Genetics, Vol. 150, 1585-1593, December 1998, Copyright © 1998

DNA Polymorphism in Lycopersicon and Crossing-Over per Physical Length

Wolfgang Stephana and Charles H. Langleyb
a Department of Biology, University of Rochester, Rochester, New York 14627
b Section of Evolution and Ecology, University of California, Davis, California 95616

Corresponding author: Wolfgang Stephan, Department of Biology, University of Rochester, Rochester, NY 14627-0211., stephan{at}troi.cc.rochester.edu (E-mail).

Communicating editor: G. B. GOLDING

Surveys in Drosophila have consistently found reduced levels of DNA sequence polymorphism in genomic regions experiencing low crossing-over per physical length, while these same regions exhibit normal amounts of interspecific divergence. Here we show that for 36 loci across the genomes of eight Lycopersicon species, naturally occurring DNA polymorphism (scaled by locus-specific divergence between species) is positively correlated with the density of crossing-over per physical length. Large between-species differences in the amount of DNA sequence polymorphism reflect breeding systems: selfing species show much less within-species polymorphism than outcrossing species. The strongest association of expected heterozygosity with crossing-over is found in species with intermediate levels of average nucleotide diversity. All of these observations appear to be in qualitative agreement with the hitchhiking effects caused by the fixation of advantageous mutations and/or "background selection" against deleterious mutations.




This article has been cited by other articles:


