Friday, October 7, 2016

Pagani et al., Paragraphs 6-11:

Pagani et al
Nature
Published online
(Link)

Paragraphs 6-11:

"Using fineSTRUCTURE, we find in the genomes of Papuans and Philippine Negritos more short haplotypes assigned as African than seen in genomes for individuals from other non-African populations (Extended Data Fig. 7). This pattern remains after correcting for potential confounders such as phasing errors and sampling bias (Supplementary Information 2.2.1). These shorter shared haplotypes would be consistent with an older population split [25].  Indeed, the Papuan–Yoruban median genetic split time (using multiple sequential Markovian coalescent (MSMC)) of 90 kya predates the split of all mainland Eurasian populations from Yorubans at ~75 kya (Supplementary Table 1:2.2.3-I, Extended Data Fig. 4, Fig. 2a).  This result is robust to phasing artefacts (Extended Data Fig. 8, see Methods). Furthermore, the Papuan–Eurasian MSMC split time of ~40 kya is only slightly older than splits between west Eurasian and East Asian populations dated at ~30 kya (Extended Data Fig. 4).  The Papuan split times from Yoruba and Eurasia are therefore incompatible with a simple bifurcating population tree model.

"At least two main models could explain our estimates of older divergence dates for Sahul populations from Africa than mainland Eurasians in our sample:  1) admixture in Sahul with a potentially un-sampled archaic human population that split from modern humans either before or at the same time as did Denisova and Neanderthal; or 2) admixture in Sahul with a modern human population (extinct OoA line; xOoA) that left Africa after the split between modern humans Africa after the split between modern humans.

"We consider support for these two non-mutually exclusive scenarios.  Because the introgressing lineage has not been observed with aDNA, standard methods are limited in their ability to distinguish between these hypotheses. Furthermore, we show (Supplementary Information 2.2.7) that single-site statistics, such as Pattersons D [9],[18] and sharing of non-African Alleles (nAAs), are inherently affected by confounding effects owing to archaic introgression in non-African populations [23]Our approach therefore relies on multiple lines of evidence using haplotype-based MSMC and fineSTRUCTURE comparisons (which we show should have power at this timescale [26]; Supplementary Information 2.2.13).

"We located and masked putatively introgressed [27] Denisova haplotypes from the genomes of Papuans, and evaluated phasing errors by symmetrically phasing Papuans and Eurasians genomes (Methods). Neither modification (Fig. 2a, Supplementary Information 2.2.9, Supplementary Table 1:2.2.9-I) changed the estimated split time (based on MSMC) between Africans and Papuans (Methods, Supplementary Information 2.2.8, Extended Data Fig. 8, Supplementary Table 1.2.8-I). MSMC dates behave approximately linearly under admixture (Extended Data Fig. 8), implying that the hypothesized lineage may have split from most Africans around 120 kya (Supplementary Information 2.2.4 and 2.2.8).
 
"We compared the effect on the MSMC split times of an xOoA or a Denisova lineage in Papuans by extensive coalescent simulations Supplementary Information 2.2.8). We could not simulate the large Papuan–African and Papuan–Eurasian split times inferred from the data, unless assuming an implausibly large contribution from a Denisova-like population. Furthermore, while the observed shift in the African–Papuan MSMC split curve can be qualitatively reproduced when including a 4% genomic component that diverged 120 kya from the main human lineage within Papuans, a similar quantity of Denisova admixture does not produce any significant effect (Extended Data Fig. 8). This favours a small presence of xOoA lineages rather than Denisova admixture alone as the likely cause of the observed deep African–Papuan split. We also show (Methods) that such a scenario is compatible with the observed mitochondrial DNA and Y chromosome lineages in Oceania, as also previously argued [13,28].

"We further tested our hypothesized xOoA model by analysing haplotypes in the genomes of Papuans that show African ancestry not found in other Eurasian populations. We re-ran fineSTRUCTURE adding the Denisova, Altai Neanderthal and the Human Ancestral Genome sequences [29] to a subset of the diversity set.  FineSTRUCTURE infers haplotypes that have a most recent common ancestor (MRCA) with another individual. Papuan haplotypes assigned as African had, regardless, an elevated level of non-African derived alleles (that is, nAAs fixed ancestral in Africans) compared to such haplotypes in Eurasians. They therefore have an older mean coalescence time with our African samples."
 

