Divergence and support among slightly suboptimal likelihood gene trees

Contemporary phylogenomic studies frequently incorporate two-step coalescent analyses wherein the first step is to infer individual-gene trees, generally using maximum-likelihood implemented in the popular programs PhyML or RAxML . Four concerns with this approach are that these programs only present a single fully resolved gene tree to the user despite potential for ambiguous support, insufficient phylogenetic signal to fully resolve each gene tree, inexact computer arithmetic affecting the reported likelihood of gene trees, and an exclusive focus on the most likely tree while ignoring trees that are only slightly suboptimal or within the error tolerance. Taken together, these four concerns are sufficient for RAxML and Phy ML users to be suspicious of the resulting (perhaps over-resolved) gene-tree topologies and (perhaps unjustifiably high) bootstrap support for individual clades. In this study, we sought to determine how frequently these concerns apply in practice to contemporary phylogenomic studies that use RAxML for gene-tree inference. We did so by re-analyzing 100 genes from each of ten studies that, taken together, are representative of many empirical phylogenomic studies. Our seven findings are as follows. First, the few search replicates that are frequently applied in phylogenomic studies are generally insufficient to find the optimal gene-tree topology. Second, there is often more topological variation among slightly suboptimal gene trees relative to the best-reported tree than can be safely ignored. Third, the Shimodaira–Hasegawa-like approximate likelihood ratio test is highly effective at identifying dubiously supported clades and outperforms the alternative approaches of relying on bootstrap support or collapsing minimum-length branches. Fourth, the bootstrap can, but rarely does, indicate high support for clades that are not supported amongst slightly suboptimal trees. Fifth, increasing the accuracy by which RA xML optimizes model-parameter values generally has a nominal effect on selection of optimal trees. Sixth, tree searches using the GTRCAT model were generally less effective at finding optimal known trees than those using the GTRGAMMA model. Seventh, choice of gene-tree sampling strategy can affect inferred coalescent branch lengths, species-tree topology and branch support.     

HABITAT SELECTION BY MANATEES IN SARASOTA BAY, FLORIDA

Habitat selection by Florida manatees ( Trichechus manatus latirostris ) is influenced by, among other things, availability of food, thermal, and freshwater resources. However, habitat selection by females with dependent calves may differ from that of other demographic groups with regard to the relative importance of these factors. Additional factors that may influence habitat selection for females with dependent calves include ambient noise, strong currents, or increased foraging requirements. We examined distributional data for manatees from aerial surveys of the coastal waters near Sarasota, Florida, between 1994 and 2004 to determine whether habitat selection by groups of manatees that included calves differed from that of other groups. We characterized groups according to their location within seven habitat types. Enclosed bays not traversed by the Intracoastal Waterway had the highest proportions of groups with calves. Groups with calves used a No Entry refuge (from which almost all human use is barred) to a greater extent than did other groups. Overall, groups with calves exhibited significantly different habitat selection from groups without calves ( P < 0.001, χ²= 43.0, df = 6), but this was not consistent across seasons. During the winter and spring, thermal requirements influenced manatees to such an extent that all demographic groups selected habitat similarly.