Author Archives: Arun Sethuraman

Sexual selection and population fitness

Posted on 28 May, 2015 by Arun Sethuraman

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 , , , | 1 Comment

Genomic diversity and secondary contact

Posted on 21 May, 2015 by Arun Sethuraman

Under a divergence, or isolation model, the genomes of individuals in a daughter-population are expected to harbor greater differentiation relative to its sister-population, and lower differentiation within the population (after sufficient time since divergence). Divergence thus is a mechanism of … Continue reading →

Posted in evolution, genomics, next generation sequencing, population genetics, theory | Tagged , , | 1 Comment

Rooting eukaryotes in the Arctic Ocean

Posted on 14 May, 2015 by Arun Sethuraman

While the general consensus has centered around the evolution of eukaryotes within the TACK superphylum of Archaea (Thaum-, Aigar-, Cren-, and Kor-archaeota), considerable controversy yet remains with (a) the rooting of the eukaryote common ancestor, and (b) ‘missing’ links in … 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

dN(eutralist) < dS(electionist) Part 5

Posted on 16 Apr, 2015 by Arun Sethuraman

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 →

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Visualizing Linkage Disequilibrium in R

Posted on 9 Apr, 2015 by Arun Sethuraman

Patterns of Linkage Disequilibrium (LD) across a genome has multiple implications for a population’s ancestral demography. For instance, population bottlenecks predictably result in increased LD, LD between SNP’s in loci under natural selection affect each others rates of adaptive evolution, selfing/inbreeding populations … Continue reading →

Posted in bioinformatics, howto, population genetics, R | Tagged , , | 1 Comment

d(N)eutralist < d(S)electionist Part 4

Posted on 2 Apr, 2015 by Arun Sethuraman

Continuing our discussion of the neutralist-selectionist debate, recent findings by Schrider et al. (2015) bring us to the topic of selective sweeps, and their genomic signatures in a population. As we have discussed in previous posts, numerous studies (since the … Continue reading →

Posted in adaptation, evolution, mutation, population genetics, selection, theory | Tagged , , | 1 Comment

F-statistics Manhattan Plots in R

Posted on 26 Mar, 2015 by Arun Sethuraman

Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading →

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 4 Comments