 














"Figure 2a.  Evidence of an xOoA signature in the genomes of modern Papuans. a, MSMC split times plot. The Yoruba–Eurasia split curve shows the mean of all Eurasian genomes against one Yoruba genome. The grey area represents top and bottom 5% of runs. We chose a Koinanbe (sic) genome
as representative of the Sahul populations."

Sunday, October 2, 2016

Pagani et al., Paragraph 3

Pagani et al
Nature
Published online
(Link)

Paragraph 3:  "Ancient DNA (aDNA) sequencing studies have found support for admixture between early Eurasians and at least two archaic human lineages [18,19], and suggest modern humans reached Eurasia at around 100 kya [12]. In addition, aDNA from modern humans suggests population structuring and turnover, but little additional archaic admixture, in Eurasia over the last 35–45 thousand years [20–22].  Overall, these findings indicate that the majority of human genetic diversity outside Africa derives from a single dispersal event that wafollowed by admixture with archaic humans [18,23]."
 

Pagani et al, Paragraph 3 References:
 
[18] Richard E. Green, Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas, Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer, Hernán A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof, Barbara Höber, Barbara Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich, Svante Pääbo, A draft sequence of the Neandertal Genome, Science  07 May 2010:  Vol. 328, Issue 5979, pp. 710-722. (Link)

Abstract:  Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
 
 
[19] David Reich, Martin Kircher, Frederick Delfin, Madhusudan R. Nandineni, Irina Pugach, Albert Min-Shan Ko, Ying-Chin Ko, Timothy A. Jinam, Maude E. Phipps, Naruya Saitou, Andreas Wollstein, Manfred Kayser, Svante Pääbo, Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania, AJHG, Volume 89, Issue 4, pp. 516–528, 7 October 2011. (Link)
 
Summary:  It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.


[12] Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernan A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Ravao Rudan, Dejana Brajkovic, Zeljko Kucan, Ivan Gusic, Tomas Marques-Bonet, Aida M. Andres, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel, Sergi Castellano, Ancient gene flow from early modern humans into Eastern Neanderthals, Nature, Volume 530, Pages 429-433, Date published:  (25 February 2016) (Link)

Abstract:  It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

 
 
[20]  Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-Garcia, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F. G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich, Janet Kelso, T. Bence Viola, Svante Pääbo, Genome sequence of a 45,000-year-old modern human from western Siberia, Nature, Volume: 514, Pages: 445–449, Date published: 
 
Abstract:  We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.
 

[21] Qiaomei Fu, Alissa Mittnik, Philip L. F. Johnson, Kirsten Bos, Martina Lari, Ruth Bollongino, Chengkai Sun, Liane Giemsch, Ralf Schmitz, Joachim Burger, Anna Maria Ronchitelli, Fabio Martini, Renata G. Cremonesci, Jiri Svoboda, Peter Bauer, David Caramelli, Sergi Castellano, David Reich, Svante Pääbo, Johannes Krause, A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes, Current Biology, Volume 23, Issue 7, pp. 553-559, 8 April 2013.  (Link)

Results:  Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya.
 
 
[22]  Matthias Meyer, Martin Kircher, Marie-Theres Gansauge, Heng Li, Fernando Racimo, Swapan Mallick, Joshua G. Schraiber, Flora Jay, Kay Prüfer, Cesare de Fillippo, Peter H. Sudmant, Qiaomei Fu, Ron Do, Nadin Rohland, Arti Tandon, Michael Siebauer, Richard E. Green, Katarzyna Bryc, Adrian W. Briggs, Udo Stenzel, Jesse Dabney, Jay Shendure Jacob Kitzman, Michael F. Hammer, Michael V. Shunkov, Anatoli P. Derevianko, Nick Patterson,  Aida M. Andrés, Evan E. Eichler, Montgomery Slatkin, David Reich, Janet Kelso, Svante Pääbo, The Genetic History of Ice Age Europe, Nature, Volume:  534, Pages: 200–205, Date published:  7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

 
[23]  Matthias Meyer, Martin Kircher, Marie-Theres Gansauge, Heng Li, Fernando Racimo, Swapan Mallick, Joshua G. Schraiber, Flora Jay, Kay Prüfer, Cesare de Filippo, Peter H. Sudmant, Can Alkan, Qiaomei Fu, Ron Do, Nadin Rohland, Arti Tandon, Michael Siebauer, Richard E. Green, Katarzyna Bryc, Adrian W. Briggs, Udo Stenzel, Jesse Dabney, Jay Shendure, Jacob Kitzman, Michael F. Hammer, Michael V. Shunkov, Anatoli P. Derevianko, Nick Patterson, Aida M. Andrés, Montgomery Slatkin, David Reich, Janet Kelso, Svante Pääbo, A High-Coverage Genome Sequence from an Archaic Denisovan Individual, Science, 12 Oct 2012:  Vol. 338, Issue 6104, pp. 222-226.  (Link)

