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Category Archives: population genetics
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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Landscape genetics gets existential
I had a lot of ideas for future posts, but “landscape genetics” keeps pulling me back. Beyond the new methodology, reviews, and empirical findings, I suppose someone has to pump the brakes and get more existential. Rodney Dyer does just … Continue reading
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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A cladoceran invasion
My posts are about to take on a strong bias towards field work and interviews with the researchers kind enough to offer assistance to our lab as we embark on a Northern Hemisphere tour. Not only will we be sampling seaweeds … Continue reading
Posted in population genetics
Tagged Daphnia, invasion, Japan, microsatellites, mtDNA
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Easy as ABC
Determining the whens and hows of biological invasions using genetic data is a major goal of molecular ecology. One such tool is approximate Bayesian computation (ABC) which is being used for inferring invasion histories. In a new paper in Heredity, Benazzo et … Continue reading
Posted in evolution, methods, population genetics
Tagged ABC, invasion, microsatellites
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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