Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study

Evolutionary Applications
Stephen J GaughranAdalgisa Caccone

Abstract

High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in nonmodel organisms. Using >20,000 genomewide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 ind...Continue Reading

References

Nov 11, 1999·Proceedings of the National Academy of Sciences of the United States of America·A CacconeJ R Powell
Oct 31, 2002·Molecular Ecology·Claudio CiofiJeffrey R Powell
Oct 4, 2003·Science·Luciano B BeheregarayJeffrey R Powell
Apr 16, 2004·Proceedings of the National Academy of Sciences of the United States of America·Luciano B BeheregarayAdalgisa Caccone
Dec 7, 2006·Biology Letters·Michael A RusselloAdalgisa Caccone
May 2, 2007·Current Biology : CB·Michael A RusselloAdalgisa Caccone
Sep 24, 2008·Proceedings of the National Academy of Sciences of the United States of America·Nikos PoulakakisAdalgisa Caccone
Mar 18, 2009·Molecular Biology and Evolution·Bret A Payseur, Peicheng Jing
Sep 26, 2009·Nature·David ReichLalji Singh
Aug 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Kevin J EmersonChristina M Holzapfel
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jan 14, 2012·Current Biology : CB·Ryan C GarrickAdalgisa Caccone
May 29, 2013·Molecular Ecology·Shawn R NarumPaul A Hohenlohe
Dec 18, 2013·Genome Biology·Etienne LoireNicolas Galtier
Mar 8, 2014·Bioinformatics·Deren A R Eaton
Sep 17, 2014·Molecular Ecology·Ryan C GarrickAdalgisa Caccone
Dec 30, 2014·Ecology and Evolution·Alexander I Putman, Ignazio Carbone
Feb 17, 2015·Molecular Ecology Resources·Naama M KopelmanItay Mayrose
Feb 28, 2015·GigaScience·Christopher C ChangJames J Lee
May 15, 2015·Molecular Ecology·Patrick G Meirmans
Jul 18, 2015·Molecular Ecology·Christian RellstabRolf Holderegger
Jan 6, 2016·Nature Reviews. Genetics·Kimberly R AndrewsPaul A Hohenlohe
Apr 24, 2016·Molecular Ecology·Bridgett M vonHoldtRobert K Wayne
Apr 27, 2016·Current Biology : CB·Jacqueline A RobinsonRobert K Wayne
Oct 28, 2016·Molecular Ecology·Jaime A ChavesJ Albert C Uy
Aug 31, 2016·Molecular Ecology·Chris J BrauerLuciano B Beheregaray
Nov 1, 1984·Evolution; International Journal of Organic Evolution·B S Weir, C Clark Cockerham

❮ Previous
Next ❯

Citations

Jul 22, 2018·Evolutionary Applications·Margaret E HunterLouis Bernatchez
Apr 13, 2019·Evolutionary Applications·Brenton von Takach DukaiSam C Banks
Aug 29, 2019·Genes·Katharina C Wollenberg ValeroSebastian Steinfartz

❮ Previous
Next ❯

Methods Mentioned

BETA
PCA
genotyping
Illumina sequencing

Software Mentioned

pyrad
R
diveRsity
CLUMPAK
vcftools
PLINK

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.