Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography.

The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species' boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.

Nuclear and Mitochondrial Phylogenomics of the Sifakas Reveal Cryptic Variation in the Diademed Sifaka.

The most comprehensive phylogenomic reconstruction to date was generated on all nominal taxa within the lemur genus Propithecus. Over 200 wild-caught individuals were included in this study to evaluate the intra and interspecific relationships across this genus. Ultraconserved Elements (UCEs) resulted in well-supported phylogenomic trees. Complete mitochondrial genomes (CMGs) largely agreed with the UCEs, except where a mitochondrial introgression was detected between one clade of the diademed sifaka (Propithecus diadema) and the Milne-Edwards sifaka (P. edwardsi). Additionally, the crowned (P. coronatus) and Von der Decken's (P. deckeni) sifakas belonged to a single admixed lineage from UCEs. Further sampling across these two species is warranted to determine if our sampling represents a hybrid zone. P. diadema recovered two well-supported clades, which were dated and estimated as being ancient as the split between the Perrier's (P. perrierii) and silky (P. candidus) sifakas. The reconstructed demographic history of the two clades also varied over time. We then modeled the modern ecological niches of the two cryptic P. diadema clades and found that they were significantly diverged (p < 0.01). These ecological differences result in a very limited zone of geographic overlap for the P. diadema clades (<60 km2). Niche models also revealed that the Onive River acts as a potential barrier to dispersal between P. diadema and P. edwardsi. Further taxonomic work is required on P. diadema to determine if its taxonomic status should be revised. This first genomic evaluation of the genus resolved the relationships between the taxa and the recovered cryptic diversity within one species.

Complete sequence and gene organization of the mitochondrial genome for Hubbard's sportive lemur (Lepilemur hubbardorum).

The complete mitochondrial DNA (mtDNA) genome of Hubbard's or Zombitse sportive lemur (Lepilemur hubbardorum) was generated by polymerase chain reaction (PCR) amplification, primer-walking sequencing and fragment cloning. Comparative analyses of Hubbard's sportive lemur were conducted with available complete mitochondrial genome sequences from eight other lemur species. The mitochondrial genome of Hubbard's sportive lemur is 16,854 base pairs (bp) and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. Three rare start codons were found, in which GTG is the start codon for the ATPase 6 subunit gene (ATP), ATC for the NADH dehydrogenase (ND) 2 subunit gene, and ATT for the ND5 subunit gene. In the control region, sequence analysis found one repetitive unit between conserved sequence blocks (CSB)-1 and CSB-2 for L. hubbardorum. Comparative analysis of eight other lemur species showed different repetitive units between and outside of these two blocks. According to the phylogenetic analysis of the 12 heavy-strand encoded protein-coding genes, all nine lemur species representative of four lemuriformes families were monophyletic. This template and the newly designed primers described in this study will allow scientists to generate comparative sequences for all sportive lemurs to validate phylogenetic discrepancies in the genus Lepilemur and to evaluate evolutionary and biogeographic models.