Live from #Evol2016 — Tuesday highlights

The Molecular Ecologist team was all over this year’s Evolution meeting in Austin, Texas.
During our coverage of the meeting, we’ve been previewing presentations we’re excited about and recapping the highlights of each day here on the blog. As the main conference concluded on Tuesday evening, this is our final post in that format. However, you can still find all of the TME contributors on Twitter using the sidebar on the right or compiled in a handy Twitter list here. Additional meeting news and older tweets continue to pile up under the hashtag #Evol2016.
We’ll see everyone next year in the Rose City!


Among the many perks of holding the Evolution Meetings in Austin, this TME contributor was particularly excited to make the pilgrimage to the Texas Chili Parlour bar for Mad Dog Margaritas.

Highlights from Tuesday, June 21
Filepe Barreto “Functional and genomic consequences of mitonuclear coevolution during population divergence in a marine copepod” rRNA and tRNAs interacting with the mitochondrial genome (which ~20% divergent between populations) is under positive selection.

Cathy Newman and Chris Austin “Using sequence capture of UCEs for intraspecific phylogenetics and species delimitation of a large-genome salamander, Plethodon serratus” UCE loci worked well for phylogeography and species delimitation in salamanders despite huge ~20Gb genome size. Data suggested seven isolated populations are each different species.

John McCormack, Eugenia Zarza, Brant Faircloth, Whitney Tsai, Robert Bryson, John Klicka “Testing for hidden histories of gene flow in highland birds using genomic markers” Speciation with gene flow may be the norm rather than the exception.
Brian Moore; Sebastian Hoehna; Michael May; Bruce Rannala; John Huelsenbeck (Tuesday 21 June MR3):
Bayesian analysis of macroevolutionary mixtures (BAMM): A critical appraisal
Brian Moore and colleagues offered a solid, simulation-based appraisal of Bayesian
Analysis of Macroevolutionary Mixtures (a program from the Rabosky lab).
John McCormack; Eugenia Zarza; Brant Faircloth; Whitney Tsai; Robert Bryson; John Klicka (Tuesday 21 June MR5):
Testing for hidden histories of gene flow in highland birds using genomic markers
John talked about his ongoing work with Aphelocoma jays in Mexico, the prevalence and driveres of gene tree discordance in the system, which lays the basis for future comparative phylogeographic studies in this region.

Julia Clarke*; Chad Eliason; Leah Hudson; Hector Garza; Taylor Watts (Tuesday 21 June MR6)
Exceptional preservation and the fossil record of tetrapod integument
Julia talked about her lab’s nice work on evolution of integuments in tetrapods, differences in the preservation potential of hair vs. feathers in the fossil record, and how taphonomy may have influenced our views of hair and feather evolution.
Justin Havird: Expression, selection, and co-evolution in mitonuclear genes — A tide of research on mitonuclear interactions continues to swell, but that doesn’t mean there aren’t a lot of big mysteries left. This talk started to approach one of them: mitochondrial genes involved in mitonuclear interactions are expressed much higher than nuclear genes. This discrepancy might have something to do with differential rates of transcription and translation, meaning mitochondria have to be prepared with proteins since they operate at a slower pace.

Geoffrey Hill: Mitonuclear Ecology — Hill brought an end to the cytonuclear interactions symposium with a review of this hypotheses relating mitonuclear compatibility and sexual selection. Buoyed by the recent discovery of the genes that control red pigmentation in bird feathers, Hill explained that the pressures on females to insure their offsprings have optimally-matched mitotypes might play a big role in male phenotypes.
Brant Faircloth: “Able was I ere I saw assembly errors.” Faircloth’s talk focused on how the combined effects of sequencing and assembly errors influence downstream phylogenetic analysis. Using simulations, he showed sequencing error could lead to concerning numbers of incorrect bases in the final assemblies of three popular programs — trinity, abyss, and velvet. (If you’re looking to make a choice based on this metric, abyss arguably performed the best). However, even the assemblies with the highest levels of error still resulted in phylogenetic trees with identical topology and similar branch lengths as the “error-free” dataset he used as a comparison.  My take away: we should be worried enough to start considering sequencing and assembly error more seriously, but not that worried, as for whatever reason it doesn’t seem to influence the overall conclusions of phylogenomics studies.

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