SNPs in ecology, evolution and conservation

Morin, Phillip A.; Luikart, Gordon; Wayne, Robert K.

doi:10.1016/j.tree.2004.01.009

Cited by 880 publications

(896 citation statements)

References 65 publications

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“…New technologies for genetic monitoring typically rely upon single nucleotide polymorphisms, or SNPs (Morin et al, 2004). Unlike more conventional DNA markers such as microsatellites, SNPs have relatively few alleles per locus (theoretically up to four but usually only two due to mutation/drift equilibrium; Glaubitz et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2017

Preprint

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Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g. collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically-driven declines, which are unlikely to abate without intensive management efforts that often include MIS approaches. Here we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy datasets and recommend how to address the challenges of moving between traditional and next generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3209v1 | CC BY 4.0 Open Access |

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Section: Introductionmentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2017

Preprint

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“…This is based on their high abundance throughout the genome, simple mutation characteristics, low mutation rates, usability on non-invasive samples and historical DNA, and standardization possibilities between laboratories (Kraus et al, 2014;Morin et al, 2007aMorin et al, ,b, 2004Luikart et al, 2003). SNPs have become an established marker in molecular ecology, evolutionary genetics, and animal breeding (Davey et al, 2011;Kraus et al, 2014Kraus et al, , 2012Morin et al, 2004;Santure et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

et al. 2016

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a b s t r a c tThis study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.

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“…Other applications of the analysis of SNPs are, for example, population genetic studies concerning the history, structure and demography of populations or molecular systematic studies and parentage analyses (Garvin et al 2010;Morin et al 2004). The SNPs identified in this study are suitable for population genetic investigations complementing other frequently used markers such as microsatellites and AFLPs.…”

Section: Introductionmentioning

confidence: 99%

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

Seifert¹,

Vornam²,

Finkeldey³

2012

Eur J Forest Res

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European beech (Fagus sylvatica L.) is one of the most important deciduous tree species in Central Europe. The potential of beech to adapt to climate change, higher temperatures, and less precipitation in the summer months is still unknown. Most studies in beech used microsatellite, AFLP (amplified fragment length polymorphism), or isozyme markers, which have only a restricted potential to analyze adaptation. Only few studies investigated genes probably involved in the adaptation to drought stress and bud phenology in beech. In this study, SNP (single nucleotide polymorphisms) markers were developed in order to analyze adaptation and their technical advantages compared to microsatellites and AFLPs were discussed. Partial sequences of ten candidate genes probably involved in drought stress and/or bud phenology were identified at the genomic level, and SNPs and indels (insertions/deletions) in coding and non-coding regions were analyzed. Plant material was sampled along a precipitation gradient in Germany. In total, 8,145 bp were sequenced and analyzed, 4,038 bp were located in exon and 4,107 bp in intron regions. 63 SNPs and 11 indels were detected, which are differently distributed over the studied gene regions. The nucleotide diversity ranged from 0 to 6.62 (p 9 10 -3 ) and is comparable to other tree species, whereas the mean nucleotide diversity (2.64) for F. sylvatica is comparatively low. These results will help to investigate the genetic basis of drought stress and bud burst and to conduct association mapping in natural populations. Furthermore, the detected SNPs can also be used for population genetic studies.

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SNPs in ecology, evolution and conservation

Cited by 880 publications

References 65 publications

Genetic and genomic monitoring with minimally invasive sampling methods

Genetic and genomic monitoring with minimally invasive sampling methods

Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

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