Monthly Archives: January 2015

Sex chromosome evolution … in haploids, that is

Posted on 16 Jan, 2015 by Stacy Krueger-Hadfield

In diploid organisms, the rates of mutation and recombination played a pivotal role in the evolution of sex-determining regions and, thus, sex chromosomes.  We know quite a bit theoretically and empirically in XY systems in mammals and ZW systems in … Continue reading →

Posted in evolution, mutation | Leave a comment

SpaceMix, and a brief history of Spatial Genetics

Posted on 15 Jan, 2015 by Arun Sethuraman

Incorporating spatial data to inform studies of the population demography of a species has a long history of interest. From inferring geographical clines in Principal Components Analyses (Menozzi et al. 1978), using location data as “informative priors” during model-based estimation … Continue reading →

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | Leave a comment

A current review of modern and ancient eDNA

Posted on 14 Jan, 2015 by Rob Denton

There is something romantic about environmental DNA. The ability to discover the presence of almost any species just by detecting the microscopic bread crumbs they leave behind? That is really just a deerstalker and pipette away from Sherlock-level science. But if … Continue reading →

Posted in DNA barcoding, genomics, metagenomics, Paleogenomics | Tagged , | 2 Comments

A population genetic R-evolution

Posted on 14 Jan, 2015 by Stacy Krueger-Hadfield

Uphill, both ways, in the snow, without shoes … quite apt when thinking of the dark days, in the not too distant past, in which a separate input file was needed for each popgen analysis in order to use a … Continue reading →

Posted in howto, methods, population genetics, R, software, Uncategorized | 3 Comments

Whip it. Population structure and cross-species transmission of Whipworms

Posted on 13 Jan, 2015 by Noah Snyder-Mackler

This may be my second worm-related post, but it comes from the PLoS journal that is first in my heart: PLoS Neglected Tropical Diseases. And, as the journal name suggests, it is about a neglected tropical disease: the Whipworm (Trichuris … Continue reading →

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Linking gene expression and phenotype in an emerging model organism

Posted on 12 Jan, 2015 by Melissa DeBiasse

Last week in his post “Transcriptomics in the wild (populations),” TME contributor Noah Snyder-Mackler focused on a recent paper by Alvarez et al. that reviews the last decade of transcriptomic research including the goal of linking gene expression and phenotype. Researchers today routinely collect transcriptomic data for non-model … Continue reading →

Posted in genomics, howto, methods, Uncategorized | Leave a comment

Species and sensibility

Posted on 9 Jan, 2015 by Stacy Krueger-Hadfield

Pante et al. (2014) performed a literature review of marine population connectivity in order to illustrate the biased estimates of connectivity which can result from the failure to recognize an evolutionary-relevant unit, such as a species. When exploring the connectivity … Continue reading →

Posted in adaptation, community ecology, conservation, DNA barcoding, natural history, next generation sequencing, phylogenetics, population genetics, speciation, theory | 6 Comments

Recent Ancestry of the USA and the 100k Genome Project

Posted on 8 Jan, 2015 by Arun Sethuraman

Holiday presents for pop-gen enthusiasts come in the form of data – boatloads of it! The past two weeks saw the announcements of two neat studies that spell monumental steps toward our understanding of the genetics of mixed populations. With … Continue reading →

Posted in genomics, population genetics | Tagged , , | 1 Comment

Totally RAD, Part 2

Posted on 7 Jan, 2015 by Rob Denton

Edit (8/20/15): I used the wrong web address for Kimberly Andrews! Go check out her work here. Sorry Kim! Restriction site-associated DNA sequencing (RADseq) is quickly becoming the go-to methodology for collecting population genetic data, and the methodological difficulties of … Continue reading →

Posted in genomics, Molecular Ecology views, next generation sequencing, population genetics | Tagged , , | 1 Comment

Transcriptomics in the wild (populations)

Posted on 6 Jan, 2015 by Noah Snyder-Mackler

The genomics revolution is coming has already come. The past decade has seen countless advances in genomic techniques – many of which are now commonly found in any molecular ecologist’s toolbox. For example, instead of measuring gene expression in one … Continue reading →

Posted in genomics, next generation sequencing | Tagged , , | 1 Comment