ArticlePLoS biology2016
Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.
Article in PLoS biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 184 papers.
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184 citing papers in PubMed.
- Repeated genetic adaptation under demographic limits in kiwifruit.The Plant journal : for cell and molecular biology · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Genomics Approach Links ROS-Scavenging to Enhanced Lateral Root Development Under Salt Stress in Tomato.Plant, cell & environment · 2026Article
- Variance in Calvin-Benson cycle intermediate levels between closely related species in the tomato clade.Journal of experimental botany · 2026Article
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.Systematic biology · 2026Article
- Genomic and ecological drivers of parallel arid adaptation in tree grapes (Vitaceae).Nature communications · 2026Article
- The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization.Systematic biology · 2026Article
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- Phylogenetic Divergence and Domestication Jointly Shape the Tomato Root Microbiome.Plants (Basel, Switzerland) · 2026Article
- Parallel and non-parallel features of adaptive radiation in Yucatán pupfishes.bioRxiv : the preprint server for biology · 2025Article
- Introgression across Narrow Contact Zones Shapes the Genomic Landscape of Phylogenetic Variation in an African Bird Clade.Systematic biology · 2025Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- Comparative Genomics of the Testacea Group of Drosophila Reveals Introgression and Variation in Chromosome Size and Structure.Genome biology and evolution · 2025Article
- Tomato and its relatives are breaking the genomics barriers.Journal of experimental botany · 2025Review
- Comparative Analysis ofGenes · 2025Article
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Phylogenomic and super-pangenome analyses unveil the genetic landscape of tomato evolution and domestication.Plant biotechnology journal · 2025Article
- Phylogeographic evidence reveals multiple colonization events and a secondary contact zone in the Balkans for the Anthriscus sylvestris complex (Apiaceae).Scientific reports · 2025Article
- The unique morphological basis and repeated evolutionary origins of personate flowers in Penstemon.American journal of botany · 2025Article
124 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.
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