The utility of single nucleotide polymorphisms in inferences of population history

By R. T. Brumfield, Peter Beerli, Deborah A. Nickerson, S. Edwards. 2003

655 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/88f0f9ace5c8d330fcb65f713af784cc889754ea

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In Molecular Biology

Citations in the corpus

Contribution of genetics and genomics to seagrass biology and conservation (2007, background): “…as starting point for the development of second-generation molecular markers that may reflect selection (and not only neutral genetic processes), such as EST linked microsatellites (Li et al., 2002) or single nucleotide polymorphism (SNP, Brumfield et al., 2003) (see Molecular markers section).”
Standard methods for characterising subspecies and ecotypes of Apis mellifera (2013, background): “While there would be four possible nucleotides at each position of a sequence stretch, due to the low mutation rate, which is about 10-8 to 10-9 changes per nucleotide per generation (Brumfield et al., 2003), SNPs are usually bi-allelic.”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, background): “SNPs are useful markers for population genetic studies and phylogenetic analyses of recently diverged species (Brumfield et al. 2003; Liu et al. 2014; Spinks et al. 2014; Streicher et al. 2014), and they can provide accurate measures of population parameters (Kuhner et al. 2000; Arnold et al. 2013).”
THE MOLECULAR TOOLBOX: GENETIC TECHNIQUES IN WILDLIFE ECOLOGY AND MANAGEMENT (2005, background): “About 90% of variation in the human genome is the result of SNPs (Collins et al. 1998), and this genome-wide distribution of SNPs provides a highly accurate measure of genetic variation (Brumfield et al. 2003).”
GENETIC APPROACHES FOR ESTIMATING THE EFFECTIVE SIZE OF POPULATIONS (2005, background): “Newly developed types of biparentally inherited markers, such as single nucleotide polymorphisms (SNPs; Brumfield et al. 2003), should perform well with most estimators of NeV ; however, they may produce more biased estimates of historical NeI than would be obtained with microsatellites (Morin et…”
The importance of immune gene variability (MHC) in evolutionary ecology and conservation (2005, background): “While these markers are very informative for phylogenetic reconstructions and population history (bottleneck effects), for molecular clocks, to examine dispersal patterns of individuals (gene flow) and to classify individuals by relatedness and paternity analyses [25-28], the variation at neutral lo”
Highly accurate SNP genotyping from historical and low‐quality samples (2007, methodology): “Single-nucleotide polymorphism (SNP) genotyping is rapidly becoming a powerful tool for assessing genetic variation in natural populations (reviewed in Brumfield et al . 2003; Morin et al . 2004).”
Beyond FST: Analysis of population genetic data for conservation (2004, methodology): “In the past seven years, however, new statistical methods have been developed along with an increase in genetic data provided by large sample sizes and DNA markers such as microsatellites, sequences, and most recently, single nucleotide polymorphisms (SNPs; see review by Brumfield et al. 2003).”
Markers, old and new, for examining Phytophthora infestans diversity (2004, background): “A haplotype is a set of polymorphisms in a defined length of DNA sequence that can be assigned unambiguously to one chromosome (Brumfield et al., 2003) and is the raw data for much phylogeographic analysis.”
Land ahead: using genome scans to identify molecular markers of adaptive relevance (2008, methodology): “Most methods to detect historical and recent bottlenecks are based on the assumption of neutrality (Cornuet and Luikart 1996; Brumfield et al. 2003).”
Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars (2008, background): “The utilization of multi-SNP haplotypes can offset the relatively low information content of single SNP loci (Brumfield et al. 2003).”
Insect-Fungal Associations: Ecology and Evolution (2005, background): “Mutation rates estimated for microsatellites and SNPs differ by several orders of magnitude (e.g., ≈10–4 versus 10–8– 10–9, respectively; Brumfield et al. 2003).”
DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. (2007, background): “More recently, with the availability of high-throughput sequencing technology, ﬁne-scale sequence analysis methods, such as single-nucleotide polymorphism (SNP), have given a new dimension to population-level studies [44].”
Identifying future research needs in landscape genetics: where to from here? (2009, background): “Molecular markers can be carefully selected to match the research questions and spatio-temporal scales by considering not only mutation rate and variability, but also genome representativeness, inheritance and ploidy level (Brumfield et al. 2003).”
How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use (2009, background): “Today, electrophoretic marker data may seem outdated, but it has only recently become easy to sample more than 30 anonymous sequence loci (Brumfield et al. 2003), or microsatellites for most species groups.”