Category Archives: next generation sequencing

The gopher tortoise gut microbiome

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.

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Posted in community ecology, genomics, natural history, next generation sequencing, population genetics, Uncategorized | Tagged , , | Leave a comment

Gorillas (genomes) in the mist

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

                    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

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 , , , | 1 Comment

Rescue me

Whiteley et al. (2015) review genetic rescue (GR), or the increase in population fitness (growth) owing to immigration of new alleles, in a new paper in TREE. Genetic rescue is a controversial and hasn’t been applied to any great extent … Continue reading

Posted in adaptation, evolution, genomics, next generation sequencing | Tagged , , | Leave a comment

Night at the museum

Many population genetic and genomic studies document snapshots of a given population’s genetic diversity. Yet, there are many reasons to document changes over time in population parameters in response to perturbations, such as biological invasions (both in terms of the invader … Continue reading

Posted in DNA barcoding, evolution, genomics, natural history, next generation sequencing, phylogenetics, population genetics, speciation, Uncategorized | Tagged , , , | Leave a comment

Mike Sovic on what comes AftrRAD

We’ve recently been highlighting some discussions comparing different protocols for restriction site-associated DNA sequencing (RADseq). We’ve seen the pros and cons of multiple techniques, but what happens when you finally have thousands of shiny SNPs sitting on your hard drive? Multiple … Continue reading

Posted in interview, Molecular Ecology views, next generation sequencing | Tagged , | Leave a comment

New to the genome sequencing $8 menu: Nextera library preps!

Researchers are thrifty. We’re always looking for ways to make our expensive supplies and reagents go the extra mile. This shit has been going on for decades – hell, probably even centuries: I remember when I was a kid and … Continue reading

Posted in genomics, methods, next generation sequencing | Tagged , , , , | 7 Comments