The intergeneric phylogeny of Lagomorpha had been controversial for a long time before a robust phylogeny was reconstructed based on seven nuclear and mitochondrial DNA sequences. However, skull morphology of several endemic genera remained poorly understood. The morphology of supraorbital processes in Lagomorpha is normally used as a diagnostic characteristic in taxonomy, but whether shape change of this structure parallels its genetic divergence has not been investigated. In this study, we conducted a comparative analysis of the skull morphology of all 12 extant genera using geometric morphometrics. These results indicated that no significant phylogenetic signal is observed in the shape change of the dorsal and ventral views of the cranium as well as in the lateral view of the mandible. The supraorbital processes also show insignificant phylogenetic signal in shape change. Similarly, mapping the centroid size (averaged by genus) of these datasets onto the phylogeny also showed insignificant phylogenetic signal. Aside from homoplasy caused by convergent evolution of skull shape, the massive extinction of lagomorphs after the late Miocene is proposed as one of the main causes for diluting phylogenetic signals in their morphological evolution. Acknowledging the loss of phylogenetic signals in skull shape and supraorbital processes of extant genera sheds new light on the long-standing difficulties for understanding higher-level systematics in Lagomorpha.
Lagomorpha (rabbits, hares, and pikas) is one of the least diversified orders in mammals with only 12 extant genera (Hoffmann and Smith, 2005). Eight of these are monotypic taxa endemic to restricted areas and are poorly known. Among 92 extant species, three are critically endangered, ten are endangered, five are near threatened, five are vulnerable, and 31 others have a high probability for population decrease (The IUCN Red List of Threatened Species. Version 2014.3).