- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Data Supplement
-
All Versions of this Article:
genetics.105.048223v1
172/3/1607 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Thornton, K.
- Articles by Andolfatto, P.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Thornton, K.
- Articles by Andolfatto, P.
Originally published as Genetics Published Articles Ahead of Print on November 19, 2005.
Genetics, Vol. 172, 1607-1619, March 2006, Copyright © 2006
doi:10.1534/genetics.105.048223
Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila melanogaster
Kevin Thornton*,1 and
Peter Andolfatto
* Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 and Section of Ecology, Behavior and Evolution, University of California, San Diego, California 92093
1 Corresponding author: Department of Molecular Biology and Genetics, Cornell University, 227 Biotechnology Bldg., Ithaca, NY 14853.
E-mail: kt234{at}cornell.edu
Genome-wide nucleotide variation in non-African populations of Drosophila melanogaster is a subset of variation found in East sub-Saharan African populations, suggesting a bottleneck in the history of the former. We implement an approximate Bayesian approach to infer the timing, duration, and severity of this putative bottleneck and ask whether this inferred model is sufficient to account for patterns of variability observed at 115 loci scattered across the X chromosome. We estimate a recent bottleneck 0.006Ne generations ago, somewhat further in the past than suggested by biogeographical evidence. Using various proposed statistical tests, we find that this bottleneck model is able to predict the majority of observed features of diversity and linkage disequilibrium in the data. Thus, while precise estimates of bottleneck parameters (like inferences of selection) are sensitive to model assumptions, our results imply that it may be unnecessary to invoke frequent selective sweeps associated with the dispersal of D. melanogaster from Africa to explain patterns of variability in non-African populations.
This article has been cited by other articles:
 |
|
 |
|
  J. E. Pool and R. Nielsen The Impact of Founder Events on Chromosomal Variability in Multiply Mating Species Mol. Biol. Evol., August 1, 2008; 25(8): 1728 - 1736. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L.-z. Gao and H. Innan Nonindependent Domestication of the Two Rice Subspecies, Oryza sativa ssp. indica and ssp. japonica, Demonstrated by Multilocus Microsatellites Genetics, June 1, 2008; 179(2): 965 - 976. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kawabe, A. Forrest, S. I. Wright, and D. Charlesworth High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata Genetics, June 1, 2008; 179(2): 985 - 995. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Macpherson, J. Gonzalez, D. M. Witten, J. C. Davis, N. A. Rosenberg, A. E. Hirsh, and D. A. Petrov Nonadaptive Explanations for Signatures of Partial Selective Sweeps in Drosophila Mol. Biol. Evol., June 1, 2008; 25(6): 1025 - 1042. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-F. Lefebvre and D. Labuda Fraction of Informative Recombinations: A Heuristic Approach to Analyze Recombination Rates Genetics, April 1, 2008; 178(4): 2069 - 2079. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Chen, P. L. Morrell, M. de la Cruz, and M. T. Clegg Nucleotide Diversity and Linkage Disequilibrium in Wild Avocado (Persea americana Mill.) J. Hered., March 14, 2008; (2008) esn016v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Jensen, K. R. Thornton, and C. F. Aquadro Inferring Selection in Partially Sequenced Regions Mol. Biol. Evol., February 1, 2008; 25(2): 438 - 446. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. De Mita, J. Ronfort, H. I. McKhann, C. Poncet, R. El Malki, and T. Bataillon Investigation of the Demographic and Selective Forces Shaping the Nucleotide Diversity of Genes Involved in Nod Factor Signaling in Medicago truncatula Genetics, December 1, 2007; 177(4): 2123 - 2133. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Jensen, V. L. Bauer DuMont, A. B. Ashmore, A. Gutierrez, and C. F. Aquadro Patterns of Sequence Variability and Divergence at the diminutive Gene Region of Drosophila melanogaster: Complex Patterns Suggest an Ancestral Selective Sweep Genetics, October 1, 2007; 177(2): 1071 - 1085. