The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori. We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus. These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5-18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.biogeography | Callicebus | extinct mammal | island evolution | phylogeny

Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1-200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear datasets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonisation. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents, and possibly the greatest for any mammal lineage.

Abundant fossils of nesophontid lipotyphlan insectivores and capromyid rodents have been collected from late Quaternary deposits on the Cayman Islands, an island group separated by a major marine barrier from other Caribbean landmasses and isolated from anthropogenic impacts until the arrival of Columbus in 1503 CE. These collections have not previously been formally described. Using morphological and ancient DNA approaches, we document three new taxa of extinct endemic terrestrial mammals from this island group: Nesophontes hemicingulus (Grand Cayman and Cayman Brac), Capromys pilorides lewisi (Grand Cayman, Little Cayman, and Cayman Brac), and Geocapromys caymanensis (Grand Cayman and Cayman Brac). Morphometric comparisons with other extinct and living West Indian mammals indicate that the biogeographic origins of all three new taxa are from source populations on Cuba. Ancient DNA data indicate very low sequence divergence of Capromys pilorides lewisi from mainland Cuban C. pilorides (only 0.5% across the entire mitogenome). Using probabilistic analysis of existing and new radiometric dates, we calculate an estimated extinction date of 1700 CE (95% confidence interval = 1632-1774 CE) for the Cayman Brac Capromys population. This result suggests that at least one endemic Cayman terrestrial mammal population survived for well over a century following first European arrival in the Cayman Islands. The West Indies lost nearly all its species-rich late Quaternary land mammal fauna during the late Holocene due to direct or indirect human impacts, and this study provides a new baseline to understand the magnitude of human-caused mammal extinctions during the recent past. FIG. 1. Cayman Islands, showing geographical position and paleontological localities on Grand Cayman, Cayman Brac, and Little Cayman.