Abstract: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

Saturday, October 1, 2016

The Arrival of Homo sapiens into the Southern Cone at 14,000 Years Ago





















Gustavo G. Politis, Maria A. Gutiérrez, Daniel J. Rafuse, Adriana Blasi
Published: September 28, 2016

Abstract

The Arroyo Seco 2 site contains a rich archaeological record, exceptional for South America, to explain the expansion of Homo sapiens into the Americas and their interaction with extinct Pleistocene mammals. The following paper provides a detailed overview of material remains found in the earliest cultural episodes at this multi-component site, dated between ca. 12,170 14C yrs B.P. (ca. 14,064 cal yrs B.P.) and 11,180 14C yrs B.P. (ca. 13,068 cal yrs B.P.). Evidence of early occupations includes the presence of lithic tools, a concentration of Pleistocene species remains, human-induced fractured animal bones, and a selection of skeletal parts of extinct fauna. The occurrence of hunter-gatherers in the Southern Cone at ca. 14,000 cal yrs B.P. is added to the growing list of American sites that indicate a human occupation earlier than the Clovis dispersal episode, but posterior to the onset of the deglaciation of the Last Glacial Maximum (LGM) in the North America.

Monday, September 26, 2016

Pagani et al., Paragraph 2

Pagani et al
Nature
Published online
(Link)

Paragraph 2:  "The paths taken by AMHs out of Africa (OoA) have been the subject of considerable debate over the past two decades. Fossil and archaeological evidence [13,14], and craniometric studies [15] of African and Asian populations, demonstrate that Homo sapiens was present outside of Africa ~ 120–70 thousand years ago (kya) [11]. However, this colonization has been viewed as a failed expansion OoA [16] since genetic analyses of living populations have been consistent with a single OoA followed by serial founder events [17]."


Pagani et al, Paragraph 2 References:

[13]  Huw S. Groucutt, Michael D. Petraglia, Geoff Bailey, Eleanor M. L. Scerri, Ash Parton, Laine Clark-Balzan, Richard P. Jennings, Laura Lewis, James Blinkhorn, Nick A. Drake, Paul S. Breeze, Robyn H. Inglis, Maud H. Devès, Matthew Meredith-Williams, Nicole Boivin, Mark G. Thomas, Aylwyn Scally, Rethinking the dispersal of Homo sapiens out of Africa, Evolutionary Anthropology:  Issues, News, Reviews, 8 July, 2015 (Link)

Abstract:  Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.



[14]  Wu Liu, María Martinón-Torres, Yan-jun Cai, Song Xing, Hao-wen Tong, Shu-wen Pei, Mark Jan Sier, Xiao-hong Wu, R. Lawrence Edwards, Hai Cheng, Yi-yuan Li, Xiong-xin Yang, José María Bermudez de Castro, Xiu-jie Wu, The earliest unequivocally modern humans in southern China, Nature, Volume: 526, Pages: 696–699, Date published:


 
 
[15]  Hugo Reyes-Centeno, Silvia Ghirotto, Florent Detroit, Dominique Grimaud-Hervé, Guido Barbujani, Katerina Harvati, Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia, PNAS, vol. 111 no. 20 (Link)

Significance:  Current consensus indicates that modern humans originated from an ancestral African population between ∼100–200 ka. The ensuing dispersal pattern is controversial, yet has important implications for the demographic history and genetic/phenotypic structure of extant human populations. We test for the first time to our knowledge the spatiotemporal dimensions of competing out-of-Africa dispersal models, analyzing in parallel genomic and craniometric data. Our results support an initial dispersal into Asia by a southern route beginning as early as ∼130 ka and a later dispersal into northern Eurasia by ∼50 ka. Our findings indicate that African Pleistocene population structure may account for observed plesiomorphic genetic/phenotypic patterns in extant Australians and Melanesians. They point to an earlier out-of-Africa dispersal than previously hypothesized.         
                                                       
Abstract:  Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model. They suggest instead a “southern route” dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.


