Tag Archives: genomics

Gorillas (genomes) in the mist

Posted on 10 Apr, 2015 by Stacy Krueger-Hadfield

Mountain gorillas are an endangered great ape subspecies that number around 800 individuals, inhabiting mountain ranges in central Africa. They have been the subject of numerous field studies, but few genetic analyses have been carried out. Xue et al. (2015) sequenced … Continue reading →

Posted in bioinformatics, conservation, evolution, genomics, natural history, next generation sequencing, primates | Tagged , , , | Leave a comment

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

dN(eutralist) = dS(electionist) Part 3

Posted on 19 Mar, 2015 by Arun Sethuraman

In a previous post, I discussed the phenomenon of background selection, which results in rapid expungement of neutral alleles linked to loci under purifying or negative selection, and conversely, the rapid fixation of neutral variants that are linked to loci of … Continue reading →

Posted in adaptation, evolution, genomics, natural history, plants, population genetics, selection | Tagged , | Leave a comment

sedaDNA sleuths: embracing your inner Sherlock

Posted on 6 Mar, 2015 by Stacy Krueger-Hadfield

Awhile back fellow TME contributor Rob Denton posted about a recent review on environmental DNA by Pedersen et al. (2015). Environmental DNA (eDNA) is obtained from samples such as sediments, ice or water and can provide scientific sleuths with tantalizing clues about past … Continue reading →

Posted in bioinformatics, domestication, genomics, natural history, next generation sequencing, Paleogenomics | Tagged , , , | 1 Comment

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

Posted on 26 Feb, 2015 by Arun Sethuraman

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 , , | 15 Comments

Rescue me

Posted on 6 Feb, 2015 by Stacy Krueger-Hadfield

Whiteley et al. (2015) review genetic rescue (GR), or the increase in population fitness (growth) owing to immigration of new alleles, in a new paper in TREE. Genetic rescue is a controversial and hasn’t been applied to any great extent … Continue reading →

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Night at the museum

Posted on 5 Feb, 2015 by Stacy Krueger-Hadfield

Many population genetic and genomic studies document snapshots of a given population’s genetic diversity. Yet, there are many reasons to document changes over time in population parameters in response to perturbations, such as biological invasions (both in terms of the invader … Continue reading →

Posted in DNA barcoding, evolution, genomics, natural history, next generation sequencing, phylogenetics, population genetics, speciation, Uncategorized | Tagged , , , | Leave a comment

Discordance in ancestry inference using human mtDNA and autosomes

Posted on 29 Jan, 2015 by Arun Sethuraman

Mitochondrial haplotypes have been used extensively over the last few decades for inference of a population structure in humans. Key findings from these studies include what has come to be known as the “Mitochondrial Eve” hypothesis (see the controversial Cann, … Continue reading →

Posted in genomics, population genetics | Tagged , | Leave a comment