• A demonstration of conservation genomics for threatened species management

      Wright, Belinda R.; Farquharson, Katherine A.; McLennan, Elspeth A.; Belov, Katherine; Hogg, Carolyn J.; Grueber, Catherine E. (2020)
      ... We conducted whole genome sequencing (WGS) of 25 individuals from the captive breeding programme and reduced‐representation sequencing (RRS) of 98 founders of the same programme. A subset of the WGS samples was also sequenced by RRS, allowing us to directly compare genome‐wide heterozygosity with estimates from RRS data. We found good congruence in interindividual variation and gene‐ontology classifications between the two data sets, indicating that our RRS data reflect the genome well....
    • A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert

      Farré, Marta; Li, Qiye; Zhou, Yang; Damas, Joana; Chemnick, Leona G.; Kim, Jaebum; Ryder, Oliver A.; Ma, Jian; Zhang, Guojie; Larkin, Denis M.; et al. (2018)
      Background The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts. Findings Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions. Conclusions Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.
    • A suite of microsatellite markers optimized for amplification of DNA from addax (Addax nasomaculatus) blood preserved on FTA cards: Microsatellites for addax on FTA cards

      Heim, Brett C.; Ivy, Jamie A.; Latch, Emily K. (2012)
      The addax (Addax nasomaculatus) is a critically endangered antelope that is currently maintained in zoos through regional, conservation breeding programs. As for many captive species, incomplete pedigree data currently impedes the ability of addax breeding programs to confidently manage the genetics of captive populations and to select appropriate animals for reintroduction. Molecular markers are often used to improve pedigree resolution, thereby improving the long‐term effectiveness of genetic management....
    • Advances and constraints in somatic embryogenesis of Araucaria angustifolia, Acca sellowiana, and Bactris gasipaes

      Stefenon, Valdir Marcos; Ree, Joseph Francis; Pinheiro, Marcos Vinicius Marques; Goeten, Daniela; Steiner, Neusa; Guerra, Miguel Pedro (2020)
      Somatic embryogenesis (SE) is a useful biotechnological tool to promote the conservation of plant genetic resources. Araucaria angustifolia, Acca sellowiana, and Bactris gasipaes are forest species with recognized ecological, cultural, and economic importance in the subtropical Atlantic Forest and the tropical Amazon Forest…. Here we reviewed and discussed the advancements and continuing constraints in the SE of these species, pointing out the more successful procedures….
    • 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.....
    • Genetic aspects of equids with particular reference to their hybrids

      Benirschke, Kurt; Ryder, Oliver A.; (1985)
      This paper gives a brief review of the cytogenetic knowlege of equine species, the chromosomal errors currently known to exist, and an account of the interspecific hybrids that have served man during the 4500 years of domestication of horse and donkey.
    • Genetic guidelines for maintaining a conservation collection

      Maschinski, Joyce; Havens, Kayri; Font, Jeremie; Kramer, Andrea; Vitt, Pati; Neale, Jennifer Ramp; Guerrant Jr., Edward O.; Edwards, Christine; Steele, Stephanie; Maschinski, Joyce; et al. (Center for Plant ConservationEscondido, California, 2019)
      Give your reintroduced population a good chance for survival by starting with adequate numbers of plants or seeds at the beginning. Determine the source of the plants or seeds. Determine whether the source should consist of seeds or plants from a single population or from mixed populations.
    • Genetic structure of Rhinoceros Rock Iguanas, Cyclura cornuta, in the Dominican Republic, with insights into the impact of captive facilities and the taxonomic status of Cyclura on Mona Island

      Pasachnik, Stesha A.; Colosimo, Giuliano; Carreras-De León, Rosanna; Gerber, Glenn P. (2020)
      …To better understand the population structure of this species, we used a combination of mtDNA and nuclear markers to elucidate the genetic variation of wild populations across 13 sampling regions in the Dominican Republic (DR), as well as neighboring Mona Island, home to a Cyclura population of uncertain taxonomic status…. Our results suggest that the captive facilities may pose a threat to wild populations and increased regulation of these facilities is needed….
    • Impacts of early viability selection on management of inbreeding and genetic diversity in conservation

      Grueber, Catherine E.; Hogg, Carolyn J.; Ivy, Jamie A.; Belov, Katherine (2015)
      Maintaining genetic diversity is a crucial goal of intensive management of threatened species, particularly for those populations that act as sources for translocation or re‐introduction programmes. Most captive genetic management is based on pedigrees and a neutral theory of inheritance, an assumption that may be violated by selective forces operating in captivity. Here, we explore the conservation consequences of early viability selection: differential offspring survival that occurs prior to management or research observations, such as embryo deaths in utero....
    • Implications of different species concepts for conserving biodiversity

      Frankham, Richard; Ballou, Jonathan D.; Dudash, Michele R.; Eldridge, Mark D.B.; Fenster, Charles B.; Lacy, Robert C.; Mendelson, Joseph R.; Porton, Ingrid J.; Ralls, Katherine; Ryder, Oliver A. (2012)
      The ~26 definitions of species often yield different numbers of species and disparate groupings, with financial, legal, biological and conservation implications. Using conservation genetic considerations, we demonstrate that different species concepts have a critical bearing on our ability to conserve species.... Consequently, we conclude that the diagnostic phylogenetic species concept is unsuitable for use in conservation contexts, especially for classifying allopatric populations.
    • Lineage identification and genealogical relationships among captive Galápagos tortoises