[11]  Matt Grove, Henry Lamb, Helen Roberts, Sarah Davies, Mike Marshall, Richard Bates, Hei Huws, Climatic variability, plasticity, and dispersal: A case study from Lake Tana, Ethiopia, Journal of Human Evolution, Volume 87, October 2015, Pages 32–47 (Link)

Abstract:  The numerous dispersal events that have occurred during the prehistory of hominin lineages are the subject of longstanding and increasingly active debate in evolutionary anthropology. As well as research into the dating and geographic extent of such dispersals, there is an increasing focus on the factors that may have been responsible for dispersal. The growing body of detailed regional palaeoclimatic data is invaluable in demonstrating the often close relationship between changes in prehistoric environments and the movements of hominin populations. The scenarios constructed from such data are often overly simplistic, however, concentrating on the dynamics of cyclical contraction and expansion during severe and ameliorated conditions respectively. This contribution proposes a two-stage hypothesis of hominin dispersal in which populations (1) accumulate high levels of climatic tolerance during highly variable climatic phases, and (2) express such heightened tolerance via dispersal in subsequent low-variability phases. Likely dispersal phases are thus proposed to occur during stable climatic phases that immediately follow phases of high climatic variability. Employing high resolution palaeoclimatic data from Lake Tana, Ethiopia, the hypothesis is examined in relation to the early dispersal of Homo sapiens out of East Africa and into the Levant. A dispersal phase is identified in the Lake Tana record between c. 112,550 and c. 96,975 years ago, a date bracket that accords well with the dating evidence for H. sapiens occupation at the sites of Qafzeh and Skhul. Results are discussed in relation to the complex pattern of H. sapiens dispersal out of East Africa, with particular attention paid to the implications of recent genetic chronologies for the origin of non-African modern humans.


[16]  Paul Mellars, Kevin C. Gori, Martin Carr, Pedro A. Soares, Martin B. Richards, Genetic and archaeological perspectives on the initial modern human colonization of southern Asia, PNAS, vol. 110 no. 26 (Link)

Abstract:  It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.

[17]  Franck Prugnolle, Andrea Manica, François Balloux, Geography predicts neutral genetic diversity of human populations, Current Biology, Volume 15, Issue 5, pp. 159–R160, 8 March 2005 (Link)

Abstract:  A leading theory for the origin of modern humans, the ‘recent African origin’ (RAO) model [1] , postulates that the ancestors of all modern humans originated in East Africa and that, around 100,000 years ago, some modern humans left the African continent and subsequently colonised the entire world, displacing previously established human species such as Neanderthals in Europe [2,3] . This scenario is supported by the observation that human populations from Africa are genetically the most diverse [2] and that the genetic diversity of non-African populations is negatively correlated with their genetic differentiation towards populations from Africa [3] .

Thursday, September 22, 2016

Some comments on "Genomic analyses inform on migration events during the peopling of Eurasia"

Pagani et al
Nature
Published online
(Link)

"High-coverage whole-genome sequence studies have so far focused on a limited number[1] of geographically restricted populations [2–5], or been targeted at specific diseases, such as cancer[6]. Nevertheless,  the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history[7–9] and refuelled the debate on the mutation rate in humans [10].  Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets.  We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record [11], and admixture between AMHs and Neanderthals predating the main Eurasian expansion [12], our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago."

My comments: 

Sounds good to me.  I would add that it is pretty backward to think that there is no "Eurasian" ancestry in Africans.  And if there is "Eurasian" ancestry in Africans, due to obvious high mobility of hominins backward and forwards across and between continents for hundreds of thousands of years, (and most large mammals for that matter) then most of these calculations regarding the degree of archaic and modern admixture in the hominin past are grossly under-estimated (since the degree of admixture in non-Africans has been inferred against Africans, and assumes that Africans [incorrectly] have no Neanderthal or Denisovan admixture.)  Furthermore, the time estimates of population splits would be different if we started to include the idea of high mobility and "soft" splits between hominin populations and continents.

Unfortunately, we rarely see sophisticated models accounting for bidirectional gene flow, high mobility, and other possible confounding phenomena.   The models reflect the same "just so" human origin genetic story, with ever so minor a variation, and are carefully crafted so as not to too directly tread on the toes of a small number of prominent and entrenched paleoanthropologists and human origin geneticists.

At least this paper managed to state the obvious that AMH was present in Eurasia earlier than 75,000 years ago (given those "80,000 year old" Daoxian AMH teeth).

:)

Yes, I'm smiling, but only because I don't work professionally in any field related to the cloying, over specialized, highly politicized and narrow field of human origin genetics.