Interesting new paper: "Proving universal common ancestry with similar sequences"

Just discovered an interesting paper by Leonardo de Oliveira Martins and David Posada.  It is titled "Proving universal common ancestry with similar sequences."  It relates to a paper by Douglas Theobald: "A formal test of the theory of universal common ancestry. Nature 2010; 465:219-22." Although the latter paper is not openly available the more recent one is.  


The new paper is worth a look.  Not sure about the Theobald one as I do not have access from home.


Am hoping Leonardo writes more about this in his blog: Bayesian Procedures in Biology ....

Antibiotic use in animals (may) lead to superbugs in people #mBIO

New paper in mBIO of potential interest from Lance Price et al.:  Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock.  For those not in the know, mBIO is a relatively new Open Access journal from the American Society for Microbiology.  The paper discusses genomic studies of MRSA which has led the authors to conclude that antibiotic use in animals may contribute to the rise and spread of superbugs in people.

From here. Maximum-parsimony tree of the 89 CC398 isolates (including ST398SO385) based on 4,238 total SNPs, including 1,102 parsimony-informative SNPs with a CI of 0.9591. Clades and groups of importance are labeled in a hierarchical fashion to facilitate description in the text. The tree was rooted with clade I based on an iterative selection process that identified this group as the most ancestral (see Materials and Methods). COO, country of origin; AT, Austria; BE, Belgium; CA, Canada; CH, Switzerland; CN, China; DE, Germany; DK, Denmark; ES, Spain; FI, Finland; FR, France; GF, French Guiana; HU, Hungary; IT, Italy; NL, The Netherlands; PE, Peru; PL, Poland; PT, Portugal; SI, Slovenia; US, United States; P, pig; H, human; R, horse; T, turkey; B, bovine; MET, methicillin susceptibility; R, resistant; S, susceptible.

The figure above is the only figure in the main text of the paper.  There are others in supplemental information which seems a bit strange to me - why put anything in supplemental information when the paper is only released online?  Or at least have thumbnail images for all figures in the main text ...

Anyway, the paper and press release got picked up by many newsy places.  See for example:

• Pig-to-Human 'Superbug' May Be Due to Animal Antibiotics (US News)
• MRSA Staph Strain Developed Drug Resistance in Your Burger (US News)
• How Using Antibiotics In Animal Feed Creates Superbugs (NPR blog)
• MRSA in Livestock May Spread to Humans (ABC news)
• Staph Turns into Drug-Resistant Superbug on Farms (SciAm blog)

I note - the Press Release is MUCH better than the last one that was about a paper by Price that I wrote about here: The Tree of Life: #PLoSOne paper keywords revealing: (#Penis #Microbiome #Circumcision #HIV); press release misleading ...  Lance was awesomally quick to respond to my complaints about that PR.  The PR for this paper is not so bad --- a bit over the top in some of the quotes - but no need for comments I think. 

Citation:

Price LB, et al. 2012. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. mBio 3(1):e00305-11. doi:10.1128/mBio.00305-11.

UPDATE 2/21 5:30 PM: an alternative (and much more pleasing) press release from ASM is here.

Draft blog post cleanup #1: Divide and Conquer to Find Orthologs

OK - I am cleaning out my draft blog post list.  I start many posts and don't finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is the first ---

Saw an interesting paper worth checking out:
PLoS ONE: Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach



It describes not only a way to speed up continual ortholog annotation in bacterial and archaeal genomes but also is linked to an ongoing open code development project.

Here is the abstract:

Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively expensive in terms of hardware requirements or computational time (requiring an estimated 18 months or more on a typical server). Here, we present xBASE-Orth, a system for ongoing ortholog annotation, which applies a “divide and conquer” approach and adopts a pragmatic scheme that trades accuracy for speed. Starting at species level, xBASE-Orth carefully constructs and uses pan-genomes as proxies for the full collections of coding sequences at each level as it progressively climbs the taxonomic tree using the previously computed data. This leads to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale. Using xBASE-Orth, we analyzed an NCBI collection of 1,288 bacterial and 94 archaeal complete genomes with more than 4 million coding sequences in 5 weeks and predicted more than 700 million ortholog pairs, clustered in 175,531 orthologous groups. We have also identified sets of highly conserved bacterial and archaeal orthologs and in so doing have highlighted anomalies in genome annotation and in the proposed composition of the minimal bacterial genome. In summary, our approach allows for scalable and efficient computation of the bacterial and archaeal ortholog annotations. In addition, due to its hierarchical nature, it is suitable for incorporating novel complete genomes and alternative genome annotations. The computed ortholog data and a continuously evolving set of applications based on it are integrated in the xBASE database, available at http://www.xbase.ac.uk/.

Definitely worth checking out.

Coming up on http://phyloseminar.org Jason Stajich (aka @hyphaltip) #fungi #genomics

Upcoming seminar on Phyloseminar.Org

Jason Stajich speaks Wednesday, June 29th at noon PST on "Fungal phylogenomics: Getting lost in the moldy forest."
Fungi occupy diverse ecological niches in roles from nutrient cycling in rainforest floors to aggressive plant and animal pathogens. Molecular phylogenetics has helped resolve many of branches on the Fungal tree of life and enabling studies of evolution across this diverse kingdom. The genome sequences from hundreds of fungi now permit the study of change in genes and gene content in this phylogenetic context and to connect molecular evolution with adaptation to ecological niches or changes in lifestyles. I will describe our work in studies contrasting pathogenic and non-pathogenic fungi and efforts to unravel the evolution of multicellularity in fungi comparing unicellular basal fungi with multicellular mushrooms and molds.
The development of tools for data mining and use of fungal genomics is also driving the pace of molecular biology and genetics of fungi. I will highlight new approaches to make this easier and the ways data integration can inform and transform studies of functional biology of fungi.

Japan	04:00 (04:00 AM) on Thursday, June 30
New Zealand	07:00 (07:00 AM) on Thursday, June 30
West Coast USA	12:00 (12:00 PM) on Wednesday, June 29
East Coast USA	15:00 (03:00 PM) on Wednesday, June 29
England	20:00 (08:00 PM) on Wednesday, June 29
France	21:00 (09:00 PM) on Wednesday, June 29

Learn how to connect ahead of time. To hear about upcoming talks, send an email to phyloseminar+subscribe@googlegroups.com or follow @ematsen.
If you can't make it, don't fret-- you can always watch the recording