Sackler Institute of Comparative Genomics

New York City, NY, United States

Sackler Institute of Comparative Genomics

New York City, NY, United States
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Vynne C.,University of Washington | Vynne C.,World Wildlife Fund | Skalski J.R.,University of Washington | Machado R.B.,Conservation International Brazil | And 8 more authors.
Conservation Biology | Year: 2011

Most protected areas are too small to sustain populations of wide-ranging mammals; thus, identification and conservation of high-quality habitat for those animals outside parks is often a high priority, particularly for regions where extensive land conversion is occurring. This is the case in the vicinity of Emas National Park, a small protected area in the Brazilian Cerrado. Over the last 40 years the native vegetation surrounding the park has been converted to agriculture, but the region still supports virtually all of the animals native to the area. We determined the effectiveness of scat-detection dogs in detecting presence of five species of mammals threatened with extinction by habitat loss: maned wolf (Chrysocyon brachyurus), puma (Puma concolor), jaguar (Panthera onca), giant anteater (Myrmecophaga tridactyla), and giant armadillo (Priodontes maximus). The probability of scat detection varied among the five species and among survey quadrats of different size, but was consistent across team, season, and year. The probability of occurrence, determined from the presence of scat, in a randomly selected site within the study area ranged from 0.14 for jaguars, which occur primarily in the forested areas of the park, to 0.91 for maned wolves, the most widely distributed species in our study area. Most occurrences of giant armadillos in the park were in open grasslands, but in the agricultural matrix they tended to occur in riparian woodlands. At least one target species occurred in every survey quadrat, and giant armadillos, jaguars, and maned wolves were more likely to be present in quadrats located inside than outside the park. The effort required for detection of scats was highest for the two felids. We were able to detect the presence for each of five wide-ranging species inside and outside the park and to assign occurrence probabilities to specific survey sites. Thus, scat dogs provide an effective survey tool for rare species even when accurate detection likelihoods are required. We believe the way we used scat-detection dogs to determine the presence of species can be applied to the detection of other mammalian species in other ecosystems. © 2010 Society for Conservation Biology.


News Article | December 14, 2016
Site: www.eurekalert.org

New York (Dec.14, 2016) - Marine scientists have discovered that two species of dolphin in the waters off Bangladesh are genetically distinct from those in other regions of the Indian and western Pacific Oceans, a finding that supports a growing body of evidence that the Bay of Bengal harbors conditions that drive the evolution of new life forms, according to a new study by the American Museum of Natural History(AMNH), WCS (Wildlife Conservation Society), and the cE3c - Centre for Ecology, Evolution and Environmental Changes (Universidade de Lisboa). In the comparative study using DNA collected from both Indo-Pacific humpback dolphins (Sousa chinensis) and Indo-Pacific bottlenose dolphins (Tursiops aduncus) and data from previous genetic studies, the authors of a newly published paper in Conservation Genetics have found that both populations of both species are distinct from populations in other parts of the Indian Ocean and western Pacific. This discovery follows the recent description of a possible new species of "river shark" in the same waters. The authors of the study titled "Oceanic drivers of population differentiation in Indo-Pacific bottlenose (Tursiops aduncus) and humpback (Sousa spp.) dolphins of the northern Bay of Bengal" are: Dr. Ana R. Amaral of cE3c, Universidade de Lisboa, Portugal and AMNH's Sackler Institute of Comparative Genomics; Brian D. Smith and Rubaiyat M. Mansur of WCS; and Dr. Howard C. Rosenbaum of WCS and affiliated with AMNH. "Our findings indicate that there is a connection between the presence of these distinct populations of dolphins and the unique oceanic habitat that is found in the Bay of Bengal," said Amaral, the lead author of the study. "The combination of a biologically rich yet isolated seascape could be driving speciation, or the emergence of new species." Located in the northern Indian Ocean, the Bay of Bengal receives vast amounts of freshwater and organic matter from the Meghna, Brahmaputra, and Ganges Rivers; the confluence also supports the world's largest mangrove forest. In deeper waters, a submarine canyon called the Swatch-of-No-Ground (SoNG) recycles nutrients through upwelling, all of which creates a biologically productive coastal region with a complex interchange of currents that creates conditions for species to become isolated from other parts of the Indian Ocean. During the study, researchers collected skin samples from 32 coastal Indo-Pacific and humpback dolphins. Genetic sequences were then extracted from the samples for comparison with previously published sequences for both species. The researchers found both dolphins to be genetically discrete from nearby populations, a tantalizing result that the authors say merits further investigation. "The discovery of genetically distinct dolphin populations helps us to expand the body of knowledge of how these dolphin species have changed over time," said Howard Rosenbaum, Director of WCS's Ocean Giants Program who added that "these results have significant implications for identifying unique marine mammal populations, which in turn have important conservation implications for safeguarding the long-term biodiversity in this region." "This is great news for Bangladesh," said Rubaiyat Mansur, Principal Researcher for WCS's Bangladesh Program. "Despite the challenges of wildlife conservation in our country, we take great pride in protecting our wildlife as evidenced by the recent declaration of Bangladesh's first marine protected area in the Swatch-of-No-Ground submarine canyon and adjacent estuarine waters." The Indo-Pacific bottlenose dolphin that ranges between the Indian and western Pacific Oceans is a smaller version of the better-known common bottlenose dolphin (Tursiops truncatus). The waters of the Bay of Bengal's SoNG canyon are home to one of the world's largest populations of Indo-Pacific bottlenose dolphins. Humpback dolphins in particular have been a topic of much debate among taxonomists due to the variations in appearance and genetics of animals that inhabit coastal waters from western Africa to the western Pacific. The genus Sousa now contains four species, one of which -- the Australian humpback dolphin (Sousa sahulensis) -- was recently designated as a separate species after a number of comparative studies combining morphology and genetic markers. While the humpback dolphins in the Bay of Bengal are currently considered as a population of Indo-Pacific humpback dolphins (Sousa chinensis), the population occurs right in between the known ranges of the Indo-Pacific species and the Indian Ocean humpback dolphin (Sousa plumbea). This study's comparison of mitochondrial DNA across populations reveals a closer connection between the Bay of Bengal's humpback dolphins and the more distantly located Australian humpback dolphin. Both dolphin species are threatened by entanglement and death in gill nets; many of the individual dolphins photographed by researchers bear the scars of fishing gear entanglement while these are only the ones that escaped. "The results of this study raise important questions about the exact conservation status of these small cetaceans of the Bay of Bengal," said Brian Smith, a co-author on the study and Director of WCS's Asian Freshwater and Coastal Cetacean Program. "Our findings highlight areas for further inquiry as well as the importance of protecting these marine mammals from the threat of fishing entanglement." This work was supported by the IWC Small Cetacean Conservation Fund and Ocean Park Conservation Foundation, Hong Kong. MISSION: WCS saves wildlife and wild places worldwide through science, conservation action, education, and inspiring people to value nature. To achieve our mission, WCS, based at the Bronx Zoo, harnesses the power of its Global Conservation Program in nearly 60 nations and in all the world's oceans and its five wildlife parks in New York City, visited by 4 million people annually. WCS combines its expertise in the field, zoos, and aquarium to achieve its conservation mission. Visit: newsroom.wcs.org Follow: @WCSNewsroom. For more information: 347-840-1242.


