All bash scripts for analyses run for my PhD thesis 'Population genomics of Antipodean and Gibson’s albatross and use of genetic markers for threatened seabird species identification'.
!!insert link to pdf of final thesis!!
CHAPTER 3. Using genetic markers to identify seabirds caught in Aotearoa New Zealand fisheries
Fisheries bycatch mortality is a significant threat facing seabirds worldwide. Yet, understanding which species and populations are most impacted is hindered by uncertainties when identifying bycatch specimens. Birds can be damaged beyond recognition by fishing gear or may present challenges to observers who are not fully trained to identify closely related seabird taxa. Here, we have developed a geneticsbased pipeline using mitochondrial DNA markers for identifying bycatch in Aotearoa New Zealand waters across 36 species including albatrosses (Diomedeidae), storm petrels (Hydrobatidae), petrels (Procellariidae), cormorants (Phalacrocoracidae) and penguins (Spheniscidae). Analysis of Cytochrome Oxidase I (COI) sequences was successful in identifying all taxa to genus level, and 75% to species level. All but one species (Salvin’s albatross, Thalassarche salvini) that could not be successfully identified using COI sequence could be individually identified from their more highly variable mitochondrial Control Region sequences. Subspecies of Cape petrel (Daption capense capense/D. c. australe), Antipodean albatross (Diomedea antipodensis antipodensis/D. a. gibsoni) and Buller’s albatross (T. bulleri bulleri/T. b. platei) could not be distinguished using either of these loci. However, assembly and assessment of whole mitogenomes for 86 Antipodean albatross individuals did reveal a diagnostic region for these subspecies. A decision tree for species identification from an otherwise morphologically unidentifiable specimen is presented. Our new methodology should prove to be a valuable complement for the current formal identification process of seabird bycatch in South Pacific fisheries and thereby help to inform future fisheries management and seabird conservation.
Albatrosses are a highly threatened family of seabirds that are facing widespread declines, largely attributed to incidental fisheries bycatch mortality. Protection relies upon sound knowledge of distinct breeding units, but population structure has been difficult to detect due to low levels of genetic differentiation between closely related taxa. Whole-genome data have not yet been used to investigate this issue, and genomic resources for albatrosses are currently limited to a few fragmented genome assemblies. Here, we present high-quality reference genomes for both the Antipodean and Gibson’s wandering albatrosses (Diomedea antipodensis antipodensis and D. a. gibsoni), sequenced using Oxford Nanopore Technology and assembled with the Flye assembly algorithm. Both assemblies were around 1.25 Gb in length and comprised 255 and 313 scaffolds for the Antipodean and Gibson’s assemblies, respectively. Although not chromosome-resolution assemblies, the largest 60 scaffolds had BUSCO completeness of ~97%. As well, alignment of the two genomes, and alignment of each genome to an available chromosome-level assembly of the common tern (Sterna hirundo) suggests that most chromosomes are likely represented by only a few large scaffolds. These two high-quality reference genomes for albatross will allow population-level analysis of genomic diversity, gene flow and adaptive diversity to inform taxonomy and conservation management in a changing world.
Understanding the genetic structure of populations is important for identifying management units for conservation. When populations have low genetic diversity, or are closely related, single genetic markers may not be able to fully resolve population genetic structure. However, recent advances in DNA sequencing have provided the opportunity to use large whole-genome datasets to test for genetic differentiation, providing more confidence. Here, we use whole-genome data to investigate the genetic population structure of the highly threatened Antipodean (D. antipodensis antipodensis) and Gibson’s albatross (D. a. gibsoni). Whole-genome resequencing data from 86 individuals sampled across Antipodes Island (D. a. antipodensis) and the Auckland Islands (D. a. gibsoni) produced a dataset of 60,488 neutrally evolving and 21 outlier (putatively adaptive) SNPs. Analyses with both datasets revealed significant genetic differentiation between the Antipodean and Gibson’s albatross with no evidence of contemporary gene flow between the island populations. Within-population structure was also identified for the Gibson’s albatross using the neutral dataset, with genetic differentiation among sample sites from different islands (Adams Island and Disappointment Island) which could be the result of their natal philopatry. The identification of strong genome-wide differentiation between the Antipodean and Gibson’s albatross is concordant with other evidence of population differentiation (morphological and behavioural). These findings suggest a need to reconsider the taxonomic status and threat classification of the two subspecies to ensure adequate protection for each taxon.