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Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to provide species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba towards Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to the Cuban species, N. major rather than N. micrus as previously speculated. Our proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.

Here we provide a compilation of bat distribution records based on neontological and paleontological data, updating the known distribution in Matanzas province, the Isle of Pines, and Central Cuba. From 97 collecting localities in the Province of Matanzas, we report 27 taxa out of the 34 known from the Cuban archipelago; 21 of them are extant while the other six are extinct. Antrozous koopmani and Natalus primus are considered locally extinct in Matanzas, as in most of the archipelago today, but had a wider distribution in the past that lasted until very late in the Holocene. The extinct endemics, Artibeus anthonyi, and Phyllops vetus, are reported for the first time in the province, and the distribution records of Phyllops falcatus, Lasiurus pfeifferi, Lasiurus insularis, Chilonatalus macer, and Eumops ferox are updated and expanded. These records make Matanzas the second richest province in bat diversity of the Cuban archipelago and an area of considerable conservation potential.