In the comparative study using DNA collected from both Indo-Pacific humpback dolphins (Sousa chinensis) and Indo-Pacific bottlenose dolphins (Tursiops aduncus) and data from previous genetic studies, the authors of a newly published paper in Conservation Genetics have found that both populations of both species are distinct from populations in other parts of the Indian Ocean and western Pacific. This discovery follows the recent description of a possible new species of "river shark" in the same waters. The authors of the study titled "Oceanic drivers of population differentiation in Indo-Pacific bottlenose (Tursiops aduncus) and humpback (Sousa spp.) dolphins of the northern Bay of Bengal" are: Dr. Ana R. Amaral of cE3c, Universidade de Lisboa, Portugal and AMNH's Sackler Institute of Comparative Genomics; Brian D. Smith and Rubaiyat M. Mansur of WCS; and Dr. Howard C. Rosenbaum of WCS and affiliated with AMNH. "Our findings indicate that there is a connection between the presence of these distinct populations of dolphins and the unique oceanic habitat that is found in the Bay of Bengal," said Amaral, the lead author of the study. "The combination of a biologically rich yet isolated seascape could be driving speciation, or the emergence of new species." Located in the northern Indian Ocean, the Bay of Bengal receives vast amounts of freshwater and organic matter from the Meghna, Brahmaputra, and Ganges Rivers; the confluence also supports the world's largest mangrove forest. In deeper waters, a submarine canyon called the Swatch-of-No-Ground (SoNG) recycles nutrients through upwelling, all of which creates a biologically productive coastal region with a complex interchange of currents that creates conditions for species to become isolated from other parts of the Indian Ocean. During the study, researchers collected skin samples from 32 coastal Indo-Pacific and humpback dolphins. Genetic sequences were then extracted from the samples for comparison with previously published sequences for both species. The researchers found both dolphins to be genetically discrete from nearby populations, a tantalizing result that the authors say merits further investigation. "The discovery of genetically distinct dolphin populations helps us to expand the body of knowledge of how these dolphin species have changed over time," said Howard Rosenbaum, Director of WCS's Ocean Giants Program who added that "these results have significant implications for identifying unique marine mammal populations, which in turn have important conservation implications for safeguarding the long-term biodiversity in this region." "This is great news for Bangladesh," said Rubaiyat Mansur, Principal Researcher for WCS's Bangladesh Program. "Despite the challenges of wildlife conservation in our country, we take great pride in protecting our wildlife as evidenced by the recent declaration of Bangladesh's first marine protected area in the Swatch-of-No-Ground submarine canyon and adjacent estuarine waters." The Indo-Pacific bottlenose dolphin that ranges between the Indian and western Pacific Oceans is a smaller version of the better-known common bottlenose dolphin (Tursiops truncatus). The waters of the Bay of Bengal's SoNG canyon are home to one of the world's largest populations of Indo-Pacific bottlenose dolphins. Humpback dolphins in particular have been a topic of much debate among taxonomists due to the variations in appearance and genetics of animals that inhabit coastal waters from western Africa to the western Pacific. The genus Sousa now contains four species, one of which—the Australian humpback dolphin (Sousa sahulensis)—was recently designated as a separate species after a number of comparative studies combining morphology and genetic markers. While the humpback dolphins in the Bay of Bengal are currently considered as a population of Indo-Pacific humpback dolphins (Sousa chinensis), the population occurs right in between the known ranges of the Indo-Pacific species and the Indian Ocean humpback dolphin (Sousa plumbea). This study's comparison of mitochondrial DNA across populations reveals a closer connection between the Bay of Bengal's humpback dolphins and the more distantly located Australian humpback dolphin. Both dolphin species are threatened by entanglement and death in gill nets; many of the individual dolphins photographed by researchers bear the scars of fishing gear entanglement while these are only the ones that escaped. "The results of this study raise important questions about the exact conservation status of these small cetaceans of the Bay of Bengal," said Brian Smith, a co-author on the study and Director of WCS's Asian Freshwater and Coastal Cetacean Program. "Our findings highlight areas for further inquiry as well as the importance of protecting these marine mammals from the threat of fishing entanglement." Explore further: Scientists find that dolphin in Australian waters is a new species More information: Ana R. Amaral et al, Oceanographic drivers of population differentiation in Indo-Pacific bottlenose (Tursiops aduncus) and humpback (Sousa spp.) dolphins of the northern Bay of Bengal, Conservation Genetics (2016). DOI: 10.1007/s10592-016-0913-7


