ArticleBMC genetics2010
SNP identification, verification, and utility for population genetics in a non-model genus.
Article in BMC genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it, 70 citations in OpenAlex.
- Pooled it
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- Genetic Characterization of a Captive Colony of Pigtailed Macaques (Journal of the American Association for Laboratory Animal Science : JAALAS · 2017Article
- Steep, coincident, and concordant clines in mitochondrial and nuclear-encoded genes in a hybrid zone between subspecies of Atlantic killifish, Fundulus heteroclitus.Ecology and evolution · 2016Article
- Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error.BMC research notes · 2015Article
- Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).PloS one · 2015Article
- Genetic diversity analysis of highly incomplete SNP genotype data with imputations: an empirical assessment.G3 (Bethesda, Md.) · 2014Article
- Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic killifish (Fundulus heteroclitus).BMC evolutionary biology · 2014Article
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- Patterns of transcriptome divergence in the male accessory gland of two closely related species of field crickets.Genetics · 2013Article
- Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).PloS one · 2013Article
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- Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing.BMC genomics · 2012Article
- Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail.BMC genomics · 2012Article
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- Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data.Frontiers in genetics · 2012Article
- Ecologically and evolutionarily important SNPs identified in natural populations.Molecular biology and evolution · 2011Article
- Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundBy targeting SNPs contained in both coding and non-coding areas of the genome, we are able to identify genetic differences and characterize genome-wide patterns of variation among individuals, populations and species. We investigated the utility of 454 sequencing and MassARRAY genotyping for population genetics in natural populations of the teleost, Fundulus heteroclitus as well as closely related Fundulus species (F. grandis, F. majalis and F. similis).
resultsWe used 454 pyrosequencing and MassARRAY genotyping technology to identify and type 458 genome-wide SNPs and determine genetic differentiation within and between populations and species of Fundulus. Specifically, pyrosequencing identified 96 putative SNPs across coding and non-coding regions of the F. heteroclitus genome: 88.8% were verified as true SNPs with MassARRAY. Additionally, putative SNPs identified in F. heteroclitus EST sequences were verified in most (86.5%) F. heteroclitus individuals; fewer were genotyped in F. grandis (74.4%), F. majalis (72.9%), and F. similis (60.7%) individuals. SNPs were polymorphic and showed latitudinal clinal variation separating northern and southern populations and established isolation by distance in F. heteroclitus populations. In F. grandis, SNPs were less polymorphic but still established isolation by distance. Markers differentiated species and populations.
conclusionsIn total, these approaches were used to quickly determine differences within the Fundulus genome and provide markers for population genetic studies.
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