A FORTRAN program for the calculation and analysis of two-locus linkage disequilibrium coefficients

Black, William C.; Krafsur, E. S.

doi:10.1007/bf00305981

Cited by 157 publications

(154 citation statements)

References 20 publications

Supporting

Mentioning

145

Contrasting

Unclassified

Order By: Relevance

“…The v.2.1 implements extensions of the original methods described in Stephens et al (2001) and Stephens and Donnelly (2003). Linkage disequilibrium estimates between the STR and their respective Alu were quantified using the adaptation of Black and Krafsur (1985) algorithms contained in the computer program GENETIX 4.05 (Belkhir et al 1996(Belkhir et al -2004. The apportionment of genetic variance was checked by analysis of molecular variance (AMOVA) through the ARLEQUIN computer package (Excoffier et al 2005).…”

Section: Methodsmentioning

confidence: 99%

The ins and outs of population relationships in west-Mediterranean islands: data from autosomal Alu polymorphisms and Alu/STR compound systems

González-Pérez¹,

Moral²,

Via³

et al. 2007

J Hum Genet

View full text Add to dashboard Cite

The islands of the West Mediterranean have played a central role in numerous archaeological, historical and anthropological studies due to their active participation in the history of main Mediterranean civilisations. However, genetic data failed to fit in both their degree of internal differentiation and relationships. A set of 18 Alu markers and three short tandem repeats (STRs) closely linked to the CD4, F13B and DM Alu have been analysed in seven samples from Majorca, Corsica, Sardinia and Sicily to explore some of these issues. Our samples show a high genetic heterogeneity inside and among islands for the Alu data. Global differentiation among islands (F ST 2.2%) is slightly higher than that described for Europeans and North Africans. Both the estimated divergence times among samples and the high population heterogeneity revealed by Alu data are compatible with population differences since the first islands' settlement in the Paleolithic period. However, the high within-population diversities and the remarkable homogeneity observed in both STR and Alu/STR haplotype variation indicated that, at least since Neolithic times, gene flow has been acting in west Mediterranean. Genetic drift in west-coast Sardinia and gene flow in west Sicily have contributed to their general differentiation, whereas Corsica, Majorca and east Sicily seem to reflect more recent historical relationships from continental south Europe.

show abstract

Section: Methodsmentioning

confidence: 99%

The ins and outs of population relationships in west-Mediterranean islands: data from autosomal Alu polymorphisms and Alu/STR compound systems

González-Pérez¹,

Moral²,

Via³

et al. 2007

J Hum Genet

View full text Add to dashboard Cite

show abstract

“…The FORTRAN program of Black & Krafsur (1985) was used to calculate two-locus composite linkage disequilibrium coefficients from the allozyme frequencies and from those estimated for the recessive phenotypes at the shell colour and banding loci. Ohta's methods (1982a,b) were applied, in the hope of distinguishing between deterministic and stochastic effects that can produce linkage disequilibrium.…”

Section: Discussionmentioning

confidence: 99%

Application of ecological genetics techniques to test for selection by habitat on allozymes in Cepaea nemoralis (L.)

Wilson

1996

Heredity

View full text Add to dashboard Cite

Techniques of ecological genetics were applied to the distribution of gene frequencies at seven polymorphic enzyme loci among populations of Cepaea nemoralis in lowland England in an attempt to detect evidence of natural selection operating at the molecular level. In Warwickshire, the frequencies of MDH-1 alleles differed significantly, and those at PEP-D nearly so, between ancient woodlands and old open habitats. However, these differences were not repeated elsewhere. Overall, the pattern of gene frequencies at the molecular level was uncoupled from that at the morphological level, where there was evidence of natural selection on shell colour and banding patterns. The brown phenotype did not appear to be selected in relation to the visible background but, in Gloucestershire, was found to be at a higher frequency on the upper slopes than at lower altitudes along the Cotswold escarpment.

show abstract

“…Disequilibrium in a single population Genotypic disequilibria were estimated for all pairwise combinations of loci in all 81 populations following the method of Weir (1979Weir ( , 1990 An unbiased estimate of Burrows's composite measure of linkage disequilibrium is given by (Cockerham & Weir, 1977;Black & Krafsur, 1985):…”

Section: Plant Materialsmentioning

confidence: 99%

Geographical structure of gene diversity in Quercus petraea (Matt.) Liebl. II: Multilocus patterns of variation

Kremer¹,

Zanetto²

1997

Heredity

View full text Add to dashboard Cite

INRA, Laboratoire c/a genetique et d'amélioration des arbres forestiers, UP 45, 33611 Gazinet Cedex, France Two-locus composite disequilibria were estimated for all 28 pairs of loci (from eight loci) in 81 populations of Quercus petraea spread over the natural distribution of the species. Significant disequilibria were found in almost all populations for two pairs (Aap-A/Lap-A, Mr-A/Dia-A) that have also shown strong linkage in cosegregation analysis. These pairs belong to the so-called complex loci producing nearly identical gene products and that are tightly linked. Significant disequilibria were also found for other pairs of loci that are linked to a smaller degree. The amount of disequilibrium followed a geographical pattern. The number of pairs showing significant disequilibria per population was higher on the edges of the natural range (Norway, Great Britain, Turkey). Disequilibria for the two pairs (Aap-A/Lap-A, Mr-AIDia-A) were also higher at the edges of the distribution and were correlated with longitude. Population differentiation resulting from the associations of alleles at different loci was increased when the correlations of allele frequencies at the within-and between-population level were of different magnitude. It is suspected that correlations at the between-population level may arise from historical causes rather than gametic disequilibrium. Finally, the first canonical variate (multivariate score) including allelic frequencies of all eight loci follows a strong longitudinal pattern of variation.

show abstract

A FORTRAN program for the calculation and analysis of two-locus linkage disequilibrium coefficients

Cited by 157 publications

References 20 publications

The ins and outs of population relationships in west-Mediterranean islands: data from autosomal Alu polymorphisms and Alu/STR compound systems

The ins and outs of population relationships in west-Mediterranean islands: data from autosomal Alu polymorphisms and Alu/STR compound systems

Application of ecological genetics techniques to test for selection by habitat on allozymes in Cepaea nemoralis (L.)

Geographical structure of gene diversity in Quercus petraea (Matt.) Liebl. II: Multilocus patterns of variation

Contact Info

Product

Resources

About