Geographical structure of gene diversity in Quercus petraea (Matt.) Liebl. I. Monolocus patterns of variation

Kremer, Antoine; Zanetto, Anne

doi:10.1038/hdy.1995.167

Cited by 86 publications

(83 citation statements)

References 32 publications

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“…Purifying selection within candidate genes could have generated background selection at the associated polymorphism, thus producing lower F ST values (Maruki et al 2012). However, the overall F ST of SNPs was of the same magnitude as earlier reported values for other genetic markers (Zanetto and Kremer 1995;Mariette et al 2002;Alberto et al 2010). Thus it seems unlikely that purifying selection may have shifted the levels of population differentiation.…”

Section: Local Adaptation Along the Environmental Gradientsmentioning

confidence: 57%

“…Despite the low level of population differentiation reported by traditional F ST estimations in oaks (Zanetto and Kremer 1995;Mariette et al 2002;Alberto et al 2010), we incorporated genetic structure into the model through the Bayesian clustering method implemented in Structure v. 2.3 (Pritchard et al 2000). The structure of the populations of the altitudinal gradient was previously assessed with a set of 14 neutral nuclear microsatellites, in a previous study (see Alberto et al 2010 for details).…”

Section: Statistical Analysesmentioning

confidence: 99%

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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: Local Adaptation Along the Environmental Gradientsmentioning

confidence: 57%

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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“…Liebl.) in Europe using several isozyme markers (Zanetto & Kremer, 1995). A total of 81 populations were sampled over most of the European range of this species.…”

Section: Numerical Examplementioning

confidence: 99%

“…We will present the exact or approximate bootstrap estimators and will compare them to the direct estimators obtained analytically in Pons & Petit (1995) and which will be referred to simply as the 'direct estimators'. These results will be illustrated using data on isozyme polymorphism in sessile oak (Zanetto & Kremer, 1995). The comparison of the bootstrap estimators with the corresponding bootstrap simulated values will provide an evaluation of the approximations we used in the analytical derivations of the variances.…”

Section: Introductionmentioning

confidence: 99%

Bootstrap variance of diversity and differentiation estimators in a subdivided population

Petit

Pons

1998

Heredity

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We have recently proposed new estimators of the parameters of genetic diversity and differentiation and of their variances for a haploid locus in a population subdivided into a large number of subpopulations, with a two-stage sampling of populations and individuals. Here they are compared with bootstrap estimators. Several resampling methods are evaluated: sampling of populations only, individuals within populations only, or both. Theoretical results and a numerical example show that the most appropriate bootstrap variance estimators are obtained by resampling the populations alone and not both populations and individuals. However, some bias is apparent in the bootstrap methods, and the direct estimators proposed previously should therefore be preferred.

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“…When analyzing the genetic structure of populations using enzyme-coding loci, Zanetto and Kremer [21] observed significant differences in the frequencies of alleles in oak populations. Streiff et al [10] used isozymes and six microsatelite loci to study the diversity and fine-scale genetic structure within a native oak forest containing Quercus robur and Q. petraea in the northwest of France.…”

Section: Introductionmentioning

confidence: 99%

Genetic differences within natural and planted stands of Quercus petraea

2011

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Five sessile oak [Quercus petraea (Matt.) Liebl.] stands from the Czech Republic were studied to learn about the impact of different types of forest management regimes on the genetic differences among tree populations and on population structures. One population had not been markedly affected by human activity, two populations represented unplanted stands that were extensively managed for a long period of time using the coppice system, and two populations were planted stands. Approximately 100 trees from each stand were mapped and subsequently genotyped using 10 nuclear microsatellite loci. We determined the spatial genetic structure of each population and the genetic differentiation among the populations. We found that: (i) the populations were genetically differentiated, but the differences between the unplanted and planted stands were not markedly significant; (ii) the genetic differentiation among the populations depended on the geographical distribution of the populations; (iii) within unplanted stands, a strong spatial genetic structure was seen; and (iv) within planted stands, no spatial genetic structure was observed. Our findings implies that the analysis of spatial genetic structure of the sessile oak forest stand can help reveal and determine its origin.

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Geographical structure of gene diversity in Quercus petraea (Matt.) Liebl. I. Monolocus patterns of variation

Cited by 86 publications

References 32 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

Bootstrap variance of diversity and differentiation estimators in a subdivided population

Genetic differences within natural and planted stands of Quercus petraea

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