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The scale of population structure in Arabidopsis thaliana

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Platt, A. (Alexander), Horton, Matthew, Huang, Yu S., Li, Y. (Yan), Anastasio, Alison Elizabeth, Mulyati, Ni Wayan, Ågren, Jon, Bossdorf, Oliver, Byers, Diane, Donohue, Kathleen, Ph.D. et al.

. (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genetics, Vol.6 (No.2). e1000843. ISSN 1553-7390

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Official URL: http://dx.doi.org/10.1371/journal.pgen.1000843

Abstract

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

Item Type:

Journal Article

Subjects:

Q Science > QK Botany
Q Science > QH Natural history > QH426 Genetics

Divisions:

Faculty of Science > Life Sciences (2010- ) > Warwick HRI (2004-2010)

Library of Congress Subject Headings (LCSH):

Arabidopsis thaliana, Plant population genetics, Plant populations, Fertilization of plants

Journal or Publication Title:

PLoS Genetics

Publisher:

Public Library of Science

ISSN:

1553-7390

Official Date:

12 February 2010

Dates:

Date	Event
12 February 2010	Published

Volume:

Vol.6

Number:

No.2

Page Range:

e1000843

Identification Number:

10.1371/journal.pgen.1000843

Status:

Peer Reviewed

Access rights to Published version:

Open Access

Funder:

National Science Foundation (U.S.) (NSF), National Institutes of Health (U.S.) (NIH)

Grant number:

DEB-0519961 (NSF), GM073822 (NIH), GM07994 (NIH), DEB - 0723935 (NSF)

References:

1. Kliman RM, Andolfatto P, Coyne JA, Depaulis F, Kreitman M, et al. (2000)
The Population Genetics of the Origin and Divergence of the Drosophila
simulans Complex Species. Genetics 156: 1913–1931.
2. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human
population structure on large genetic association studies. Nat Genet 36:
512–517. doi:10.1038/ng1337.
3. Voight BF, Pritchard JK (2005) Confounding from cryptic relatedness in casecontrol
association studies. PLoS Genet 1: e32. doi:10.1371/journal.pgen.
0010032.
4. Buckler ES, Thornsberry JM, Kresovich S (2001) Molecular Diversity, Structure
and Domestication of Grasses. Genetics Research 77: 213–218. doi:10.1017/
S0016672301005158.
5. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, et al. (2002) The
genome sequence and structure of rice chromosome 1. Nature 420: 312–316.
doi:10.1038/nature01184.
6. Rafalski A, Morgante M (2004) Corn and humans: recombination and linkage
disequilibrium in two genomes of similar size. Trends in Genetics 20: 103–111.
doi:10.1016/j.tig.2003.12.002.
7. Mitchell-Olds T (1995) Interval Mapping of Viability Loci Causing Heterosis in
Arabidopsis. Genetics 140: 1105–1109.
8. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, et al.
(2002) The cost of inbreeding in Arabidopsis. Nature 416: 531–534.
doi:10.1038/416531a.
9. Beck JB, HeikeSchmuths, Barbara A.Schaal (2008) Native range genetic
variation in Arabidopsis thaliana is strongly geographically structured and
reflects Pleistocene glacial dynamics. Molecular Ecology 17: 902–915.
doi:10.1111/j.1365-294X.2007.03615.x.
10. Pico FX, Mendez-Vigo B, Martı´nez-Zapater JM, Alonso-Blanco C (2008)
Natural Genetic Variation of Arabidopsis thaliana Is Geographically Structured
in the Iberian Peninsula. Genetics 180: 1009–1021. doi:10.1534/genetics.
108.089581.
11. O’Kane SL, Al-Shehbaz IA (1997) A Synopsis of Arabidopsis (Brassicaceae).
Novon 7: 323–327. doi:10.2307/3391949.
12. Wright S (1943) Isolation by Distance. Genetics 28: 114–138.
13. Maruyama T (1972) Rate of Decrease of Genetic Variability in a Two-
Dimensional Continuous Population of Finite Size. Genetics 70: 639–651.
14. Barton NH, Wilson I (1995) Genealogies and Geography. Philosophical
Transactions: Biological Sciences 349: 49–59. doi:10.2307/56123.
15. Wilkins JF (2004) A Separation-of-Timescales Approach to the Coalescent in a
Continuous Population. Genetics 168: 2227–2244. doi:10.1534/genetics.
103.022830.
16. Knowles LL, Carstens BC (2007) Estimating a geographically explicit model of
population divergence. Evolution 61(3): 477–493.
17. Guillot G, Estoup A, Mortier F, Cosson JF (2005) A Spatial Statistical Model for
Landscape Genetics. Genetics 170: 1261–1280. doi:10.1534/genetics.
104.033803.
18. Storfer A, Murphy MA, Evans JS, Goldberg CS, Robinson S, et al. (2006)
Putting the /‘landscape/’ in landscape genetics. Heredity 98: 128–142.
19. Wilkins JF, Marlowe FW (2006) Sex-biased migration in humans: what should
we expect from genetic data? BioEssays 28: 290–300. doi:10.1002/bies.20378.
20. Guillot G, Leblois R, Coulon A, Frantz AC (2009) Statistical methods in spatial
genetics. Molecular Ecology 18: 4734–4756. doi:10.1111/j.1365-294X.
2009.04410.x.
21. Atwell S, et al. Genome-wide association study of 107 phenotypes in a common
set of Arabidopsis thaliana inbred lines. Nature. in press.
22. Li Y (2007) Purification of Arabidopsis DNA in 96-Well Plate Using the
PUREGENE DNA Purification Kit. p87. In book: Genetic variation: a
laboratory manual Weiner MP, Gabriel S, Stephens JC, eds. Cold Spring
harbor laboratory Press, Cold Spring Harbor, New York.
23. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C (2005) The pattern of
polymorphism in Arabidopsis thaliana. PLoS Biol 3: e196. doi:10.1371/
journal.pbio.0030196.
24. Warthmann N, Fitz J,WeigelD(2007)MSQT for choosing SNP assays from multiple
DNA alignments. Bioinformatics 23: 2784–2787. doi:10.1093/bioinformatics/
btm428.
25. Heyer LJ, Kruglyak S, Yooseph S (1999) Exploring Expression Data:
Identification and Analysis of Coexpressed Genes. Genome Res 9: 1106–1115.
26. Weir BS, Cockerham CC (1984) Estimating F-Statistics for the Analysis of
Population Structure. Evolution 38: 1358–1370.
27. Lewis P, Zaykin D (2001) Genetic Data Analysis: Computer program for the
analysis of allelic data Version 1.0 (d16c).
Arabidopsis Population Structure
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