Population genetics of STR loci in Caucasians

Balding, David J.; Greenhalgh, M.; Nichols, Richard A.

doi:10.1007/bf02432124

Cited by 46 publications

(33 citation statements)

References 19 publications

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“…Unlike frequentist methods, BayeScan takes into account heterogeneous rates of migration between populations, corresponding to a situation likely to occur in natural populations. A Bayesian approach is used to estimate the posterior probabilities of two alternative models estimating the locus-population-specific F ST as described by Balding et al (1996): a "neutral model" including only population effects (b j ) and thus accounting only for demographic effects and a "selection model" including both population effects (b j ) and locus effects (a i ) indicative of selection. A negative a i value indicates balancing selection whereas a positive a i value indicates directional selection.…”

Section: Statistical Analysesmentioning

confidence: 99%

Imprints of Natural Selection Along Environmental Gradients in Phenology-Related Genes ofQuercus petraea

et al. 2013

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We explored single nucleotide polymorphism (SNP) variation in candidate genes for bud burst from Quercus petraea populations sampled along gradients of latitude and altitude in Western Europe. SNP diversity was monitored for 106 candidate genes, in 758 individuals from 32 natural populations. We investigated whether SNP variation reflected the clinal pattern of bud burst observed in common garden experiments. We used different methods to detect imprints of natural selection (F ST outlier, clinal variation at allelic frequencies, association tests) and compared the results obtained for the two gradients. F ST outlier SNPs were found in 15 genes, 5 of which were common to both gradients. The type of selection differed between the two gradients (directional or balancing) for 3 of these 5. Clinal variations were observed for six SNPs, and one cline was conserved across both gradients. Association tests between the phenotypic or breeding values of trees and SNP genotypes identified 14 significant associations, involving 12 genes. The results of outlier detection on the basis of population differentiation or clinal variation were not very consistent with the results of association tests. The discrepancies between these approaches may reflect the different hierarchical levels of selection considered (inter-and intrapopulation selection). Finally, we obtained evidence for convergent selection (similar for gradients) and clinal variation for a few genes, suggesting that comparisons between parallel gradients could be used to screen for major candidate genes responding to natural selection in trees.L OCAL adaptation of temperate forest trees to environmental variation has been widely investigated in common garden experiments or provenance tests (Langlet 1971;Matyas 1996; König 2005 for reviews). Comparisons of populations sampled over wide ranges have revealed continuous patterns of differentiation along environmental gradients (Wright 1976;Morgenstern 1996). Clinal variation along geographic gradients (latitude, altitude, longitude) is frequently reported for phenological traits (see Alberto et al. 2013 for a review). Congruent clines have been identified across species and across experiments within species, suggesting the occurrence of directional selection in response to identical environmental gradients. For example, in northern temperate spruces and pines, populations from northern latitudes flush earlier than southern populations (Wright 1976;Morgenstern 1996) and steep clines have been observed in species extending over large ranges of latitude (Pinus sylvestris in Scandinavia, Giertych 1991; Picea sitchensis in North America, Mimura and Aitken 2007). Bud burst clines have also been observed in northern temperate broadleaved trees, but following the opposite trend. In beech (von Wuehlisch et al. 1995), birch (Worrell et al. 2000), and sessile oak (Liepe 1993;Deans and Harvey 1995;Ducousso et al. 1996), southern populations flush earlier than northern populations. Similar clinal variation has also been repo...

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Section: Statistical Analysesmentioning

confidence: 99%

Imprints of Natural Selection Along Environmental Gradients in Phenology-Related Genes ofQuercus petraea

et al. 2013

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“…This procedure would, however, be appropriate only if F were constant across loci and we will see (Fig. 1) that such an hypothesis is not supported by the data (see also Balding et a!., 1996). Possible reasons include differing mutation rates or selection processes at distinct loci.…”

Section: Combining In Formationmentioning

confidence: 94%

Significant genetic correlations among Caucasians at forensic DNA loci

Balding

Nichols

1997

Heredity

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Although the effect of population differentiation on the forensic use of DNA profiles has been the subject of controversy for some years now, the debate has largely failed to focus on the genetical questions directly relevant to the forensic context. We re-analyse two published data sets and find that they convey much the same message for forensic inference, in contrast with the dramatically differing conclusions of the original authors. The analysis is likelihood-based and combines information across loci and across populations without assuming constant genetic differentiation. Our results suggest that the relevant genetic correlation coefficients are too large to be ignored in forensic work: although DNA profile evidence is typically very strong, the effect of genetic correlations can be important in some cases. Such correlations can, however, be accommodated in an appropriate assessment of evidential strength so that population genetic issues should not present a barrier to the efficient and fair use of DNA profile evidence.

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“…In forensic casework, this is rarely the case and allele proportion estimates are used from databases covering a large, heterogeneous population [11]. Extensions of this work to allow for uncertainties in allele frequencies and the coancestry coefficient will also be discussed in Section 5.…”

Section: Assumptionsmentioning

confidence: 99%

Object-oriented Bayesian networks for paternity cases with allelic dependencies

Hepler

Weir

2008

Forensic Science International: Genetics

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This study extends the current use of Bayesian networks by incorporating the effects of allelic dependencies in paternity calculations. The use of object-oriented networks greatly simplify the process of building and interpreting forensic identification models, allowing researchers to solve new, more complex problems. We explore two paternity examples: the most common scenario where DNA evidence is available from the alleged father, the mother and the child; a more complex casewhere DNA is not available from the alleged father, but is available from the alleged father's brother. Object-oriented networks are built, using HUGIN, for each example which incorporate the effects of allelic dependence caused by evolutionary relatedness.

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Population genetics of STR loci in Caucasians

Cited by 46 publications

References 19 publications

Imprints of Natural Selection Along Environmental Gradients in Phenology-Related Genes ofQuercus petraea

Imprints of Natural Selection Along Environmental Gradients in Phenology-Related Genes ofQuercus petraea

Significant genetic correlations among Caucasians at forensic DNA loci

Object-oriented Bayesian networks for paternity cases with allelic dependencies

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