Blind population genetics survey of tropical rainforest trees

Duminil, Jérôme; Caron, Henri; Scotti, Ivan; Cazal, Saint-Omer; Petit, Rémy J.

doi:10.1111/j.1365-294x.2006.03040.x

Cited by 61 publications

(71 citation statements)

References 42 publications

(66 reference statements)

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“…In particular, by using genetic assignment without any a priori information (Pritchard et al 2000, Duminil et al 2006) many studies highlighted different levels of hybridization rate among European white oak species (Valbuena et al 2005, Gugerli et al 2007, Curtu et al 2007b, Salvini et al 2009.…”

Section: Discussionmentioning

confidence: 99%

Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae)

et al. 2015

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Antonecchia G., Fortini P., Lepais O., Gerber S., Legér P., Scippa G.S., Viscosi V., 2015. Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae). Ann. For. Res. 58(2): 205-216.Abstract. Incomplete reproductive barriers between species, especially in sympatric areas where several species coexist, may result in hybridization and an increase in genetic diversity. Here we assessed the amount of genetic diversity in a community of three interfertile and sympatric European oaks (Quercus frainetto Ten., Q. petraea Liebl. Matt. and Q. pubescens Willd.) situated in central Italy. We used 11 microsatellite markers derived from Expressed Sequence Tag (EST-SSRs) and we implemented a Bayesian clustering analysis to assign individuals to species or hybrids. All genotyped loci were polymorphic for all the species and three genetic clusters corresponding to each species were detected. Significant differences and a higher level of gene flow were observed between the three oak species. Occurrence of hybrids varied markedly within the studied area: hybrids between Q. petraea and Q, pubescens were the most frequent, while hybrids between Q. petraea and Q. frainetto were particularly rare. Q. pubescens and Q. petraea showed the highest number of alleles compared to Q. frainetto, which was characterized by a low number of private, but highly frequent, alleles. However, Q. frainetto showed a lower genetic diversity and a stronger reproductive isolation from the other two oak species.

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Section: Discussionmentioning

confidence: 99%

Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae)

et al. 2015

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“…Bayesian approaches have the ability to detect hidden substructures through pooling sets of individuals independently of the actual sample structure and to infer genetic relationships among populations. Accordingly, Bayesian approaches have proved valuable in analyzing microsatellite data obtained from populations of woody species in several recent studies (Heuertz et al 2004;Tsuda and Ide 2005;Williams et al 2005;Duminil et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan

Hiraoka

Tomaru

2009

J Plant Res

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Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species' range. Although population differentiation was very low (F (ST) = 0.027; R (ST) = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H (E) = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.

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“…Moreover, in all of these studies the identification of genetic diagnostic elements is dependent on the morphological determination of pure species. In contrast, the Bayesian approach used here allows us to define the genetic boundaries of pure species independently from any feature other than genetic data, thus allowing more accurate estimates of species status (Duminil et al, 2006) and gene exchange. We found a similar proportion of each parental morphotype among the putative hybrid individuals (Figure 2) and very good correspondence between morphotype and molecular-based assignation for the putative purebreds.…”

Section: Hybrid Identitymentioning

confidence: 99%

Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex)

et al. 2009

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Powerful and accurate detection of first-generation (F1) hybrids and backcrosses in nature is needed to achieve a better understanding of the function and dynamics of introgression. To document the frequency of ongoing interspecific gene exchange between two Mediterranean evergreen oaks, the cork oak (Quercus suber) and the holm oak (Q. ilex), we analyzed 1487 individuals originating from across the range of the two species using eight microsatellite loci and two Bayesian clustering approaches (implemented in the programs STRUCTURE and NEWHY-BRIDS). Simulated data were used to assess the differences between the two clustering methods and to back up the choice of the threshold value for the posterior probability to discriminate admixed from pure individuals. We found that the use of STRUCTURE resulted in the highest power to detect hybrids, whereas NEWHYBRIDS provided the highest accuracy. Irrespective of the approach, the two species were clearly distinguished as independent genetic entities without any prior information. In contrast with previous reports, we found no evidence for unidirectional introgression. The overall hybridization rate was very low (o2% of introgressed individuals). Only two individuals were identified as F1 hybrids and five as early backcrosses. This work shows that the combined application of the two complementary Bayesian approaches and their systematic validation with simulations, fit for the case at hand, helps gain resolution in the identification of admixed individuals.

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Blind population genetics survey of tropical rainforest trees

Cited by 61 publications

References 42 publications

Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae)

Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae)

Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan

Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex)

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