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Quaternary paleontological and archaeological evidence often is crucial for uncovering the historical mechanisms shaping modern diversity and distributions. We take an interdisciplinary approach using multiple lines of evidence to understand how past human activity has shaped long-term animal diversity in an island system. Islands afford unique opportunities for such studies given their robust fossil and archaeological records. Herein, we examine the only non-volant terrestrial mammal endemic to the Bahamian Archipelago, the hutia Geocapromys ingrahami. This capromyine rodent once inhabited many islands but is now restricted to several small cays. Radiocarbon dated fossils indicate that hutias were present on the Great Bahama Bank islands before humans arrived at AD ~800-1000; all dates from other islands post-date human arrival. Using ancient DNA from a subset of these fossils, along with modern representatives of Bahamian hutia and related taxa, we develop a fossil-calibrated phylogeny. We found little genetic divergence among individuals from within either the northern or southern Bahamas but discovered a relatively deep North-South divergence (~750 ka). This result, combined with radiocarbon dating and archaeological evidence, reveals a pre-human biogeographic divergence, and an unexpected human role in shaping Bahamian hutia diversity and biogeography across islands.

Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understanding the ecological and evolutionary implications of these losses. While ancient DNA (aDNA) techniques have advanced rapidly in recent decades, aDNA from tropical species, especially birds, has been historically difficult to obtain, leaving a gap in our knowledge of the extinction processes that have influenced current distributions and biodiversity. Here we report the recovery of a nearly complete mitochondrial genome from a 2,500 year old (late Holocene) bone of an extinct species of bird, Caracara creightoni, recovered from the anoxic saltwater environment of a blue hole in the Bahamas. Our results suggest that this extinct species is sister (1.6% sequence divergence) to a clade containing the extant C. cheriway and C. plancus. Caracara creightoni shared a common ancestor with these extant species during the Pleistocene (1.2-0.4 MYA) and presumably survived on Cuba when the Bahamas was mostly underwater during Quaternary interglacial intervals (periods of high sea levels). Tropical blue holes have been collecting animals for thousands of years and will continue to improve our understanding of faunal extinctions and distributions. In particular, new aDNA techniques combined with radiocarbon dating from Holocene Bahamian fossils will allow us to place other extinct (species-level loss) and extirpated (population-level loss) vertebrate taxa in improved phylogenetic, evolutionary, biogeographic, and temporal contexts., (Copyright © 2019 Elsevier Inc. All rights reserved.)

We report Quaternary vertebrate and plant fossils from Sawmill Sink, a "blue hole" (a water-filled sinkhole) on Great Abaco Island, The Bahamas. The fossils are well preserved because of deposition in anoxic salt water. Vertebrate fossils from peat on the talus cone are radiocarbon-dated from approximately 4,200 to 1,000 cal BP (Late Holocene). The peat produced skeletons of two extinct species (tortoise Chelonoidis undescribed sp. and Caracara Caracara creightoni) and two extant species no longer in The Bahamas (Cuban crocodile, Crocodylus rhombifer; and Cooper's or Gundlach's Hawk, Accipiter cooperii or Accipiter gundlachii). A different, inorganic bone deposit on a limestone ledge in Sawmill Sink is a Late Pleistocene owl roost that features lizards (one species), snakes (three species), birds (25 species), and bats (four species). The owl roost fauna includes Rallus undescribed sp. (extinct; the first Bahamian flightless rail) and four other locally extinct species of birds (Cooper's/Gundlach's Hawk, A. cooperii/gundlachii; flicker Colaptes sp.; Cave Swallow, Petrochelidon fulva; and Eastern Meadowlark, Sturnella magna) and mammals (Bahamian hutia, Geocapromys ingrahami; and a bat, Myotis sp.). The exquisitely preserved fossils from Sawmill Sink suggest a grassy pineland as the dominant plant community on Abaco in the Late Pleistocene, with a heavier component of coppice (tropical dry evergreen forest) in the Late Holocene. Important in its own right, this information also will help biologists and government planners to develop conservation programs in The Bahamas that consider long-term ecological and cultural processes.