. just diagnosed an exaggerated accumulation of mutations within a region that included all genetic areas they already knew as highly prone to mutations. If this were the case, their investigation was useless and we should rather direct our efforts in distinguishing the behaviour and mutation rates related to either coding or non-coding DNA.
In her age calculations for Y-DNA haplogroups Karafet bases herself on the assumptions of others, e.g. Jobling et al. (2004). The latter just doubles the previous estimates concerning STR (Pritchard et al.,2000) and SNP (Thomson et al.,2000) due to the new insight of generation intervals of 35 years:
“The appropriate choice of generation time for ancient populations remains unclear, but the use of 35 years would almost double the TMRCA estimates.”
Thus her study also depends heavily on older studies that make some curious assumptions on Chimp and Junk Y-DNA, including Jobling’s claim that Y-DNA “carries few genes”, leaving one-half of Y-DNA virtually without any potential coding blueprint.
Thomson et al. (2000): “For the ages of major events in these trees, an estimate for the mutation (single-nucleotide substitution) rate was needed. To obtain this rate, the number of substitutions was found between a chimpanzee sequence and a human sequence for the genomic region in question. From this information, the mutation rates per site per year for the three genes were estimated“.
Note that these mutations rates are now probably way too high due to positive selection that occurred among chimps. This study of Thomson was cited by Jobling as: “The largest study of Y-SNP variation free from ascertainment bias, which is based on DHPLC [denaturing high-performance liquid chromatography] and proposes a common ancestor ~59 kya.”
Karafet’s assumptions on STR are based on similar principles: […] our analysis has several modeling limitations. […] In particular, we ignore population structure. Second, we assume selective neutrality of the Y chromosome.[…] It would be of considerable biological interest if natural selection were shown to have been an important force on the human Y chromosome, but the value of the Y chromosome as a tool for interpreting human history would then be reduced (Pritchard et al.,1999).
Jobling: “The human population is so large that, even given the low average mutation rate of ~2 × 10–8 per base per generation,we expect recurrent mutations to occur at every base of the Y chromosome in each global generation.”
Of course this can’t be true for coding DNA, where only a few DNA configurations are viable.

Jobling referring to Kayser (2000): “Studies that use mutation rates in calculations […] often quote average rates, such as 3.17 × 10–3 per microsatellite per generation”. Note this study of Kayser was cited by Jobling as: “Still the largest published study to measure the mutation rates at Y-chromosomal microsatellites using father–son pairs. This is more laborious than using deep-rooting pedigrees or sperm pools, but produces more reliable measurements.”
Jobling: “Sequencing of the chimpanzee genome is underway, and promises a cornucopia of information about the evolution of our own genome. Assembly of a chimp genome sequence using the human sequence as a framework will be straightforward for most chromosomes, but it might prove difficult for the Y chromosome because of its evolutionary lability. It is to be hoped that expenditure of effort on the Y chromosome will be comparable to that on other chromosomes, and that its reputation as a gene-poor junk-rich delinquent will not lead to a reluctance to include it wholeheartedly in the sequencing effort.”
The investigation of Hughes et al. shows that Y-DNA is neither subject to evolutionary lability nor does it substantiate claims of being a “gene-poor junk-rich delinquent.”

So what it is all about?
Chimps deviated from humans because of some peculiar selective pressures that concern sperm competition (Nascimento et al., 2008).
This deviation thus probably affected chimps rather than humanoids, what seems to be confirmed by what was already known in the seventies, that Gorilla sperm is more similar to human sperm than the sperm of chimps (Seuánez, 1976).
This can only make sense if Y-DNA of chimps deviated from the common stock rather than the y-DNA of humans. The Gorilla-Chimp-Human group split off too early from Orangutan to presume a specific correlation of Human DNA to Orangutan to be worthwhile, unless gorillas, like chimps, deviated disproportionally from the common human lineage since the Orangutan split. In that case, even primitive “Orangutan-like” features would be valuable for making better age estimations than chimps, at least concerning the Y-chromosome.

