Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics

Abstract

The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multilocus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multilocus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as operational taxonomic units, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.

Not as Ubiquitous as We Thought: Taxonomic Crypsis, Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

“…Due to the increasing awareness that the sole use of concatenated sequence data for phylogenetic analyses can produce misleading results due to gene tree/species tree discordance [58], we compared the results of standard gene concatenation with those of Bayesian Concordance Analyses (BCA, [36]) and Bayesian Inference of Species Trees [37]. The primary concordance tree obtained from the BCA was similar to the topology obtained in the phylogenetic analyses of the concatenated data set (Figure 3A).…”

Limited geographic variation in the acoustic structure of and responses to adult male alarm barks of African green monkeys

“…In contrast, the alarm calls of western grey and eastern rufous mouse lemurs ( Microcebus murinus and M. rufus ), despite diverging 6.7–7.3 MYA (Weisrock et al 2012), do not differ (Zimmermann et al 2000). One explanation for these differences could be that African green monkey barks, similar to the loud calls of leaf monkeys and crested gibbons, also play a role outside of alarm contexts (Struhsaker 1967), and they may therefore be less subjected to stabilising selection than the more stimulus-specific mouse lemur alarms.…”

A multilocus phylogeny reveals deep lineages within African galagids (Primates: Galagidae)

“…We restricted the analysis to 16 taxa because gene tree-species tree analyses are computationally intensive and a larger dataset could have made it difficult or impossible to reach proper convergence among repeated analyses [60,61,119]. Taxon coverage for individual genes varied from 81.3% (13 out of 16 taxa for ABCA1) to 100% (average 94.7%) (see Additional file 7: Table S7a).…”

“…Coalescence methods have recently been applied to primate phylogenies [60-64], and are likely to provide a more realistic picture of the primate tree [62,65]. Hence, as a second step, we applied a coalescence-based species tree approach to phylogenetic inference within galagids, and compared our results to those obtained from concatenated analyses.…”