We report a mid- to late-Holocene, non-cultural vertebrate assemblage from Garden Cave (site EL-229), Eleuthera Island, The Bahamas, with 2450 fossils representing 26 species. The chronology is based on accelerator mass spectrometer (AMS) radiocarbon (14C) dates determined directly on individual bones of the hutia ( Geocapromys ingrahami), an extirpated species of rodent that dominates the bone assemblage at Garden Cave. Four AMS 14C dates from our excavation range from 1340 to 1280 cal. BP (surface of the site) to 4860 to 4830 cal. BP with depth. A hutia bone lying on the surface from elsewhere in the cave dated to 450 to 290 cal. BP, which is roughly the time of European and African contact on Eleuthera. Other extirpated species from Garden Cave are tortoise ( Chelonoidis sp.), rock iguana ( Cyclura sp.), skink ( Mabuya sp.), parrot ( Amazona leucocephala), crow ( Corvus nasicus), and southeastern myotis ( Myotis austroriparius). Each of these species may have survived on Eleuthera until sometime after the initial human occupation of the island (~1000 cal. BP), although we have direct AMS 14C dates for only the hutia. During the time of fossil deposition in Garden Cave, sea levels were approaching that of today, yet land areas were considerably larger than now, connecting Eleuthera to New Providence, and potentially to Exuma as well. Such relatively recent connections are important in explaining past and present distributions of terrestrial plants and animals.

We report 95 vertebrate taxa (13 fishes, 11 reptiles, 63 birds, 8 mammals) from late Pleistocene bone deposits in Sawmill Sink, Abaco, The Bahamas. The >5,000 fossils were recovered by scuba divers on ledges at depths of 27-35 m below sea level. Of the 95 species, 39 (41%) no longer occur on Abaco (4 reptiles, 31 birds, 4 mammals). We estimate that 17 of the 39 losses (all of them birds) are linked to changes during the Pleistocene-Holocene Transition (PHT) (∼ 15-9 ka) in climate (becoming more warm and moist), habitat (expansion of broadleaf forest at the expense of pine woodland), sea level (rising from -80 m to nearly modern levels), and island area (receding from ∼ 17,000 km(2) to 1,214 km(2)). The remaining 22 losses likely are related to the presence of humans on Abaco for the past 1,000 y. Thus, the late Holocene arrival of people probably depleted more populations than the dramatic physical and biological changes associated with the PHT.

Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.