Developing a universal beaked whale genotyping panel for assessing population level impacts of anthropogenic activities
Abstract
Beaked whales (Ziphiidae) are vulnerable to a variety of natural and anthropogenic impacts that have resulted in mortality events. H owever, current research tools limit our ability to link these deaths to populations of origin, and in some cases, even to the speci es involved as beaked whale species can be notoriously difficult to identify from morphological features. Here we propose developing new genomic tools that will provide insight into the population-level effects of atypical mass stranding events (ASEs). While the g enomics revolution is providing unprecedented insight into marine mammal ecology and evolution, most approaches require high quality /quantity DNA. However, the vast majority of samples collected from beaked whales are from dead stranded animals that are often much decomposed or from skeletal remains, both of which typically only yield low quality/quantity DNA. Moreover, new techniques for the minimally-invasive monitoring of cetaceans, such as the collection of DNA from exhalations (blow), faeces, and other environmental DNA sources (eDNA, e.g., from water that whales have passed through) also yield only small amounts of DNA of variable quality. Cle arly, new genomics methods need to be developed to reliably provide genomic-level information from across diverse sample types. Here we propose to address this issue by developing a reproducible set or panel of genomic markers that will provide species and sex ide ntification, as well as individual and population level information, across a range of beaked whale species. This suite of markers w ill be developed by leveraging existing genomic resources, partly generated during a previous ONR grant. The panel will be validated using high quality DNA templates from a variety of species which we already hold. The panel will be trialed with low quality/quanti ty DNA template samples using different methods (PCR-based vs bait capture approaches) to determine the optimal workflow, using know n, validated genotypes where possible. The new genotyping panel will then be applied to samples collected during recent ASEs and fro m eDNA sources from free-swimming animals to provide insight into the species, sex, relatedness, and population identity of beaked w hales
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Oct 22, 2021
- Source ID
- N000142112712
Entities
People
- Emma L. Carroll
Organizations
- Office of Naval Research
- United States Navy
- University of Auckland