The final day of the 2015 CBA conference on species delimitation featured another set of very interesting talks.
Sally Potter presented her and colleagues' exome capture pipeline for the study of skinks. Admittedly this was already so specific and applied that one would not expect to walk away with many concrete ideas for one's own work unless one wants to use pretty much the same method, but she also mentioned a species tree method that had so far escaped my attention.
ASTRAL is supposedly very fast for large numbers of loci; it is said to be "improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods". Statistical consistency sounds nice, but when I played around with them for a bit back when those precursor methods didn't really convince me. Still, ASTRAL may be worth a try at some point in the future.
Luciano Beheregaray gave a very densely packed talk about teasing apart biogeographic history and ecological selection in complex tropical ecosystems. His examples were mostly lizards and fishes from South America. There sure are a lot of people working on lizards, or at least that is the feeling you get when a lizard researcher organises the conference...
Lyn Cook then went through three case studies to examine the degree of subjectivity in species delimitation and to what degree reticulation causes problems. Although one of her first slides implied that horizontal gene transfer across larger phylogenetic was going to be one of the issues, all her cases ultimately involved phylogenetically very close groups. They were a completely asexually reproducing scale insect ("no sex for at least two million years"), three species of Butcherbirds showing the signature of past hybridisation during ice ages, and the groundsel species Senecio lautus. I must admit that I do not quite understand the problem in the latter case, as to me everything clearly indicated that it is indeed only one species with several ecotypes.
At any rate, her take home messages were to be explicit about the species concept used in a study, not least because it is a prerequisite for reproducibility, and to ask oneself if it is important to recognise a lineage at the species level. Does it really add to our understanding? Will it really improve conservation management? And so on. She also drew attention to the irony of the most clear-cut cases of "separately evolving lineages" - in many people's minds a very objective criterion - being the ones with the most subjective species limits, because in asexual organisms every individual is its own lineage and you can only draw the line arbitrarily.
I probably learned the most today in Dave Rowell's talk about chromosomal rearrangements leading to cryptic speciation. It seems to be fairly easy for two V-shaped chromosomes with the centromers at the ends to fuse together, and the result is then an X-shaped chromosome with the centromer in the middle. Even more surprisingly, this does not necessarily cause trouble in meiosis, so it will not lead to speciation even if one population has 40 and the other only 20 chromosomes because they all got glued together in twos. However, if two populations of the same species happen to make different fusion pairings, then there is trouble, and any hybrid offspring will be highly sterile, leading to rapid speciation.
The talk was also very enjoyable and humorous: "For the under-thirties..." (proceeds to explain what meiosis is).
The final presentation, apart from a talk for the public that I didn't attend, was by John La Salle of the Atlas of Living Australia, which is of course an indispensable resource for biodiversity research in this country. He focused mostly on the recently released PhyloLink tool that allows the user of ALA to import their own phylogenetic tree and link it to other data, map clades onto the landscape, etc. PhyloLink is an extension of PhyloJIVE, which in turn was developed by a team including my former line manager Joe Miller.