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,…
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…
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…
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…
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,…
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…
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…
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…
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…
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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