• A comparative genomics multitool for scientific discovery and conservation

      Genereux, Diane P.; Serres, Aitor; Armstrong, Joel; Johnson, Jeremy; Marinescu, Voichita D.; Murén, Eva; Juan, David; Bejerano, Gill; Casewell, Nicholas R.; Chemnick, Leona G.; et al. (2020)
      The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
    • Appendix 4: Annotated bibliography of books, journals, and web sites on captive management.

      Kenyon Barboza, K.; Coates, Linda L.; Kleiman, Devra G. (University of Chicago Press, 2010)
      ...Wild Mammals in Captivity presents the most current thinking and practice in the care and management of wild mammals in zoos and other institutions. In one comprehensive volume, the editors have gathered the most current information from studies of animal behavior; advances in captive breeding; research in physiology, genetics, and nutrition; and new thinking in animal management and welfare.....
    • Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

      Damas, Joana; Hughes, Graham M.; Keough, Kathleen C.; Painter, Corrie A.; Persky, Nicole S.; Corbo, Marco; Hiller, Michael; Koepfli, Klaus-Peter; Pfenning, Andreas R.; Zhao, Huabin; et al. (2020)
      The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
    • Comparative biology of mammalian telomeres: hypotheses on ancestral states and the roles of telomeres in longevity determination: The comparative biology of mammalian telomeres

      Gomes, Nuno M. V.; Ryder, Oliver A.; Houck, Marlys L.; Charter, Suellen J.; Walker, William; Forsyth, Nicholas R.; Austad, Steven N.; Venditti, Chris; Pagel, Mark; Shay, Jerry W.; et al. (2011)
      ...We examined telomeres/telomerase in cultured cells from >?60 mammalian species to place different uses of telomeres in a broad mammalian context. Phylogeny?based statistical analysis reconstructed ancestral states. Our analysis suggested that the ancestral mammalian phenotype included short telomeres (
    • Genome-wide characterization of centromeric satellites from multiple mammalian genomes

      Alkan, C.; Cardone, M. F.; Catacchio, C. R.; Antonacci, F.; O'Brien, S. J.; Ryder, Oliver A.; Purgato, S.; Zoli, M.; Della Valle, G.; Eichler, E. E.; et al. (2011)
      ...We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes....
    • Hunters versus hunted: New perspectives on the energetic costs of survival at the top of the food chain

      Williams, Terrie M.; Jørgensen, Mads Peter-Heide; Pagano, Anthony M.; Bryce, Caleb M. (2020)
      Global biotic and abiotic threats, particularly from pervasive human activities, are progressively pushing large, apex carnivorous mammals into the functional role of mesopredator. Hunters are now becoming the hunted….
    • Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification

      Meredith, R.W.; Janecka, J.E.; Gatesy, J.; Ryder, Oliver A.; Fisher, C.A.; Teeling, E.C.; Goodbla, A.; Eizirik, E.; Simao, T.L.L.; Stadler, T.; et al. (2011)
      ...We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods....
    • Vocal cues to male androgen levels in giant pandas

      Charlton, Benjamin D.; Keating, Jennifer L.; Kersey, David; Rengui, Li; Huang, Yan; Swaisgood, Ronald R. (2011)
      Little is known about the potential of non-human mammal vocalizations to signal information on the hormonal status of the caller. In the current study, we used endocrine data and acoustic analyses to determine whether male giant panda bleats provide reliable information about the caller's current androgen levels. Our results revealed significant relationships between acoustic features of male giant panda bleats and the caller's faecal androgen metabolite concentrations….
    • Winning the genetic lottery: Biasing birth sex ratio results in more grandchildren

      Thorgerson, C.M.; Brady, C.M.; Howard, H.R.; Mason, G.J.; Vicino, Greg A. (2013)
      Population dynamics predicts that on average parents should invest equally in male and female offspring; similarly, the physiology of mammalian sex determination is supposedly stochastic, producing equal numbers of sons and daughters. However, a high quality parent can maximize fitness by biasing their birth sex ratio (SR) to the sex with the greatest potential to disproportionately outperform peers. All SR manipulation theories share a fundamental prediction: grandparents who bias birth SR should produce more grandoffspring via the favored sex. The celebrated examples of biased birth SRs in nature consistent with SR manipulation theories provide compelling circumstantial evidence. However, this prediction has never been directly tested in mammals, primarily because the complete three-generation pedigrees needed to test whether individual favored offspring produce more grandoffspring for the biasing grandparent are essentially impossible to obtain in nature. Three-generation pedigrees were constructed using 90 years of captive breeding records from 198 mammalian species. Male and female grandparents consistently biased their birth SR toward the sex that maximized second-generation success. The most strongly male-biased granddams and grandsires produced respectively 29% and 25% more grandoffspring than non-skewing conspecifics. The sons of the most male-biasing granddams were 2.7 times as fecund as those of granddams with a 50∶50 bias (similar results are seen in grandsires). Daughters of the strongest female-biasing granddams were 1.2 times as fecund as those of non-biasing females (this effect is not seen in grandsires). To our knowledge, these results are the first formal test of the hypothesis that birth SR manipulation is adaptive in mammals in terms of grandchildren produced, showing that SR manipulation can explain biased birth SR in general across mammalian species. These findings also have practical implications: parental control of birth SR has the potential to accelerate genetic loss and risk of extinction within captive populations of endangered species.