Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes

Abstract

Many authors have claimed that short branches in the Tree of Life will be very difficult to resolve with strong support, even with the large multilocus data sets now made possible by genomic resources. Short branches may be especially problematic because the underlying gene trees are expected to have discordant phylogenetic histories when the time between branching events is very short. Although there are many examples of short branches that are difficult to resolve, surprisingly, no empirical studies have systematically examined the relationships between branch lengths, branch support, and congruence among genes. Here, we examine these fundamental relationships quantitatively using a data set of 20 nuclear loci for 50 species of snakes (representing most traditionally recognized families). A combined maximum likelihood analysis of the 20 loci gives strong support for 69% of the nodes, but many remain weakly supported, with bootstrap values for 20% ranging from 21% to 66%. For the combined-data tree, we find significant correlations between the length of a branch, levels of bootstrap support, and the proportion of genes that are congruent with that branch in the separate analyses of each gene. We also find that strongly supported conflicts between gene trees over the resolution of individual branches are common (roughly 35% of clades), especially for shorter branches. Overall, our results support the hypothesis that short branches may be very difficult to confidently resolve, even with large, multilocus data sets. Nevertheless, our study provides strong support for many clades, including several that were controversial or poorly resolved in previous studies of snake phylogeny.

Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny

“…of GenBankReferencesCyt.bC‐mosRag‐1 Afronatrix anoscopus ROM19842Liberia AF420073 AF471123 EU402832 Lawson et al., 2005, de Queiroz, Lawson, and Lemos‐Espinal 2002, and Wiens et al. (2008) Amphiesma stolatum _1HT0548China LC325319 LC325765 –This study Amphiesma stolatum _2HT0798Sri Lanka LC325347 LC325793 LC326030 This study Amphiesma stolatum _3GP2213China KJ685693 KJ685643 KJ685585 Guo et al. (2014) Aspidura guentheri RAP0437Sri Lanka KC347472 KC347380 KC347418 Pyron, Kandambi et al.…”

Diversification rates and species richness across the Tree of Life

“…Branch lengths (e.g. clade ages) may be more important than topology for comparative analyses, and may remain similar even as topologies change (especially as most topological uncertainty may be associated with short branch lengths [45,46]). However, non-monophyly of clades might influence some results.…”

Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes

“…To provide a phylogenetic perspective on the evolution of elevated TTX resistance in snakes and to aid in our interpretation of Na v 1.4 sequence data, we collected TTX-resistance data from a diverse sample of colubroid snakes. We collected data from 16 snake species (n = 116 individuals) representing most of the major colubroid lineages (57,58) and from one lizard outgroup taxon (n = 5). We augmented these data with results from some of our other work (19,20,42,59) to provide the most complete picture of TTX resistance in squamate reptiles to date (29 species; n = 424) (Fig.…”