Updates from the lab.
Updates from the lab.
Along with a group of 200+ collaborators from 20 countries and as part of the Avian Phylogenomics Project, we recently published the largest genome-scale phylogeny for a vertebrate group. Using whole genomes, we were able to generate the most statistically robust phylogeny for birds using data sets composed of several types of data (exons, introns, UCEs, and indels). The article was covered extensively in the popular press by Bloomberg, The Guardian, NPR, The Washington Post, The Economist, National Geographic, Scientific American, Nature, Newsweek and more.
cc-by Doug Fisher
As part of the Avian Phylogenomics Project, we published three genomes representing crocodilians (alligators, crocodiles, and gharials) in Science. Using UCEs and other genomic data types drawn from these genome sequences, we determined that crocodilians have the slowest (or among the slowest) rates of molecular evolution among vertebrates. The article was covered extensively in the popular press by LA Times, Bloomberg, Nature World News, and National Geographic, among others.
We recently published a manuscript in collaboration with Brian Smith, Robb Brumfield, Mike Harvey, and John McCormack in Nature which challenges the idea that landscape change is the primary driver of species diversification. The article was covered in the popular press internationally by Folha De Sao Paulo and El Espectador, and a number of science blogs.
With collaborators Nick Crawford, James Parham, and Brian Simison, we've published a manuscript describing the first genome-scale analysis of major turtle lineages, and we used that phylogeny to propose a name for the crown clade of turtles and archosaurs, "Archelosauria". This manuscript was covered widely, and was also names the "Editor's Choice" at Molecular Phylogenetics and Evolution.
We recently worked with collaborators Keping Sun, Ed Braun, and Rebecca Kimball on a manuscript that uses UCEs to study the evolutionary origin(s) of eyespots (ocelli) in peafowl. The article was covered in the popular press by National Geographic, PhysOrg, and Science Magazine News Sifter. Adam Jones also provides a nice summary of the manuscript over at F1000.
We recently published a manuscript with long-term collaborator Travis Glenn and others that used low-coverage genome sequencing to develop a database of microsatellite loci (n = 13,790 loci) for use with Schistosoma haematobium - an important urogenital parasite affecting an estimated 112 million patients, worldwide. We then used a small subset of these loci to investigate genetic diversity of Schistosoma haematobium populations across Africa.
Elizabeth Pennisi pens an article in this week's Science (342:26-27) that discusses UCEs in the context of target enrichment and the impact that the enrichment of conserved loci (e.g., Faircloth et al. 2012) has had on the phylogenetics community. Our publications resolving deep relationships among turtles (Crawford et al. 2012), deep relationships among birds (McCormack et al. 2012), and shallow relationships among rainforest birds are discussed (Smith et al. 2013).
In a Special News Feature of BioTechniques, Patrick Lo discusses how the UCE method that we developed is changing the way that we collect data informing phylogenetic studies. The article discusses our first in vitro test of the UCE approach that was published in Systematic Biology (Faircloth et al. 2012). The article also discusses several other manuscripts that have implemented a similar approach to the one we published early during 2012.
People said it could not be done and others suggested, several times, that it was not possible. However, they were incorrect. Today, our paper using data from enriched UCEs to answer questions at the population level was published in Systematic Biology. This manuscript was headed up by Brian Smith and Mike Harvey in Robb Brumfield's group LSU. Brant worked with Brian, Mike, and Robb on setting up their bioinformatics workflow and processing the data. There's some additional coverage over at Haldane's Sieve, including a guest post by Mike.
Our recent manuscript inferring a phylogeny of birds using ultraconserved elements has been published in PLoS One. The manuscript has received great coverage from several independent blogs, including posts by 10,000 Birds, the American Birding Association and The Ornithology Blog. We also posted a pre-print version of the manuscript to arXiv, as we've started to do with most of our manuscripts, where possible.
Our manuscript inferring a sister relationship between turtles and archosaurs was among the top 10 downloaded and cited articles published in Biology Letters during 2012. The turtle manuscript was also covered by several press outlets including Nature News, the AFP, PhysOrg, and Science Friday, among others. The findings of our study refute earlier work that used microRNAs to show turtles are more closely related to lizards and snakes (i.e., Lepidosaurs).
The Smithsonian Tropical Research Institute film and video crew put together an excellent introductory video to a portion of the field component of our Dimensions of Biodiversity project on Barro Colorado Island in Panama. The video discusses the project in the context of its goal to test the Enemy Susceptibility Hypothesis, which attempts to explain tropical forest diversity and the rarity of certain tropical forest tree species as a result of their susceptibility to pathogenic fungi.