The Scale of Population Structure in
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.
Vyšlo v časopise:
The Scale of Population Structure in. PLoS Genet 6(2): e32767. doi:10.1371/journal.pgen.1000843
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1000843
Souhrn
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.
Zdroje
1. KlimanRM
AndolfattoP
CoyneJA
DepaulisF
KreitmanM
2000 The Population Genetics of the Origin and Divergence of the Drosophila simulans Complex Species. Genetics 156 1913 1931
2. MarchiniJ
CardonLR
PhillipsMS
DonnellyP
2004 The effects of human population structure on large genetic association studies. Nat Genet 36 512 517 doi:10.1038/ng1337
3. VoightBF
PritchardJK
2005 Confounding from cryptic relatedness in case-control association studies. PLoS Genet 1 e32 doi:10.1371/journal.pgen.0010032
4. BucklerES
ThornsberryJM
KresovichS
2001 Molecular Diversity, Structure and Domestication of Grasses. Genetics Research 77 213 218 doi:10.1017/S0016672301005158
5. SasakiT
MatsumotoT
YamamotoK
SakataK
BabaT
2002 The genome sequence and structure of rice chromosome 1. Nature 420 312 316 doi:10.1038/nature01184
6. RafalskiA
MorganteM
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-OldsT
1995 Interval Mapping of Viability Loci Causing Heterosis in Arabidopsis. Genetics 140 1105 1109
8. BustamanteCD
NielsenR
SawyerSA
OlsenKM
PuruggananMD
2002 The cost of inbreeding in Arabidopsis. Nature 416 531 534 doi:10.1038/416531a
9. BeckJB
SchmuthsHeike
SchaalBarbaraA.
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. PicoFX
Mendez-VigoB
Martínez-ZapaterJM
Alonso-BlancoC
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'KaneSL
Al-ShehbazIA
1997 A Synopsis of Arabidopsis (Brassicaceae). Novon 7 323 327 doi:10.2307/3391949
12. WrightS
1943 Isolation by Distance. Genetics 28 114 138
13. MaruyamaT
1972 Rate of Decrease of Genetic Variability in a Two-Dimensional Continuous Population of Finite Size. Genetics 70 639 651
14. BartonNH
WilsonI
1995 Genealogies and Geography. Philosophical Transactions: Biological Sciences 349 49 59 doi:10.2307/56123
15. WilkinsJF
2004 A Separation-of-Timescales Approach to the Coalescent in a Continuous Population. Genetics 168 2227 2244 doi:10.1534/genetics.103.022830
16. KnowlesLL
CarstensBC
2007 Estimating a geographically explicit model of population divergence. Evolution 61(3) 477 493
17. GuillotG
EstoupA
MortierF
CossonJF
2005 A Spatial Statistical Model for Landscape Genetics. Genetics 170 1261 1280 doi:10.1534/genetics.104.033803
18. StorferA
MurphyMA
EvansJS
GoldbergCS
RobinsonS
2006 Putting the /‘landscape/’ in landscape genetics. Heredity 98 128 142
19. WilkinsJF
MarloweFW
2006 Sex-biased migration in humans: what should we expect from genetic data? BioEssays 28 290 300 doi:10.1002/bies.20378
20. GuillotG
LebloisR
CoulonA
FrantzAC
2009 Statistical methods in spatial genetics. Molecular Ecology 18 4734 4756 doi:10.1111/j.1365-294X.2009.04410.x
21. AtwellS
Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines. Nature. in press
22. LiY
2007 Purification of Arabidopsis DNA in 96-Well Plate Using the PUREGENE DNA Purification Kit. p87.
WeinerMP
GabrielS
StephensJC
Genetic variation: a laboratory manual In book: Cold Spring harbor laboratory Press, Cold Spring Harbor, New York
23. NordborgM
HuTT
IshinoY
JhaveriJ
ToomajianC
2005 The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3 e196 doi:10.1371/journal.pbio.0030196
24. WarthmannN
FitzJ
WeigelD
2007 MSQT for choosing SNP assays from multiple DNA alignments. Bioinformatics 23 2784 2787 doi:10.1093/bioinformatics/btm428
25. HeyerLJ
KruglyakS
YoosephS
1999 Exploring Expression Data: Identification and Analysis of Coexpressed Genes. Genome Res 9 1106 1115
26. WeirBS
CockerhamCC
1984 Estimating F-Statistics for the Analysis of Population Structure. Evolution 38 1358 1370
27. LewisP
ZaykinD
2001 Genetic Data Analysis: Computer program for the analysis of allelic data Version 1.0 (d16c).
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2010 Číslo 2
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Genome-Wide Association Study in Asian Populations Identifies Variants in and Associated with Systemic Lupus Erythematosus
- Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Genome
- The Genetic Interpretation of Area under the ROC Curve in Genomic Profiling
- Cdk2 Is Required for p53-Independent G/M Checkpoint Control