First some highlights from talks on phylogenetic reconstruction in general:
1. The species trees have arrived.
2. 5 to 20 'independent' loci analyzed via partitioned analyses in MrBayes or RaxML are the standard for high-end phylogenetic analyses (of non-model groups). Most people were concatenating, but that may be changing (see point 1).
3. Branch lengths are a growing concern in Bayesian phylogenetic analyses. Both Joseph W. Brown (Michigan) & Jeremy M. Brown (UT Austin) showed that our prior assumptions about branch lengths require revision. Joseph Brown gave a nice example of how shifting to more appropriate (i.e., better fitting) assumptions about branch lengths can turn bad trees to good in the case of paleognathus birds.
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