Category Archives: next generation sequencing

Mixed modeling of methylation measures (increase your power by 60%)

Posted on 7 Jul, 2015 by Noah Snyder-Mackler

Do you want to increase your power to detect differentially methylated CpG sites by 60%*? Yes?! Then do I have the pre-print for you.

Posted in bioinformatics, genomics, methods, next generation sequencing, software | Tagged , , | 1 Comment

The evolution of phylogeography in the next gen era: 20 years in review

Posted on 15 Jun, 2015 by Melissa DeBiasse

Phylogeographers have long known about the limitations of single locus studies (ie, the effects of selective sweeps, stochasticity in lineage sorting among loci) and that adding loci improves the accuracy of demographic parameter estimates. As we continue to shift towards collecting multi-locus datasets thanks to high throughput … Continue reading →

Posted in evolution, genomics, Molecular Ecology, the journal, next generation sequencing, phylogeography, Uncategorized | 3 Comments

Genomic diversity and secondary contact

Posted on 21 May, 2015 by Arun Sethuraman

Under a divergence, or isolation model, the genomes of individuals in a daughter-population are expected to harbor greater differentiation relative to its sister-population, and lower differentiation within the population (after sufficient time since divergence). Divergence thus is a mechanism of … Continue reading →

Posted in evolution, genomics, next generation sequencing, population genetics, theory | Tagged , , | 1 Comment

Another lesson in genomics experimental design and avoiding batch effects

Posted on 12 May, 2015 by Noah Snyder-Mackler

Twitter has been abuzz with Orna Man and Yoav Gilad’s (re)analysis of the data from a recent PNAS paper: “Comparison of the transcriptional landscapes between human and mouse tissues”. The PNAS paper concluded that the gene expression profiles of different … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing, RNAseq | Tagged , , | 3 Comments

A mammoth bottleneck prior to extinction

Posted on 28 Apr, 2015 by Noah Snyder-Mackler

Here’s to back-to-back posts on extinct mammalian genomes! Woolly mammoth genomes are all the rage. How do I know? Just check out the new book, pre-print, and paper that were recently published.

Posted in conservation, genomics, next generation sequencing, Paleogenomics, population genetics | Tagged , , | Leave a comment

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

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

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

Speciation by selection (and drift) in the sea

Posted on 9 Mar, 2015 by Melissa DeBiasse

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 | 1 Comment