Wolfe J.M.,Yale University | Wolfe J.M.,Sackler Institute of Comparative Genomics | Hegna T.A.,Yale University | Hegna T.A.,Western Illinois University
Cladistics | Year: 2014

The study of ontogeny as an integral part of understanding the pattern of evolution dates back over 200 years, but only recently have ontogenetic data been explicitly incorporated into phylogenetic analyses. Pancrustaceans undergo radical ontogenetic changes. The spectacular upper Cambrian "Orsten" fauna preserves phosphatized fossil larvae, including putative crown-group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages remains a source of debate, causing spurious placements in a traditional morphological analysis. We introduce a new coding method where each semaphoront (discrete larval or adult stage) is considered an operational taxonomic unit. This avoids a priori assumptions of heterochrony. Characters and their states are defined to identify changes in morphology throughout ontogeny. Phylogenetic analyses of semaphoronts produced possible relationships of each Orsten fossil to the crown-group clade expected from morphology shared with extant larvae. Bredocaris is a member of the stem lineage of Thecostraca or (Thecostraca + Copepoda), and Yicaris and Rehbachiella are probably members of the stem lineage of Cephalocarida. These placements rely directly on comparisons between extant and fossil larval character states. The position of Phosphatocopina remains unresolved. This method may have broader applications to other phylogenetic problems which may rely on ontogenetically variable homology statements. © The Willi Hennig Society 2013.


Siddall M.E.,Sackler Institute of Comparative Genomics | Min G.-S.,Inha University | Fontanella F.M.,Brigham Young University | Phillips A.J.,Sackler Institute of Comparative Genomics | And 2 more authors.
Parasitology | Year: 2011

The evolutionary history of leeches is employed as a general framework for understanding more than merely the systematics of this charismatic group of annelid worms, and serves as a basis for understanding blood-feeding related correlates ranging from the specifics of gut-associated bacterial symbionts to salivary anticoagulant peptides. A variety of medicinal leech families were examined for intraluminal crop bacterial symbionts. Species of Aeromonas and Bacteroidetes were characterized with DNA gyrase B and 16S rDNA. Bacteroidetes isolates were found to be much more phylogenetically diverse and suggested stronger evidence of phylogenetic correlation than the gammaproteobacteria. Patterns that look like co-speciation with limited taxon sampling do not in the full context of phylogeny. Bioactive compounds that are expressed as gene products, like those in leech salivary glands, have passed the test of evolutionary selection. We produced and bioinformatically mined salivary gland EST libraries across medicinal leech lineages to experimentally and statistically evaluate whether evolutionary selection on peptides can identify structure-function activities of known therapeutically relevant bioactive compounds like antithrombin, hirudin and antistasin. The combined information content of a well corroborated leech phylogeny and broad taxonomic coverage of expressed proteins leads to a rich understanding of evolution and function in leech history. Copyright © Cambridge University Press 2011.

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