Tag Archives: population structure

Genomic history of Eurasia

Posted on 11 Jun, 2015 by Arun Sethuraman

The route of modern humans out of Africa has been contentious, with archaeological and genetic finds pointing towards a route through Egypt, versus one through Ethiopia. Pagani et al. (2015) analyze the genomic admixture of individuals sampled from both Egypt … Continue reading →

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Gene flow and Population Fitness

Posted on 7 May, 2015 by Arun Sethuraman

Fitness effects of gene flow (both advantageous and deleterious) have garnered plenty of recent press and scientific exploration. At the population level, the concepts and consequences are notoriously familiar. In the context of immigration, they reduce to existing genetic variation, … Continue reading →

Posted in adaptation, evolution, genomics, natural history, population genetics, selection, speciation, theory | Tagged , , , , , | 1 Comment

Quantifying risks of consanguineous mating in humans

Posted on 30 Apr, 2015 by Arun Sethuraman

The efficacy of selection in purging a deleterious mutation from a randomly mating population depends on numerous factors, including dominance effects of alleles – see my previous posts. Simplistically, most new mutations are expected to be heterozygotic, and be purged … Continue reading →

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Procrustes Analyses in R

Posted on 23 Apr, 2015 by Arun Sethuraman

Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geographical and genetic distributions of species, following the lead of Wang et … Continue reading →

Posted in genomics, howto, population genetics, R, software | Tagged , , , | 3 Comments

Comparing runs and counting K

Posted on 18 Feb, 2015 by Rob Denton

If you are someone who has any interaction with population genetics, the letter K may cause you a distinct feeling of uneasiness. Identifying the number of distinct genetic clusters (often represented as K) in a data set is a primary component in … Continue reading →

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Phonemes and Genomes

Posted on 5 Feb, 2015 by Arun Sethuraman

Human phonemes and genomes are thought to have evolved hand-in-glove out of Africa. Several recent studies have attempted to capture a picture of this global variation in languages and peoples, often supporting (and rejecting) a serial founder model (eg. see … Continue reading →

Posted in bioinformatics, evolution, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

Discordance in ancestry inference using human mtDNA and autosomes

Posted on 29 Jan, 2015 by Arun Sethuraman

Mitochondrial haplotypes have been used extensively over the last few decades for inference of a population structure in humans. Key findings from these studies include what has come to be known as the “Mitochondrial Eve” hypothesis (see the controversial Cann, … Continue reading →

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SpaceMix, and a brief history of Spatial Genetics

Posted on 15 Jan, 2015 by Arun Sethuraman

Incorporating spatial data to inform studies of the population demography of a species has a long history of interest. From inferring geographical clines in Principal Components Analyses (Menozzi et al. 1978), using location data as “informative priors” during model-based estimation … Continue reading →

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Recent Ancestry of the USA and the 100k Genome Project

Posted on 8 Jan, 2015 by Arun Sethuraman

Holiday presents for pop-gen enthusiasts come in the form of data – boatloads of it! The past two weeks saw the announcements of two neat studies that spell monumental steps toward our understanding of the genetics of mixed populations. With … Continue reading →

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Geophylogeny plots in R for Dummies

Posted on 27 Nov, 2014 by Arun Sethuraman

Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with … Continue reading →

Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE | Tagged , | 4 Comments