Category Archives: linkfest

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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What we’re reading: Genetic diversity and life history, evolutionary rescue, and scientists on social media

In the journals Romiguier, J., P. Gayral, M. Ballenghien, A. Bernard, V. Cahais, A. Chenuil, Y. Chiari, R. Dernat, L. Duret, N. Faivre, E. Loire, J. M. Lourenco, B. Nabholz, C. Roux, G. Tsagkogeorga, A. A.-T. Weber, L. A. Weinert, … Continue reading

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What we’re reading: Selection for heterozygosity in threatened seals, and testing Fst outlier tests

In the journals Forcada J and Hoffman JI. 2014. Climate change selects for heterozygosity in a declining fur seal population. Nature. 511:462–465. doi: 10.1038/nature13542. Variation in SAM [Southern Annular Mode of the Antarctic atmosphere] significantly affects most of the life … Continue reading

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