Journal•ISSN: 1471-8278
Molecular Ecology Notes
Wiley-Blackwell
About: Molecular Ecology Notes is an academic journal. The journal publishes majorly in the area(s): Microsatellite & Population. It has an ISSN identifier of 1471-8278. Over the lifetime, 1855 publications have been published receiving 102717 citations.
Topics: Microsatellite, Population, Polymorphic Microsatellite Marker, Locus (genetics), Genetic diversity
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TL;DR: Genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data.
Abstract: genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/
15,786 citations
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TL;DR: MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
Abstract: DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO - CHECKER is WINDOWS ®-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. MICRO CHECKER can be freely downloaded from http://www.microchecker.hull.ac.uk/.
9,953 citations
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TL;DR: Distortion as discussed by the authors provides a general method for visualizing membership coefficients in multilocus genotypes from structured populations, and can be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
Abstract: In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as STRUCTURE . DISTRUCT provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. DISTRUCT , available at www.cmb.usc.edu/∼ noahr/distruct.html, can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
4,668 citations
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TL;DR: A simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish is presented.
Abstract: Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd.uchicago.edu/structure.html.
4,274 citations
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3,792 citations