Category Archives: next generation sequencing

Comparing your options for phylogenomic data

Posted on 16 Dec, 2015 by Rob Denton

The choices for current-generation (last generation?) molecular markers are grouped in two primary camps. First, the “reduced representation” methods: take some DNA, cut it up with specific enzymes, tag those pieces, read the sequences. These methods produce lots and lots of … Continue reading →

Posted in methods, next generation sequencing, phylogenetics | Tagged , , | 2 Comments

It's not you, it's my genes: Sexual fidelity tradeoffs in prairie voles

Posted on 15 Dec, 2015 by Noah Snyder-Mackler

Many of you may probably already know the monogamous prairie vole as the yin to the promiscuous montane vole’s yang. Prairie voles are socially monogamous, which is an extremely rare trait among mammals. This trait has made the prairie vole … Continue reading →

Posted in adaptation, evolution, genomics, next generation sequencing, selection | Tagged , , | 3 Comments

The next, next generation: long reads facilitate assembly & annotation in large genome species

Posted on 10 Dec, 2015 by Melissa DeBiasse

The typical procedure for constructing a draft genome or transcriptome using current second generation, high throughput sequencing platforms involves generating short reads about 150 base pairs long, assembling those short reads into larger contigs, putting the contigs in the correct order to create … Continue reading →

Posted in genomics, next generation sequencing, plants, Uncategorized | 1 Comment

Pre-adapted algal ancestors colonized land

Posted on 7 Dec, 2015 by Stacy Krueger-Hadfield

The colonization of land by plants 450 Mya marked a major transition on Earth and was one of the critical events that led to the emergence of extant terrestrial ecosystems. Chief among the challenges the terrestrial environment presented for these … Continue reading →

Posted in adaptation, bioinformatics, Coevolution, evolution, genomics, haploid-diploid, next generation sequencing, phylogenetics, plants, transcriptomics | Tagged | Leave a comment

Life fast, diapause young: The African turquoise killifish genome

Posted on 7 Dec, 2015 by Noah Snyder-Mackler

Your newly sequenced genome isn’t going to get into Nature, Science, or Cell just because it “hasn’t been done before”. You need to have a hook. And speaking of hooks, there are two new fish genome papers out in Cell! … Continue reading →

Posted in genomics, natural history, next generation sequencing, selection, Uncategorized | Tagged , , | Leave a comment

Bees brought to their knees

Posted on 27 Nov, 2015 by Stacy Krueger-Hadfield

As regular readers of TME will have read, this past summer was a whirlwind of sampling in which I took the briefest of holidays in the Southwest of England before attending the European Phycological Congress (read about the congress here and here). … Continue reading →

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

The Goldilocks zone of missing data

Posted on 16 Sep, 2015 by Rob Denton

Reduced representation sequencing approaches, such as RADseq and UCEs, have provided some fascinating inferences in recent years, but something has always been missing in these analyses: data. As sampled taxa become more divergent, the price paid for more loci is … Continue reading →

Posted in evolution, methods, next generation sequencing, phylogenetics | Tagged , , , | 1 Comment

And who made your beer?

Posted on 27 Aug, 2015 by Arun Sethuraman

In the spirit of it being almost Friday, and while we’re on the topic of your favorite beverages – perhaps wine puts you to sleep, couldn’t care less where it came from, but prefer the bitterness of lager beers at your … Continue reading →

Posted in adaptation, evolution, genomics, natural history, next generation sequencing, phylogenetics, population genetics, selection, speciation, yeast | Tagged , , , , | 2 Comments

Where's your wine from?

Posted on 20 Aug, 2015 by Arun Sethuraman

Human-mediated selection of yeast cultures has played a huge role in the development of numerous unique strains of Sacchromyces cerevisiae, often attributed to production of a wide variety of wines the world over. Previous studies have indicated a single domesticated … Continue reading →

Posted in domestication, evolution, genomics, horizontal gene transfer, microbiology, Molecular Ecology, the journal, next generation sequencing, phylogenetics, phylogeography, population genetics, STRUCTURE, yeast | Tagged , , , | 1 Comment

Who came first – the Paleo- or Native American?

Posted on 23 Jul, 2015 by Arun Sethuraman

In yet another infamous Science vs Nature race, two studies published this Tuesday toss more cans of worms at the ongoing debate about the founding of the Americas – with disparate findings. Uh oh. Skoglund et al. Nature (2015) Genetic … Continue reading →

Posted in genomics, next generation sequencing, Paleogenomics, population genetics | Tagged , , , , | 2 Comments