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Author Archives: Jeremy Yoder
For viruses, ecology shapes the speed of evolutionary change
Molecular ecologists are interested in understanding what patterns in genetic variation across and among populations can tell us about the ecology of the living things we study. But a paper published in the latest issue of The American Naturalist demonstrates … Continue reading
What we're reading: Next-generation admixture estimates, mutation rates shaped by epidemiology, and whatever happened to that data?
In the journals Skotte L, TS Korneliussen, and A Albrechtsen. 2013. Estimating individual admixture proportions from next generation sequencing data. Genetics doi: 10.1534/genetics.113.154138. This paper presents a new method for inferring individ- ual’s ancestry that takes the uncertainty introduced in … Continue reading
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What we're reading: Compressed genomes, drafting genes, and the third post-publication peer reviewer
In the journals Deorowicz, S., A. Danek, and S. Grabowski. 2013. Genome compression: A novel approach for large collections. Bioinformatics 1–7. doi: 10.1093/bioinformatics/btt460. More precisely, our novel Ziv-Lempel-style compression algorithm squeezes a single human genome to ~400KB. The key to … Continue reading
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Using R to run parallel analyses of population genetic data in STRUCTURE: ParallelStructure
In this guest post, Francois Besnier explains how to use ParallelStructure, his new R package for running STRUCTURE analyses in parallel computing environments. To start with, thanks to The Molecular Ecologist blog team (Tim and Jeremy) for the invitation to … Continue reading
Posted in howto, population genetics, R, software, STRUCTURE
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What we're reading: Species delimitation failure, the twisty history of a retrovirus, and breeding a better tomato
In the journals Carstens, B. C., T. a Pelletier, N. M. Reid, and J. D. Satler. 2013. How to fail at species delimitation. Molecular Ecology 22:4369–4383. doi: 10.1111/mec.12413. … in most contexts it is better to fail to delimit species … Continue reading
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What we're reading: Rams' horns, beetles' testes, the rules of CC-BY reuse, and "Gatcaatgaggtgga …"
In the journals Johnston SE, J Gratten, C Berenos, JG Pilkington, TH Clutton-Brock, JM Pemberton, and J Slate. 2013. Life history trade-offs at a single locus maintain sexually selected genetic variation. Nature doi: 10.1038/nature12489. We found that an allele conferring … Continue reading
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By popular request …
The original data set of Joshua tree presence locations, which I used as an example in my post about estimating species distribution models in R, is now available for download from Dryad. Thanks to my coauthors for agreeing to share … Continue reading
Posted in data archiving, howto, methods
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What we're reading: Adaptive introgression reviewed, overdominance and heterozygosity, and predatory re-publication of CC-BY articles
In the journals Hedrick, PW. 2013. Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. Molecular Ecology doi: 10.1111/mec.12415. … potential examples of adaptive introgression in animals, including balancing selection for … Continue reading
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Domesticated genes gone wild
Artificial selection of domesticated plants and animals has been cited as a test case for natural selection since Charles Darwin first conceived the latter concept. But we generally consider that these two forms of selection operate to very different ends—that … Continue reading
Posted in adaptation, domestication, population genetics
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