A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

Advances in high‐throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration are rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions...

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Veröffentlicht in:Molecular ecology resources Jg. 19; H. 2; S. 497 - 511
Hauptverfasser: Komoroske, Lisa M., Miller, Michael R., O'Rourke, Sean M., Stewart, Kelly R., Jensen, Michael P., Dutton, Peter H.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Wiley Subscription Services, Inc 01.03.2019
Schlagworte:
Animals
Aquatic Organisms - classification
Aquatic Organisms - genetics
Chelonia mydas
Cheloniidae
Collaboration
Conservation genetics
Ecological monitoring
genetic databases
Genetics
genome
Genomes
Genotype
Genotypes
Genotyping
Genotyping Techniques - methods
geographical distribution
high-throughput nucleotide sequencing
High-Throughput Nucleotide Sequencing - methods
high‐throughput sequencing
Life history
loci
Marine technology
Polymorphism, Single Nucleotide
RAD‐Seq
reptiles
Reptiles & amphibians
sea turtle
sea turtles
sequence capture
Single-nucleotide polymorphism
Species
species identification
Turtles
Turtles - classification
Turtles - genetics
Wildlife
Wildlife conservation
Wildlife management
sequence capture
sea turtle
RAD-Seq
reptiles
high-throughput sequencing
conservation genetics
ISSN:1755-098X, 1755-0998, 1755-0998
Online-Zugang:Volltext
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Zusammenfassung:Advances in high‐throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration are rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high‐throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Here, we present a versatile marine turtle HTS targeted enrichment platform adapted from the recently developed Rapture (RAD‐Capture) method specifically designed to meet these research needs. Our results demonstrate consistent enrichment of targeted regions throughout the genome and discovery of candidate variants in all species examined for use in various conservation genetics applications. Accurate species identification confirmed the ability of our platform to genotype over 1,000 multiplexed samples and identified areas for future methodological improvement such as optimization for low initial concentration samples. Finally, analyses within green turtles supported the ability of this platform to identify informative SNPs for stock structure, population assignment and other applications over a broad geographic range of interest to management. This platform provides an additional tool for marine turtle genetic studies and broadens capacity for future large‐scale initiatives such as collaborative global marine turtle genetic databases.
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ISSN:1755-098X
1755-0998
1755-0998
DOI:10.1111/1755-0998.12980