Chimpanzee–human last common ancestor
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The chimpanzee–human last common ancestor, or CHLCA, is the last common ancestor shared by the extant Homo (human) and Pan (chimpanzee) genera of hominini. Due to complex hybrid speciation, it is not possible to give a precise estimate on the age of this ancestral individual. While "original divergence" between populations may have occurred as early as 13 million years ago (Miocene), hybridization may have been ongoing until as recent as 4 million years ago (Pliocene).
Speciation from Pan to Homo appears to have been a long, drawn-out process. After the "original" divergence(s), there were, according to Patterson (2006), periods of hybridization between population groups and a process of alternating divergence and hybridization that lasted over several millions of years. Sometime during the late Miocene or early Pliocene the earliest members of the human clade completed a final separation from the lineage of Pan — with dates estimated by several specialists ranging from 13 million  to as recent as 4 million years ago. The latter date and the argument for hybridization events are rejected by Wakeley (see current estimates regarding complex speciation).
Richard Wrangham (2001) argued that the CHLCA species was very similar to the common chimpanzee (Pan troglodytes) — so much so that it should be classified as a member of the Pan genus and be given the taxonomic name Pan prior. However, to date no fossil has been identified as a probable candidate for the CHLCA or the taxon Pan prior.
In human genetic studies, the CHLCA is useful as an anchor point for calculating single-nucleotide polymorphism (SNP) rates in human populations where chimpanzees are used as an outgroup, that is, as the extant species most genetically similar to Homo sapiens.
The earliest studies[year needed] of apes suggested the CHLCA may have been as old as 25 million years; however, protein studies in the 1970s suggested the CHLCA was less than 8 million years in age. Genetic methods based on orangutan–human and gibbon–human LCA times were then used to estimate a chimpanzee–human LCA of 5 to 7 million years.
Some researchers tried to estimate the age of the CHLCA (TCHLCA) using biopolymer structures that differ slightly between closely related animals. Among these researchers, Allan C. Wilson and Vincent Sarich were pioneers in the development of the molecular clock for humans. Working on protein sequences they eventually (1971) determined that apes were closer to humans than some paleontologists perceived based on the fossil record. Later,[year needed] Vincent Sarich concluded that the TCHLCA was no greater than 8 million years in age, with a favored range between 4 and 6 million years before present.
This paradigmatic age has stuck with molecular anthropology until the late 1990s. Since the 1990s, the estimate has again been pushed towards more-remote times, because studies have found evidence for a slowing of the molecular clock as apes evolved from a common monkey-like ancestor with monkeys and humans evolved from a common ape-like ancestor with non-human apes.
Since the 1990s, the estimation of the TCHLCA has become less certain, and there is genetic as well as paleontological support for increasing TCHLCA beyond the 5 to 7 million years range accepted during the 1970s and 1980s. An estimate of TCHLCA at 10 to 13 million years was proposed in 1998, and a range of 7 to 10 million years ago is assumed by White et al. (2009):
In effect, there is now no a priori reason to presume that human-chimpanzee split times are especially recent, and the fossil evidence is now fully compatible with older chimpanzee–human divergence dates [7 to 10 Ma...— White et al. (2009), 
A source of confusion in determining the exact age of the Pan–Homo split is evidence of a more complex speciation process rather than a clean split between the two lineages. Different chromosomes appear to have split at different times, possibly over as much as a 4-million-year period, indicating a long and drawn out speciation process with large-scale hybridization events between the two emerging lineages as late as 6.3 to 5.4 million years ago according to Patterson et al. (2006). The assumption of late hybridization was in particular based on the similarity of the X chromosome in humans and chimpanzees, suggesting a divergence as late as some 4 million years ago. This conclusion was rejected as unwarranted by Wakeley (2008), who suggested alternative explanations, including selection pressure on the X chromosome in the populations ancestral to the CHLCA.
Complex speciation and incomplete lineage sorting of genetic sequences seem to also have happened in the split between the human lineage and that of the gorilla, indicating "messy" speciation is the rule rather than the exception in large primates. Such a scenario would explain why the divergence age between the Homo and Pan has varied with the chosen method and why a single point has so far been hard to track down.
Moorjani et al. (2016) found transitions at CpG sites in genome sequences exhibit a more clocklike behavior than other substitutions, resulting in an estimated human and chimpanzee divergence time of 12.1 million years.
The taxon "tribe Hominini" was proposed on basis of the idea that, regarding a trichotomy, the least similar species should be separated from the other two. Originally, this produced a separated Homo genus, which, predictably, was deemed the "most different" among the three genera that includes Pan and Gorilla. However, later discoveries and analyses revealed that Pan and Homo are closer genetically than are Pan and Gorilla; thus, Pan was referred to the tribe Hominini with Homo. Gorilla now became the separated genus and was referred to the new taxon 'tribe Gorillini' (see evolutionary tree here).