Home page
 GeneticsHome page
L. C. Moyle and T. Nakazato
Comparative Genetics of Hybrid Incompatibility: Sterility in Two Solanum Species Crosses
Genetics, July 1, 2008; 179(3): 1437 - 1453.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
T. Paape, B. Igic, S. D. Smith, R. Olmstead, L. Bohs, and J. R. Kohn
A 15-Myr-Old Genetic Bottleneck
Mol. Biol. Evol., April 1, 2008; 25(4): 655 - 663.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
A.-C. Thuillet, M. I. Tenaillon, L. K. Anderson, S. E. Mitchell, S. Kresovich, S. M. Stack, B. Gaut, and J. Doebley
A Weak Effect of Background Selection on Trinucleotide Microsatellites in Maize
J. Hered., January 1, 2008; 99(1): 45 - 55.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
U. Arunyawat, W. Stephan, and T. Stadler
Using Multilocus Sequence Data to Assess Population Structure, Natural Selection, and Linkage Disequilibrium in Wild Tomatoes
Mol. Biol. Evol., October 1, 2007; 24(10): 2310 - 2322.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
T. L. Turner and M. W. Hahn
Locus- and Population-Specific Selection and Differentiation between Incipient Species of Anopheles gambiae
Mol. Biol. Evol., September 1, 2007; 24(9): 2132 - 2138.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S.-B. Chang, L. K. Anderson, J. D. Sherman, S. M. Royer, and S. M. Stack
Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome 1
Genetics, August 1, 2007; 176(4): 2131 - 2138.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
K. Fengler, S. M. Allen, B. Li, and A. Rafalski
Distribution of Genes, Recombination, and Repetitive Elements in the Maize Genome
Crop Sci., July 16, 2007; 47(S2): S-83 - S-95.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
L. C. Moyle
Comparative Genetics of Potential Prezygotic and Postzygotic Isolating Barriers in a Lycopersicon Species Cross
J. Hered., March 1, 2007; 98(2): 123 - 135.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. Beye, I. Gattermeier, M. Hasselmann, T. Gempe, M. Schioett, J. F. Baines, D. Schlipalius, F. Mougel, C. Emore, O. Rueppell, et al.
Exceptionally high levels of recombination across the honey bee genome
Genome Res., November 1, 2006; 16(11): 1339 - 1344.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. R. See, S. Brooks, J. C. Nelson, G. Brown-Guedira, B. Friebe, and B. S. Gill
Gene evolution at the ends of wheat chromosomes.
PNAS, March 14, 2006; 103(11): 4162 - 4167.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
T. Borge, M. T. Webster, G. Andersson, and G.-P. Saetre
Contrasting Patterns of Polymorphism and Divergence on the Z Chromosome and Autosomes in Two Ficedula Flycatcher Species
Genetics, December 1, 2005; 171(4): 1861 - 1873.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. Roselius, W. Stephan, and T. Stadler
The Relationship of Nucleotide Polymorphism, Recombination Rate and Selection in Wild Tomato Species
Genetics, October 1, 2005; 171(2): 753 - 763.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. J. Schmid, S. Ramos-Onsins, H. Ringys-Beckstein, B. Weisshaar, and T. Mitchell-Olds
A Multilocus Sequence Survey in Arabidopsis thaliana Reveals a Genome-Wide Departure From a Neutral Model of DNA Sequence Polymorphism
Genetics, March 1, 2005; 169(3): 1601 - 1615.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. C. Moyle and E. B. Graham
Genetics of Hybrid Incompatibility Between Lycopersicon esculentum and L. hirsutum
Genetics, January 1, 2005; 169(1): 355 - 373.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. E. Stajich and M. W. Hahn
Disentangling the Effects of Demography and Selection in Human History
Mol. Biol. Evol., January 1, 2005; 22(1): 63 - 73.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. J. Betancourt, Y. Kim, and H. A. Orr
A Pseudohitchhiking Model of X vs. Autosomal Diversity
Genetics, December 1, 2004; 168(4): 2261 - 2269.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. Scotti-Saintagne, S. Mariette, I. Porth, P. G. Goicoechea, T. Barreneche, C. Bodenes, K. Burg, and A. Kremer
Genome Scanning for Interspecific Differentiation Between Two Closely Related Oak Species [Quercus robur L. and Q. petraea (Matt.) Liebl.]
Genetics, November 1, 2004; 168(3): 1615 - 1626.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
F. A. Feltus, J. Wan, S. R. Schulze, J. C. Estill, N. Jiang, and A. H. Paterson
An SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments
Genome Res., September 1, 2004; 14(9): 1812 - 1819.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. I. Tenaillon, J. U'Ren, O. Tenaillon, and B. S. Gaut
Selection Versus Demography: A Multilocus Investigation of the Domestication Process in Maize
Mol. Biol. Evol., July 1, 2004; 21(7): 1214 - 1225.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. K. Anderson, N. Salameh, H. W. Bass, L. C. Harper, W. Z. Cande, G. Weber, and S. M. Stack
Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize
Genetics, April 1, 2004; 166(4): 1923 - 1933.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
H. Innan and W. Stephan
Distinguishing the Hitchhiking and Background Selection Models
Genetics, December 1, 2003; 165(4): 2307 - 2312.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. A. Sheldahl, D. M. Weinreich, and D. M. Rand
Recombination, Dominance and Selection on Amino Acid Polymorphism in the Drosophila Genome: Contrasting Patterns on the X and Fourth Chromosomes
Genetics, November 1, 2003; 165(3): 1195 - 1208.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. K. Anderson, G. G. Doyle, B. Brigham, J. Carter, K. D. Hooker, A. Lai, M. Rice, and S. M. Stack
High-Resolution Crossover Maps for Each Bivalent of Zea mays Using Recombination Nodules
Genetics, October 1, 2003; 165(2): 849 - 865.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
D. Charlesworth, B. K. Mable, M. H. Schierup, C. Bartolome, and P. Awadalla
Diversity and Linkage of Genes in the Self-Incompatibility Gene Family in Arabidopsis lyrata
Genetics, August 1, 2003; 164(4): 1519 - 1535.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
E. D. Akhunov, A. W. Goodyear, S. Geng, L.-L. Qi, B. Echalier, B. S. Gill, Miftahudin, J. P. Gustafson, G. Lazo, S. Chao, et al.
The Organization and Rate of Evolution of Wheat Genomes Are Correlated With Recombination Rates Along Chromosome Arms
Genome Res., May 1, 2003; 13(5): 753 - 763.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. D. Cutter and B. A. Payseur
Selection at Linked Sites in the Partial Selfer Caenorhabditis elegans
Mol. Biol. Evol., May 1, 2003; 20(5): 665 - 673.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. S. Senchina, I. Alvarez, R. C. Cronn, B. Liu, J. Rong, R. D. Noyes, A. H. Paterson, R. A. Wing, T. A. Wilkins, and J. F. Wendel
Rate Variation Among Nuclear Genes and the Age of Polyploidy in Gossypium
Mol. Biol. Evol., April 1, 2003; 20(4): 633 - 643.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. I. Tenaillon, M. C. Sawkins, L. K. Anderson, S. M. Stack, J. Doebley, and B. S. Gaut
Patterns of Diversity and Recombination Along Chromosome 1 of Maize (Zea mays ssp. mays L.)
Genetics, November 1, 2002; 162(3): 1401 - 1413.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
A. J. Betancourt and D. C. Presgraves
Linkage limits the power of natural selection in Drosophila
PNAS, October 15, 2002; 99(21): 13616 - 13620.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. J. Betancourt, D. C. Presgraves, and W. J. Swanson
A Test for Faster X Evolution in Drosophila
Mol. Biol. Evol., October 1, 2002; 19(10): 1816 - 1819.
[Full Text] [PDF]

