What We’re Reading- Dec 2, 2016

Birds of Differentially Colored Feathers Still Flock Together
Yellow-winged warblers (left in picture) are threatened with extinction in Canada under SARA, and a candidate species for the ESA in the United States. Hybridization with the more widely distributed blue-winged warbler (right in picture) is considered a threat to the species. This paper (open) compared genomic signatures between the species and observed that 4 of the 6 regions of divergence were related to genes involved in color variation. The researchers also modeled gene flow between the species, where a model of long-term, rather than recent anthropogenically driven, hybridization has occurred. Thus this study has implications for understanding the genomic architecture of feather colors, and significant conservation implications including management of phenotypic variation despite new evidence questioning the validity of species assignment.

Conservation Genomics Costs WHAT?!
SNPits blogger Emily turned her post “Are Microsatellite Studies Publishable?” into a full journal article (sub).  While the blog post specifically addressed how genotyping markers for conservation studies changed over time, the paper focuses on the costs of genotyping depending on if microsatellites or SNPs are the marker of choice.  Using cost curves and varying salient genotyping parameters (number of loci and multiplex panels used, sequencing facility charges, sample pooling, etc), she shows that microsatellite based projects are less costly than RAD-Seq.  However, researchers must weigh costs versus accuracy and precision of the resultant datasets.  The paper offers practical suggestions for conservation researchers to decrease their project costs, particularly by negotiating with their sequencing facility.

It is noteworthy that the analysis of labor costs is somewhat skewed.  While wet bench labor may be well estimated as it scales with project size, data analysis labor costs were only quantified for a single project.  Thus, data analysis for multiple projects was not included in the analysis, but could be estimated by downloading the cost curves (provided as supplemental material) and factoring in a multiplier.

Side pictures by Jim Zipp vai ARKive.

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