Author Archives: Ethan Linck

Molecular Inversion Probes: phylogenomics without the excess?

Posted on 18 Jul, 2016 by Ethan Linck

The onset of the phylogenomic era has revolutionized molecular ecology and systematics, helping resolve relationships throughout the tree of life that have long eluded researchers working with only a handful of loci and morphological data. Phylogenetic studies of nonmodel organisms … Continue reading →

Posted in genomics, next generation sequencing, phylogenetics, phylogeography, population genetics, transcriptomics | Tagged , | Leave a comment

Live from #Evol2016 — Tuesday highlights

Posted on 22 Jun, 2016 by Ethan Linck

The Molecular Ecologist team was all over this year’s Evolution meeting in Austin, Texas. During our coverage of the meeting, we’ve been previewing presentations we’re excited about and recapping the highlights of each day here on the blog. As the main conference … Continue reading →

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Mitogenomes from extinct New Zealand wrens shed light on the oldest songbird lineage

Posted on 7 Jun, 2016 by Ethan Linck

The order Passeriformes, commonly known as “perching birds” or “songbirds,” contains over half of all known avian species. Sister to all other Passeriformes are the acanthisittid wrens, a small and enigmatic family of New Zealand endemics. Though their providential phylogenetic … Continue reading →

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RADseq and missing data: some considerations

Posted on 10 May, 2016 by Ethan Linck

Unlike Sanger sequencing, where loci are directly targeted for each individual and sequencing errors are relatively rare, massively multilocus datasets from next generation sequencing platforms are characterized by large amounts of missing data. This is particularly true for restriction digest … Continue reading →

Posted in bioinformatics, genomics, methods, Molecular Ecology, the journal, next generation sequencing, phylogenetics, population genetics, theory | Tagged , , , | 6 Comments

hyRAD and museum genomics

Posted on 5 Apr, 2016 by Ethan Linck

While the RAPTURE may have arrived, the development of novel restriction digest-based library prepartation techniques — and portmanteaus — continues unabated. In a paper published in PLoS ONE last month (and previously available as a preprint on bioRxiv), Tomasz Suchan … Continue reading →

Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics | 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

Quick and dirty tree building in R

Posted on 26 Feb, 2016 by Ethan Linck

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading →

Posted in howto, methods, phylogenetics, R, software | Tagged , , , , , , , | 3 Comments

Supergenes and Sparrows with Four Sexes

Posted on 10 Feb, 2016 by Ethan Linck

Supergenes are groups of tightly-linked genes that influence suites of traits relevant to fitness. While long a fixture of evolutionary genetics theory, their role in empirical studies of non-model organisms has been relatively limited, due to limitations in both our … Continue reading →

Posted in adaptation, evolution, genomics, horizontal gene transfer, natural history, population genetics, selection | Tagged , , , , | 2 Comments