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Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array
Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to coll...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10499200/ https://www.ncbi.nlm.nih.gov/pubmed/37703242 http://dx.doi.org/10.1371/journal.pone.0291187 |
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author | Baker, Charles Scott Claridge, Diane Dunn, Charlotte Fetherston, Thomas Baker, Dorothy Nevé Klinck, Holger Steel, Debbie |
author_facet | Baker, Charles Scott Claridge, Diane Dunn, Charlotte Fetherston, Thomas Baker, Dorothy Nevé Klinck, Holger Steel, Debbie |
author_sort | Baker, Charles Scott |
collection | PubMed |
description | Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy’s Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville’s beaked whales (Mesoplodon densirostris). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville’s beaked whales, suggested the potential for further resolution of differences between oceanic populations. |
format | Online Article Text |
id | pubmed-10499200 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-104992002023-09-14 Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array Baker, Charles Scott Claridge, Diane Dunn, Charlotte Fetherston, Thomas Baker, Dorothy Nevé Klinck, Holger Steel, Debbie PLoS One Research Article Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy’s Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville’s beaked whales (Mesoplodon densirostris). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville’s beaked whales, suggested the potential for further resolution of differences between oceanic populations. Public Library of Science 2023-09-13 /pmc/articles/PMC10499200/ /pubmed/37703242 http://dx.doi.org/10.1371/journal.pone.0291187 Text en © 2023 Baker et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Baker, Charles Scott Claridge, Diane Dunn, Charlotte Fetherston, Thomas Baker, Dorothy Nevé Klinck, Holger Steel, Debbie Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array |
title | Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array |
title_full | Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array |
title_fullStr | Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array |
title_full_unstemmed | Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array |
title_short | Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville’s beaked whales, with assisted localization from an acoustic array |
title_sort | quantification by droplet digital pcr and species identification by metabarcoding of environmental (e)dna from blainville’s beaked whales, with assisted localization from an acoustic array |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10499200/ https://www.ncbi.nlm.nih.gov/pubmed/37703242 http://dx.doi.org/10.1371/journal.pone.0291187 |
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