Mann and Weiss (1996), proposed that the tribe Hominini should encompass Pan as well as Homo, but grouped within separate subtribes. They would classify Homo and all bipedal apes to the subtribe Hominina and Pan to the subtribe Panina. (Wood (2010) discusses the different views of this taxonomy.) Richard Wrangham (2001) argued that the CHLCA species was very similar to chimpanzees (Pan troglodytes) — so much so that it should be classified as a member of the Pan genus and be given the taxonomic name Pan prior. To date, no fossil has been identified as a potential candidate for the CHLCA or the taxon Pan prior.
The "human-side" descendants of the CHLCA species are specified as members of the tribe Hominini, that is to the inclusion of the genus Homo and its closely related genus Australopithecus, but to the exclusion of the genus Pan — meaning all those human-related genera of tribe Hominini that arose after speciation from the line with Pan. Such grouping represents "the human clade" and its members are called "hominins". A "chimpanzee clade" was posited by Wood and Richard, who referred it to a "Tribe Panini", which was envisioned from the family Hominidae being composed of a trifurcation of subfamilies.
Sahelanthropus tchadensis is an extinct hominid species with a morphology apparently as expected of the CHLCA; and it lived some 7 million years ago — which is very close to the time of the chimpanzee–human divergence. But it is unclear whether it should be classified as a member of the Hominini tribe, that is, a hominin, or as a direct ancestor of Homo and Pan and a potential candidate for the CHLCA species itself.
Few fossil specimens on the "chimpanzee-side" of the split have been found; the first fossil chimpanzee, dating between 545 and 284 kyr (thousand years, radiometric), was discovered in Kenya's East African Rift Valley (McBrearty, 2005). All extinct genera listed in the taxobox are ancestral to Homo, or are offshoots of such. However, both Orrorin and Sahelanthropus existed around the time of the divergence, and so either one or both may be ancestral to both genera Homo and Pan.
Due to the scarcity of fossil evidence for CHLCA candidates, Dr. Aurélien Mounier, a researcher at Cambridge University's Leverhulme Centre for Human Evolutionary Studies, has started a project to create a "virtual fossil" by applying digital "morphometrics" and statistical algorithms to fossils from across the evolutionary history of both Homo and Pan, having previously used this technique to visualize a skull of the last common ancestor of Neanderthal and Homo sapiens.
- Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (June 2006). "Genetic evidence for complex speciation of humans and chimpanzees". Nature 441 (7097): 1103–8. doi:10.1038/nature04789. PMID 16710306.
- Arnason U, Gullberg A, Janke A (December 1998). "Molecular timing of primate divergences as estimated by two nonprimate calibration points". J. Mol. Evol. 47 (6): 718–27. doi:10.1007/PL00006431. PMID 9847414.
- Wakeley J (March 2008). "Complex speciation of humans and chimpanzees". Nature 452 (7184): E3–4; discussion E4. doi:10.1038/nature06805. PMID 18337768. "Patterson et al. suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and—even if the null model could be rejected—they do not consider other explanations of a short divergence time on the X chromosome. These include natural selection on the X chromosome in the common ancestor of humans and chimpanzees, changes in the ratio of male-to-female mutation rates over time, and less extreme versions of divergence with gene flow. I therefore believe that their claim of hybridization is unwarranted."
- "Out of the Pan, Into the Fire" in: Frans B. M. De Waal, ed. (2001). Tree of Origin: What Primate Behavior Can Tell Us About Human Social Evolution. pp. 124–126. ISBN 9780674010048.
- "If man and old world monkeys last shared a common ancestor 30 million years ago, then man and African apes shared a common ancestor 5 million years ago..." Sarich & Wilson (1971)
- Venn, Oliver; Turner, Isaac; Mathieson, Iain; de Groot, Natasja; Bontrop, Ronald; McVean, Gil (June 2014). "Strong male bias drives germline mutation in chimpanzees". Science. 33 (6189): 1272–1275. Bibcode:2014Sci...344.1272V. doi:10.1126/science.344.6189.1272.
- Based on a revision of the divergence of Hominoidea from Cercopithecoidea at more than 50 Mya (previously set at 30 Mya). "Consistent with the marked shift in the dating of the Cercopithecoidea/Hominoidea split, all hominoid divergences receive a much earlier dating. Thus the estimated date of the divergence between Pan (chimpanzee) and Homo is 10–13 MYBP and that between Gorilla and the Pan/Homo linage ≈17 MYBP." Arnason U, Gullberg A, Janke A (December 1998). "Molecular timing of primate divergences as estimated by two nonprimate calibration points". J. Mol. Evol. 47 (6): 718–27. doi:10.1007/PL00006431. PMID 9847414.
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- "'Virtual fossil' reveals last common ancestor of humans and Neanderthals | University of Cambridge". 2015-12-18. Retrieved 2016-07-14.
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