Data Visualization in Population Genetics: Admixture and Phylogeny
This is just a short note to reflect on the two principal ways of visualizing population genetic data: Circular and Linear. Both phylogenetic trees and admixture proportions can be visualized this way. See below some examples (I give no references…
Ancient Kostenki 14 (Markina Gora) DNA: A Glimpse into a Population on Its Way from America to Africa
Science DOI: 10.1126/science.aaa0114 Genomic Structure in Europeans Dating Back at Least 36,200 Years Andaine Seguin-Orlando, Thorfinn S. Korneliussen, Martin Sikora, Anna-Sapfo Malaspinas, Andrea Manica, Ida Moltke, Anders Albrechtsen, Amy Ko, Ashot Margaryan, Vyacheslav Moiseyev, Ted Goebel, Michael Westaway, David Lambert,…
Ancient Ust’-Ishim DNA as Seen From the Americas
Nature 514, 445–449 (23 October 2014) doi:10.1038/nature13810 Genome sequence of a 45,000-year-old modern human from western Siberia Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prufer, Cesare de Filippo,…
Web Gems, November 22, 2013
I’ve been monitoring global web responses to Raghavan et al.’s “Upper Palaeolithic Siberian Genome Reveals Dual Ancestry of Native Americans” that appear in the comments sections on Dienekes, Gene Expression and Eurogenes sites. The Web Gem Reward of this week goes…
The End of Out-of-Africa: A Copernican Reassessment of the Patterns of Genetic Variation in the Old World
Over at Anthrogenica, I’ve been having some heated (as always) but this time also productive discussions regarding the interpretation of currently available genetic evidence. In the following I will sketch out a hypothesis that increasingly makes sense to me. 1….
A Signal of Neandertal Admixture in Modern Human mtDNA?
Russian Journal of Genetics, September 2013, Vol. 49, No. 9, 975-978 Mitochondrial DNA Polymorphisms Shared Between Modern Humans and Neanderthals: Adaptive Convergence or Evidence for Interspecific Hybridization Malyarchuk, Boris A. Abstract An analysis of the variability of the nucleotide sequences in the…
Neandertal Admixture in Africans: A Back-Migration to Sub-Saharan Africa Confirmed
Genome Biology and Evolution 2013 Oct 25. Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from non-African Populations. Shuoguo Wang, Joseph Lachance, Sarah Tishkoff, Jody Hey, and Jinchuan Xing Abstract Recent studies have found evidence of…
Ancient Mal’ta and Afontova Gora DNA Again
Now that Michael Balter’s news piece is out, I can retrieve my original post written in the wake of Eske Willerslev’s presentation at the Paleoamerican Odyssey conference in Santa Fe. Eske Willerslev‘s paper was on ancient DNA from the Mal’ta and Afontova…
Reader Questions 1: In Search of Archaic Hominin Survivals in Eurasia. Tutkaul Culture
This is a new category of posts on this weblog. Every now and then a reader sends me a question and sometimes I get interested and try to answer. There seems to be a steady interest on the part of…
An Out-of-America Signal as Seen Through Human Regulatory Genes
PLoS Genet 9(4): e1003404. doi:10.1371/journal.pgen.1003404 Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence Omer Gokcumen, Qihui Zhu, Lubbertus C. F. Mulder, Rebecca C. Iskow, Christian Austermann, Christopher D. Scharer, Towfique Raj, Jeremy M. Boss, Shamil…
Is Taiwan to Austronesians what America is to Modern Humans?
American Journal of Physical Anthropology 150 (4): 551–564, April 2013 Ascertaining the Role of Taiwan as a Source for the Austronesian Expansion Sheyla Mirabal, Alicia M. Cadenas, Ralph Garcia-Bertrand, and Rene J. Herrera. Taiwanese aborigines have been deemed the ancestors…
Archaic Admixture in Africa, a Final Solution for Cultural Anthropology and the New World Roots of the Oldest Dog: News from Around the Web
I haven’t been blogging for a while because of a new demanding leadership job. It will keep me busy, so I’m shifting to more of a bite-size blog post format. In the meantime, I’ve been active on Gisele Horvat’s Human…
Yuzhnyi Olenii Ostrov: Ancient mtDNA Evidence for Amerindian Admixture in Europe
Ph.D. dissertation, University of Adelaide, School of Earth and Environmental Sciences, Australian Centre for Ancient DNA Ecology and Evolutionary Biology, 2011 Mitochondrial DNA in Ancient Human Populations of Europe Clio Der Sarkissian Abstract. The distribution of human genetic variability is…
Out-of-Africa as Ghost Science
PNAS doi: 10.1073/pnas.1212380109 The Great Human Expansion Brenna M. Henn, Luca L. Cavalli-Sforza, and Marcus W. Feldman Genetic and paleoanthropological evidence is in accord that today’s human population is the result of a great demic (demographic and geographic) expansion that…
Intense Admixture: Khoisan Clicks and Khoisan Genes in Southeastern Bantu
European Journal of Human Genetics 2012, 1-7 DOI:10.1038/ejhg.2012.192 Genetic Perspectives on the Origin of Clicks in Bantu Languages from Southwestern Zambia Chiara Barbieri, Anne Butthof, Koen Bostoen, and Brigitte Pakendorf Some Bantu languages spoken in southwestern Zambia and neighboring regions…
Clicks and Genes: Linguistic and Genetic Perspectives on Khoisan Prehistory
Science DOI: 10.1126/science.1227721 Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History Carina M. Schlebusch, Pontus Skoglund, Per Sjödin, Lucie M. Gattepaille, Dena Hernandez, Flora Jay, Sen Li, Michael De Jongh, Andrew Singleton, Michael G. B. Blum,…
Rare Haplotypes in Koreans: Evidence for a Back Migration into Africa?
