The 2017 standalone meeting of the Society of Systematic Biologists included expert-led debates on major issues in molecular systematics. Didn’t make it to Baton Rouge? Don’t worry – Bryan McLean and I report on the main points below, and highlight some of our favorite lightening talks of the day. We will post part two of our SSB summary next week.
In the early years of molecular systematics, there was a lot of focus on how to estimate a gene tree accurately from one or a few loci. After Maddison 1997, we started to expect (and often found) significant variation among gene trees. Now, our focus has shifted to understanding the sources of this variation and accommodating gene tree independence in our phylogenetic reconstructions.
In the phylogenomic era, we may be tempted to think that because we can collect so many data, we can solve all difficult phylogenetic problems. However, it is crucial to keep working to improve theory and methods. For example, while ILS is often accommodated by current models, other sources of gene tree variation (selection, horizontal transfer) are still harder to distinguish. The phylogenetic scale of the question (shallow vs. deep) should also inform models, as the relative importance of each process is somewhat scale-dependent.
Methods that identify gene tree outliers can be help identify patterns that are not consistent with model expectations. Posterior predictive simulations can also identify model inadequacies. Both of these approaches can be used to help us understand underlying biological processes. Still, another major need is in understanding how filtering different classes of outlier gene trees from analyses could bias results.
Put simply, there is a real need in molecular phylogenetics for ongoing theoretical and simulation work, as well as new ways to conceptualize phylogeny. Can we really keep considering phylogenies as bifurcating trees given the complexities of gene flow, horizontal gene transfer, hybridization, etc?
Species delimitation is still a developing field in molecular systematics. (This assumes, of course, that “species” are real things). Broad goals of delimitation are to identify groups, find the relationships among them, and estimate gene flow, migration, and divergence times. On our species delimitation wish list- a method/program that incorporates this multi-step process into one.
Would we feel more confident about delimitation if we thought about it as population delimitation? By a show of hands, many people said no! Delimitation of groups at lower levels is also a challenge.
Delimitation based on genetic signatures alone can get murky. Want less subjectivity? More integrative methods of delimitation such as iBPP (see our thoughts here and here) are attractive because they can incorporate rely on information other than just genes. Just beware of circularity when including other traits (e.g., those that have been previously defined by experts as taxonomically important).
The importance of species delimitation reverberates to higher levels as well. For example, does inaccurate species delimitation affect our other questions of trait evolution, for example? Must we put taxa into “species” bins? Or is a “tip” a “tip”? Luke Harmon thinks that the impacts of these issues on comparative studies are largely unknown.
Regardless of your view on species delimitation, there is no doubt that accurate delimitation is fundamental for conservation. Species are the unit recognized under the Endangered Species Act. Does that mean we should err on the side of delimiting more species? Or would this dilute conservation efforts?
Gustavo Bravo: Higher plumage brightness is associated with exposed habitats in dry regions in antbirds.
Laurel Yohe: Molecular evolution of the Trpc2 gene can predict olfactory morphology in bats.
Paul Hime: A single species hypothesis is rejected for the Hellbender, whose spatial patterns of gene flow and genetic diversity are non-random.
Neotropical bellflowers show repeated evolution of bat and hummingbird pollination, but floral traits show differences in evolutionary mode.
Long-distance migration has evolved multiple times in swallows (Hirundinidae) from an intermediate migrating ancestor.
From the Twittersphere