MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi
Abstract Morphological identification of digested prey remains from a generalist predator can be challenging, especially when attempting to match degraded remains to taxonomic keys. DNA techniques, whereby prey is sequenced and matched to large public nucleotide sequence databases, are increasingly...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-01-01
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| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.263 |
| _version_ | 1818715247114977280 |
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| author | Ilana Nimz Mark A. Renshaw John Baczenas Cynthia Vanderlip K. David Hyrenbach Matthew Iacchei |
| author_facet | Ilana Nimz Mark A. Renshaw John Baczenas Cynthia Vanderlip K. David Hyrenbach Matthew Iacchei |
| author_sort | Ilana Nimz |
| collection | DOAJ |
| description | Abstract Morphological identification of digested prey remains from a generalist predator can be challenging, especially when attempting to match degraded remains to taxonomic keys. DNA techniques, whereby prey is sequenced and matched to large public nucleotide sequence databases, are increasingly being used to augment morphological identification. We used “metaBARFcoding” (DNA metabarcoding) to target a region of the cytochrome c oxidase subunit I (COI) mitochondrial gene to identify prey in highly digested regurgitations from Christmas shearwaters Puffinus nativitatis at Hōlanikū (Kure Atoll). Metabarcoding was used to bulk‐process 92 water samples from regurgitations collected from 2009 to 2017, providing an overview of the seabird's diet. We additionally Sanger‐sequenced 100 prey items from 50 randomly chosen regurgitations to verify that metabarcoding characterized key components of the diet. The metabarcoding technique identified 87 unique taxa from 29 families of fish and squid, spanning diverse taxa, including reef‐associated, pelagic–oceanic, and mesopelagic species. Rare prey (frequency of occurrence ≤5% of samples) constituted 66% of the species richness, demonstrating the highly diverse diet of this generalist predator. Overall, 81% of the families detected in the contemporary diet were previously documented in Christmas shearwater diets from the Northwestern Hawaiian Islands. Our results indicate that metabarcoding the COI region is useful in identifying a wide range of taxa from highly digested regurgitations, thus facilitating this approach to study seabird diets. |
| first_indexed | 2024-12-17T19:00:20Z |
| format | Article |
| id | doaj.art-c1dc8dd52fed4bd88eb00737e5af846a |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-12-17T19:00:20Z |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-c1dc8dd52fed4bd88eb00737e5af846a2022-12-21T21:36:07ZengWileyEnvironmental DNA2637-49432022-01-014125426810.1002/edn3.263MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), HawaiʻiIlana Nimz0Mark A. Renshaw1John Baczenas2Cynthia Vanderlip3K. David Hyrenbach4Matthew Iacchei5Hawaiʻi Pacific University Waimānalo Hawaiʻi USAOceanic Institute at Hawaiʻi Pacific University Waimānalo Hawaiʻi USAHawaiʻi Pacific University Waimānalo Hawaiʻi USAState of Hawaiʻi Department of Land and Natural Resources Honolulu HawaiʻI USAHawaiʻi Pacific University Waimānalo Hawaiʻi USAHawaiʻi Pacific University Waimānalo Hawaiʻi USAAbstract Morphological identification of digested prey remains from a generalist predator can be challenging, especially when attempting to match degraded remains to taxonomic keys. DNA techniques, whereby prey is sequenced and matched to large public nucleotide sequence databases, are increasingly being used to augment morphological identification. We used “metaBARFcoding” (DNA metabarcoding) to target a region of the cytochrome c oxidase subunit I (COI) mitochondrial gene to identify prey in highly digested regurgitations from Christmas shearwaters Puffinus nativitatis at Hōlanikū (Kure Atoll). Metabarcoding was used to bulk‐process 92 water samples from regurgitations collected from 2009 to 2017, providing an overview of the seabird's diet. We additionally Sanger‐sequenced 100 prey items from 50 randomly chosen regurgitations to verify that metabarcoding characterized key components of the diet. The metabarcoding technique identified 87 unique taxa from 29 families of fish and squid, spanning diverse taxa, including reef‐associated, pelagic–oceanic, and mesopelagic species. Rare prey (frequency of occurrence ≤5% of samples) constituted 66% of the species richness, demonstrating the highly diverse diet of this generalist predator. Overall, 81% of the families detected in the contemporary diet were previously documented in Christmas shearwater diets from the Northwestern Hawaiian Islands. Our results indicate that metabarcoding the COI region is useful in identifying a wide range of taxa from highly digested regurgitations, thus facilitating this approach to study seabird diets.https://doi.org/10.1002/edn3.263cytochrome c oxidase subunit I (COI)dietDNA metabarcodingeDNAfood webmitochondrial DNA |
| spellingShingle | Ilana Nimz Mark A. Renshaw John Baczenas Cynthia Vanderlip K. David Hyrenbach Matthew Iacchei MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi Environmental DNA cytochrome c oxidase subunit I (COI) diet DNA metabarcoding eDNA food web mitochondrial DNA |
| title | MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi |
| title_full | MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi |
| title_fullStr | MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi |
| title_full_unstemmed | MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi |
| title_short | MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi |
| title_sort | metabarfcoding dna barcoding of regurgitated prey yields insights into christmas shearwater puffinus nativitatis foraging ecology at holaniku kure atoll hawai i |
| topic | cytochrome c oxidase subunit I (COI) diet DNA metabarcoding eDNA food web mitochondrial DNA |
| url | https://doi.org/10.1002/edn3.263 |
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