Author Archives: Jeremy Yoder

About Jeremy Yoder

Jeremy Yoder is a postdoctoral associate in the Department of Plant Biology at the University of Minnesota. He also blogs at Denim and Tweed and Nothing in Biology Makes Sense!, and tweets under the handle @jbyoder.

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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Fishing for genetic signals of adaptation

One of the biggest promises of modern DNA sequencing methods is the ability to track the adaptation of living populations at a fine genetic scale, in essentially real time. It’s already been done in a number of experimental evolution systems: … 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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The #IcedBudgetChallenge: Tell Congress to thaw out funding for NSF and NIH!

So a friend nominated me in this viral scheme to raise funds for ALS research, about which you may have heard lately. I’m all in favor of finding a cure for ALS—my grandfather died of it—but I’m also pretty skeptical … 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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You can evolve there from here. And from here. And here …

If evolutionary history somehow reverted back to the “warm little pond” in which life began, and started over from almost-scratch, would the re-diversification of life end up, four billion years later, pretty much as we see it today? I think … 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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What we’re reading: Estimating linkage in resequencing data, genomics of host-parasite coevolution, and scientific work-life balance

In the journals Maruki, T., and M. Lynch. 2014. Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data. Genetics 197:1303–1313. doi: 10.1534/genetics.114.165514. … we developed a maximum-likelihood estimator of linkage disequilibrium for use with error-prone sampling data. Computer simulations … Continue reading

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