Category Archives: methods

Incorporating phenotype and genotype in model-based species delimitation

  Species are the fundamental unit of biology but identifying them is a challenging task that receives a lot of theoretical and empirical attention. In a recent Evolution paper, Solís‐Lemus et al. (2015) introduce a new model-based method that integrates phenotypic and genetic data … Continue reading

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Posted in methods, speciation, species delimitation, theory | Leave a comment

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 , , , , | 5 Comments

A population genetic R-evolution

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 | Leave a comment

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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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

Increase your broader impacts with Data Nuggets

  This week we have a special guest post by Elizabeth Schultheis, a PhD candidate at Michigan State University and the Kellogg Biological Station, to describe her Data Nuggets project. Previous guest posts have discussed other great projects happening in the … Continue reading

Posted in career, citizen science, community, funding, methods | 1 Comment

Isolation by environment explains why the grass isn’t always greener

Ever since Sewall Wright introduced isolation by distance in 1943, the interplay between genetic differentiation and geographic distance has been a foundational, sometimes frustrating, aspect of population genetics studies. But distance isn’t just distance. The walk to my car isn’t any longer when … Continue reading

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The big chief at Molecular Ecology Resources: Interviewing Shawn Narum

What are the most exciting parts of doing science? The first look at results? The sheen of your publication finally in print? That initial foray out into the field? What about the moment you figure out a way to make a … Continue reading

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The latest gadget for the molecular ecologist’s toolkit

Designing a sampling scheme to collect an organism of interest for a population genetic/genomic study can be fraught with difficulty. How best to sample? Randomly? Or, along a grid? How many individuals to sample? Thirty? Or, perhaps, the sample size … Continue reading

Posted in genomics, methods, Molecular Ecology, the journal, natural history, pedigree, population genetics, software | 1 Comment

From cats to rats: two studies on domestication and tameness

Anyone who has ever read Charles Darwin is acutely aware of his fascination with domestication – particularly how he fancied fancy pigeons. Darwin drew on his domestication obsession while writing his book, The Variation of Animals and Plants under Domestication, … Continue reading

Posted in adaptation, association genetics, domestication, genomics, methods, next generation sequencing, phylogenetics, quantitative genetics | Tagged , , , , , | Leave a comment