Category Archives: theory

Selection scans, and the genomics of adaptive/maladaptive introgression

Natural selection, and the adaptive evolution of hybrid reproductive incompatibilities post divergence are known to be major drivers of speciation. At the phenotype level, these manifest as fitness differences between introgressing populations. At the genomic level, speciation “genes” or “islands” … Continue reading

RedditDiggMendeleyPocketShare and Enjoy
Posted in adaptation, Coevolution, evolution, genomics, Molecular Ecology, the journal, mutation, natural history, population genetics, selection, speciation, theory | Tagged , , , , | Leave a comment

IMa2p – Parallel Isolation with Migration Analyses

I figured that it was time to write an update on my post from a year ago on Bayesian MCMC in inferring ancestral demography. Recently, my postdoctoral advisor, Jody Hey and I released a version of the popular IMa2 program, … Continue reading

Posted in bioinformatics, genomics, howto, software, theory | Tagged , , , , , | Leave a comment

Genomic diversity and secondary contact

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

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

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

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 , , | Leave a comment

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

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

How (not) to review papers on inclusive fitness

There are few evolutionary concepts as polarizing as Hamilton’s rule. Some researchers feel that there is no mathematical grounding for it, while others beg to differ. Yet empirical evidence in support of Hamilton’s rule is scarce (but check out this … Continue reading

Posted in adaptation, population genetics, societal structure, theory | Leave a comment

dN(eutralist) > dS(electionist)? Part 2

Last week’s post dealt with the debate over differences in the efficacy of purifying selection across human genomes. This week, we’ll look at the differences in de novo mutation rates across populations. The human de novo mutation rate has gone … Continue reading

Posted in evolution, mutation, theory | Tagged , , , | Leave a comment

dN(eutralist) > dS(electionist)? Part 1

In a new series of posts, I will now proffer neutralist and selectionist reviews of recent publications. I point readers to an excellent review of the debate by Masatoshi Nei (2005). Besides being a fun exercise in PoV’s, I hope … Continue reading

Posted in evolution, genomics, mutation, population genetics, theory | Tagged , , | 14 Comments

Genome-wide effects of artificial selection

Humans have been artificially selecting for favorable traits in crops, pets, and livestock over millennia. Years of theoretical predictions and experimental evolution studies have shown the detrimental effects of increased homozygosity, and the population-wide advantages of artificially maintaining heterozygosity. Two … Continue reading

Posted in bioinformatics, evolution, genomics, methods, mutation, population genetics, theory | Leave a comment