Something to Crow About: SMRT Sequencing Aids Conservation of Rare Hawaiian Bird

Brought to the brink of extinction, the future of Hawaii’s only lineage of the crow family (Corvidae) is looking up thanks to intensive conservation genomics efforts using PacBio de novo assemblies.
In Hawaiian mythology, the ‘alalā is said to lead souls to their final resting place on the cliffs of Ka Lae, the southernmost tip on the Big Island of Hawaii. As one of the largest native bird populations, it also had a vital role in the ecosystem, helping to disperse and germinate seeds of many indigenous plant species.
Disease, predators and shrinking habitats led to a complete loss of the species in the wild. A captive breeding program led by San Diego Zoo Global managed to save nine ‘alalā and has successfully bred around 140 more to date. But the captive birds also face challenges, including low hatching success and signs of poor genetic diversity due to inbreeding, with the majority of the population linked to a single founding pair.
Not satisfied with following family trees to determine suitable mating pairs, a research team from the San Diego Zoo Institute for Conservation Research, the University of Hawaii, and other organizations produced a high-quality genome assembly based on SMRT Sequencing.  The team believed a comprehensive genome assembly could provide a more detailed picture of population-level genomic diversity and genetic load of Corvus hawaiiensis, as well as more accurate estimates of molecular relatedness to guide breeding decisions. And they were right.
Led by Jolene Sutton, assistant professor at the University of Hawaii, Hilo, the team created an assembly which has provided critical insights into inbreeding and disease susceptibility. They found that the ‘alalā genome is substantially more homozygous compared with more outbred species, and created annotations for a subset of immunity genes that are likely to be important for conservation applications.
As reported in the latest issue of Genes — and featured on its cover — the quality of the assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems.
“Such genome-level data offer unprecedented precision to examine the causes and genetic consequences of population declines, and to apply these results to conservation management,” the authors state. “Although pair selection and managed breeding using the pedigree has kept the inbreeding level of the ‘alalā population at a relatively low level over the past 20 years, the intensive and ongoing conservation management of the species requires a more detailed approach.”
Since the generation of the ‘alalā assembly, several projects have been initiated that rely heavily on use of the new resource, the authors state. To better understand the impact of population bottlenecks over the past 100 years, and to provide a clearer picture of how much diversity can likely be maintained into the future, the team is using targeted SNP-capture to compare genomic diversity in museum and modern ‘alalā, for example. Plans are also underway to genotype every individual ‘alalā against this new reference to further inform the choice of breeding pairs in captivity as well as the management of an ‘alalā release project started in 2017.
“Genomic data derived from our analyses are an essential component of the current and future recovery of the ‘alalā,” the authors write. “As the size of both the captive and wild ‘alalā populations continue to increase, the integration of genomic data as part of the conservation management effort will help to maximize the genetic health of the species well into the future.”