• 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-related patterns of neophobia in an endangered island crow: implications for conservation and natural history

      Greggor, Alison L.; Masuda, Bryce M.; Flanagan, Alison M.; Swaisgood, Ronald R. (2020)
      Theory suggests that the balance between unknown dangers and novel opportunities drives the evolution of species-level neophobia. Juveniles show lower neophobia than adults, within mammals and birds, presumably to help minimize the costs of avoiding beneficial novelty, and adults tend to be more neophobic, to reduce risks and focus on known stimuli. How these dynamics function in island species with fewer dangers from predators and toxic prey is not well understood. Yet, predicting neophobia levels at different age classes may be highly valuable in conservation contexts, such as species' translocation programmes, where responses to novelty can influence the effectiveness of prerelease training and animals' survival postrelease. To better understand how neophobia and its age-related patterns are expressed in an island corvid, we surveyed object neophobia in 84% of the world's critically endangered ‘alal?, Corvus hawaiiensis. Individuals repeatedly demonstrated high neophobia, suggesting that neither captivity nor their island evolution has erased this corvid-typical trait. Unexpectedly, juveniles were exceedingly more neophobic than adults, a pattern in stark contrast to common neophobia predictions and known mammalian and avian studies. We discuss the potential conservation ramifications of this age-structured result within the larger context of neophobia theory. Not only may the expression of neophobia be more complicated than previously thought but predicting such responses may also be important for conservation management that requires exposing animals to novelty.
    • Changes in vocal repertoire of the Hawaiian crow, Corvus hawaiiensis, from past wild to current captive populations

      Tanimoto, Ann M.; Hart, Patrick J.; Pack, Adam A.; Switzer, Richard A.; Banko, Paul C.; Ball, Donna L.; Sebastián-González, Esther; Komarczyk, Lisa; Warrington, Miyako H. (2017)
      ...We compared the vocal repertoire of three of the last four wild 'alalā pairs from the early 1990s to three current captive pairs on the Island of Hawai'i to determine how acoustic behaviour has been affected by changes in their social and physical environment. Over 18 h of recordings from wild breeding pairs were analysed and compared with 44 h from captive breeding pairs....
    • Discovery of species-wide tool use in the Hawaiian crow

      Rutz, Christian; Klump, Barbara C.; Komarczyk, Lisa; Leighton, Rosanna; Kramer, Joshua; Wischnewski, Saskia; Sugasawa, Shoko; Morrissey, Michael B.; James, Richard; St Clair, James J. H.; et al. (2016)
      ...Here we show that another tropical corvid, the ‘Alalā (C. hawaiiensis; Hawaiian crow), is a highly dexterous tool user. Although the ‘Alalā became extinct in the wild in the early 2000s, and currently survives only in captivity5, at least two lines of evidence suggest that tool use is part of the species’ natural behavioural repertoire: juveniles develop functional tool use without training, or social input from adults; and proficient tool use is a species-wide capacity....
    • 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.
    • Inter-aviary distance and visual access influence conservation breeding outcomes in a territorial, endangered bird

      Flanagan, Alison M.; Rutz, Christian; Farabaugh, Susan M.; Greggor, Alison L.; Masuda, Bryce M.; Swaisgood, Ronald R. (2020)
      Species extinctions are becoming a global crisis, affecting biodiversity and ecosystem services, with island populations being particularly vulnerable. In response, conservation managers are increasingly turning to ex situ conservation breeding programs to establish assurance populations and provide a source for release and re-establishment of wild populations. The 'Alalā (Hawaiian crow, Corvus hawaiiensis) is a critically endangered and territorial island corvid that became extinct in the wild in 2002, following a severe and prolonged population decline during the late 20th century....
    • 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....
    • Vocal repertoire and signal characteristics of 'Alalā, the Hawaiian Crow (Corvus hawaiiensis)

      Tanimoto, Ann M.; Hart, Patrick J.; Pack, Adam A.; Switzer, Richard A. (2017)
      The critically endangered Hawaiian Crow or ′Alalā (Corvus hawaiiensis) is currently extinct in the wild and the remaining 115 individuals are being captively managed on Hawai′i and Maui Islands by the Zoological Society of San Diego. Here we provide the first comprehensive analysis of the vocal repertoire of this species....