Category Archives: genomics

The gopher tortoise gut microbiome

Posted on 14 Apr, 2015 by Noah Snyder-Mackler

A few weeks ago I wrote about a study on socially structured gut microbiomes in wild baboons. Well, now I’m here to tell you about a new study that examined the population structure of tortoise gut microbiomes.

Posted in community ecology, genomics, natural history, next generation sequencing, population genetics, Uncategorized | Tagged , , | 1 Comment

Gorillas (genomes) in the mist

Posted on 10 Apr, 2015 by Stacy Krueger-Hadfield

Mountain gorillas are an endangered great ape subspecies that number around 800 individuals, inhabiting mountain ranges in central Africa. They have been the subject of numerous field studies, but few genetic analyses have been carried out. Xue et al. (2015) sequenced … Continue reading →

Posted in bioinformatics, conservation, evolution, genomics, natural history, next generation sequencing, primates | Tagged , , , | Leave a comment

Don't trust your data: reviewing Bioinformatics Data Skills

Posted on 8 Apr, 2015 by Rob Denton

The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post. There is little debate on the importance of bioinformatics for the present and future of science. As molecular ecologists, we are likely more aware of this … Continue reading →

Posted in bioinformatics, book review, genomics, software | Tagged | 2 Comments

A transcriptomic approach for reduced representation in population genomics

Posted on 6 Apr, 2015 by Melissa DeBiasse

                    Many population genomics studies use methods that provide a reduced representation of the genome, for example RADseq or UCEs. Targeting a subset of the genome reduces the cost of sequencing … Continue reading →

Posted in genomics, howto, methods, Molecular Ecology, the journal, next generation sequencing, RNAseq | Leave a comment

F-statistics Manhattan Plots in R

Posted on 26 Mar, 2015 by Arun Sethuraman

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 →

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 4 Comments

Killer genetic differentiation

Posted on 25 Mar, 2015 by Rob Denton

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 →

Posted in genomics, population genetics | Tagged , | Leave a comment

Haploid-diploidy, a (brief?) history

Posted on 20 Mar, 2015 by Stacy Krueger-Hadfield

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 , , , , , | 2 Comments

dN(eutralist) = dS(electionist) Part 3

Posted on 19 Mar, 2015 by Arun Sethuraman

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 →

Posted in adaptation, evolution, genomics, natural history, plants, population genetics, selection | Tagged , | Leave a comment

Socially structured gut microbiomes in wild baboons

Posted on 17 Mar, 2015 by Noah Snyder-Mackler

“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 , , | 5 Comments

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

Posted on 16 Mar, 2015 by Stacy Krueger-Hadfield

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