• Conservation genomics of threatened animal species

      Steiner, Cynthia C.; Putnam, Andrea S.; Hoeck, Paquita E. A.; Ryder, Oliver A. (2013)
      The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation.…
    • Fitness costs associated with ancestry to isolated populations of an endangered species

      Wilder, Aryn P.; Navarro, Asako Y.; King, Shauna N. D.; Miller, William B.; Thomas, Steven M.; Steiner, Cynthia C.; Ryder, Oliver A.; Shier, Debra M. (2020)
      ... The endangered Pacific pocket mouse (Perognathus longimembris pacificus) persists in three isolated populations in southern California. Mitochondrial and microsatellite data indicated that effective population sizes were extremely small (Ne< 50), and continued declines prompted a conservation breeding program founded by individuals from each population....
    • 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....
    • Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species

      Willoughby, Janna R.; Ivy, Jamie A.; Lacy, Robert C.; Doyle, Jacqueline M.; DeWoody, J. Andrew (2017)
      Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.
    • Inbreeding, immune defence and ectoparasite load in different mockingbird populations and species in the Galápagos Islands

      Hoeck, Paquita E. A.; Keller, Lukas F. (2012)
      ...Using 26 microsatellite loci and genetic data from museum specimens and contemporary samples, we calculated short‐term and long‐term inbreeding in 13 different mockingbird populations covering the range of all 4 species in the Galápagos Islands and compared them with three different measures of innate immunity and ectoparasite load. We found no significant effect of either measure of inbreeding on natural antibody or complement enzyme titres, heterophil‐lymphocyte ratio or feather louse abundance....
    • Kinship-based management strategies for captive breeding programs when pedigrees are unknown or uncertain

      Putnam, Andrea S.; Ivy, Jamie A. (2014)
      …Using the demographic parameters of a North American captive population of Arabian oryx (Oryx leucoryx), 2 kinship-based breeding-pair selection strategies were modeled for their performance in handling pedigrees with varying degrees of parentage uncertainty…. Both kinship-based breeding-pair selection strategies significantly outperformed the nonkinship-based strategies.
    • Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore

      McLennan, E. A.; Grueber, Catherine E.; Wise, P.; Belov, K.; Hogg, Carolyn J. (2020)
      …We used an introduced population of Tasmanian devils Sarcophilus harrisii descended from two genetically differentiated source populations to illustrate the benefits of genetic admixture for translocation programmes. Devils are endangered due to an infectious cancer causing 80% population declines across their range since disease emergence in 1996…. As part of their conservation management, devils were introduced to Maria Island, Tasmania in an assisted colonization in 2012 with supplementations in 2013 and 2017….
    • No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding

      Gooley, Rebecca M.; Hogg, Carolyn J.; Belov, Katherine; Grueber, Catherine E. (2017)
      Inbreeding depression occurs when inbred individuals experience reduced fitness as a result of reduced genome-wide heterozygosity. The Tasmanian devil faces extinction due to a contagious cancer, devil facial tumour disease (DFTD). An insurance metapopulation was established in 2006 to ensure the survival of the species and to be used as a source population for re-wilding and genetic rescue. The emergence of DFTD and the rapid decline of wild devil populations have rendered the species at risk of inbreeding depression. We used 33 microsatellite loci to (1) reconstruct a pedigree for the insurance population and (2) estimate genome-wide heterozygosity for 200 individuals. Using heterozygosity-fitness correlations, we investigated the effect of heterozygosity on six diverse fitness measures (ulna length, asymmetry, weight-at-weaning, testes volume, reproductive success and survival). Despite statistically significant evidence of variation in individual inbreeding in this population, we found no associations between inbreeding and any of our six fitness measurements. We propose that the benign environment in captivity may decrease the intensity of inbreeding depression, relative to the stressful conditions in the wild. Future work will need to measure fitness of released animals to facilitate translation of this data to the broader conservation management of the species in its native range.
    • 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....
    • Reciprocal translocation of small numbers of inbred individuals rescues immunogenetic diversity

      Grueber, Catherine E.; Sutton Jolene T.; Heber Sol; Briskie James V.; Jamieson, Ian G.; Robertson Bruce C. (2017)
      Genetic rescue can reduce inbreeding depression and increase fitness of small populations, even when the donor populations are highly inbred. In a recent experiment involving two inbred island populations of the New Zealand South Island robin, Petroica australis, reciprocal translocations improved microsatellite diversity and individual fitness....
    • 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.
    • The impacts of inbreeding, drift and selection on genetic diversity in captive breeding populations

      Willoughby, J.R.; Fernandez, N.B.; Lamb M.C.; Ivy, Jamie A.; Lacy, R.C.; DeWoody, J.A. (2015)
      The goal of captive breeding programmes is often to maintain genetic diversity until re‐introductions can occur.... Our results suggest that although the effects of drift may not be fully mitigated, MK reduces the loss of alleles due to inbreeding more effectively than random mating or docility selection….
    • Unexpected positive and negative effects of continuing inbreeding in one of the world's most inbred wild animals

      Weiser Emily L.; Grueber, Catherine E.; Kennedy, Euan S.; Jamieson, Ian G. (2015)
      ...The Chatham Island black robin represents a case of extreme inbreeding following two severe population bottlenecks…. The positive and negative effects we found emphasize that continuing inbreeding can have important effects on individual fitness, even in populations that are already highly inbred....
    • Use of molecular data in zoo and aquarium collection management: Benefits, challenges, and best practices

      Norman, Anita J.; Putnam, Andrea S.; Ivy, Jamie A. (2019)
      The global zoo and aquarium community widely recognizes that its animal collections and cooperative breeding programs are facing a sustainability crisis. It has become commonly accepted that numerous priority species cannot be maintained unless new management strategies are adopted....
    • Using molecular methods to improve the genetic management of captive breeding programs for threatened species

      Ivy, Jamie A.; Lacy, Robert C.; DeWoody, J. Andrew; Bickham, John W.; Michler, Charles H.; Nichols, Krista M.; Rhodes, Gene E.; Woeste, Keith E. (Cambridge University PressCambridge, 2010)
      ...the genetic goals of captive population management are to minimize genetic drift, retain genetic diversity, restrict inbreeding, and limit adaptation to captivity (Lacy 1994). The foundations of most captive breeding programs are pedigree analyses, which are used to manage both the demography and genetics of captive populations (Ballou & Foose 1996)....