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Sep 15, 2023 •452 likes •614 views

Ancient DNA: would the real Neandertal please stand up? Multiregional continuity model : Transition between archaic and modern forms took place within a single evolutionary lineage. The single lineage is composed of geographic

  1. Ancient DNA: would the real Neandertal please stand up? Multiregional continuity model : • Transition between archaic and modern forms took place within a single evolutionary lineage. • The single lineage is composed of geographic sub-populations connected by gene flow . • Gene flow prevents independent evolution in the sub-populations • The lineage originated in Africa about 2 million years ago in Homo erectus • H. erectus left Africa and disperses into other parts of the world • Regional variation reflects natural selection for local adaptations • H. sapiens emerged from a lineage-wide process of evolution • Archaic forms of Homo are subspecies (e.g., H. sapiens neanderthalensis ) Replacement model : • H. sapiens evolved as a new species in a sub-population (probably Africa) • The H. sapiens lineage originated about 150-200, thousand years ago • H. sapiens lefts Africa and dispersed to other parts of the world. • H. sapiens displaces the pre-existing hominids; no interbreeding occurs • Under this model the preexisting populations of Homo in Europe and elsewhere are species (e.g., H. erectus; H. ergaster; H. heidelbergensis; H. neanderthalensis ) 1

  2. Ancient DNA: would the real Neandertal please stand up? Eur. Eur. Afr. Asia Afr. Asia H. sapiens (modern) Modern human “Out of Africa” dispersal 100,000 ybp H. sapiens (archaic) 500,000 ybp H. erectus 1,800,000 ybp H. habilis Multiregional continuity model Replacement model Ancient DNA: would the real Neandertal please stand up? 2

  3. Gibraltar 2 Neandertal child 3

  4. Ancient DNA: would the real Neandertal please stand up? Loads of data are relevant to the controversy: • Anatomical structures • Archeological evidence • Genetics (Modern Humans and Neandertals; we will focus on these…) Anatomical structures indicate substantial differences: Neandertal morphology: • evolved over a period of 220,000 years (350k to130k ybp). • final morphological form reached at 130,000 ybp. • Neandertals are first hominids to adapt to cold mid-latitude climates. “Human” morphology: • appear in fossil record about 140,000 ybp (robust) • Appear elsewhere around 60,000 ybp • Modern humans arrive in Europe 40,000 ybp and begin to displace (?) Neandertals 1. Some argue that coexistence of morphologically distinct forms, and subsequent displacement, supports the “replacement” model. 2. Others point out that coexistence in Europe could have lasted as long as 10,000 years and that some early modern humans exhibit a mosaic of archaic and modern features. [ But, discrete Neandertals and modern humans coexisted in Middle East for about 55,000 years ] [A morphologically intermediate skeleton was found in Portugal, having a Neandertal-like skeleton and more modern skull. The conclusions that this might be a hybrid is controversial. The date of the skeleton (24,500) is very late, and there are issues about what a hybrid anatomy should look like] 4

  5. Archeological evidence : Neandertals and modern humans: • very similar up to 40-50,000 ybp • After 40-50,000 ybp anatomically modern humans undergo a “creative explosion” • The “creative explosion” appears to have begun in Africa and spread outward. 1. Supporters of the replacement model argue that this period of innovation has a genetic basis and represents gene flow as well as cultural flow 2. Supporters of the continuity model argue that transmission could have been purely by social mechanisms and point out that there are no changes in skull morphology during the period of the outward spreading of the “creative explosion” Sites in southern France reveal populations of Neandertals using (mimicking) the culture of modern humans associated with the creative explosion. No clearly intermediate morphologies at this site. Extant human mtDNA polymorphism supports “Out of Africa” African populations have the most polymorphism. Some argue that they must be oldest, because they have accumulated the most mutations. Africans dominate the root of the human mtDNA tree Consistent with the “Out of Africa model”; i.e, that Africa was the source for contemporary human mtDNA diversity 5

