Journal ArticleDOI
Micro-Checker: Software for identifying and correcting genotyping errors in microsatellite data
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TLDR
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/.read more
Citations
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Journal ArticleDOI
Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers
TL;DR: This synthesis presents a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike and aims to encourage the use and consistent reporting of thorough marker screening to ensure high quality data.
Journal ArticleDOI
Genotyping errors: causes, consequences and solutions.
TL;DR: A protocol for estimating error rates is proposed and it is recommended that these measures be systemically reported to attest the reliability of published genotyping studies.
Journal ArticleDOI
Speciation through sensory drive in cichlid fish
Ole Seehausen,Ole Seehausen,Yohey Terai,Isabel S. Magalhaes,Isabel S. Magalhaes,Karen L. Carleton,Hillary D. J. Mrosso,Ryutaro Miyagi,Inke van der Sluijs,Maria Victoria Schneider,Martine E. Maan,Hidenori Tachida,Hiroo Imai,Norihiro Okada +13 more
TL;DR: This work identifies the ecological and molecular basis of divergent evolution in the cichlid visual system, demonstrates associated divergence in male colouration and female preferences, and shows subsequent differentiation at neutral loci, indicating reproductive isolation.
Journal ArticleDOI
Current trends in microsatellite genotyping.
Erwan Guichoux,Lélia Lagache,Stefanie Wagner,Stefanie Wagner,Philippe Chaumeil,Patrick Léger,Olivier Lepais,Olivier Lepais,Camille Lepoittevin,Thibaut Malausa,E. Revardel,Franck Salin,Rémy J. Petit +12 more
TL;DR: To make the most of the latest technical developments, the need for a well‐established strategy including standardized high‐throughput bench protocols and specific bioinformatic tools, from primer design to allele calling is outlined.
Journal ArticleDOI
Larval Export from Marine Reserves and the Recruitment Benefit for Fish and Fisheries
Hugo B. Harrison,Hugo B. Harrison,David H. Williamson,Richard D. Evans,Richard D. Evans,Glenn R. Almany,Simon R. Thorrold,Garry R. Russ,Kevin A. Feldheim,Lynne van Herwerden,Serge Planes,Maya Srinivasan,Michael L. Berumen,Michael L. Berumen,Geoffrey P. Jones +14 more
TL;DR: Using genetic parentage analyses, patterns of larval dispersal for two species of exploited coral reef fish within a network of marine reserves on the Great Barrier Reef are resolved and provide compelling evidence that adequately protected reserve networks can make a significant contribution to the replenishment of populations on both reserve and fished reefs at a scale that benefits local stakeholders.
References
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Journal ArticleDOI
GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism
Michel Raymond,François Rousset +1 more
Journal ArticleDOI
Statistical confidence for likelihood-based paternity inference in natural populations
TL;DR: This study derives likelihood ratios for paternity inference with codominant markers taking account of typing error, and defines a statistic Δ for resolving paternity, and demonstrates the method is robust to their presence under commonly encountered conditions.
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