Cilia & Emy
We recently hosted our friends from Greece, Dr. Cilia Antoniou from the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) and the Hellenic Centre for Marine Research (HCMR), and Emy Karameta from the University of Athens. They visited the lab for a few weeks to collect SNP data for their phylogeography and species delimitation projects focusing on taxa found in the beautiful Aegean Islands. Cilia and Emy are instructors at the annual Computational Molecular Evolution Workshop. Emy is studying agama lizards (Stellagama stellio) in the Mediterranean as well as the phylogeography of other co-distributed species found across the Islands. Cilia is studying a wide variety of taxa, including hares (not rabbits), dolphins, and even land snails. We’re looking forward to seeing them again in the UK in 2015, and then visiting them on their home turf in Crete in 2016.
A new paper published in the journal Molecular Phylogenetics & Evolution contains a new recipe for making phylogenetic sausage,
“We suggest that the coalescence protocol utilized by McCormack et al. (2012) is the equivalent of making phylogenetic sausage. In the messy construction of a sausage, a butcher grinds together chunks of undesirable cuts (e.g., lips, heart valves, assorted fatty bits, etc.), mixes this flotsam with spices, forcibly extrudes the concoction into a casing made of intestinal lining, and forms a product of passable palatability. Likewise, in the first step of the shortcut coalescence procedure, undesirable gene trees were reconstructed from small, uninformative bits of the genome (Fig. 7; Table 1) that in some cases have wildly varying rates of evolution in different mammalian lineages (Fig. 10). The arbitrarily resolved, inaccurate gene trees were then forced into a final species tree casing under the assumption that all gene tree conflicts are due to deep coalescence. Utilizing this crude and messy process, a phylogenetic hypothesis.”
–Gatesy & Springer 2014. Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Molecular Phylogenetics & Evolution 80, 231-266.
I applaud the authors for their novel contribution of a phylogenetic sausage recipe.
If it’s not too late, then perhaps the journal could use one of these possible cover images:
Cover Submission V.2: Rooted 3-taxa Phylogenetic Sausage Tree
Cover Submission V.1: Unrooted 4-taxa Phylogenetic Sausage Tree
Mariana and Adam at the Burke Museum.
Our friend and colleague Dr. Mariana Morando visited the lab for a week to collect SNP data for some Argentinian lizards. Mariana is on sabbatical this year at BYU in the Jack Sites lab. Mariana set a new record for quickest ddRADseq data collection in our lab – she went from DNA to finished libraries in just 2.5 days! Congratulations to Mariana on a job well done.
NSF just released the updated program solicitation for the Postdoctoral Research Fellowships in Biology (PRFB), and one of the three key BIO programs is Research Using Biological Collections. This is an exciting update for museum-based researchers. They are looking to fund transformative approaches that use biological collections in innovative ways to address big challenges in biology. From the solicitation, “Priority may be given to applicants who integrate biological collections and associated resources with other types of data in an effort to forge new insight into areas traditionally funded by BIO. Examples of key questions in biology of interest include, but are not limited to, links between genotype and phenotype, evolutionary developmental biology, comparative approaches in functional and developmental neurobiology, and the biophysics of nanostructures. Using collections as a resource for grand challenge questions in biology is expected to present new opportunities to advance understanding of biological processes and systems, inspiring new discoveries in areas with relevance to other disciplines with overlapping interests in biological systems. Applicants must document access to the selected collection(s) in the research and training plan.”
You can read the full solicitation here.
We recently released a new software package (shinyPhrynomics) for single nucleotide polymorphism (SNP) data analysis. The software package is a collection of R codes for transforming your SNP data matrix into various popular phylogenetic program formats, including RAxML, MrBayes, and SNAPP. Options for plotting data include summaries of genetic variation and missing data.
These tools are available for download and via a friendly online graphical user interface.
Check out our new Software page for links to this and other data analysis tools and methods.