Category Archives: population genetics

A mammoth bottleneck prior to extinction

Posted on 28 Apr, 2015 by Noah Snyder-Mackler

Here’s to back-to-back posts on extinct mammalian genomes! Woolly mammoth genomes are all the rage. How do I know? Just check out the new book, pre-print, and paper that were recently published.

Posted in conservation, genomics, next generation sequencing, Paleogenomics, population genetics | Tagged , , | Leave a comment

Clonal conundrum, part deux

Posted on 24 Apr, 2015 by Stacy Krueger-Hadfield

In the second installment of the clonal conundrum, one hallmark of clonality is one that surprisingly hasn’t been validated that many times using species that have both sexually and asexually reproducing populations. Theoretically, clonal reproduction should generate massive … Heterozygote excess … Continue reading →

Posted in conservation, DNA barcoding, domestication, evolution, haploid-diploid, population genetics | Tagged , , , , | Leave a comment

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

Clonal conundrum, part un

Posted on 19 Apr, 2015 by Stacy Krueger-Hadfield

Molecular ecologists are faced with a clonal conundrum when we wish to investigate the evolutionary ecology of clonal organisms. An attack of the clones is not something that should frighten one away …

Posted in Coevolution, community ecology, conservation, domestication, evolution, haploid-diploid, natural history, population genetics | 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 →

Posted in evolution, mutation, natural history, plants, population genetics, theory | Tagged , , | Leave a comment

The gopher tortoise gut microbiome

Posted on 14 Apr, 2015 by Noah Snyder-Mackler

A few weeks ago I wrote about a study on socially structured gut microbiomes in wild baboons. Well, now I’m here to tell you about a new study that examined the population structure of tortoise gut microbiomes.

Posted in community ecology, genomics, natural history, next generation sequencing, population genetics, Uncategorized | Tagged , , | 1 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

Live fast and reproduce young

Posted on 1 Apr, 2015 by Rob Denton

Here is one for the “simple, elegant science” folder: a new paper in PNAS by Julia Schroeder and colleagues that demonstrates a fitness disadvantage in offspring from older parents. While there a multitude of papers out there showing that gametes have … Continue reading →

Posted in pedigree, population genetics, societal structure | Tagged , | Leave a comment

How (not) to review papers on inclusive fitness

Posted on 30 Mar, 2015 by Noah Snyder-Mackler

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