SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it

J Lachance, SA Tishkoff - Bioessays, 2013 - Wiley Online Library
Whole genome sequencing and SNP genotyping arrays can paint strikingly different pictures
of demographic history and natural selection. This is because genotyping arrays contain …

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms.

JE Seeb, G Carvalho, L Hauser… - Molecular ecology …, 2011 - search.ebscohost.com
An introduction to articles published within the issue is presented, including an approach to
discover single-nucleotide polymorphisms (SNP) for population genetics study of the ringed …

Single nucleotide polymorphism markers with applications in conservation and exploitation of aquatic natural populations

R Wenne - Animals, 2023 - mdpi.com
Simple Summary In recent decades, societies, states and local authorities have become
increasingly aware that for effective long-term management and protection of aquatic …

How array design creates SNP ascertainment bias

J Geibel, C Reimer, S Weigend, A Weigend, T Pook… - PloS one, 2021 - journals.plos.org
Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely
used marker type in population genetic analyses over the last 10 years. However, compared …

Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish

IR Bradbury, S Hubert, B Higgins… - Evolutionary …, 2013 - Wiley Online Library
As populations diverge, genomic regions associated with adaptation display elevated
differentiation. These genomic islands of adaptive divergence can inform conservation …

Characterizing genic and nongenic molecular markers: Comparison of microsatellites and SNP s

J DeFaveri, H Viitaniemi, E Leder… - Molecular ecology …, 2013 - Wiley Online Library
The implications of transitioning to single nucleotide polymorphism (SNP s) from
microsatellite markers (MS s) have been investigated in a number of population genetics …

SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

P Ollitrault, J Terol, A Garcia-Lor, A Bérard… - BMC genomics, 2012 - Springer
Background With the increasing availability of EST databases and whole genome
sequences, SNPs have become the most abundant and powerful polymorphic markers …

A GT‐seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non‐model organisms

ML Bootsma, KM Gruenthal… - Molecular Ecology …, 2020 - Wiley Online Library
Targeted amplicon sequencing methods, such as genotyping‐in‐thousands by sequencing
(GT‐seq), facilitate rapid, accurate, and cost‐effective analysis of hundreds of genetic loci in …

Genotyping‐by‐sequencing of genome‐wide microsatellite loci reveals fine‐scale harvest composition in a coastal Atlantic salmon fishery

IR Bradbury, BF Wringe, B Watson… - Evolutionary …, 2018 - Wiley Online Library
Individual assignment and genetic mixture analysis are commonly utilized in contemporary
wildlife and fisheries management. Although microsatellite loci provide unparalleled …

Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

F Curk, G Ancillo, F Ollitrault, X Perrier… - PloS one, 2015 - journals.plos.org
Most cultivated Citrus species originated from interspecific hybridisation between four
ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further …