Category Archives: genomics

From crocodiles to coconuts

The first plant trypanosomatids were discovered in plant tissues over 100 years ago, but we know very little about their biology, life cycle or how they have adapted to life inside plants. Jaskowska et al. (2015) provide a review of … Continue reading

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Posted in adaptation, Coevolution, evolution, genomics, natural history | Leave a comment

Discordance in ancestry inference using human mtDNA and autosomes

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

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New to the genome sequencing $8 menu: Nextera library preps!

Researchers are thrifty. We’re always looking for ways to make our expensive supplies and reagents go the extra mile. This shit has been going on for decades – hell, probably even centuries: I remember when I was a kid and … Continue reading

Posted in genomics, methods, next generation sequencing | Tagged , , , , | 7 Comments

A current review of modern and ancient eDNA

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

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Linking gene expression and phenotype in an emerging model organism

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

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Recent Ancestry of the USA and the 100k Genome Project

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

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Totally RAD, Part 2

Restriction site-associated DNA sequencing (RADseq) is quickly becoming the go-to methodology for collecting population genetic data, and the methodological difficulties of a technique that is exploding in popularity are coming along with it. Last month, Stacy pointed you towards a … Continue reading

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Transcriptomics in the wild (populations)

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

Totally RAD

Puritz et al. (2014) weigh the pros and cons of, the aptly titled, “RAD fad” in a comment recently published online in Molecular Ecology. They challenge: (1) the assertion that the original RAD protocol minimizes the impact of PCR artifacts … Continue reading

Posted in bioinformatics, genomics, methods, next generation sequencing, Uncategorized | 2 Comments

Migration Circos plots in R

We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading

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