CAMDA 2012 Conference, July 13, 2012 Rare Haplotypes in the Korean Population Sepp Hochreiter, Gunter Klambauer, Gundula Povysil, and Djork‐Arné Clevert Link (Full Text PDF) These days you never know where research related to modern human origins will be reported…
How Europeans Got to Be ~10% American Indian
Genetics doi: 10.1534/genetics.112.145037 Ancient Admixture in Human History Nick Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, and David Reich Population mixture is an important process in biology. We present a suite of methods…
A High Coverage of the Denisovan Hominin
Science 30 August 2012 DOI: 10.1126/science.1224344 A High-Coverage Genome Sequence from an Archaic Denisovan Individual 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,…
Nivkh and Chukotko-Kamchatkan Linguistic Relationship and Its Genetic Correlates
Lingua Vol. 8, Issue 121, June 2011, 1359-1376 http://dx.doi.org/10.1016/j.lingua.2011.03.001 The Relationship of Nivkh to Chukotko-Kamchatkan Revisited Michael Fortescue With the availability today of reliable materials for comparing the languages that in the past have been lumped together under the rubric…
The Caucasus is the Americas of Western Eurasia: Intragroup-Genetic and Linguistic Diversity Are Inversely Correlated
Dienekes continues to refute himself and adopt my ideas. In his latest ADMIXTURE experiment he announces “The most salient point about this analysis is the central position of the Caucasus component vis-a-vis the others, consistent with my womb of nations…
Archaic Introgression and the Derived Nature of African Lineages at STAT2 Gene
American Journal of Human Genetics 91, 2012, 265-274. http://dx.doi.org/10.1016/j.ajhg.2012.06.015. A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea Fernando L. Mendez, Joseph C. Watkins, and Michael F. Hammer. Signals of…
The Xavante Indians and Genetic Divergence Between American Indians and Africans
PLoS ONE 7 (8): e42702. doi:10.1371/journal.pone.0042702 Genome-Wide Analysis in Brazilian Xavante Indians Reveals Low Degree of Admixture Patricia C. Kuhn, Andréa R. V. Russo. Horimoto, José Maurício Sanches, João Paulo B. Vieira Filho, Luciana Franco, Amaury Dal Fabbro, Laercio Joel…
Social Anthropology and the Bantu Expansion
Razib is now officially a fantasy science blogger. When he recently called his readers “stupid, ignorant or lazy” and put up a stringent comments policy (I bet inspired by my own) rallying them to show their “A-game,” I knew it…
A Seismic Shift in Human Origins Research, or a Downward Slide?
A new research paper is out which has created a lot of media buzz. “Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers, “ by Joseph Lachance et al. reports “archaic admixture” in three African hunter-gathering populations…
Khoisans Are Genetically Admixed and Not Basal to Other Humans, Hadza Are Recently Admixed
In my last post I discussed the ways in which phylogenetic trees constructed on the basis of genetic data confound population relationships derived from common descent and from admixture. Unless admixture is taken into account, the sampled populations may end…
How to Interpret Patterns of Genetic Variation? Admixture, Divergence, Inbreeding, Cousin Marriage
Two different but important population genetics papers have come out. One is Steven Bray et al. (2010) “Signatures of Founder Effects, Admixture, and Selection in the Ashkenazi Jewish Population.” The other one is Isabel Alves et al. (2012) “Genomic Data…
A Three-Wave Model for the Peopling of the Americas, or a Three-Wave Back-Migration from the Americas to the Old World
Nature (2012) doi:10.1038/nature11258 Reconstructing Native American population history Reich, David, et al. The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred…
Out-of-Africa in the Mid-Pleistocene: A New Interdisciplinary Paradigm or a New Myth?
In the comments section on this blog, Dienekes raises the issue of interdisciplinary support for the out-of-America theory. Since I’m a big proponent of interdisciplinarity, the seeming convergence of genetics, archeology and paleobiology on the origin of modern humans in…
Neandertal Admixture in microRNA Genes
Molecular Biology and Evolution (27 January 2012), doi:10.1093/molbev. An Ancestral miR-1304 Allele Present in Neanderthals Regulates Genes Involved in Enamel Formation and Could Explain Dental Differences with Modern Humans Lopez-Valenzuela, Maria, Oscar Ramirez, Antonio Rosas, Samuel Garcıa-Vargas, Marco de la…
American Indians, Neanderthals and Denisovans: PCA and ADMIXTURE
Dienekes continued his search for “archaic admixture” in world populations. This time he blended ADMIXTURE and PCA approaches to plot 5 composite populations detected by ADMIXTURE in the Harvard HGDP set. American Indians are back in. The ADMIXTURE plot replicates…
Archaic Morphology and American Indian Biological Variability
On the heels of my last post about the possibly systematic trend to ignore American Indian samples in the studies of worldwide variation, there’s a new paper dealing with the discovery of human remains with archaic morphology as late as…
Admixture: An Amerindian Component in Eurasian Populations
About a year ago, one of genome bloggers, Diogenes, discovered, using ADMIXTURE, an intriguing “Amerindian” component in a wide range of East and West Eurasian populations. Here are the results of his ADMIXTURE runs. Grey represents the component that’s modal…
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