King Kong illustrates interspecies mating is hard to imagine.

Male Y-DNA developed rapidly, but this doesn’t prove ancestral males developed preferences for certain kinds of ancestral females. Actually, strikingly low differences at X-chromosome levels between humans and chimps even allow both species to have evolved together for a much longer time than the differences on Y (and other chromosome differences) suggest. Free mixing may apply even more to early humans, where evolutionary forces that concern sexuality remained lower. If a certain group of early “chumans” (ancestral chimp-humans) developed a chimp-like sexual behaviour that caused females to be so very promiscuous as to trigger male sperm competition, then mainstream “chuman” males just didn’t get a chance anymore to add to the genepool of the most promiscuous group. On the other hand, males that already developed better sperm strategies lost their competitive edge in mainstream communities where female behaviour was less explicit. The female chimp has an estrus cycle of about 34 to 35 days. While in heat, the bare skin on her bottom becomes pink and swollen, and she may mate with several males. When did the males develop their mating preferences? And when females lost their attractiveness to one of the emerging species? Sperm behaviour may have been the prime cause of the split, since I don’t think humans are known for being particularly selective in finding a mating partner. That humans and chimps stopped mating/mixing thus may have been interluded by a lost sperm-competition among males, rather than cross-group infertility. Somehow early humans did not follow this sexual chimp-culture, or else (in this view) the split wouldn’t have occurred due to the sexual advantage of chimp males. Maybe early human males became discouraged by the explicit promiscuity and swollen bottoms of the females demanding sperm competition, or the early chimp females became discouraged beforehand to show their pink bottoms to the early human losers of the sperm competition around. Still chimp females and chimp males could have entered the human genepool for a longer period, unless of course the Y-DNA changes among chimps were also a response to a new chimp-female receptivity of a certain kind of chuman-sperm. However, evidence of a shared female evolution – if any – tends to outweigh all potential evidence of hybridization.
Speciation does not happen if Panmixia outweighs Fixation. In a simple formula:

P = 1 – F
P – “factor of Panmixia”
F – “factor of Fixation”

In this case F(ixation) could have happened because of two concurrent reproduction strategies among males, without isolation. Panmixia could have been fully in place for female “chumans”, to the point that they might have remained indistinguishable one from the other for some time. The view that early hominids may have been human-chimpanzee hybrids has no empirical support in the animal world. However, Panmixia does not necessarily imply hybridization at any stage. The same lack of empirical evidence makes the Multiregional Hypothesis so very hard to prove. There is no empirical data on animals that persistently violate biological barreers. Humans, however, are essentially different from animals in much of their behavior, and the uniqueness of humans implies no other examples, thus the non-existence of empirical data that concern animal observation by definition. In my view, maximum Panmixia is likely as a feature of incipient humans, and “maybe” of chumans as well. Fixation as an exclusive result of sexual behavior and sperm competition thus would be perfectly in line with the Multiregional view.
The only way to account for the accumulation of human Y mutations over the whole population is to assume that Y evolved in a process of change that involved the regular replacement of the whole male population of the species, always departing from a single ancestor. There certainly are quite a few mutations since the human-chimp split date and it just doesn’t make sense to imagine evolution as a one step event. Parallel lineages may have occurred sometimes though successful mutations only occur once, and most probably one at a time. Moreover, there is not any reason to assume that each successful mutation on Y implies the emergence of a new species versus the extinction of ancestral species. Thus the selective forces not only resulted into the continuous reconstruction of Y (Hughes et al.), but also into the continuous reconstruction of the whole male population, departing each time from a single male ancestor – no matter how small the change and on what part of the Y the successful mutation occurred. The only precondition, of course, would be real selective advantage. The main implication to what this means to the nature of Y-DNA is: much less junk than was ever assumed. The evolutionary changes of orthologous MSY sequences that were a “little bit faster” could confuse mutation rates even more. Actually, in my view evolving Y DNA does not allow so much random change, except for the acceleration of decay. I suspect the existence of non-conventional mechanisms leading to successful mutations. Furthermore, diminished random change would inevitably slow down the formation of new stable markers that are truly “random”.