      Benavides, Edgar; Russello, Michael; Boyer, Donal; Wiese, Robert J.; Kajdacsi, Brittney; Marquez, Lady; Garrick, Ryan; Caccone, Adalgisa (2012)
      Genetic tools have become a critical complement to traditional approaches for meeting short‐ and long‐term goals of ex situ conservation programs. The San Diego Zoo (SDZ) harbors a collection of wild‐born and captive‐born Galápagos giant tortoises (n = 22) of uncertain species designation and unknown genealogical relationships. Here, we used mitochondrial DNA haplotypic data and nuclear microsatellite genotypic data to identify the evolutionary lineage of wild‐born and captive‐born tortoises of unknown ancestry, to infer levels of relatedness among founders and captive‐born tortoises, and assess putative pedigree relationships assigned by the SDZ studbook....
    • Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies

      Steiner, Cynthia C.; Mitelberg, A.; Tursi, R.; Ryder, Oliver A. (2012)
      …Here we studied the phylogenetic relationships of all extant species of Equidae by analyzing 22 partial mitochondrial and nuclear genes using maximum likelihood and Bayesian inferences that account for heterogeneous gene histories. We also examined genetic signatures of lineage sorting and/or genetic introgression in zebras by evaluating patterns of intraspecific genetic variation….
    • 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....
    • Population demography and heterozygosity-fitness correlations in natural guppy populations: an examination using sexually selected fitness traits

      Grueber, Catherine E.; Fitzpatrick, John L.; Devigili, Alessandro; Gasparini, Clelia; Ramnarine, Indar W.; Evans, Jonathan P. (2017)
      ...Here, we examined the relationship between individual microsatellite heterozygosity and a range of sexually selected traits in 660 male guppies from 22 natural populations in Trinidad....
    • Reducing the extinction risk of populations threatened by infectious diseases

      Glassock, Gael L.; Grueber, Catherine E.; Belov, Katherine; Hogg, Carolyn J. (2021)
      Extinction risk is increasing for a range of species due to a variety of threats, including disease. Emerging infectious diseases can cause severe declines in wild animal populations, increasing population fragmentation and reducing gene flow. Small, isolated, host populations may lose adaptive potential and become more susceptible to extinction due to other threats. Management of the genetic consequences of disease-induced population decline is often necessary. Whilst disease threats need to be addressed, they can be difficult to mitigate. Actions implemented to conserve the Tasmanian devil (Sarcophilus harrisii), which has suffered decline to the deadly devil facial tumour disease (DFTD), exemplify how genetic management can be used to reduce extinction risk in populations threatened by disease. Supplementation is an emerging conservation technique that may benefit populations threatened by disease by enabling gene flow and conserving their adaptive potential through genetic restoration. Other candidate species may benefit from genetic management via supplementation but concerns regarding outbreeding depression may prevent widespread incorporation of this technique into wildlife disease management. However, existing knowledge can be used to identify populations that would benefit from supplementation where risk of outbreeding depression is low. For populations threatened by disease and, in situations where disease eradication is not an option, wildlife managers should consider genetic management to buffer the host species against inbreeding and loss of genetic diversity.
    • Society, demography and genetic structure in the spotted hyena.

      Holekamp, Kay E.; Smith, Jennifer E.; Strelioff, Christopher C.; Van Horn, Russell C.; Watts, Heather E. (2012)
      Spotted hyenas (Crocuta crocuta) are large mammalian carnivores, but their societies, called ‘clans’, resemble those of such cercopithecine primates as baboons and macaques with respect to their size, hierarchical structure, and frequency of social interaction among both kin and unrelated group‐mates. However, in contrast to cercopithecine primates, spotted hyenas regularly hunt antelope and compete with group‐mates for access to kills, which are extremely rich food sources, but also rare and ephemeral....
    • The Frozen Zoo

      Ryder, Oliver A. (2012)
      Wildlife gene banks provide a tool for studying species and monitoring conservation efforts
    • Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

      McLennan, Elspeth A.; Wright, Belinda R.; Belov, Katherine; Hogg, Carolyn J.; Grueber, Catherine E. (2019)
      Molecular markers are a useful tool allowing conservation and population managers to shed light on genetic processes affecting threatened populations. However, as technological advancements in molecular techniques continue to evolve, conservationists are frequently faced with new genetic markers, each with nuanced variation in their characteristics as well as advantages and disadvantages for informing various questions....
    • Twenty-nine polymorphic microsatellite loci in Cyclura carinata, the Turks and Caicos Iguana, a critically endangered island endemic

      Welch, M.E.; Long, G.J.; Berk, J.W.; Getz, A.H.; Gerber, Glenn P.; Wallace, L.E. (2011)
      Cyclura carinata, a critically endangered Caribbean rock iguana, now occupies less than 5% of its historic range. Remaining populations are genetically structured, but available tools are insufficient to identify taxonomic units. Ten polymorphic microsatellites isolated from C. carinata, and 19 loci developed for congeners are identified....
    • Unexpected shallow genetic divergence in Turks Island boas (Epicrates c. chrysogaster) reveals single evolutionarily significant unit for conservation

      Reynolds, R.G.; Gerber, Glenn P.; Fitzpatrick, B.M. (2011)
      ... The subspecies has likely been extirpated from several islands in its historic range, and all remaining populations are threatened with extirpation owing to habitat loss, introduced feral predators, malicious killing, and vehicle strikes. To assist conservation efforts, we undertook a genetic analysis of 53 individual E. c. chrysogaster, representing five island populations, with the goal of identifying existing population structure and genetic diversity. For each snake sampled, we sequenced one mitochondrial and two nuclear genes, resulting in 1591 bp of sequence, and screened nine microsatellite loci....