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.