Category Archives: theory

Genomics of Hybridization – Part II, Top three of 2015

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading

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Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment

Genomics of Hybridization – Part 1

In a series of articles, I will discuss recent advances in hybridization genomics – the fundamentals of adaptive introgression, “islands of speciation”, differential gene flow, and linked selection have been discussed in my previous posts (here, here, and also at … Continue reading

Posted in adaptation, evolution, genomics, methods, natural history, next generation sequencing, pedigree, phylogenetics, plants, population genetics, RNAseq, software, speciation, species delimitation, STRUCTURE, theory, transcriptomics | Tagged , , , , , , | Leave a comment

On getting empirical with the obvious

I’ve been thinking lately about the value in doing “simple” things. As a PhD student, my time is constantly incentivised by productivity (what am I doing right now that is working towards a publication?). But that doesn’t jive well with … Continue reading

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On false positives in Isolation with Migration analyses

The IM suite of tools (IM, IMa, IMa2, IMa2p, etc.) are used widely by molecular ecologists at large for the analyses and estimation of ancestral demography under an Isolation with Migration (IM) model. However, these tools come with fundamental assumptions … Continue reading

Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory | Tagged , , , , , , , | Leave a comment

On background selection in Ficedula flycatchers

Several recent studies (including those I wrote about last week) use genome-wide scans of differentiation to understand evolutionary mechanisms behind high or low divergence. However, there has been contentious support for and against these differentiation islands being due to differential … Continue reading

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Sweptaway – Part 2

Numerous methods have been developed over the last few years for the detection of selective sweeps (hard and soft – see my previous post). This week, we look at three new studies that (a) compare existing methods to detect sweeps … Continue reading

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Sweptaway – Part 1

Brace yourselves for a series of new posts on selection, especially with articles from the special Molecular Ecology issue on “Detecting selection in natural populations: making sense of genome scans and towards alternative solutions” starting to roll out! Selective sweeps … Continue reading

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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

Posted in adaptation, Coevolution, evolution, genomics, Molecular Ecology, the journal, mutation, natural history, population genetics, selection, speciation, theory | Tagged , , , , | 2 Comments

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

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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