Wednesday, August 19, 2015

Systematic Biology

I thought that I should draw your attention to the current issue of the journal Systematic Biology, which contains more contributions about reticulate relationships than I have seen there before.

These include:

♦ Andrew R. Francis and Mike Steel (2015) Which phylogenetic networks are merely trees with additional arcs? Systematic Biology 64: 768-777. doi:10.1093/sysbio/syv037

A theoretical paper discussed by Leo in a previous blog post (Networks vs augmented trees).

♦ Jonathan Brassac and Frank R. Blattner (2015) Species-level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in silico cloning of multiple nuclear loci. Systematic Biology 64: 792-808. doi:10.1093/sysbio/syv035

Contains a tree of relationships among the diploid species, with the tetraploid and hexaploid species manually added as reticulations, to create a hybridization network.

♦ Noah W. M. Stenz, Bret Larget, David A. Baum, and Cécile Ané (2015) Exploring tree-like and non-tree-like patterns using genome sequences: an example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. Systematic Biology 64: 809-823. doi:10.1093/sysbio/syv039

Contains a series of trees but no network. Nevertheless, the authors' analyses "identify instances of introgression and detect one clear case of reticulation among ecotypes that have come into contact".

♦ David A. Morrison (2015) Aristotle's Ladder, Darwin's Tree: The Evolution of Visual Metaphors for Biological Order, by J. David Archibald. Systematic Biology 64: 892-895. doi:10.1093/sysbio/syv038

A book review that castigates the book's author for hardly mentioning networks when writing about phylogenetic metaphors. There is a table summarizing some of the relevant publication history.

There is also one paper that possibly should be about networks but doesn't actually mention them.

♦ Thomas C. Giarla and Jacob A. Esselstyn (2015) The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews. Systematic Biology 64: 727-740. doi:10.1093/sysbio/syv029

The authors collected data on "hundreds of ultraconserved elements and whole mitochondrial genomes" from multiple individuals of several species of shrews (Crocidura). They conclude that "the low support we obtained for backbone relationships ... reflects a real and appropriate lack of certainty. Our results illuminate the challenges of estimating a bifurcating tree in a rapid and recent radiation, providing a rare empirical example of a nearly simultaneous series of speciation events".

A NeighborNet analysis of the provided mitochondrial data is shown in the first figure. Clearly, all it says is that the individuals group into species, but there is no information in the data about the relationships among the species.

A NeighborNet analysis of the SNPs from the ultraconserved elements is shown in the second figure. This network is not that different, in that it does little more than group the individuals into species, with little information about relationships.

However, note also that the largest reticulation involves sp_FMNH146788 and mindorus_FMNH221890. These two samples are not closely related in the mitochondrial network. This hints that the sp_FMNH146788 sample may be a genotypic mixture, due perhaps to hybridization or introgression. The authors treat the specimen as representing a "heretofore undescribed taxon that shares introgressed mitochondrial DNA with true C. ninoyi."

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