Genetic Data Analysis II. Methods for Discrete Population Genentic Data

By J. Ross-Ibarra. 2002

943 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2c4a06641330dcbcb8069d644807e772d934e010

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In Genetics

Citations in the corpus

A comparison of phasing algorithms for trios and unrelated individuals. (2006, methodology): “Use genotypes for pairs of markers to estimate 2 r with the EM algorithm (pairwise) (Weir 1996).”
The VGAM Package for Categorical Data Analysis (2010, background): “There are quite a number of population genetic models based on the multinomial distribution, e.g., Weir (1996), Lange (2002).”
Molecular differentiation, diversity, and folk classification of “sweet” and “bitter” cassava (Manihot esculenta) in Caiçara and Caboclo management systems (Brazil) (2007, positive): “The heterozygosity (H) will be refereed as the genetic diversity index as proposed by Weir (1996).”
Ecological consequences of genetic diversity. (2008, background): “…to depict genetic diversity for discrete traits (Table 1), and although they are often tailored to account for the type of inheritance of a particular genetic marker (Weir 1996), for the most part they all reflect either the number (richness) and ⁄ or relative frequencies (evenness) of alleles.”
Increased inbreeding and inter-species gene flow in remnant populations of the rare Eucalyptus benthamii (2005, methodology): “Genetic differentiation among all populations and pairs of population were compared using FST statistics, calculated according to Weir (1996) using the GDA package.”
Deriving genotypes from RAD-seq short-read data using Stacks (2017, methodology): “If requested, the populations program will calculate a nucleotide-level F ST value, using an analysis of molecular variance framework 45 , between each pair of populations ( --fstats ).”
Population structure and long-range linkage disequilibrium in a durum wheat elite collection (2005, positive): “Significance (p values) of LD for SSR pairs was determined by permutation (Weir 1996); for each pair, 100,000 permutations were performed.”
A Rice Diversity Panel Evaluated for Genetic and Agro‐Morphological Diversity between Subpopulations and its Geographic Distribution (2011, neutral): “1 (Weir, 1996; Excoffier et al., 2005).”
Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.) (2010, methodology): “Allele frequency correlations (r2) according to Weir (1996) were calculated using the LD function.”
Population structure in the Atlantic salmon: insights from 40 years of research into genetic protein variation (2005, background): “This requires careful consideration of sampling theory and hypothesis testing (Weir, 1996), particularly when drawing inferences regarding the species or genome as a whole, and the rejection of null hypotheses is based on the balance of probability.”
Managing biological and genetic diversity in tropical agroforestry (2004, background): “In addition, the extent and causes of genetic variation provide the basis of any evolutionary studies (Weir 1996).”
Association mapping of yield and its components in rice cultivars (2007, methodology): “The distribution of molecular genetic variation among and within the eight clusters of accessions was estimated by AMOVA, which revealed 41% of total variation was among the clusters whereas 51% of the variation was within the clusters (Table 3).”
Arlequin (version 3.0): An integrated software package for population genetics data analysis (2005, background): “• Calculation of several measures of linkage disequilibrium (LD) like D , D ’, or r 2 (Hedrick 1987), and test of non-random association of alleles at different loci when the gametic phase is known (Weir 1996) or unknown (Slatkin and Excof ﬁ er 1996).”
Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity in Sugarcane Germplasm Collections (2006, background): “The polymorphism information content (PIC), which measures information content as a function of a marker system’s ability to distinguish between genotypes (Weir, 1990), varied among the primer combinations ranging from 0.11 in CDPK 1 Arbi 1 to 0.36 in PODK 1 Arbi2 with an average of 0.24.”