Population genomics of Antipodean and Gibson’s albatross and use of genetic markers for threatened seabird species identification

Biodiversity loss is occurring at an unprecedented rate, and seabirds are one of the most threatened taxa. This is of serious concern because of their important role as top predators in the marine ecosystem, which makes their protection and recovery an important goal of conservation. A range of factors have been implicated in the decline of seabird populations, and mortality due to incidental bycatch in fisheries is considered one of the biggest threats. The implementation of effective measures to protect seabirds against bycatch mortality relies on accurate assessment of the risk to populations. This can be hindered because of difficulties delineating and identifying species from bycatch using morphology, or uncertainty about population units and taxonomy. The Antipodean and Gibson’s albatross (Diomedea antipodensis antipodensis and D. a. gibsoni) are taxa of particular concern due to recent population declines, largely as a result of incidental fisheries bycatch mortality. However, the effectiveness of current conservation measures is unclear due to the taxonomic uncertainty of these taxa and the lack of information about distinct population units. The aims of this thesis were to investigate the use of genetic markers for assessment of seabird taxa highly threatened by fisheries to inform conservation management by 1) developing genetic markers to identify seabird bycatch from fisheries, 2) assemble high-quality reference genomes for the Antipodean and Gibson’s albatrosses and 3) use whole-genome data to assess their population genetic structure.

Mitochondrial DNA (mtDNA) markers were assessed for their utility in genetic identification of seabirds caught in New Zealand fisheries. Analysis of sequences across 36 species indicated cytochrome oxidase I (COI) was useful as a broadly applicable genetic marker for species identification, with successful identification of 28 of 36 species. To provide additional resolution, mtDNA control region sequences were used to successfully identify species not resolved using COI sequence. Three subspecies pairs were unable to be distinguished using either marker. However, assembly of whole mitogenomes for one of these pairs, the Antipodean and Gibson’s albatross, revealed a diagnostic variable repeat region suitable for taxon identification for this species. A workflow for genetic identification of seabird specimens was developed and is presented. These methodologies can be implemented in fisheries management for identification of bycaught seabirds, to assess the risk of fisheries to different species.

De novo whole-genome sequences were generated and assembled for both the Antipodean and Gibson’s albatross using samples collected from the respective breeding sites on Antipodes Island and the Auckland Islands. DNA sequencing was performed using Oxford Nanopore Technology chemistry and the Flye algorithm used for genome assembly. The final reference genomes were approximately 1.25 Gigabase pairs (Gb) in length and comprising 255 and 313 scaffolds for the Antipodean and Gibson’s assembly respectively, although the largest 60 scaffolds of each genome showed BUSCO completeness of ~97%. Approximately 10% of each genome was composed of repetitive elements. These highly contiguous and complete reference genomes will be a valuable resource for future population genomic analysis of the Antipodean and Gibson’s albatrosses, as demonstrated in further chapters of this thesis.

Population genetic structure and differentiation of the Antipodean and Gibson’s albatross was assessed using whole-genome resequencing data for 43 individuals from each taxon. Overall, 6.7 million single-nucleotide polymorphisms (SNPs) were identified. After filtering, final datasets of 60,488 neutrally evolving, and 21 outlier (putatively adaptive) independently segregating SNPs were obtained. Analysis of these datasets revealed low but significant genetic differentiation between the Antipodean and Gibson’s albatross, with no evidence of contemporary gene flow. Further assessment using the neutral dataset revealed apparent fine-scale structure within the Gibson’s albatross population, with birds breeding on different islands showing a degree of genetic differentiation. Discovery of significant genome-wide differentiation between the Antipodean and Gibson’s albatross agrees with other evidence (morphological and behavioural) of population differentiation. This identification of distinct breeding units will help to inform improved management of the taxa and may prompt reconsideration of their taxonomic status. The high-quality reference genomes are the first for Diomedea albatrosses and some of the first presented across the albatross family. These provide a valuable resource for study of albatross phylogeny and evolution. Improvements in resolution of taxon discrimination and genetic structure highlights the promise of genomic data for informing management of populations of closely related seabirds. Overall, this thesis research demonstrates the value of both genetics and genomics for precise assessment and monitoring of threatened populations, which is critical for effective conservation.