Moving from trends to benchmarks by using regression tree analysis to find inbreeding thresholds in a critically endangered bird

Nest quality predicts the probability of egg loss in the critically endangered 'Alalā (Corvus hawaiiensis)

Conservation breeding programs for endangered species face challenges, notably in the development of husbandry techniques, complicated by the impracticality of conducting controlled experiments. To reduce uncertainty regarding what works in conservation breeding programs, it is essential to capture data. In avian breeding programs, the construction of quality nests and appropriate incubation and handling of eggs by the parents are essential prerequisites to the successful production of offspring. Here, we study factors influencing nest-building and parental incubation outcomes in 'alalā (Corvus hawaiiensis), which is extinct in the wild and numbers fewer than 130 individuals in human care. Using parent-incubated egg data from 2018 to 2021 (171 clutches, 55 pairs), we evaluated the role of husbandry factors in determining the quality of nests constructed by 'alalā and the likelihood of nest quality and other social and environmental factors to predict egg loss (breaking, cannibalization, or ejection of an egg from the nest). More than half of all eggs laid failed to reach the hatch date. Nest quality was the most influential predictor of egg loss, with eggs in higher quality nests more likely to reach the hatch date. Male age also influenced egg loss, with very young (3 years old) and older males (⪞12 years old) experiencing more egg loss. Furthermore, the two facilities and two aviary types also differed in the quality of nests 'alalā constructed, indicating that nest-building behavior can be influenced by husbandry practices. These findings reduce uncertainty and provide insights for recommended management interventions to facilitate successful reproduction in human care.

Reduction of genetic diversity in 'Alalā (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alalā were more numerous, to samples taken between 1973 and 1998, when 'Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.

Adapting conservation breeding techniques using a data-driven approach to restore the 'Alalā (Hawaiian crow, Corvus hawaiiensis)

For some critically endangered species, conservation breeding is a vital steppingstone toward re-establishing wild populations. The 'Alalā (Hawaiian crow, Corvus hawaiiensis), currently extinct in the wild, exists today only in a conservation breeding program, which, for many years, utilized successful hands-on husbandry approaches such as separating and resocializing pairs, providing partially manmade nests, artificially incubating eggs, and puppet rearing nestlings. Yet, a top priority of any conservation breeding program is to retain natural behaviors essential to postrelease survival and reproduction, to achieve successful reintroduction and restoration to the wild. We describe how we are adapting 'Alalā husbandry techniques to strengthen pair bonds through full-time socialization, enable pairs to build robust nests, encourage females to incubate eggs to hatch, and provide pairs and their offspring with vital parental rearing experiences. We discuss the use of standardized, data-driven methods to objectively track our progress towards successful parental breeding and to select release candidates based on their likelihood to survive and breed in the wild. The information shared in this report can be applied to other conservation breeding programs, particularly those implementing or transitioning to husbandry techniques geared towards preparing species to thrive in the wild.

Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome-wide association approach to test the locus-specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern.

Ex situ breeding programs benefit from science-based cooperative management

Science-based management confers a variety of benefits to wildlife populations that are cooperatively managed by zoos and aquariums, including those managed through the Association of Zoos and Aquariums. Briefly, when management strategies are successful, they result in reproductively robust populations that better retain genetic diversity and limit inbreeding than unmanaged populations. Although the benefits of demographic and genetic management have been well documented throughout both the scientific and popular literature, it has also been established that the majority of managed populations in zoos and aquariums are not meeting the minimum criteria believed to convey long-term biological viability. For most of these populations, an inability to meet viability criteria is not an inherent failure of how cooperative management is implemented. Furthermore, in recent years, we have perceived that the need to meet specific viability goals sometimes has obscured the benefits that these populations receive from rigorous, science-based management. To better clarify the conversation surrounding population viability in zoos and aquariums, we seek to decouple viability measures and how they predict population persistence from the benefits conferred to populations through science-based management. A primary goal of population management is to facilitate the persistence of priority species for longer than would be expected if no such management were implemented. Although current viability measures and future projections of viability are important tools for assessing the likelihood of population persistence, they are not indicators of which populations may most benefit from science-based management. Here, we review the history and purpose of applying science-based management to zoo and aquarium populations, describe measures of population viability and caution against confusing those measures of viability with population management goals or long-term population sustainability, and clearly articulate the benefits conferred to zoo and aquarium populations by science-based management.

Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (R_xy ), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (R_AB ), allele-sharing co-ancestry (AS)) across five species bred in captivity-including three birds and two mammals-with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using R_xy , R_AB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either R_xy or R_AB . Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.