Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodologica...
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ftzenodo:oai:zenodo.org:7055748 2023-06-06T11:48:05+02:00 Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone Walton, Kerry Scarsbrook, Lachie Mitchell, Kieren Verry, Alexander Marshall, Bruce Rawlence, Nicolas Spencer, Hamish 2022-08-18 https://zenodo.org/record/7055748 https://doi.org/10.5061/dryad.3ffbg79mq unknown https://zenodo.org/communities/dryad https://zenodo.org/record/7055748 https://doi.org/10.5061/dryad.3ffbg79mq oai:zenodo.org:7055748 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode ancient DNA Haliotidae Haliotis invertebrates Mollusca Phylogeography info:eu-repo/semantics/other dataset 2022 ftzenodo https://doi.org/10.5061/dryad.3ffbg79mq 2023-04-13T21:55:20Z Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research. See main text of manuscript. Dataset Antipodes Islands Zenodo Campbell Island ENVELOPE(169.500,169.500,-52.500,-52.500) New Zealand |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
ancient DNA Haliotidae Haliotis invertebrates Mollusca Phylogeography |
spellingShingle |
ancient DNA Haliotidae Haliotis invertebrates Mollusca Phylogeography Walton, Kerry Scarsbrook, Lachie Mitchell, Kieren Verry, Alexander Marshall, Bruce Rawlence, Nicolas Spencer, Hamish Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone |
topic_facet |
ancient DNA Haliotidae Haliotis invertebrates Mollusca Phylogeography |
description |
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research. See main text of manuscript. |
format |
Dataset |
author |
Walton, Kerry Scarsbrook, Lachie Mitchell, Kieren Verry, Alexander Marshall, Bruce Rawlence, Nicolas Spencer, Hamish |
author_facet |
Walton, Kerry Scarsbrook, Lachie Mitchell, Kieren Verry, Alexander Marshall, Bruce Rawlence, Nicolas Spencer, Hamish |
author_sort |
Walton, Kerry |
title |
Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone |
title_short |
Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone |
title_full |
Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone |
title_fullStr |
Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone |
title_full_unstemmed |
Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone |
title_sort |
raw data and alignments for: application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a new zealand abalone |
publishDate |
2022 |
url |
https://zenodo.org/record/7055748 https://doi.org/10.5061/dryad.3ffbg79mq |
long_lat |
ENVELOPE(169.500,169.500,-52.500,-52.500) |
geographic |
Campbell Island New Zealand |
geographic_facet |
Campbell Island New Zealand |
genre |
Antipodes Islands |
genre_facet |
Antipodes Islands |
op_relation |
https://zenodo.org/communities/dryad https://zenodo.org/record/7055748 https://doi.org/10.5061/dryad.3ffbg79mq oai:zenodo.org:7055748 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.3ffbg79mq |
_version_ |
1767953981263314944 |