Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs

Abstract

Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships poorly supported or entirely unresolved. We used genomic resources to develop 11 novel markers from nine chromosomes, representing approximately 9 kb of nuclear sequence data. In combination with previously published nuclear and mitochondrial loci, this yields a data set of more than 16 kb and adds approximately 275 kb of DNA sequence to current databases. Our phylogenetic analyses confirm hypotheses of lemuriform monophyly and provide robust resolution of the phylogenetic relationships among the five lemuriform families. We verify that the genus Daubentonia is the sister lineage to all other lemurs. The Cheirogaleidae and Lepilemuridae are sister taxa and together form the sister lineage to the Indriidae; this clade is the sister lineage to the Lemuridae. Divergence time estimates indicate that lemurs are an ancient group, with their initial diversification occurring around the Cretaceous-Tertiary boundary. Given the power of this data set to resolve branches in a notoriously problematic area of primate phylogeny, we anticipate that our phylogenomic toolkit will be of value to other studies of primate phylogeny and diversification. Moreover, the methods applied will be broadly applicable to other taxonomic groups where phylogenetic relationships have been notoriously difficult to resolve.

Figure 1.

Lemur Bayesian consensus phylogram using 18 nuclear loci combined. This phylogram is based on the combined posterior distribution of four independent analyses of the combined and partitioned nuclear data sets. The topology is identical to those resolved using maximum parsimony (MP) and maximum likelihood (ML). Nodes with strong measures of branch support (posterior probabilities = 1.0, MP bootstrap >90%, ML >90%) are marked with filled black circles. Branch support values are indicated in Table 3. Open vertical boxes span the two infraorders of strepsirrhine primates. Shaded boxes encompass family-level taxonomic groups.

Figure 2.

Bayesian primary concordance tree. The Bayesian primary concordance tree is shown, resulting from analyses of 13 nuclear loci, using the program BUCKy (Larget 2006). Numbers on branches represent the average concordance factor. The 95% confidence intervals that are not exclusively 1.0 are included in parentheses. Results are identical across analyses using α priors of 0.1, 1, and 10. Loci not used in this analysis are listed in the Supplementary material.

Figure 3.

Divergence time estimates for the strepsirrhine lineages. An ultrametric tree with divergence time estimates resulting from the combined posterior distribution of four independent BEAST analyses (see Methods) of the combined nuclear data set. The results are based on prior date estimates of (1) the 6 Mya (5–7 Mya) split between Homo sapiens and Pan troglodytes (Kumar et al. 2005) and (2) the 40 Mya (38–42 Mya) split between the Lorisidae and Galagidae (Seiffert et al. 2003). Shaded gray boxes and numbers within brackets span the 95% highest posterior density of divergence time estimates. The scale bar is divided up by time (in millions of years before present) according to the Cretaceous, Tertiary, and Quaternary periods. The Tertiary period is shown according to epochs (Pa indicates Paleocene; Eo, Eocene; Ol, Oligocene; Mi, Miocene; Pl, Pliocene). Full details of time estimates from all BEAST analyses are presented in Table 4.