Category Archives: next generation sequencing

Genomic diversity and secondary contact

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

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Posted in evolution, genomics, next generation sequencing, population genetics, theory | Tagged , , | Leave a comment

Another lesson in genomics experimental design and avoiding batch effects

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 , , | 2 Comments

A mammoth bottleneck prior to extinction

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

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 , , | 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

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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

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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

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