MBE Advance Access originally published online on August 4, 2007
Molecular Biology and Evolution 2007 24(10):2310-2322; doi:10.1093/molbev/msm162
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Articles |
Using Multilocus Sequence Data to Assess Population Structure, Natural Selection, and Linkage Disequilibrium in Wild Tomatoes
Section of Evolutionary Biology, Department Biologie II, University of Munich (LMU), Planegg-Martinsried, Germany
E-mail: staedler{at}zi.biologie.uni-muenchen.de.
Accepted for publication July 31, 2007.
We employed a multilocus approach to examine the effects of population subdivision and natural selection on DNA polymorphism in 2 closely related wild tomato species (Solanum peruvianum and Solanum chilense), using sequence data for 8 nuclear loci from populations across much of the species’ range. Both species exhibit substantial levels of nucleotide variation. The species-wide level of silent nucleotide diversity is 18% higher in S. peruvianum (
sil 
2.50%) than in S. chilense (sil 2.12%). One of the loci deviates from neutral expectations, showing a clinal pattern of nucleotide diversity and haplotype structure in S. chilense. This geographic pattern of variation is suggestive of an incomplete (ongoing) selective sweep, but neutral explanations cannot be entirely dismissed. Both wild tomato species exhibit moderate levels of population differentiation (average FST 0.20). Interestingly, the pooled samples (across different demes) exhibit more negative Tajima’s D and Fu and Li's D values; this marked excess of low-frequency polymorphism can only be explained by population (or range) expansion and is unlikely to be due to population structure per se. We thus propose that population structure and population/range expansion are among the most important evolutionary forces shaping patterns of nucleotide diversity within and among demes in these wild tomatoes. Patterns of population differentiation may also be impacted by soil seed banks and historical associations mediated by climatic cycles. Intragenic linkage disequilibrium (LD) decays very rapidly with physical distance, suggesting high recombination rates and effective population sizes in both species. The rapid decline of LD seems very promising for future association studies with the purpose of mapping functional variation in wild tomatoes.
Key Words: population structure • population expansion • clinal variation • ongoing selective sweep • linkage disequilibrium • wild tomatoes
1 Present address: Department of Genetics, Kasetsart University, Bangkok, Thailand.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. D. Quang, S. Ikeda, and K. Harada Patterns of Nucleotide Diversity at the Methionine Synthase Locus in Fragmented and Continuous Populations of a Wind-Pollinated Tree, Quercus mongolica var. crispula J. Hered., June 16, 2009; (2009) esp036v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Stadler, B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations Genetics, May 1, 2009; 182(1): 205 - 216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Ross-Ibarra, M. Tenaillon, and B. S. Gaut Historical Divergence and Gene Flow in the Genus Zea Genetics, April 1, 2009; 181(4): 1399 - 1413. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Nadachowska and W. Babik Divergence in the Face of Gene Flow: The Case of Two Newts (Amphibia: Salamandridae) Mol. Biol. Evol., April 1, 2009; 26(4): 829 - 841. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Riebler, L. Held, and W. Stephan Bayesian Variable Selection for Detecting Adaptive Genomic Differences Among Populations Genetics, March 1, 2008; 178(3): 1817 - 1829. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Stadler, U. Arunyawat, and W. Stephan Population Genetics of Speciation in Two Closely Related Wild Tomatoes (Solanum Section Lycopersicon) Genetics, January 1, 2008; 178(1): 339 - 350. [Abstract] [Full Text] [PDF]
|
|