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Casillas, A. Barbadilla, and C. M. Bergman Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila Mol. Biol. Evol., October 1, 2007; 24(10): 2222 - 2234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Jensen, K. R. Thornton, C. D. Bustamante, and C. F. Aquadro On the Utility of Linkage Disequilibrium as a Statistic for Identifying Targets of Positive Selection in Nonequilibrium Populations Genetics, August 1, 2007; 176(4): 2371 - 2379. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Zeng, S. Shi, and C.-I Wu Compound Tests for the Detection of Hitchhiking Under Positive Selection Mol. Biol. Evol., August 1, 2007; 24(8): 1898 - 1908. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Bergman and D. Bensasson Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster PNAS, July 3, 2007; 104(27): 11340 - 11345. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Ross-Ibarra, P. L. Morrell, and B. S. Gaut Colloquium Papers: Plant domestication, a unique opportunity to identify the genetic basis of adaptation PNAS, May 15, 2007; 104(suppl_1): 8641 - 8648. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Orengo and M. Aguade Genome Scans of Variation and Adaptive Change: Extended Analysis of a Candidate Locus Close to the phantom Gene Region in Drosophila melanogaster Mol. Biol. Evol., May 1, 2007; 24(5): 1122 - 1129. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sanchez-Gracia and J. Rozas Unusual Pattern of Nucleotide Sequence Variation at the OS-E and OS-F Genomic Regions of Drosophila simulans Genetics, April 1, 2007; 175(4): 1923 - 1935. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Mustonen and M. Lassig Adaptations to fluctuating selection in Drosophila PNAS, February 13, 2007; 104(7): 2277 - 2282. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Sisson, Y. Fan, and M. M. Tanaka Sequential Monte Carlo without likelihoods PNAS, February 6, 2007; 104(6): 1760 - 1765. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. R. Thornton and J. D. Jensen Controlling the False-Positive Rate in Multilocus Genome Scans for Selection Genetics, February 1, 2007; 175(2): 737 - 750. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. C. Presgraves and W. Stephan Pervasive Adaptive Evolution among Interactors of the Drosophila Hybrid Inviability Gene, Nup96 Mol. Biol. Evol., January 1, 2007; 24(1): 306 - 314. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Bachtrog and P. Andolfatto Selection, Recombination and Demographic History in Drosophila miranda Genetics, December 1, 2006; 174(4): 2045 - 2059. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. C. Presgraves Intron Length Evolution in Drosophila Mol. Biol. Evol., November 1, 2006; 23(11): 2203 - 2213. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Casa, S. E. Mitchell, J. D. Jensen, M. T. Hamblin, A. H. Paterson, C. F. Aquadro, and S. Kresovich Evidence for a Selective Sweep on Chromosome 1 of Cultivated Sorghum Crop Sci., November 1, 2006; 46(Supplement_1): S-27 - S-40. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. Pool and C. F. Aquadro History and Structure of Sub-Saharan Populations of Drosophila melanogaster Genetics, October 1, 2006; 174(2): 915 - 929. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Cutter, S. E. Baird, and D. Charlesworth High Nucleotide Polymorphism and Rapid Decay of Linkage Disequilibrium in Wild Populations of Caenorhabditis remanei Genetics, October 1, 2006; 174(2): 901 - 913. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. M. Panhuis and W. J. Swanson Molecular Evolution and Population Genetic Analysis of Candidate Female Reproductive Genes in Drosophila Genetics, August 1, 2006; 173(4): 2039 - 2047. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. L. Morrell, D. M. Toleno, K. E. Lundy, and M. T. Clegg Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity Genetics, July 1, 2006; 173(3): 1705 - 1723. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. M. Teshima, G. Coop, and M. Przeworski How reliable are empirical genomic scans for selective sweeps? Genome Res., June 1, 2006; 16(6): 702 - 712. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. T. Hamblin, A. M. Casa, H. Sun, S. C. Murray, A. H. Paterson, C. F. Aquadro, and S. Kresovich Challenges of Detecting Directional Selection After a Bottleneck: Lessons From Sorghum bicolor Genetics, June 1, 2006; 173(2): 953 - 964. [Abstract] [Full Text] [PDF]
|
|