Home page
 GeneticsHome page
A. Navarro and N. H. Barton
The Effects of Multilocus Balancing Selection on Neutral Variability
Genetics, June 1, 2002; 161(2): 849 - 863.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
D. Zwettler, C. P. Vieira, and C. Schlotterer
Polymorphic Microsatellites in Antirrhinum (Scrophulariaceae), a Genus With Low Levels of Nuclear Sequence Variability
J. Hered., May 1, 2002; 93(3): 217 - 221.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. Graustein, J. M. Gaspar, J. R. Walters, and M. F. Palopoli
Levels of DNA Polymorphism Vary With Mating System in the Nematode Genus Caenorhabditis
Genetics, May 1, 2002; 161(1): 99 - 107.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. M. Comeron and M. Kreitman
Population, Evolutionary and Genomic Consequences of Interference Selection
Genetics, May 1, 2002; 161(1): 389 - 410.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B. A. Payseur and M. W. Nachman
Gene Density and Human Nucleotide Polymorphism
Mol. Biol. Evol., March 1, 2002; 19(3): 336 - 340.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
V. Dvornyk, A. Sirvio, M. Mikkonen, and O. Savolainen
Low Nucleotide Diversity at the pal1 Locus in the Widely Distributed Pinus sylvestris
Mol. Biol. Evol., February 1, 2002; 19(2): 179 - 188.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Kauer, B. Zangerl, D. Dieringer, and C. Schlotterer
Chromosomal Patterns of Microsatellite Variability Contrast Sharply in African and Non-African Populations of Drosophila melanogaster
Genetics, January 1, 2002; 160(1): 247 - 256.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
I. E. Peralta and D. M. Spooner
Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill.] Wettst. subsection Lycopersicon)
Am. J. Botany, October 1, 2001; 88(10): 1888 - 1902.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. A. F. Noor, A. L. Cunningham, and J. C. Larkin
Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome
Genetics, October 1, 2001; 159(2): 581 - 588.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
E. Baudry, C. Kerdelhue, H. Innan, and W. Stephan
Species and Recombination Effects on DNA Variability in the Tomato Genus
Genetics, August 1, 2001; 158(4): 1725 - 1735.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. A. Filatov, V. Laporte, C. Vitte, and D. Charlesworth
DNA Diversity in Sex-Linked and Autosomal Genes of the Plant Species Silene latifolia and Silene dioica
Mol. Biol. Evol., August 1, 2001; 18(8): 1442 - 1454.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. I. Tenaillon, M. C. Sawkins, A. D. Long, R. L. Gaut, J. F. Doebley, and B. S. Gaut
Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.)
PNAS, July 19, 2001; (2001) 151244298.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
P. Andolfatto and M. Przeworski
Regions of Lower Crossing Over Harbor More Rare Variants in African Populations of Drosophila melanogaster
Genetics, June 1, 2001; 158(2): 657 - 665.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
N. A. Eckardt
Functional Evolutionary Genetics and Plant Adaptation: Linking Phenotype and Genotype
PLANT CELL, June 1, 2001; 13(6): 1249 - 1254.
[Full Text] [PDF]

