Category Archives: next generation sequencing

To find duplicated loci in vertebrate polyploids, try thinking small

Posted on 23 Mar, 2016 by Rob Denton

Big sequencing efforts have gone a long way to help understand the complexities of polyploidy. However, the bioinformatic approaches to sorting and scoring alleles in next-gen data are generally designed for easy of use in diploid species. Unlike a diploid species, where … Continue reading →

Posted in genomics, methods, next generation sequencing, Uncategorized | Tagged , , | 3 Comments

RADseq vs. UCEs, round 3

Posted on 18 Mar, 2016 by Ethan Linck

Though reduced-representation genome sequencing (or high-throughput, or nextgen, or massively parallel sequencing, or…) has become standard practice for molecular ecology labs over the past few years, the relative merits of different library preparation methods remains an active area of research. … Continue reading →

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

The Truth

Posted on 17 Mar, 2016 by Arun Sethuraman

Spoiler Alert: I’ve taken plenty of care to try and not spill the beans on any plotlines, but you have been forewarned that there may be some aspects of the science that’s discussed on the show that I attempt to … Continue reading →

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Veritas Genetics offers $999 (human) genome sequences

Posted on 3 Mar, 2016 by Jeremy Yoder

Veritas Genetics, a company co-founded by Harvard University geneticist George Church* announced today that it will sequence your genome for less than $1,000. One dollar less, specifically. Up to now, “personal genome” services like 23andMe have used methods that don’t … Continue reading →

Posted in association genetics, bioinformatics, genomics, medicine, next generation sequencing | Tagged , , | 3 Comments

The 2016 Workshop on Genomics summary

Posted on 29 Feb, 2016 by Elin Videvall

I recently had the pleasure to spend two and a half weeks in the beautiful medieval town of Český Krumlov, Czech Republic. The reason was the popular Workshop on Genomics that was running and I was one of the TAs … Continue reading →

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The Neanderthal admixture plot thickens…

Posted on 25 Feb, 2016 by Arun Sethuraman

Previous studies of archaic admixture from Altai Neanderthals and Denisovans into modern humans outside of Africa have put forth several lines of evidence for gene flow from Neanderthals into common ancestors of Eurasian populations, from Denisovans into ancestors of modern … Continue reading →

Posted in bioinformatics, evolution, genomics, mutation, natural history, next generation sequencing, Paleogenomics, population genetics, speciation | Tagged , , , | 2 Comments

Welcome to the Rapture

Posted on 16 Feb, 2016 by Reid Brennan

The advent of massively parallel, high throughput sequencing has undoubtedly revolutionized biology. However, have you ever wanted to run a parentage analysis, assess basic population structure, or perform any of the other countless applications where hundreds of thousands of SNPs … Continue reading →

Posted in methods, next generation sequencing | 2 Comments

Genomics of Hybridization – Part II, Top three of 2015

Posted on 28 Jan, 2016 by Arun Sethuraman

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 →

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

Posted on 21 Jan, 2016 by Arun Sethuraman

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

Posted on 7 Jan, 2016 by Arun Sethuraman

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 →

Posted in adaptation, evolution, genomics, natural history, next generation sequencing, phylogeography, population genetics, selection, STRUCTURE | Tagged , , , , , , | Leave a comment