Male competition - Humans lost! (Travis the Ladykiller).

Let’s not be confused here about the word evolution. Evolution in this context implies adaptation and non-random change caused by natural selection. Most of all, true evolution implies non-neutral Y markers, not the statistic accumulation of variance or diversity of junk DNA. Obviously, this is not what population geneticists should want to have in calculating their mutation rates since neutrality is their explicit and prime assumption. In all the relevant papers this assumed neutrality is explicitly mentioned.
The variation of coding sites is very low, since mutations on coding DNA could invoke a tricky situation. Except for decay, evolutionary change of coding DNA is usually limited to a set of polymorphisms. For instance, if only 10 polymorphisms are viable and doing about the same then this is all we will ever see, no matter how much time will pass. Evolution of polymorphisms is not infinite. That is why you can grow the eyes of a mouse on the legs of a fly, using genes that are essentially similar to all species. This probably means that new mutations rather originate from another source, somewhere else on the chromosome. There is no accepted theory on the emergence of successful mutations as far I know, though there are theories on the coding potential of palindromic elements, inverted repeats that like direct repeats can also be tandem repeats. My guess is that to gain a competitive edge you’ll need an increased supply of these repeats, like chimps have, i.e. some kind of genetic lab where new configurations can be tested without compromising existing,i.e. functional genes. Somehow these palindromes find their source in blueprints and we don’t know yet how loosely related they really are to coding sites. Definitely we can observe constraints to the variance of STR – this could be one.
The effective mutation rates of sites subject to selection is lower than for sites not subject to selection. Population geneticists may be quite used to dealing with this, even without the need for deeper understanding: HVR vs coding region equal to fast STRs vs slow STRs. This may be no big deal, but only in the case very little of the Y actually codes for proteins. We don’t know how much is coding, we are only starting to understand the functionality of Y-DNA, like the study also indicates. If slow STR are indeed (loosely) linked to coding regions, and fast STR to HVR, then non-neutrality should be an issue to consider. Non-coding parts may be closely associated to coding parts and actually this is what the rapidly “evolving” chimp Y-DNA suggests:

“By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years. The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor.”

Note the “lost part” of chimp Y-DNA is a powerful indication of the one-sided nature of chimp evolution, apparently causing a considerable degree of collateral damage. Remarkably, Gorilla DNA didn’t attest such loss of the ancestral state. The X-degenerate region on the Y chromosome has retained all 16 genes for gorilla’s and humans alike, while chimpanzee has lost 4 of the 16 genes since the divergence of the two species.
Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation.”
The impact of change on human Y evolution remains unclear in the study. There can’t be any doubt that genetic decay was a principal dynamic all along in the evolution of Y chromosomes, but chimp DNA show us that “wholesale renovation is the paramount
theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs.”

The dynamics of change are so widely different between chimps and humans, that the massive chimpanzee ampliconic regions being 44% larger than in human must have some evolutionary advantage.

Previous models of Y-chromosome evolution treated the chromosome as a uniform, homogeneous substrate for evolutionary change. In fact, the evolution of ampliconic sequences has outpaced that of X-degenerate sequences
Unlike the human MSY, nearly all of the chimpanzee MSY palindromes exist in multiple copies, so that each palindrome arm has potential partners for both intra- and interpalindrome gene conversion (non-reciprocal transfer) – Hughes et al., 2010

