Category Archives: phylogenetics

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

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

RedditDiggMendeleyPocketShare and Enjoy
Posted in genomics, next generation sequencing, Paleogenomics, phylogenetics | Tagged , , , , , , , | Leave a comment

New World snakes are “mimics until proven otherwise”

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 , , | Leave a comment

RADseq and missing data: some considerations

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 , , , | 3 Comments

Island-Hopping with an E.I.D.

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

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

Posted in data archiving, evolution, howto, phylogenetics, Uncategorized | Leave a comment

New branches on the tree of life

(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 , , , , | Leave a comment

hyRAD and museum genomics

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 , , , , , | Leave a comment