  6. Ancient DNA: • single neandertal • 30,000 years old (max 100,000) • HVI of mt control region: 387 bp • Great effort to authenticate the ancient DNA (aDNA) Krings et al. (1997) conclude: • Neandertals went extinct without contributing mtDNA to modern humans • Used as outgroup, the Neandertal sequence supports the “Out of Africa” hypothesis of modern humans • Modern human and Neandertal mtDNA coalesce at 500,000 ybp There are now 8 Neandertal aDNA sequences The shaded area indicates the known range of Neanderthals. Mezmaiskaya is the location where the baby Neanderthal whose DNA was sequenced was found. An earlier Neanderthal DNA sequence was determined from bones found in Feldhofer Cave in Germany. 6

  7. Ancient DNA: would the real Neandertal please stand up? Neanderthal Homo sapiens sapiens Homo sapiens idaltu 160,000 years old, Clearly suggest African origin The oldest modern human DNA is not from Africa Remember that Homo sapiens idaltu is from Africa Given an African origin for H. sapiens , these genetic results clearly indicate an Neandertal im portant role for genetic drift in explaining the m odern patterns of genetic diversity of hum ans Oldest Modern Human DNA [LM3: > 55,000 ybp] � LM3 is the oldest reliably dated modern human. � LM3 lived >55,000 ybp � LM3 was Australian � The LM3 mtDNA lineage diverged before the MRCA of living humans, but has gone extinct Contemporary diversity at a single locus cannot be used to infer the pattern of human evolution 7

  8. All the phylogenetic analyses that include Neandertal DNA indicate a substantial divergence of the mtDNA lineages BUT, what about genetic drift? Random sampling from one generation to the next means that some lineages will become extinct by chance alone; i.e., stochastic lineage sorting will occur mtDNA represents just a single genetic locus! Australian LM3 Homo neandertalensis Homo sapiens sapiens Homo sapiens idaltu This Human and Neanderthal pair are each others closes genetic relatives [ in this sample of lineages] 8

  9. So, divergence of lineages is not evidence on its own. Coalescent models can be used to answer the question: “ How much introgression could have occurred without leaving any evidence of Neandertal mtDNA in the modern human population ?” Species 1 Species 2 Species 3 Species 4 - you want to look at such patterns over many loci! Published in PLOS (2005) 9

  10. Assumptions: • Complete displacement along a narrow front of a spatially expanding human population. • Population growth is logistic. This means that introgressed neandertal genes are not lost by drift; rather they are amplified. If we assume a different model, as much as 25% introgression could occur and we would not see any Neandertal mtDNA lineages within the human population Some alternative views: � A robust modern human mandible � Reanalysis of Neandertal data � Discovered in 2002 (pub. 2003) � Published in 2002 � Dated to 34-36,000 ybp � Results sensitive to substitution model � “presents a mosaic of archaic, early � Divergence of Neandertal lineage is not modern human, and possible Neandertal supported under more sophisticated morphological features” substitution models Best-fit model Best-fit model Suboptimal model What should a hybrid look line, anyway? 10

  11. The controversies continue. The replacement model seems to have greater support. Would the real Neandertal please stand up? That was the story in 2005 Possible survival of archaic alleles more closely related to Neanderthals Potential introgression of Neanderthal alleles Minimum contribution of archaic gene pool to modern humans: 5% 11

  12. In 2006 began the discipline of Neanderthal genomics… Nature VOL 444 16 November 2006 1 million base pairs 62,250 base pairs Estimate effective Estimated coalescent population sizes times Hum an-chim p : ~ 98% identical (~ 35 million nucleotide differences) Hum an-Neanderthal : ~ 99.5% identical (~ 1.5 million differences) Estimated time of split of The earliest point at which ancestral populations genealogies diverged that ultimately gave rise to the hum and Neanderthal reference sequences (95% CI on contribution of Neanderthal to human genome: 0 – 20%) 12

  13. Nature VOL 444 16 November 2006 Modern Humans N e : ~ 10,000 Archaic Humans N e : ~ 20-40,000 Chimp (gorilla, orang) N e : ~ 20-40,000 Human-Neanderthal CA N e : ~ 3,000 (0-12,000) Neanderthal X chromosome shows higher divergence than autosomes: gene flow from human males to Neanderthals (mtDNA datasets do not record male Neanderthal contributions to modern humans) In 2006 began the discipline of Neanderthal genomics… Expect to see a complete Neanderthal genome sequence sometime in the next few years; it holds the promise of answering many controversial questions about human evolution That was the story in 2006 13

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