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

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, longbranch 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. Includes supplementary materials

Tammar wallabies (Macropus eugenii) associate safety with higher levels of nocturnal illumination

Moonlight is commonly reported to increase the time nocturnal animals allocate to antipredator vigilance and to affect space use patterns because predation risk increases as a function of light intensity. The majority of studies reporting moon-light effects have been conducted on small-body sized mammals which are relatively vulnerable to a variety of predators. Moonlight effects were studied experimentally on a mid-sized mammal, the tammar wallaby (Macropus eugenii), a macropodid marsupial. Four groups of six adult female wallabies were observed for 6 days during each of three moon phases (no moon, quarter moon and full moon). In addition to natural illumination, wallabies were exposed to 2 days each of three artificial light treatments (no light, red light, white light) during each moon phase treatment. Subjects were videotaped at night with an image intensifier affixed to a video camera. Time budgets were calculated from the video record, and later analyzed in a repeated-measures factorial ANOVA. There was no effect of natural moonlight on time allocation, suggesting that wallabies had no endogenous cycle associated with moonlight. There were effects of artificial illumination and of the experimental group on time allocation. Wallabies tended to forage more and allocate less time to antipredator vigilance under the two light treatments, suggesting that, unlike previous studies on a variety of other taxa, they associated safety with increased illumination. We speculate that differences among groups might reflect the different seasons over which wallabies were studied. Results suggest that the nocturnally active tammar wallaby exercises caution in the dark.14 page(s

Individual Gene Trees

Bayesian majority-rule consensus trees reconstructed for the 12 individual nuclear loci and the concatenated mitochondrial loci. Trees are presented as phylograms with branch lengths representing the average number of substitutions per site. Numbers on branches represent posterior probabilities

Pruning example

This is the R script used to prune alleles from the sequence data sets and the corresponding tips in the posterior distribution of trees. Example files for one gene are included along with a "Read me" file with a few more snippets of information

Individual Gene Alignments

A compressed file containing the 12 nuclear and one mitochondrial data sets. Each gene is aligned as used in the original study and is presented in NEXUS format