Impact of Amplified Fragment Length Polymorphism Size Homoplasy on the Estimation of Population Genetic Diversity and the Detection of Selective Loci

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Genetics

• Publication date

  2008-05-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1534/genetics.107.083246PMID 18493070PMCID PMC2390631
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2008influential reference
• Heterogeneous Genomic Differentiation Between Walking-Stick Ecotypes: “Isolation by Adaptation” and Multiple Roles for Divergent Selection

  2008influential reference
• Genome scan of Diabrotica virgifera virgifera for genetic variation associated with crop rotation tolerance

  2007influential reference
• The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes.

  2007cited by this paper
• Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists

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  2006influential reference
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  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
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• INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergence

  2005cited by this paper
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  2004influential reference
• Genetic diversity in Tetrachaetum elegans, a mitosporic aquatic fungus

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• A microsatellite-based multilocus screen for the identification of local selective sweeps.

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  2001cited by this paper
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  2000influential reference
• A Simple method for the detection of size homoplasy among amplified fragment length polymorphism fragments

  2000cited by this paper
• AFLP genotyping and fingerprinting.

  1999cited by this paper
• Evaluation of AFLP in Beta

  1999influential reference
• Estimating population structure in diploids with multilocus dominant DNA markers

  1999influential reference
• A method for estimating nucleotide diversity from AFLP data.

  1999influential reference
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  1997cited by this paper
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  1996influential reference
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  1995cited by this paper
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  1991cited by this paper
• ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE

  1984cited by this paper
• GENETIC STRUCTURE OF POPULATIONS.

  1975cited by this paper
• Analysis of gene diversity in subdivided populations.

  1973cited by this paper
• Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms.

  1973cited by this paper
• Genetical Structure of Populations

  1950cited by this paper
• Genetical structure of populations.

  1950cited by this paper
• The Distribution of Gene Frequencies in Populations.

  1937cited by this paper
• THE DISTRIBUTION OF GENE FREQUENCIES IN POPULATIONS.

  1937cited by this paper

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