Estimation, variance and optimal sampling of gene diversity II. Diploid locus

Pons, Odile; Petit, Rémy J.

doi:10.1007/bf00220868

Cited by 199 publications

(220 citation statements)

References 9 publications

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“…The same populations were used, but the samples were smaller, because cloning of sequences from plants heterozygous for length differences limited the sample size that was possible. All samples are sufficient for accurate withinpopulation diversity estimates (since samples .5 alleles improve accuracy only slightly; see Pons and Chaouche 1995).…”

Section: Methodsmentioning

confidence: 99%

High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

et al. 2008

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Differences in neutral diversity at different loci are predicted to arise due to differences in mutation rates and from the ''hitchhiking'' effects of natural selection. Consistent with hitchhiking models, Drosophila melanogaster chromosome regions with very low recombination have unusually low nucleotide diversity. We compared levels of diversity from five pericentromeric regions with regions of normal recombination in Arabidopsis lyrata, an outcrossing close relative of the highly selfing A. thaliana. In contrast with the accepted theoretical prediction, and the pattern in Drosophila, we found generally high diversity in pericentromeric genes, which is consistent with the observation in A. thaliana. Our data rule out balancing selection in the pericentromeric regions, suggesting that hitchhiking is more strongly reducing diversity in the chromosome arms than the pericentromere regions.

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Section: Methodsmentioning

confidence: 99%

High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

et al. 2008

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“…For the mt data, within population genetic diversity (H S ), total genetic diversity (H T ) and genetic differentiation among populations (G ST ) were calculated according to Pons and Petit (1995) using the programme, CON-TRIB. Allelic richness (A S ) based on a rarefaction factor of 13 was calculated in FSTAT.…”

Section: Genetic Diversity and Differentiationmentioning

confidence: 99%

Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies

et al. 2009

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Norway spruce of northern Europe expanded at the end of the last glacial out of one refugium in Russia. To provide a detailed insight into how the genetic structure in the northern European lineage of this species has been shaped by postglacial migration, recurrent pollen flow and marginality, we here compare variation at seven highly variable nuclear microsatellite loci in 37 populations (1715 trees) with mitochondrial DNA variation. Microsatellite diversity was high (H E ¼ 0.640) and genetic differentiation was low (F ST ¼ 0.029). The microsatellite structure supported a mitochondrial DNA (mtDNA)-based hypothesis of two migration routes out of a single Russian refugium; one northwestern over Finland to northern Scandinavia, and one southwestern across the Baltic Sea into southern Scandinavia. Microsatellite diversity was maintained along the southwestern migration routes, whereas a significant decrease was observed towards the north. In contrast, the mtDNA diversity suggested higher amounts of historical gene flow towards the north than along the southwestern migration route. This suggests that the loss of nuclear diversity after postglacial colonization has been efficiently replenished by pollen-mediated gene flow in the south. Towards the north, smaller effective population size because of more limited seed and pollen production may have caused decreased nuclear diversity and increased inbreeding, reflecting the ecological marginality of the species in the north.

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“…The speed of colonisation was calculated by determining how long it takes for a column in the grid to become 10% colonised, which approximately corresponds to the likelihood of a pollen grain being present in a pollen core sample. Diversity statistics were determined (according to Nei, 1973, see also Pons and Petit, 1995) for average population (H S ) and total (H T ) genetic diversity and differentiation (G ST ) at a number of patch sizes to determine which was the most appropriate sample scale. Model data were extracted from regions 2, 4 and 6 (Figure 1), with 20 populations of 10 individuals randomly sampled for 10 different patch sizes in each region.…”

Section: Preliminary Studymentioning

confidence: 99%

An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis

Davies

White

Lowe³

2004

Heredity

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A simulation-based modelling approach is used to examine the effects of stratified seed dispersal (representing the distribution of the majority of dispersal around the maternal parent and also rare long-distance dispersal) on the genetic structure of maternally inherited genomes and the colonization rate of expanding plant populations. The model is parameterized to approximate postglacial oak colonization in the UK, but is relevant to plant populations that exhibit stratified seed dispersal. The modelling approach considers the colonization of individual plants over a large area (three 500 km Â 10 km rolled transects are used to approximate a 500 km Â 300 km area). Our approach shows how the interaction of plant population dynamics with stratified dispersal can result in a spatially patchy haplotype structure. We show that while both colonization speeds and the resulting genetic structure are influenced by the characteristics of the dispersal kernel, they are robust to changes in the periodicity of long-distance events, provided the average number of long-distance dispersal events remains constant. We also consider the effects of additional physical and environmental mechanisms on plant colonization. Results show significant changes in genetic structure when the initial colonization of different haplotypes is staggered over time and when a barrier to colonization is introduced. Environmental influences on survivorship and fecundity affect both the genetic structure and the speed of colonization. The importance of these mechanisms in relation to the postglacial spread and genetic structure of oak in the UK is discussed.

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Estimation, variance and optimal sampling of gene diversity II. Diploid locus

Cited by 199 publications

References 9 publications

High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies

An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis

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