Environmental (e)DNA metabarcoding for estimating haplotype diversityand population differentiation of social odontocetes
Abstract
We propose to estimate diversity and differentiation of mitochondrial (mt)DNA haplotypesusing samples of environmental (e)DNA collec ted in the proximity of abundant species, specifically from large groups of social odontocetes that are common on the Navy s testing ranges. Using next-generation sequencing methods for eDNA metabarcoding we can identify multiple haplotypes (sequence variants) and the relative frequency of haplotypes (using the number of sequencing reads) from replicate eDNA samples of large groups. We will al so investigate the potential to characterize the frequency of Single Nucleotide Polymorphisms (SNPs) from eDNA by sequencing short s egments of nuclear DNA. A discovery curve, or similar rarefaction method, will be used to estimate and compare haplotype diversity a s well as the number of samples needed to recover most or all of the diversity in each group. A robotic autosampler will be trialed to help standardize methods of field collection. In Year 1 (FY21), we will take advantage of operational support for field collectio n provided by a separately funded ONR program to samples large groups of Delphinus sp. in the vicinity of Catalina Island (N00014-19 -1-2572). Funding is also requested for fieldwork in Year 2, with the location and subject species to be decided depending on result s of the first year and ONR priorities. We will complete analyses and report preparation in Year 3.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Sep 07, 2021
- Source ID
- N000142112713
Entities
People
- Scott Baker
Organizations
- Office of Naval Research
- Oregon State University
- United States Navy