• A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species

      Sutton, Jolene; Helmkampf, Martin; Steiner, Cynthia C.; Bellinger, M. Renee; Korlach, Jonas; Hall, Richard; Baybayan, Primo; Muehling, Jill; Gu, Jenny; Kingan, Sarah; et al. (2018)
      Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the ʻAlalā (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawaiʻi, the ʻAlalā survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the ʻAlalā genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications
    • Age-dependent, negative heterozygosity-fitness correlations and local effects in an endangered Caribbean reptile, Iguana delicatissima

      Judson, Jessica L Martin; Knapp, Charles R.; Welch, Mark E. (2018)
      Inbreeding depression can have alarming impacts on threatened species with small population sizes. Assessing inbreeding has therefore become an important focus of conservation research. In this study, heterozygosity-fitness correlations (HFCs) were measured by genotyping 7 loci in 83 adult and 184 hatchling Lesser Antillean Iguanas, Iguana delicatissima, at a communal nesting site in Dominica to assess the role of inbreeding depression on hatchling fitness and recruitment to the adult population in this endangered species. We found insignificant correlations between multilocus heterozygosity and multiple fitness proxies in hatchlings and adults. Further, multilocus heterozygosity did not differ significantly between hatchlings and adults, which suggests that the survivorship of homozygous hatchlings does not differ markedly from that of their heterozygous counterparts. However, genotypes at two individual loci were correlated with hatching date, a finding consistent with the linkage between specific marker loci and segregating deleterious recessive alleles. These results provide only modest evidence that inbreeding depression influences the population dynamics of I. delicatissima on Dominica.;
    • Chromosomal variation and perinatal mortality in San Diego zoo Soemmerring's gazelles

      Steiner, Cynthia C.; Charter, Suellen J.; Goddard, Natalie; Davis, Heidi; Brandt, Margot; Houck, Marlys L.; Ryder, Oliver A. (2015)
      …For the past 35 years, the San Diego Zoo Global (SDZG) captive population of Soemmerring's gazelles has revealed complex karyotypes resulting from chromosomal translocations with diploid numbers ranging from 34 to 39... Low levels of genetic distance and nucleotide diversity among individuals, in addition to high relatedness values, suggested that outbreeding is less of a concern than inbreeding for maintaining a sustainable captive population….
    • 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.…
    • Effects of inbreeding and parental incubation on captive breeding success in Hawaiian crows

      Hoeck, Paquita E. A.; Wolak, Matthew E.; Switzer, Richard A.; Kuehler, Cyndi M.; Lieberman, Alan A. (2015)
      We used 17 years of captive breeding records of the Hawaiian crow (Corvus hawaiiensis) to study the effects of individual and parental level of inbreeding on survival through early life…. Our study contributes to evidence that the strength of inbreeding depression is particularly severe in early life traits. It shows that the negative effects of inbreeding on reproductive success should be accounted for even in benign captive environments where survival is maximized and suggests that parental incubation should be favored over artificial incubation in avian captive breeding programs.
    • Evidence for dominant males but not choosy females in an insular rock iguana

      Moss, Jeanette B.; Gerber, Glenn P.; Schwirian, Aumbriel; Jackson, Anna C.; Welch, Mark E. (2018)
      In natural populations susceptible to inbreeding depression, behaviors such as female promiscuity and disassortative mating may enhance the production of outbred progeny and help maintain genetic variation at the population-level. However, empirical tests of such hypotheses have largely focused on mating systems in which female choice is known to play a large role....
    • 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....
    • Great ape genetic diversity and population history

      Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.; Li, Heng; Kelley, Joanna L.; Lorente-Galdos, Belen; Veeramah, Krishna R.; Woerner, August E.; O’Connor, Timothy D.; Santpere, Gabriel; et al. (2013)
      Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria–Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
    • Heterozygosity–Fitness Correlations Reveal Inbreeding Depression in Neonatal Body Size in a Critically Endangered Rock Iguana

      Moss, Jeanette B.; Gerber, Glenn P.; Welch, Mark E. (Oxford University Press (OUP), 2019)
      Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.
    • Inbreeding and inbreeding avoidance in wild giant pandas

      Hu, Yibo; Nie, Yonggang; Wei, Wei; Ma, Tianxiao; Van Horn, Russell C.; Zheng, Xiaoguang; Swaisgood, Ronald R.; Zhou, Zhixin; Zhou, Wenliang; Yan, Li; et al. (2017)
      Inbreeding can have negative consequences on population and individual fitness, which could be counteracted by inbreeding avoidance mechanisms. However, the inbreeding risk and inbreeding avoidance mechanisms in endangered species are less studied....
    • Species concepts for conservation – Reply to Russello and Amato

      Frankham, Richard; Lacy, Robert C.; Ballou, Jonathan D.; Dudash, Michele R.; Eldridge, Mark D.B.; Fenster, Charles B.; Mendelson, Joseph R.; Porton, Ingrid J.; Ralls, Katherine; Ryder, Oliver A. (2014)
      There are two critical steps required in assessing the taxonomic identity of populations (especially fragmented ones) for conservation purposes. The first is to define the criteria for distinguishing species and the second is to implement the delineation....
    • The influence of captive breeding management on founder representation and inbreeding in the ‘Alalā, the Hawaiian crow

      Hedrick, Philip W.; Hoeck, Paquita E. A.; Fleischer, Robert C.; Farabaugh, Susan M.; Masuda, Bryce M. (2016)
      The ‘Alalā (Corvus hawaiiensis), or the Hawaiian crow, was historically only found on the island of Hawai‘i, declined greatly in the twentieth century, and was last seen in the wild in 2002. A captive breeding program was initiated in the 1970s and 113 individuals were in captivity in 2014....
    • Trouble in paradise

      Toledo, Luís Felipe; de Paula, Catia Dejuste; Pessier, Allan P. (2016)
      The article discusses the reasons for occurrences of deformed and blind toads in large numbers on Brazilian island such as Fernando de Noronha, Brazil. It highlights several causes for amphibian malformations including chemical pollutants, overexposure to ultraviolent radiation and inbreeding....