Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in<i><scp>P</scp>opulus</i>

Lindtke, Dorothea; Buerkle, C. Alex; Barbará, Thelma; Heinze, Berthold; Castiglione, Stefano; Bartha, Dénes; Lexer, Christian

doi:10.1111/j.1365-294x.2012.05744.x

Cited by 50 publications

(131 citation statements)

References 82 publications

(186 reference statements)

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“…In plants, resistance genes have been put forward for their potential role in the origin and maintenance of reproductive barriers through hybrid necrosis (Bomblies and Weigel 2007;Bomblies 2009). The two European Populus species, Populus alba and Populus tremula, have been described as species with incomplete reproductive barriers that hybridize despite relatively high levels of genomic divergence Lindtke et al 2012;Stölting et al 2013), largely concordant with available models of Bporous genomes^and heterogenous genomic divergence (Wu 2001;Feder et al 2012). Postzygotic selection has recently been put forward as a mechanism potentially maintaining the species barrier, but the exact selective factors acting on hybrid seedlings are currently unknown (Lindtke et al 2014).…”

Section: Introductionmentioning

confidence: 84%

“…European Populus species have previously been shown to present high levels of genomic divergence Lindtke et al 2012;Stölting et al 2013). The impact of R-gene clusters on the genomics of population divergence of Populus species with porous genomes is poorly known, even though R-genes were put forward as gene families that, through diversification by tandem duplication followed by genomic reorganization and gene conversion, have contributed greatly to the evolution of biological responses in poplars (Tuskan et al 2006).…”

Section: Discussionmentioning

confidence: 99%

“…These individuals were previously characterized as parental species or hybrids according to their hybrid index measured as the admixture proportion (Q) assessed with 77 microsatellite markers Lindtke et al 2012). Individuals were classified as P. alba when Q>0.95, as hybrids when 0.95>Q>0.05, and as P. tremula when Q< 0.05.…”

Section: Plant Materialsmentioning

confidence: 99%

“…Genetic markers positioned outside of R-gene clusters on chromosomes III and IV and markers from chromosomes I, VI, and X (Fig. 1), available from a previous study (Lindtke et al 2012), were also used for comparative purposes. These additional chromosomes were selected as a reference for genetic diversity outside of R-gene clusters.…”

Section: Molecular Genetic Markersmentioning

confidence: 99%

“…The overall genetic structure and diversity of European Populus hybrid zones have been previously studied (Lexer et al 2005Lindtke et al 2012). In this study, descriptive population genetic parameters focused on gene diversity (He), allelic richness corrected for sample size, and genetic differentiation (F ST ) between parental species in each hybrid zone are provided only for the target and reference genomic regions (see above).…”

Section: Genetic Diversitymentioning

confidence: 99%

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Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Caseys

Stölting

Barbará

et al. 2015

Tree Genetics & Genomes

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Resistance genes (R-genes) are essential for longlived organisms such as forest trees, which are exposed to diverse herbivores and pathogens. In short-lived model species, R-genes have been shown to be involved in species isolation. Here, we studied more than 400 trees from two natural hybrid zones of the European Populus species Populus alba and Populus tremula for microsatellite markers located in three R-gene clusters, including one cluster situated in the incipient sex chromosome region. The results indicate that all three R-gene clusters present extensive linkage disequilibrium (LD). Outlier tests suggest balancing selection as a potential driver of R-gene diversity, but divergent selection was also detected. Nucleotide-binding site leucine-rich repeat (NBS-LRR) type R-gene clusters exhibit low species differentiation and appear to be affected by shared selection pressures between species, recurrent interspecific gene flow, or both. Our results are consistent with a role for R-gene clusters in the evolution of chromosome XIX, recently put forward as an incipient sex chromosome in Populus.

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Section: Introductionmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Plant Materialsmentioning

confidence: 99%

Section: Molecular Genetic Markersmentioning

confidence: 99%

Section: Genetic Diversitymentioning

confidence: 99%

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Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Caseys

Stölting

Barbará

et al. 2015

Tree Genetics & Genomes

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Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns

2018

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Natural selection plays a variety of roles in hybridization, speciation, and admixture. Most research has focused on two extreme cases: crosses between closely related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. But many natural populations must fall into intermediate regimes, with multiple types of gene interaction, and these are more difficult to study. Here, we develop a simple fitness landscape model, and show that it naturally interpolates between previous modeling approaches, which were designed for the extreme cases, and invoke either mildly deleterious recessives, or discrete hybrid incompatibilities. Our model yields several new predictions, which we test with genomic data from Mytilus mussels, and published data from plants (Zea, Populus, and Senecio) and animals (Mus, Teleogryllus, and Drosophila). The predictions are generally supported, and the model explains a number of surprising empirical patterns. Our approach enables novel and complementary uses of genome‐wide datasets, which do not depend on identifying outlier loci, or “speciation genes” with anomalous effects. Given its simplicity and flexibility, and its predictive successes with a wide range of data, the approach should be readily extendable to other outstanding questions in the study of hybridization.

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Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow

et al. 2018

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Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system‐specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome‐wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non‐neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non‐neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.

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Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation inPopulus

Cited by 50 publications

References 82 publications

Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns

Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow

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