• An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile

      Hekkala, Evon; Shirley, Matthew H.; Amato, George; Austin, James D.; Charter, Suellen J.; Thorbjarnarson, John; Vliet, Kent A.; Houck, Marlys L.; Desalle, Rob; Blum, Michael J. (2011)
      ...Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long‐standing arguments over the species’ taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River....
    • Informing species conservation at multiple scales using data collected for marine mammal stock assessments

      Grech, Alana; Sheppard, James; Marsh, Helene (2011)
      Background Conservation planning and the design of marine protected areas (MPAs) requires spatially explicit information on the distribution of ecological features. Most species of marine mammals range over large areas and across multiple planning regions. The spatial distributions of marine mammals are difficult to predict using habitat modelling at ecological scales because of insufficient understanding of their habitat needs, however, relevant information may be available from surveys conducted to inform mandatory stock assessments. Methodology and Results We use a 20-year time series of systematic aerial surveys of dugong (Dugong dugong) abundance to create spatially-explicit models of dugong distribution and relative density at the scale of the coastal waters of northeast Australia (∼136,000 km2). We interpolated the corrected data at the scale of 2 km * 2 km planning units using geostatistics. Planning units were classified as low, medium, high and very high dugong density on the basis of the relative density of dugongs estimated from the models and a frequency analysis. Torres Strait was identified as the most significant dugong habitat in northeast Australia and the most globally significant habitat known for any member of the Order Sirenia. The models are used by local, State and Federal agencies to inform management decisions related to the Indigenous harvest of dugongs, gill-net fisheries and Australia's National Representative System of Marine Protected Areas. Conclusion/Significance In this paper we demonstrate that spatially-explicit population models add value to data collected for stock assessments, provide a robust alternative to predictive habitat distribution models, and inform species conservation at multiple scales.
    • Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix

      Springer, Mark S.; Meredith, Robert W.; Gatesy, John; Emerling, Christopher A.; Park, Jong; Rabosky, Daniel L.; Stadler, Tanja; Steiner, Cynthia C.; Ryder, Oliver A.; Janečka, Jan E.; et al. (2012)
      Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.
    • Molecular systematics of eastern North American Phalangodidae (Arachnida: Opiliones: Laniatores), demonstrating convergent morphological evolution in caves

      Hedin, Marshal; Thomas, Steven M.; (2010)
      The phalangodid harvestmen (Opiliones: Laniatores) fauna of the southeastern United States has remained obscure since original descriptions of many genera and species over 60 years ago. The obscurity of this interesting group is pervasive, with uncertainty regarding basic systematic information such as generic limits, species limits, and geographic distributions....
    • Patterns of genetic partitioning and gene flow in the endangered San Bernardino kangaroo rat (Dipodomys merriami parvus) and implications for conservation management

      Hendricks, Sarah; Navarro, Asako Y.; Wang, Thea B.; Wilder, Aryn P.; Ryder, Oliver A.; Shier, Debra M. (2020)
      ...We examined the genetic diversity, population structure, and phylogeography of this subspecies using partial mitochrondrial DNA sequencing and microsatellite genotyping. Our study indicates that currently, the three remaining populations seem to be highly fragmented....
    • Sumatran tiger (Panthera tigris sumatrae): A review of conservation status

      Wibisono, Hariyo T.; Pusparini, Wulan; (2010)
      The majority of wild Sumatran tigers are believed to live in 12 Tiger Conservation Landscapes covering approximately 88 000 km2. However, the actual distribution of tigers across Sumatra has never been accurately mapped. Over the past 20 years, conservation efforts focused on the Sumatran tigers have increased, but the population continues to decline as a result of several key threats. To identify the status of the Sumatran tiger distribution across the island, an island-wide questionnaire survey comprised of 35 respondents from various backgrounds was conducted between May and June 2010. The survey found that Sumatran tigers are positively present in 27 habitat patches larger than 250 km2 and possibly present in another 2. In addition, a review on major published studies on the Sumatran tiger was conducted to identify the current conservation status of the Sumatran tiger. Collectively, these studies have identified several key factors that have contributed to the decline of Sumatran tiger populations, including: forest habitat fragmentation and loss, direct killing of tigers and their prey, and the retaliatory killing of tigers due to conflict with villagers. The present paper provides management authorities and the international community with a recent assessment and a base map of the actual distribution of Sumatran tigers as well as a general overview on the current status and possible future conservation challenges of Sumatran tiger management.