Category Archives: genomics

F-statistics Manhattan Plots in R

Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading

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Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 2 Comments

Killer genetic differentiation

Like most of you out there, I sometimes get bogged down in literature, and the pressure to keep up with new methods can lead to a towering “to-read” folder. I feel forced to read many of these papers no matter … Continue reading

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Haploid-diploidy, a (brief?) history

Haploid-diploid life cycles are not only good exercise for the brain, but they’re also fantastic study systems to investigate a myriad of questions. Yet, the majority of molecular studies have focused on the diploid-dominated life cycles of animal and plant … Continue reading

Posted in DNA barcoding, domestication, evolution, genomics, haploid-diploid, natural history, population genetics, selection, speciation | Tagged , , , , , | Leave a comment

dN(eutralist) = dS(electionist) Part 3

In a previous post, I discussed the phenomenon of background selection, which results in rapid expungement of neutral alleles linked to loci under purifying or negative selection, and conversely, the rapid fixation of neutral variants that are linked to loci of … Continue reading

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Socially structured gut microbiomes in wild baboons

“You can pick your friends and you can pick your nose, but you can’t pick your friend’s nose.” Well, that old adage may still be true, but baboons certainly pick (up) their friends’ gut microbes. A new study by Jenny … Continue reading

Posted in community ecology, genomics, metagenomics, natural history, primates | Tagged , , | 1 Comment

To sequence a genome or not to sequence a genome, that is the question

In a paper out last month in the Journal of Phycology, Bhattacharya et al. (2015) provide a perspective on the need for more algal genomes. [A] relevant question on the minds of many phycologists might be: do we really need more algal … Continue reading

Posted in bioinformatics, evolution, genomics, horizontal gene transfer, mutation, next generation sequencing, selection | Tagged , , , , | Leave a comment

Speciation by selection (and drift) in the sea

Marine systems challenge the view that speciation is the result of geographic isolation. Many marine taxa have large effective population sizes, which slows lineage sorting, larval dispersal phases that may extend for days, weeks, and sometimes months, potentially connecting far flung populations, … Continue reading

Posted in genomics, next generation sequencing, selection, speciation | Leave a comment

sedaDNA sleuths: embracing your inner Sherlock

Awhile back fellow TME contributor Rob Denton posted about a recent review on environmental DNA by Pedersen et al. (2015). Environmental DNA (eDNA) is obtained from samples such as sediments, ice or water and can provide scientific sleuths with tantalizing clues about past … Continue reading

Posted in bioinformatics, domestication, genomics, natural history, next generation sequencing, Paleogenomics | Tagged , , , | Leave a comment

dN(eutralist) > dS(electionist)? Part 1

In a new series of posts, I will now proffer neutralist and selectionist reviews of recent publications. I point readers to an excellent review of the debate by Masatoshi Nei (2005). Besides being a fun exercise in PoV’s, I hope … Continue reading

Posted in evolution, genomics, mutation, population genetics, theory | Tagged , , | 13 Comments

The conservation genomics gap

Is genomic data a boon or a hurdle for conservation? Aaron Shafer and Jochen Wolf take a strong stance on the issue in a newly-published review in Trends in Ecology and Evolution: genomic data could be really useful for conservation, but not … Continue reading

Posted in conservation, genomics | Tagged | 5 Comments