Category Archives: linkfest

What we’re reading: The diversification of bacteria, landscape genomics of cottonwood, and the skewed sex ratio of science

In the journals Plata G., C.S. Henry, and D. Vitkup. 2014. Long-term phenotypic evolution of bacteria. Nature. doi: 10.1038/nature13827. Overall, bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow … Continue reading

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What we’re reading: The color of cichlids, projected genomes, and simplifying NSF proposals

In the journals Albertson RC, KE Powder, Y Hu, KP Coyle, RB Roberts, and KJ Parsons. 2014. Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes. Molecular Ecology, 23: 5135–5150. doi: 10.1111/mec.12900. … … Continue reading

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What we’re reading: A meta-analysis of meta-analyses, plants’ cytoplasmic genomes, and science under political attack

In the journals Koricheva, J. and J. Gurevitch. 2014. Uses and misuses of meta-analysis in plant ecology. Journal of Ecology, 102: 828–844. doi: 10.1111/1365-2745.12224. We found many cases of imprecise and inaccurate usage of the term ‘meta-analysis’ in plant ecology, … Continue reading

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What we’re reading: QTLs of pine growth, climate-niche evolution, and the shape of Twitter conversations

In the journals Li Z., H.R. Hällingback, S. Abrahamsson, A Fries, B.A. Gull, M.J. Sillanpää and M.R. García-Gil. 2014. Functional multi-locus QTL mapping of temporal trends in Scots pine wood traits. G3: Genes | Genomes | Genetics. doi: 10.1534/g3.114.014068. Two … Continue reading

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What we’re reading: Sorting out whole-genome duplication, adaptation without tradeoffs, and is science leaving its logistic growth phase?

In the journals McGrath CL, J-F Gout, P Johri, TG Doak, and M Lynch. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. 2014. Genome Res. 24: 1665-1675. doi: 10.1101/gr.173740.114. Finally, multiple sources of evidence indicate that [Paramecium] … Continue reading

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What we’re reading: A guide to Bioconductor, Latin American admixture, and the sordid truth about academic job hunting

In the journals Lawrence M., M. Morgan. 2014. Scalable genomics with R and Bioconductor. arXiv:1409.2864. This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages … Continue reading

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What we’re reading: Bayesian phylogenetics for whole genomes and coevolutionary interactions in epidemiology

In the journals Aberer A.J., K. Kobert, and A. Stamatakis. 2014. ExaBayes: Massively parallel Bayesian tree inference for the whole-genome era. Mol. Biol. Evol. 31(10): 2553-2556. doi: 10.1093/molbev/msu236. Modern sequencing technology now allows biologists to collect the entirety of molecular … Continue reading

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What we’re reading: The phylogenomics of peanut allergens, saving the world with (and from) evolution, and how to make better figures

In the journals Ratnaparkhe MB, T-H Lee, X Tan, X Wang, J Li, C Kim, LK Rainville, C Lemke, RO Compton, J Robertson, M Gallo, DJ Bertioli, and AH Paterson. 2014. Comparative and evolutionary analysis of major peanut allergen gene … Continue reading

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What we’re reading: Hyper-mutating symbionts, cichlid genomes, and active learning in biology class

In the journals Remigi P, D Capela, C Clerissi, L Tasse, R Torchet, et al. 2014, Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer. PLoS Biology. 12(9): e1001942. doi: 10.1371/journal.pbio.1001942. Following introduction of the symbiotic plasmid … Continue reading

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What we’re reading: Genomic selection scans, local adaptation, and the grass is actually pretty green on this side of the publishing fence

In the journals Cadzow M, J Boocock, HT Nguyen, P Wilcox, TR Merriman and MA Black. 2014. A bioinformatics workflow for detecting signatures of selection in genomic data. Front. Genet. 5:293. doi: 10.3389/fgene.2014.00293. Here we describe a basic workflow, constructed … Continue reading

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