Home page
 Plant Physiol.Home page
N. C. Collins, T. Lahaye, C. Peterhänsel, A. Freialdenhoven, M. Corbitt, and P. Schulze-Lefert
Sequence Haplotypes Revealed by Sequence-Tagged Site Fine Mapping of the Ror1 Gene in the Centromeric Region of Barley Chromosome 1H
Plant Physiology, March 1, 2001; 125(3): 1236 - 1247.
[Abstract] [Full Text]

Home page
 GeneticsHome page
C. H. Langley, B. P. Lazzaro, W. Phillips, E. Heikkinen, and J. M. Braverman
Linkage Disequilibria and the Site Frequency Spectra in the su(s) and su(wa) Regions of the Drosophila melanogaster X Chromosome
Genetics, December 1, 2000; 156(4): 1837 - 1852.
[Abstract] [Full Text]

Home page
 GeneticsHome page
B. A. Payseur and M. W. Nachman
Microsatellite Variation and Recombination Rate in the Human Genome
Genetics, November 1, 2000; 156(3): 1285 - 1298.
[Abstract] [Full Text]

Home page
 GeneticsHome page
M. W. Nachman and S. L. Crowell
Contrasting Evolutionary Histories of Two Introns of the Duchenne Muscular Dystrophy Gene, Dmd, in Humans
Genetics, August 1, 2000; 155(4): 1855 - 1864.
[Abstract] [Full Text]

Home page
 GeneticsHome page
J. C. Fay and C.-I Wu
Hitchhiking Under Positive Darwinian Selection
Genetics, July 1, 2000; 155(3): 1405 - 1413.
[Abstract] [Full Text]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B. S. Gaut, M. Le Thierry d'Ennequin, A. S. Peek, and M. C. Sawkins
Maize as a model for the evolution of plant nuclear genomes
PNAS, June 20, 2000; 97(13): 7008 - 7015.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. Navarro, A. Barbadilla, and A. Ruiz
Effect of Inversion Polymorphism on the Neutral Nucleotide Variability of Linked Chromosomal Regions in Drosophila
Genetics, June 1, 2000; 155(2): 685 - 698.
[Abstract] [Full Text]

Home page
 GeneticsHome page
R. T. Chetelat, V. Meglic, and P. Cisneros
A Genetic Map of Tomato Based on BC1 Lycopersicon esculentum Solanum lycopersicoides Reveals Overall Synteny but Suppressed Recombination Between These Homeologous Genomes
Genetics, February 1, 2000; 154(2): 857 - 867.
[Abstract] [Full Text]

Home page
 GeneticsHome page
T. Takano-Shimizu
Local Recombination and Mutation Effects on Molecular Evolution in Drosophila
Genetics, November 1, 1999; 153(3): 1285 - 1296.
[Abstract] [Full Text]

Home page
 GeneticsHome page
J. Wang and W. G. Hill
Effect of Selection Against Deleterious Mutations on the Decline in Heterozygosity at Neutral Loci in Closely Inbreeding Populations
Genetics, November 1, 1999; 153(3): 1475 - 1489.
[Abstract] [Full Text]

Home page
 GeneticsHome page
F. Liu, D. Charlesworth, and M. Kreitman
The Effect of Mating System Differences on Nucleotide Diversity at the Phosphoglucose Isomerase Locus in the Plant Genus Leavenworthia
Genetics, January 1, 1999; 151(1): 343 - 357.
[Abstract] [Full Text]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. I. Tenaillon, M. C. Sawkins, A. D. Long, R. L. Gaut, J. F. Doebley, and B. S. Gaut
Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.)
PNAS, July 31, 2001; 98(16): 9161 - 9166.
[Abstract] [Full Text] [PDF]