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MBE Advance Access published online on November 6, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp267
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Intragenic Recombination Events and Evidence for Hybrid Speciation in Nicotiana (Solanaceae)

Laura J. Kelly*,{dagger},1, Andrew R. Leitch{dagger}, James J. Clarkson*, Robin B. Hunter*,{ddagger}, Sandra Knapp§ and Mark W. Chase*

* Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3DS, UK
{dagger} Queen Mary University of London, School of Biological and Chemical Sciences, E1 4NS, London, UK
{ddagger} Smith College, Northampton, Massachusetts 01063, USA
§ Department of Botany, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK

1 Author for correspondence, Present Address: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK; E-mail: l.kelly{at}rbge.ac.uk; Tel: +44 (0)131 248 2957, Fax: +44 (0)131 248 2901.

Received for publication August 26, 2009. Revision received October 30, 2009. Accepted for publication November 3, 2009.

Reticulate evolution may function both at the species-level, through homoploid and polyploid hybridization, and below the species level, through inter- and intragenic recombination. These processes represent challenges for the reconstruction of evolutionary relationships between species, because they cannot be represented adequately with bifurcating trees. We use data from low-copy nuclear genes to evaluate long-standing hypotheses of homoploid (interspecific) hybrid speciation in Nicotiana (Solanaceae) and reconstruct a complex series of reticulation events that have been important in the evolutionary history of this genus. Hybrid origins for three diploid species (N. glauca, N. linearis and N. spegazzinii) are inferred on the basis of gene tree incongruence, evidence for inter-allelic recombination between likely parental alleles, and support for incompatible splits in Lento plots. Phylogenetic analysis of recombinant gene sequences illustrates that recombinants may be resolved with one of their progenitor lineages with a high posterior probability under Bayesian inference, and thus there is no indication of the conflict between phylogenetic signals that results from reticulation. Our results illustrate the importance of hybridization in shaping evolution in Nicotiana and also show that intragenic recombination may be relatively common. This finding demonstrates that it is important to investigate the possibility of recombination when aiming to detect hybrids from DNA sequence data and reconstruct patterns of reticulate evolution between species.

Key Words: gene tree • homoploid hybridization • intragenic recombination • Nicotiana • reticulate evolution • supernetwork


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