Through the influence of Howells, many other anthropologists and biologists have confused multiregionalism with polygenism i.e. separate or multiple origins for different populations. Alan Templeton for example notes that this confusion has led to the error that gene flow between different populations was added to the Multiregional hypothesis as a "special pleading in response to recent difficulties", despite the fact: "parallel evolution was never part of the multiregional model, much less its core, whereas gene flow was not a recent addition, but rather was present in the model from the very beginning" (emphasis in original). Despite this, multiregionalism is still confused with polygenism, or Coon's model of racial origins, from which Wolpoff and his colleagues have distanced themselves. Wolpoff has also defended Wiedenreich's Polycentric hypothesis from being labeled polyphyletic. Weidenreich himself in 1949 wrote: "I may run the risk of being misunderstood, namely that I believe in polyphyletic evolution of man".
Stringer distinguishes the original or "classic" Multiregional model as having existed from 1984 (its formulation) until 2003, to a "weak" post-2003 variant that has "shifted close to that of the Assimilation Model".
Proponents of the multiregional hypothesis see regional continuity of certain morphological traits spanning the Pleistocene in different regions across the globe as evidence against a single replacement model from Africa. In general, three major regions are recognized: Europe, China, and Indonesia (often including Australia). Wolpoff cautions that the continuity in certain skeletal features in these regions should not be seen in a racial context, instead calling them morphological clades; defined as sets of traits that "uniquely characterise a geographic region". According to Wolpoff and Thorne (1981): "We do not regard a morphological clade as a unique lineage, nor do we believe it necessary to imply a particular
taxonomic status for it". Critics of multiregionalism have pointed out that no single human trait is unique to a geographical region (i.e. confined to one population and not found in any other) but Wolpoff et al. (2000) note that regional continuity only recognizes combinations of features, not traits if individually accessed, a point they elsewhere compare to the forensic identification of a human skeleton:
Combinations of features are "unique" in the sense of being found in only one region, or more weakly limited to one region at high frequency (very rarely in another). Wolpoff stresses that regional continuity works in conjunction with genetic exchanges between populations. Long-term regional continuity in certain morphological traits is explained by Alan Thorne's "centre and edge" population genetics model which resolves Weidenreich's paradox of "how did populations retain geographical distinctions and yet evolve together?". For example, in 2001 Wolpoff and colleagues published an analysis of character traits of the skulls of early modern human fossils in Australia and central Europe. They concluded that the diversity of these recent humans could not "result exclusively from a single late Pleistocene dispersal", and implied dual ancestry for each region, involving interbreeding with Africans.
Yet, regardless of these criticisms Habgood (2003) allows for limited regional continuity in Indonesia and Australia, recognizing four plesiomorphic features which do not appear in such a unique combination on fossils in any other region: a sagittally flat frontal bone, with a posterior position of minimum frontal breadth, great facial prognathism, and zygomaxillary tuberosities. This combination, Habgood says, has a "certain Australianness about it".
Wolpoff, initially skeptical of Thorne's claims, became convinced when reconstructing the Sangiran 17 Homo erectus skull from Indonesia, when he was surprised that the skull's face to vault angle matched that of the Australian modern human Kow Swamp 1 skull in excessive prognathism. Durband (2007) in contrast states that "features cited as showing continuity between Sangiran 17 and the Kow Swamp sample disappeared in the new, more orthognathic reconstruction of that fossil that was recently completed". Baba et al. who newly restored the face of Sangiran 17 concluded: "regional continuity in Australasia is far less evident than Thorne and Wolpoff argued".
Facial flatness as a morphological clade feature has been rejected by many anthropologists since it is found on many early African Homo erectus fossils, and is therefore considered plesiomorphic, but Wu has responded that the form of facial flatness in the Chinese fossil record appears distinct to other (i.e. primitive) forms. Toetik Koesbardiati in her PhD thesis "On the Relevance of the Regional Continuity Features of the Face in East Asia" also found that a form of facial flatness is unique to China (i.e. only appears there at high frequency, very rarely elsewhere) but cautions that this is the only available evidence for regional continuity: "Only two features appear to show a tendency as suggested by the Multiregional model: flatness at the upper face expressed by an obtuse nasio-frontal angle and flatness at the middle part of the face expressed by an obtuse zygomaxillay angle".
Since the early 1990s, David W. Frayer has described what he regards as a morphological clade in Europe. The sequence starts with the earliest dated Neanderthal specimens (Krapina and Saccopastore skulls) traced through the mid-Late Pleistocene (e.g. La Ferrassie 1) to Vindija Cave, and late Upper Palaeolithic Cro-Magnons or recent Europeans. Although many anthropologists consider Neanderthals and Cro Magnons morphologically distinct, Frayer maintains quite the opposite and points to their similarities, which he argues is evidence for regional continuity:
Frayer et al. (1993) consider there to be at least four features in combination that are unique to the European fossil record: a horizontal-oval shaped mandibular foramen, anterior mastoid tubercle, suprainiac fossa, and narrowing of the nasal breadth associated with tooth-size reduction. Regarding the latter, Frayer observes a sequence of nasal narrowing in Neanderthals, following through to late Upper Palaeolithic and Holocene (Mesolithic) crania. His claims are disputed by others, but have received support from Wolpoff, who regards late Neanderthal specimens to be "transitional" in nasal form between earlier Neanderthals and later Cro Magnons. Based on other cranial similarities, Wolpoff et al. (2004) argue for a sizable Neanderthal contribution to modern Europeans.
