Diego Mallo’s review on species trees in the open access theme issue “From DNA barcodes to biomes” compiled and edited by Paul DN Hebert, Mehrdad Hajibabaei and Peter M Hollingsworth is out.
Access content online at bit.ly/PTB1702.
The main TOC link when live will be http://rstb.royalsocietypublishing.org/content/371/1702.
Congrats to Sara for the final publication of her Seychelles skink paper !! It was a lot of work.
Rocha S, Perera A, Silva A, Posada D, Harris J. 2016. Evolutionary history of Trachylepis skinks from the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure. Biological Journal of the Linnean Society 119: 15-36.
Our review paper about next-generation sequencing simulators is out on Nature Reviews Genetics (advance online publication).
Escalona M, Rocha S, Posada D (2016). A comparison of tools for the simulation of genomic next-generation sequencing data. Nature Reviews Genetics doi:10.1038/nrg.2016.57
Online access: http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg.2016.57.html
Also, the full paper can be read through ReadCube: http://rdcu.be/iW5c
We have an extended version of the tables here: http://darwin.uvigo.es/ngs-simulators
Finally our paper on Bayesian species tree estimation is published in Systematic Biology, although it has been available (advance access) there since 2014. This is a very nice method implemented by Leo Martins in the software Guenomu, in which a species tree can be build from multiple gene-family alignments. It is based on a Bayesian hierarchical statistical model of the incongruence between gene trees and species trees that ignores the evolutionary process responsible for it, inspired by Steel and Rodrigo (2008) ML supertree approach. This method does not require the identification of orthologs and can use information from multiple individuals from the same species.
This paper is part of a special issue based on the Systematic Biology symposium that I organized in 2013 Evolution meetings at Snowbird. The introduction to this symposium is also available here.
Martins LO, Mallo D, Posada D. 2016. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Systematic Biology 65: 397-416.
Posada D. 2016. Phylogenomics for Systematic Biology. Systematic Biology 65: 353-356.
Leo and I have published another paper on the UCA test, maybe the last one of a series of papers showing why and how Theobald’s UCA test is biased, and proposing proper ways of doing this
Our first draft of the mussel genome has been published in PLoS ONE.
We are working on a much more polished genome with more depth and long reads. Hopefully it will be ready very soon. D
Diego Darriba defended today with success (“Sobresaliente cum laude“) his Ph.D thesis entitled “Selection of models of genomic evolution in HPC environments” supervised by Guillermo López (UDC), Ramón Doallo (UDC) and David Posada (UVIGO). The thesis was carried out jointly carried out at the University of Coruña (UDC) and the University of Vigo (UVIGO), and defended today at the School of Computer Science in A Coruña.
Diego is now going to start a postdoc with Alexis Stamatakis at Heidelberg Institute for Theoretical Science (HITS) in Germany.
Bernardo Rodríguez just joined our lab to do a PhD with Jose Tubio and David Posada on transposable element evolution in cancer.
Jose Tubío just joined our group as a Ramon and Cajal fellow, coming from the University of Cambridge and the Wellcome Trust Sanger Institute (UK). Jose is focused on the study of transposable elements mobilized somatically in cancer genomes, and the analysis of their impact on cancer genome structure and function, using next-generation sequencing data. He is a member of the PanCancer Initiative, an international effort for the analysis of molecular aberrations in thousands of cancer samples.
More of his research at http://www.researchgate.net/profile/Jose_Tubio.