Journal clubs - Page 9

Continuing the discussion of papers related to graph based representation of reference genomes, we will read a paper on the cortex assembler, which actually builds a graph based on sequencing data from multiple samples.

Earlier this year the American Society of Naturalists had a conference where they had a debate (old school!) on the importance of ecological limits to species diversity on large scales. The debate was, according to Trevor Price, not as heated as the one in 1860 with Soapy Sam and Huxley, but nevertheless. The debate ended without a vote and the contributors (Rabosky and Hurlbert vs Harmon and Harrison) were asked to write up their debate contributions as papers to be published in American Naturalist this May. The Harmon paper is not ready, but we will discuss Rabosky annd Hurlbert's contibution which is now out.

This coming week (19/03) we will discuss a paper by Senerchia et al. (Proc. B, 2015) on the role of transposons in hybridization and speciation. 

Please note that the meeting will take place at 13 in the aquarium.

Continuing the discussion of papers related to graph based representation of reference genomes, we will read a more practical paper this week on applying graph-based references to a complex variable region in the human genome.

This weeks Macroevolution journal club will discuss the paper Fast running restricts evolutionary change of the vertebral column in mammals by Frietson Galis and colleagues, published in PNAS 2014.

Continuing the discussion of papers related to graph based representation of reference genomes, we will read a technical paper this week on a new way to look at the structure of reference genomes. Note the time!

This weeks Macroevolution journal club will discuss the paper Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land by Sahney, Benton and Ferry, published in Biology Letters 2010.

This week we will discuss a paper by Foote et al. (Nature Genetics, 2015) on convergent evolution and adaptation to the marine environment in mammals.

One of the upcoming CELS projects is around Graph based representation of reference genomes. In the next episodes of the TGAC journal club, we will therefore discuss several papers around this subject. Some are very technical, some more applied.

This week's Macroevolution journal club deals with 17,208 bodysizes over 542 million years. It's a recent paper from Science by Heim et al.

This week we will discuss a paper by Lamichhaney et al. (Nature, 2015) on the genomic basis of beak divergence in Darwin's finches.

http://www.nature.com/nature/journal/v518/n7539/full/nature14181.html

Please note that the meeting will take place on wednesday the 25^th and not thursday, at 12 as usual!

This week, between the trial lecture and lunch, we'll be discussing a not-so-box-fresh paper from 2012 in Proceedings B by Smith, Lloyd and McGowan titled Phanerozoic marine biodiversity: rock record modelling provides an independent test of large-scale trends

Essentially it compares subsampling (Alroy's SQS) and a much applied bias-correction method to try to reconstruct diversity from fossil data.

Bring a friend and see you Friday.

This week, Andreas Hejnol will be visiting and we will read a perspective paper relevant to his group's reserach, namely "Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough" pulished in PLoSBiology in 2011 by Philippe et al. For background on metazoan phylogenies see Dunn et al. 2014

This Friday 30th of January we discuss a paper on why ungulates that have more friends also have larger brains. "Gregariousness increases brain size in ungulates", by Pérez-Barbería and Gordon (2005). NOTE: Change of time - journal club starts at 11:15!

We read a paper by on bryozoan evolution in the Isthmus of Panama in Evolutionary Ecology 2012 by Jagadeeshan and O'Dea.

This weeks MaEcovo journal club will discuss Charles Nunn and Natalie Cooper's recent paper in Evolution; Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT). Welcome all!

It is time for this year's last TGAC meeting, where we'll discuss the current "Flock of genomes" special issue of Science about 48 newly released bird genomes. With eight research articles and one review, this special issue could keep the TGAC busy for weeks, but for now I propose to focus on the article of Jarvis et al. entitled "Whole-genome analyses resolve early branches in the tree of life of modern birds".

This Friday we'll be enjoying a discussion on Phylogenetic Path Analysis, a chapter from the recently published book Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology, edited by László Zsolt Garamszegi. Whole book is available in the link above, we're gonna talk about Chapter 8: An Introduction to Phylogenetic Path Analysis by Alejandro Gonzalez-Voyer and Achaz von Hardenberg. To keep spirits high there's a number of cartoons in the chapter as well as a footnote stating that pun is intended, so it'll be a fun read.

This week we will read an a bit more ecological paper on hybridization and evolutionary outcomes entitled "Hierarchical behaviour, habitat use and species size differences shape evolutionary outcomes of hybridization in a coral reef fish" by Gainsford and colleagues to be published in Journal of Evolutionary Biology. Please note that the meeting will take place at a different location this time!

This week we'll be learning when species richness should be energy limited (I think the right answer is "sometimes"), and more interestingly; how would we know? An idea and perspective paper by Hurlbert and Stegen in Ecology Letters 2014.

Same time, same place, same people. Welcome!

Bank et al. (2014) looks like the perfect paper for a TGAC discussion: Highly relevant (arguing that selective sweep detection needs to take demography and background selection into account), brand new (currently in press corrected proof), and short (7 pages). So let's have a TGAC meeting on Tuesday, at 1 pm as usual.

This week we'll be discussing a paper by Brockhurst and co-workers in Proceedings B:  Running with the Red Queen: the role of biotic conflicts in evolution

This week we will discuss a paper entitled "Maximum likelihood inference of reticulate evolutionary histories" by Yu and co-authors from PNAS. The paper presents a new method for inferring reticulate evolutionary histories while accounting for incomplete lineage sorting.

In a second edition of TGAC-with-original-authors, we'll discuss Marcussen et al. (2014), a recent Science paper on ancient hybridization of polyploid wheat genomes. The first author Thomas Marcussen will join our discussion, and since Kjetill Jakobsen was involved in the study, we may even have two authors present to answer all our questions. We're switching back to the old meeting time, starting at 1 pm.