Thus, DNA of non-coding intron regions have a function after all, that is all about evolution. We don’t know if polymorphisms of an allel are the direct result of mutations in coding DNA, or replacements that pop up from an associated palindrome “lab”. These polymorphisms should be equivalent or functional within the same range. Repeat polymorphisms, on the other hand, could be associated to the corresponding polymorphism of an allel blueprint. Thus the non-neutral behavior could extend to much more than the few identified genes. The existence of each polymorphism thus should depend on its “evolutionary” success, and less to the statistic probability of occurrence.
In short, my point is that Y-DNA variation may be less “random” than normally assumed. Much of the “junk” exists for the specific need of genetic recycling. Moreover, “stable” regions assumed to be the source of valid marker SNP’s are subject of decay rather than being the scene of mutational dynamics. This is quite different from the blanket assumptions currently applied to access genetic variance and age. Note this issue even wasn’t ever addressed at all in mathematical assessments dealing with variance and age.
I wonder how much fastly evolving DNA could ever contribute to a really valuable deep peek into the ancestry of the human species, so let’s consider “slow STR” and evolution. It must be very worthwhile to evaluate the selective forces of Y among humans during the last 100.000 years. I could not find any reliable article on the subject, only rumors. Someone proposed reduced sizes of the male reproductive organ among Y-DNA haplogroups CF(xIJK), though the poor results I remember of a study among e.g. Germans would rather suggest the opposite. Interesting though to investigate selective forces that e.g. would explain low Y-DNA haplogroup G-values over a wide area including Europe as reminiscent of pre-Y-DNA Haplogroup IJK conditions. Male-human “sizes” definitely attest specific human selective forces (compared to other species) and definitely among humans there is a lot of variation, though I don’t have a clue to any relation to Y-DNA. So far sizes of the reproductive male organ are only a reliable Y-DNA predictor to Gorillas: merely 4 cm! There is no guarantee on any relationship and maybe the Y only involves the properties of sperm (and maybe male behaviour as well, including preferences for older females among chimps) and thus should be rather considered utterly invisible.
Old Y-DNA thus could still be preserved as a very early geographic pattern in early humans migrations, only that in the future we should compare with gorillas rather than chimps in this Y-DNA matter to retrieve valid estimations for SNP mutation rates. However, due to this latest chimp Y-DNA study it became very tenuous that – as Jobling assumed – we can still continue in the assumption of the Y-Chromosome being regarded as a neutral locus. We simply can’t presume selective pressures on male human Y-DNA to have ended already ages ago, e.g. just before the chimps deviated from the humanoid lineage. What we should know is that the Karafet assumptions are build on thin air.
The chimpanzee evolved because the sins of Eve, that decided to be promiscuous and thus degraded Adam to the state of an Ape. If so, we have to get accustomed to the idea that humans still occupy paradise and that the animals were thrown out instead. I never considered myself a descendant of Adam nor of Eve, though. Now I know why.

Forever Chimps, due to the sins of Eve.


  • J.F.Hughes et al. – Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content, 2010, link (paysite). Try here.
  • Tatiana M. Karafet et al. – New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree, 2008, link
  • H. Goto et al. – Evolution of X-degenerate Y chromosome genes in greater apes: conservation of gene content in human and gorilla, but not chimpanzee, 2009, link
  • Yali Xue et al. – Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree (2009), link
  • Mark A. Jobling and Chris Tyler-Smith – The Human Y Chromosome: An Evolutionary Marker Comes Of Age (2004), link
  • Jaclyn M Nascimento et al. – The use of optical tweezers to study sperm competition and motility in primates (2008), link
  • Russell Thomson et al. – Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data (2000), link
  • H. Seuánez, Fluorescent (F) bodies in the spermatozoa of man and the great apes (1976), link
  • Kayser, M. et al. – Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs (2000), link
  • Pritchard, J. K., Seielstad, M. T., Perez-Lezaun, A. & Feldman, M. W. – Population growth of human Y chromosomes: a study of Y chromosome microsatellites (1999), link
  • Gráinne McGuire et al. – Models of Sequence Evolution for DNA Sequences Containing Gaps (2001), link

Recommended reading:

  • John Hawks Weblog – A low human mutation rate may throw everything out of whack, link

Note: I got noticed this article was erroneously cited elsewhere to support claims in favor of lower Y-DNA based date estimates. For this reason I bolded the phrases that indicate my view that instead (much) higher Y-DNA based date estimates should be considered.