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Design of SNP markers for Aldabra giant tortoises using low coverage ddRAD-seq


Çilingir, F G; Hansen, Dennis; Ozgul, Arpat; Grossen, Christine (2021). Design of SNP markers for Aldabra giant tortoises using low coverage ddRAD-seq. Conservation Genetics Resources, 13(4):409-412.

Abstract

The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea. A total of 1674 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.33 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea.

Abstract

The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea. A total of 1674 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.33 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Scopus Subject Areas:Life Sciences > Ecology, Evolution, Behavior and Systematics
Life Sciences > Genetics
Uncontrolled Keywords:Genetics, Ecology, Evolution, Behavior and Systematics
Language:English
Date:1 December 2021
Deposited On:03 Sep 2021 06:09
Last Modified:25 Feb 2024 02:42
Publisher:Springer
ISSN:1877-7252
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1007/s12686-021-01225-4
Project Information:
  • : FunderSwiss Government Excellence Scholarship for Postdocs
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  • : FunderUZH Alumni Postdoctoral Fellowship
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  • : FunderGeorges and Antoine Claraz Foundation
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  • : FunderUniversität Zürich
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  • Content: Published Version
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)