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Vaux F, Parvizi E, Craw D, Fraser CI, Waters J. Parallel recolonizations generate distinct genomic sectors in kelp following high-magnitude earthquake disturbance. Mol Ecol 2022; 31:4818-4831. [PMID: 35582778 PMCID: PMC9540901 DOI: 10.1111/mec.16535] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022]
Abstract
Large-scale disturbance events have the potential to drastically reshape biodiversity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonized by multiple lineages, which can lead to the evolution of distinct spatial "sectors" of genetic diversity within a species. We test for disturbance-driven sectoring of genetic diversity in intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot, following the high-magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping-by-sequencing (GBS) to analyse fine-scale population structure across the uplift zone and apply machine learning to assess the fit of alternative recolonizaton models. Our analysis reveals that specimens from the uplift zone carry distinctive genomic signatures potentially linked to post-earthquake recolonization processes. Specifically, our analysis identifies two parapatric spatial-genomic sectors of D. antarctica at Turakirae Head, which experienced the most dramatic uplift. Based on phylogeographical modelling, we infer that bull kelp in the Wellington region was probably a source for recolonization of the heavily uplifted Turakirae Head coastline, via two parallel, eastward recolonization events. By identifying multiple parapatric genotypic sectors within a recently recolonized coastal region, the current study provides support for the hypothesis that competing lineage expansions can generate striking spatial structuring of genetic diversity, even in highly dispersive taxa.
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Affiliation(s)
- Felix Vaux
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Elahe Parvizi
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Dave Craw
- Department of GeologyUniversity of OtagoDunedinNew Zealand
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Walton K, Scarsbrook L, Mitchell KJ, Verry AJF, Marshall BA, Rawlence NJ, Spencer HG. Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone. Mol Ecol Resour 2022; 23:118-130. [PMID: 35951485 PMCID: PMC10087340 DOI: 10.1111/1755-0998.13696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
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.
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Affiliation(s)
- Kerry Walton
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Lachie Scarsbrook
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand.,Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, 1 South Parks Road, OX1 3TG, University of Oxford, Oxford, United Kingdom
| | - Kieren J Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Alexander J F Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand.,Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Bruce A Marshall
- Museum of New Zealand Te Papa Tongarewa, 169 Tory St, Te Aro, 6011, Wellington, New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Hamish G Spencer
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
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Scarsbrook L, Verry AJF, Walton K, Hitchmough RA, Rawlence NJ. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus
Hoplodactylus. Mol Ecol 2022; 32:2964-2984. [DOI: 10.1111/mec.16434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Lachie Scarsbrook
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Alexander J. F. Verry
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Kerry Walton
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | | | - Nicolas J. Rawlence
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
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Donald KM, McCulloch GA, Dutoit L, Spencer HG. Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We examined phylogeographic structure in the direct-developing New Zealand endemic intertidal mud whelk, Cominella glandiformis. Two hundred and ninety-six whelks from 12 sites were collected from sheltered shores around New Zealand’s four largest islands (North Island, South Island, Stewart Island and Chatham Island), encompassing the geographical range of this species. Despite being direct developers, gene flow among C. glandiformis populations may occur over short distances by adult floating, and over larger distances by rafting of egg masses. Primers were developed to amplify variable microsatellite regions at six loci. All loci were variable, with 8–34 alleles/loci. Observed and expected heterozygosities were high across all alleles, with minimal evidence of null alleles. The average number of alleles varied from 3.5 (Chatham Island) to 7.5 (Waitemata Harbour). Strong genetic structure was evident, with distinct ‘eastern’ and ‘western’ groups. Each group extended over a large geographic area, including regions of unsuitable habitat, but were linked by oceanic currents. We suggest that the intraspecific geographic genetic structure in C. glandiformis has arisen due a combination of ocean currents (promoting gene flow between geographically distant regions) and upwelling areas (limiting gene flow between certain regions).
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Affiliation(s)
| | | | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Hamish G Spencer
- Department of Zoology, University of Otago, Dunedin, New Zealand
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