Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations.

By R. Petit, J. Duminil, S. Fineschi, A. Hampe, D. Salvini, G. Vendramin. Molecular Ecology, 2005

887 citations recorded by the source corpus.

Plants offer excellent models to investigate how gene flow shapes the organization of genetic diversity. Their three genomes can have different modes of transmission and will hence experience varying levels of gene flow. We have compiled studies of genetic structure based on chloroplast DNA (cpDNA), mitochondrial DNA (mtDNA) and nuclear markers in seed plants. Based on a data set of 183 species belonging to 103 genera and 52 families, we show that the precision of estimates of genetic differentiation (G(ST)) used to infer gene flow is mostly constrained by the sampling of populations. Mode of inheritance appears to have a major effect on G(ST). Maternally inherited genomes experience considerably more subdivision (median value of 0.67) than paternally or biparentally inherited genomes (approximately 0.10). G(ST) at cpDNA and mtDNA markers covary narrowly when both genomes are maternally inherited, whereas G(ST) at paternally and biparentally inherited markers also covary positively but more loosely and G(ST) at maternally inherited markers are largely independent of values based on nuclear markers. A model-based gross estimate suggests that, at the rangewide scale, historical levels of pollen flow are generally at least an order of magnitude larger than levels of seed flow (median of the pollen-to-seed migration ratio: 17) and that pollen and seed gene flow vary independently across species. Finally, we show that measures of subdivision that take into account the degree of similarity between haplotypes (N(ST) or R(ST)) make better use of the information inherent in haplotype data than standard measures based on allele frequencies only.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/777cb6d460aba93eda5d7bf2e6f01c5bf9666171

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Citations in the corpus

Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum (2009, methodology): “The cpDNA is maternally inherited in the Betulaceae (Petit et al., 2005), and the genetic variation patterns based on this genome can be used to trace retreats and colonization routes of O.”
Using population genetic analyses to understand seed dispersal patterns (2011, methodology): “116 in the conifers surveyed (Petit et al., 2005).”
Some Evolutionary Consequences of Being a Tree (2006, background): “The impact of global change will depend to a great extent on the reaction of trees and the ecosystems they sustain (e.g., Ozanne et al. 2003; Petit et al. 2004a, 2005b).”
Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea) (2007, background): “Common maternal inheritance of organelles makes cytoplasmic DNA polymorphism an ideal tool for phylogeographical study and assessment of phylogenetic relationships between uniparental lineages disseminated by seeds (Schaal et al., 1998; McKinnon et al., 2004; Petit et al., 2005).”
Plant phylogeography based on organelle genes: an introduction (2007, result): “Table 7 provides mean values of GST from an unpublished literature review (Petit et al. 2005), comparing the results of angiosperms with those for conifers.”
Refugia within refugia: the case study of a canopy tree (Eurycorymbus cavaleriei) in subtropical China (2009, result): “Indeed, this value is high when compared with the values observed for other angiosperm species (mean value of GST = 0.637; Petit et al., 2005).”
Phylogeography of a widespread Asian subtropical tree: genetic east–west differentiation and climate envelope modelling suggest multiple glacial refugia (2014, background): “Castanopsis eyrei is a species with strong pollen flow, showing a higher pollen-to-seed migration ratio (r = 25) than the reported median value for seed plants of 17 (Petit et al., 2005).”
Latitudinal gradients as natural laboratories to infer species' responses to temperature (2013, background): “Genetic differentiation between populations is common (e.g. Petit et al. 2005), and many populations show local adaptation to their home environment (Leimu & Fischer 2008).”
Spatial Scales of Pollen and Seed-Mediated Gene Flow in Tropical Rain Forest Trees (2008, background): “One reason is that maternally inherited cpDNA variation is generally too low to allow for maternal exclusion [ 100 ].”
Phylogeography and genetic differentiation along the distributional range of the orchid Epidendrum fulgens: a Neotropical coastal species not restricted to glacial refugia (2011, background): “…of nuclear and plastid genomes allowed inferences to be made regarding the relative levels of gene flow by pollen and by seed, by comparing GST values from biparentally inherited nuclear markers (GSTb) with those from uniparentally inherited plastid markers (GSTm) (Ennos, 1994; Petit et al., 2005).”
Identifying future research needs in landscape genetics: where to from here? (2009, background): “…uniparentally inherited, haploid markers of the slowly evolving organellar DNA (i.e., mitochondria or chloroplasts) are well suited, since they have lower mutation rates and smaller effective population sizes than nuclear loci at neutral sites (Petit et al. 2005; Petit and Vendramin 2007).”
Choosing and Using a Plant DNA Barcode (2011, background): “Pollen : seed flow ratios derived from joint nuclear-organelle FST estimates typically show much higher pollen-flow than seed-flow [80–82], and measures of population differentiation for maternally inherited markers are typically much higher than for nuclear markers [81].”
Inferring the past from the present phylogeographic structure of North American forest trees : seeing the forest for the genes (2009, background): “, NST or RST) and do not take (GST) into account the relatedness among genetic variants (Pons and Petit 1996) has also become common (Petit et al. 2005).”
Phylogeographical structure and conservation genetics of wild grapevine (2006, methodology): “…et al. 2000). pollen flow seed flow ¼ 1 GSTb 1 2 1GSTc 1 1 GSTc 1 This equation has already been used to estimate the relative ratio of pollen and seed flow in different Angiosperm species for which GST values are available from both biparental and maternally inherited markers (Petit et al. 2005).”