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Tag Archives: population genetics
The Kennewick, and the Oase I
Last week was glorious for ancient DNA enthusiasts – here are some quick blurbs on findings from genomic analyses of the Kennewick man, and the Oase I individual. The ancestry and affiliations of Kennewick Man, Rasmussen et al. (2015) Nature DOI: … Continue reading
Posted in evolution, genomics, Paleogenomics, population genetics
Tagged gene flow, genomics, Homo sapiens, population genetics, population structure
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IBE/IBD Contour plots in R
Rob’s post from yesterday motivated me to find an alternate way of visualizing correlations between matrices of geographical or ecological data, and genetic data. I have seen plenty of Mantel, or partial Mantel tests of correlation, as well as plots … Continue reading
Posted in bioinformatics, howto, population genetics, R, software
Tagged data visualization, landscape genetics, methods, population genetics
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Genomic history of Eurasia
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
Posted in genomics, Paleogenomics, population genetics
Tagged gene flow, genomics, Homo sapiens, population genetics, population structure
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Sexual selection and population fitness
Sexual selection or non-random mate choice acts to ‘filter’ out less competitive/desirable phenotypes from a population. In the presence of small effect mutation loads, i.e. small fitness differences between a mutation-free population, and one with persistent deleterious mutations, sexual selection … Continue reading
Posted in adaptation, evolution, mutation, population genetics
Tagged ecological speciation, genomics, natural selection, population genetics
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Gene flow and Population Fitness
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
Quantifying risks of consanguineous mating in humans
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
Procrustes Analyses in R
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 data visualization, genomics, population genetics, population structure
3 Comments
dN(eutralist) < dS(electionist) Part 5
The neutral theory predicts that species with small census (and effective) population sizes are subject to greater drift (or allele frequency fluctuations), and vice versa. In other words, species with larger population sizes are expected to maintain more neutral diversity … Continue reading
Posted in evolution, mutation, natural history, plants, population genetics, theory
Tagged genomics, natural selection, population genetics
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