Detection of genomic regions differentiating two closely related oak species Quercus petraea (Matt.) Liebl. and Quercus robur L.

Bodénès, Catherine; JOANDET, S; Laigret, Frédéric; Kremer, Antoine

doi:10.1038/sj.hdy.6880910

Cited by 20 publications

(21 citation statements)

References 13 publications

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“…The genetic differentiation between Q. ellipsoidalis and Q. velutina increased (9%) when equal numbers of largely genetically pure ( 0.80 ancestry coefficient) individuals of the four species were analyzed, but remained the same between Q. rubra and Q. coccinea (Table S6). Genetic marker analyses in other hybridizing oak species revealed a similar pattern of low interspecific genetic differentiation, suggesting incomplete reproductive isolation between species (Bodénès et al 1997;Mariette et al 2002;Aldrich et al 2003) and/or incomplete lineage sorting (Muir and Schlö tterer 2005).…”

Section: Individualmentioning

confidence: 90%

Taxonomic Relationships and Gene Flow in Four North American Quercus Species (Quercus section Lobatae)

Owusu¹,

Sullivan²,

Weber³

et al. 2015

Systematic Botany

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Taxonomic relationships between North American red oak species (Quercus section Lobatae) are not well resolved using genetic and morphological markers. Phenotypic plasticity, recent species divergence, and hybridization may all contribute to the unclear species boundaries in red oaks. We applied twenty-eight genomic and gene-based microsatellites, including outlier loci with potential roles in reproductive isolation and adaptive divergence between species, to natural populations of four monophyletic interfertile oak species: Quercus ellipsoidalis, Q. coccinea, Q. rubra, and Q. velutina. To better resolve the taxonomic relationships in this difficult clade, we assigned individual samples to species, identified hybrids and introgressive forms, and reconstructed phylogenetic relationships among the four species after exclusion of genetically intermediate individuals. Genetic assignment analyses identified four distinct species clusters, with Q. rubra most differentiated from the three other species. However, especially between Q. ellipsoidalis and Q. velutina, a comparatively large number of misclassified individuals (7.14%), hybrids (7.14%), and introgressive forms (18.83%) were detected. After the exclusion of genetically intermediate individuals, Q. ellipsoidalis grouped as sister species to the largely parapatric Q. coccinea with high bootstrap support (91%). Genetically intermediate forms in a mixed species stand were located proximate to both potential parental species, which supports recent hybridization of Q. velutina with both Q. ellipsoidalis and Q. rubra. Analyses of genome-wide patterns of interspecific differentiation can provide a better understanding of speciation processes and taxonomic relationships in this taxonomically difficult group of red oak species.

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Section: Individualmentioning

confidence: 90%

Taxonomic Relationships and Gene Flow in Four North American Quercus Species (Quercus section Lobatae)

Owusu¹,

Sullivan²,

Weber³

et al. 2015

Systematic Botany

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“…2004). However, fixation at nuclear markers had not been observed in Q. robur or Q. petraea and polymorphisms are generally shared among species (Bodénès et al. 1997; Mariette et al.…”

Section: Discussionmentioning

confidence: 99%

“…2004). Despite a considerable degree of interspecific gene flow and a generally very low differentiation at molecular markers (Bodénès et al. 1997), differences in leaf morphological traits and ecological traits are maintained (Kremer et al.…”

Section: Introductionmentioning

confidence: 99%

QTL analysis of leaf morphological characters in a Quercus robur full‐sib family (Q. robur × Q. robur ssp. slavonica)

Gailing

2008

Plant Biology

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The distinction between white oak species (section Quercus sensu stricto) is largely based on leaf morphological characters. There is, however, considerable within-species variation and no single species-diagnostic character, possibly due to phenotypic plasticity and/or underlying genetic variation. The aim of the present study was to identify quantitative trait loci (QTL) underlying the high within-species variation for leaf morphological characters in an F(1) full-sib family derived from a cross between Q. robur and Q. robur ssp. slavonica. In accordance with an earlier QTL mapping study in an intraspecific Q. robur full-sib family, polygenic inheritance was detected for leaf morphological characters that are used to discriminate between the species Quercus robur and Q. petraea. QTLs were distributed over ten linkage groups, showed a moderate effect in terms of phenotypic variance explained (PVE) in the mapping pedigree (3.6-9.6%), but accounted for a considerable amount of the parental differences. Co-localisation of QTLs on the same linkage group in different genetic backgrounds was found for the number and percentage of intercalary veins (NV, PV) on linkage group 3 and for NV on linkage group 5, revealing a high congruence in the relative QTL positions. The generally low correspondence of the other QTLs in the different mapping pedigrees may be an effect of the genetic background and of the environment. In conclusion, leaf morphological characters were found to be under polygenic control, and a comparison to earlier published results led to the identification of two QTLs that were stable across different genetic backgrounds.

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“…Another important prerequisite for our study was to accurately delimit these two closely related interfertile oak species, which has been a long‐lasting goal for botanists and geneticists (Cousens ; Carlisle & Brown ; Bodénès et al . ; Muir et al . ; Coart et al .…”

Section: Introductionmentioning

confidence: 99%

Outlier loci highlight the direction of introgression in oaks

et al. 2012

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Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late-successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.

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Detection of genomic regions differentiating two closely related oak species Quercus petraea (Matt.) Liebl. and Quercus robur L.

Cited by 20 publications

References 13 publications

Taxonomic Relationships and Gene Flow in Four North American <I>Quercus</I> Species (<I>Quercus</I> section <I>Lobatae</I>)

Taxonomic Relationships and Gene Flow in Four North American <I>Quercus</I> Species (<I>Quercus</I> section <I>Lobatae</I>)

QTL analysis of leaf morphological characters in a Quercus robur full‐sib family (Q. robur × Q. robur ssp. slavonica)

Outlier loci highlight the direction of introgression in oaks

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