More recent claims regarding continuity in skeletal morphology in Europe focus on fossils with both Neanderthal and modern anatomical traits, to provide evidence of interbreeding rather than replacement. Examples include the Lapedo child found in Portugal and the Oase 1 mandible from Peștera cu Oase, Romania, though the "Lapedo child" is disputed by some.
A 1987 analysis of mitochondrial DNA from 147 people by Cann et al. from around the world indicated that their mitochondrial lineages all coalesced in a common ancestor from Africa between 140,000 and 290,000 years ago. The analysis suggested that this reflected the worldwide expansion of modern humans as a new species, replacing, rather than mixing with, local archaic humans outside of Africa. Such a recent replacement scenario is not compatible with the Multiregional hypothesis and the mtDNA results led to increased popularity for the alternative single replacement theory. According to Wolpoff and colleagues:
Multiregionalists have responded to what they see as flaws in the Eve theory, and have offered contrary genetic evidences. Wu and Thorne have questioned the reliability of the molecular clock used to date Eve. Multiregionalists point out that Mitochondrial DNA alone can not rule out interbreeding between early modern and archaic humans, since archaic human mitochondrial strains from such interbreeding could have been lost due to genetic drift or a selective sweep. Wolpoff for example states that Eve is "not the most recent common ancestor of all living people" since "Mitochondrial history is not population history".
In a 2005 review and analysis of the genetic lineages of 25 chromosomal regions, Alan Templeton found evidence of more than 34 occurrences of gene flow between Africa and Eurasia. Of these occurrences, 19 were associated with continuous restricted gene exchange through at least 1.46 million years ago; only 5 were associated with a recent expansion from Africa to Eurasia. Three were associated with the original expansion of Homo erectus out of Africa around 2 million years ago, 7 with an intermediate expansion out of Africa at a date consistent with the expansion of Acheulean tool technology, and a few others with other gene flows such as an expansion out of Eurasia and back into Africa subsequent to the most recent expansion out of Africa. Templeton rejected a hypothesis of complete recent African replacement with greater than 99% certainty (p < 10−17).
Recent analyses of DNA taken directly from Neanderthal specimens indicates that they or their ancestors contributed to the genome of all humans outside of Africa, indicating there was some degree of interbreeding with Neanderthals before their replacement. It has also been shown that Denisova hominins contributed to the DNA of Melanesians and Australians through interbreeding.
By 2006, extraction of DNA directly from some archaic human samples was becoming possible. The earliest analyses were of Neanderthal DNA, and indicated that the Neanderthal contribution to modern human genetic diversity was no more than 20%, with a most likely value of 0%. By 2010, however, detailed DNA sequencing of the Neanderthal specimens from Europe indicated that the contribution was nonzero, with Neanderthals sharing 1-4% more genetic variants with living non-Africans than with living humans in sub-Saharan Africa. In late 2010, a recently discovered non-Neanderthal archaic human, the Denisova hominin from south-western Siberia, was found to share 4–6% more of its genome with living Melanesian humans than with any other living group, supporting admixture between two regions outside of Africa. In August 2011, human leukocyte antigen (HLA) alleles from the archaic Denisovan and Neanderthal genomes were found to show patterns in the modern human population demonstrating origins from these non-African populations; the ancestry from these archaic alleles at the HLA-A site was more than 50% for modern Europeans, 70% for Asians, and 95% for Papua New Guineans. Proponents of the multiregional hypothesis believe the combination of regional continuity inside and outside of Africa and lateral gene transfer between various regions around the world supports the multiregional hypothesis. However, "Out of Africa" Theory proponents also explain this with the fact that genetic changes occur on a regional basis rather than a continental basis, and populations close to each other are likely to share certain specific regional SNPs while sharing most other genes in common.
Migration Matrix theory (A=Mt) indicates that dependent upon the potential contribution of Neanderthal ancestry, we would be able to calculate the percentage of Neanderthal mtDNA contribution to the human species. As we do not know the specific migration matrix, we are unable to input the exact data, which would answer these questions irrefutably.
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The CMP-N-acetylneuraminic acid hydroxylase CMAH pseudogene shows 2.9 Mya coalescence time. Hayakawa, T.; Aki, I.; Varki, A.; Satta, Y.; Takahata, N. (February 2006). "Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution". Genetics. 172 (2): 1139–46. doi:10.1534/genetics.105.046995. ISSN 0016-6731. PMC 1456212. PMID 16272417. /wiki/CMAH
The PDHA1 (pyruvate dehydrogenase) locus on the X chromosome has an estimated coalescence time of 1.86 Mya, inconsistent with a recent species origin, although the worldwide lineage pattern is unlike other autosomal sites and may be consistent with recent dispersal from Africa. Harding, Rosalind M. (16 March 1999). "More on the X files". Proceedings of the National Academy of Sciences of the United States of America. 96 (6): 2582–84. Bibcode:1999PNAS...96.2582H. doi:10.1073/pnas.96.6.2582. PMC 33533. PMID 10077551. /wiki/Pyruvate_dehydrogenase
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