Using Ultraconserved Elements to Unravel Lagomorph Phylogenetic Relationships
Portions of this work were undertaken under the auspices of NSF grant DEB–0616305 to L.A. Ruedas, who also thanks D. Lunde and A. L. Gardner (USNM) and R. Portela Míguez (MNH London) for access to specimens whose dentitions were illustrated. Support to conclude this manuscript came from UNAM-DGAPA-PAPIIT (Project IN105721).
Journal of Mammalian Evolution
Lagomorpha (lagomorphs), the order of mammals including pikas, hares, and rabbits, is distributed on all continents. The order currently is hypothesized to comprise 12 genera and 108 species, split into two families: Ochotonidae (pikas) and Leporidae (rabbits and hares). Molecular and morphological attempts have been undertaken to resolve the phylogeny of lagomorphs, although chronological relationships are still to be established. The aim of this research was to unravel lagomorph phylogeny using ultraconserved elements. We focused on Romerolagus, in light of its largely unknown phylogenetic relationships and sparse fossil record, to assess times of divergence for the genus. We obtained samples from at least one species in each of 11 genera (except Caprolagus) comprising the order and captured and sequenced ultraconserved elements (UCEs). A Maximum-Likelihood phylogenetic analysis was carried out on the 4,195 loci captured, resulting in 59,112 informative sites. We further used BEAST2 v2.6.3 on the CIPRES computing cluster to estimate the timing of cladogenesis in lagomorph evolution. Our results confirm that lagomorphs and rodents split about 65 million years ago. The former further split into its constituent families, Leporidae and Ochotonidae, about 60 million years ago. Pronolagus rupestris and Nesolagus timminsi were retrieved as basal sister taxa; the most recent common ancestor of that clade and remaining leporids was estimated to have existed about 47 million years ago. Romerolagus diazi is sister to remaining Leporidae excluding Pronolagus and Nesolagus, a topology that generally matches previously published phylogenies, although our results suggest a most recent common ancestor of Romerolagus and remaining ingroup leporids at ca. 4.8 Ma (95% highest posterior density [HPD] interval: 5.9 – 3.8 Ma), with an internal diversification in the Middle to Late Pleistocene (0.9 Ma; 95% HPD 1.8 – 0.2 Ma). Our final results yielded a robust phylogeny with high support values for every clade of the order Lagomorpha and unraveled previously unresolved phylogenetic relationships. In addition, we further conclude that the method we used, UCEs, may serve to complete the entire phylogeny of mammals by using existing museum specimens.
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Cano-Sánchez, E., Rodríguez-Gómez, F., Ruedas, L. A., Oyama, K., León-Paniagua, L., Mastretta-Yanes, A., & Velazquez, A. (2022). Using Ultraconserved Elements to Unravel Lagomorph Phylogenetic Relationships. Journal of Mammalian Evolution, 1-17.