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2022 Jun 07;136:. doi: 10.3390/genes13061026.
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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.
Figure 1. Distribution of all nine species of sifaka across Madagascar (range estimates obtained from IUCN, www.iucnredlist.org, accessed on 1 January 2020), with each individual included plotted in the matching color. Note the two clades within P. diadema are shown in light and darker orange shades. Phylogenetic tree generated in MrBayes from the 50 most informative UCEs. For simplicity, the major clades have been labelled as numbers 1–10 and colored the same across all figures.
Figure 2. Divergence dated tree including UCE data generated in BEAST v1.8.4 . Note the star at the root of the tree represents a calibration point as recovered from either ; the 10K primate tree  or , with different age estimates represented in black, blue, and green, respectively. Posterior probabilities are shown to the left of the ages (in millions of years) for all nodes. HPD bars shown were recovered from the  calibrated BEAST analysis.
Figure 3. Complete mitochondrial genome phylogenetic tree showing mitochondrial introgression between P. edwardsi (clade 1) and P. diadema clade 4. All other species were recovered as reciprocally monophyletic. Posterior probabilities shown at nodes.
Figure 4. Ecological niche models for the two Propithecus diadema clades (4 and 5) as well as P. edwardsi. Habitat that is suitable to more than one clade is indicated with hashed lines with the color depicting each clade. (a) The samples used in this study. (b) The full niche models (not restricted to forest cover) for the three groups across eastern Madagascar. (c) Only the forest-limited models for P. diadema clades 4 and 5 and indicates a limited potential contact zone of niche overlap, despite the absence of a physical barrier between these taxa. (d) Only the forest-limited models for P. edwardsi and P. diadema clade 5, with suitable habitat for both species found on either side of the Onive River. Recorded occurrences of these taxa indicate that the Onive may act as a dispersal barrier, despite this potentially suitable habitat. The models in (c,d) are limited to forest cover in 2017, the most recent year available .