Category Archives: next generation sequencing

Genomics of Hybridization – Part II, Top three of 2015

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading

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Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment

Genomics of Hybridization – Part 1

In a series of articles, I will discuss recent advances in hybridization genomics – the fundamentals of adaptive introgression, “islands of speciation”, differential gene flow, and linked selection have been discussed in my previous posts (here, here, and also at … Continue reading

Posted in adaptation, evolution, genomics, methods, natural history, next generation sequencing, pedigree, phylogenetics, plants, population genetics, RNAseq, software, speciation, species delimitation, STRUCTURE, theory, transcriptomics | Tagged , , , , , , | Leave a comment

Earthquakes and rapid evolution

The 1964 Alaskan earthquake was landscape-altering in creating/uplifting numerous islands in the Gulf of Alaska, providing an ideal system to study adaptive evolution of diversification in affected species – the threespine stickleback (Gasterosteus aculeatus) being a widely studied example. In … Continue reading

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Comparing your options for phylogenomic data

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

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

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

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

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

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

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

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Bees brought to their knees

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

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The Goldilocks zone of missing data

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

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