Category Archives: phylogenetics

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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New World snakes are "mimics until proven otherwise"

Posted on 6 Jun, 2016 by Rob Denton

Henry Walter Bates spent more than a decade living in the Amazon, having the sort of adventures that inspired generations of naturalists. His most famous and lasting contributions to natural history are his foundational descriptions of mimicry among species. The type … Continue reading →

Posted in adaptation, evolution, natural history, phylogenetics | Tagged , , | 1 Comment

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

Island-Hopping with an E.I.D.

Posted on 18 Apr, 2016 by Bryan McLean

If you live in the U.S. and feel like Zika virus is getting closer to home, that’s because it is. Although there are no known cases of Zika transmission by natural vectors in the lower 48, experts have stressed that … Continue reading →

Posted in evolution, genomics, medicine, phylogenetics, Uncategorized | Leave a comment

How to make the most out of your phylogenetic study

Posted on 14 Apr, 2016 by Christine Ewers-Saucedo

Phylogenetic studies are crucial for ecology and evolution. However, their usefulness for comparative biology or meta-analyses can vary considerably. Especially the inclusion of unidentified species (“Balanus sp.”) obstructs their use in comparative studies. How can I attach life history or morphological data … Continue reading →

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New branches on the tree of life

Posted on 12 Apr, 2016 by Kelle Freel

(Trees from Darwin (1837), Haeckel (1866), and Woese (1990)) We’ve come quite a long way since Darwin sketched out his tree in 1837 connecting, with branch tips representing animals and microbes currently in existence and branches and trunks their ancestors. … Continue reading →

Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, phylogenetics | Tagged , , , , | 1 Comment

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

The rise of the fruit flies – Can good science communication make or break a model system?

Posted on 21 Mar, 2016 by Christine Ewers-Saucedo

The answer is: probably not. It is probably more important that the organism thrives in a lab environment, reproduces and hybridizes with speed and ease, and has some additional “desirable” features: think visible mutations in the fruit fly Drosophila, constant cell … Continue reading →

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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 Evolution of Molecular Dating

Posted on 7 Mar, 2016 by Bryan McLean

Molecular dating is a key tool in deciphering the history of life. In a recent Molecular Biology and Evolution paper, Sudhir Kumar and Blair Hedges have reviewed the state of the subject, summarizing the philosophical and methodological history of this … Continue reading →

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