Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)

Molecular Ecology

Volumn 25, Issue 2, 2016, Pages 616-629

  Cornille, A ^a   Salcedo, A ^b   Kryvokhyzha, D ^a   Glemin S ^a   Holm, K ^a   Wright, S I ^b   Lascoux, M ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

bottleneck; Brassicaceae; disomic inheritance; dispersal; invasive species; time estimation; unphased SNP

Indexed keywords

ASIA; BAYES THEOREM; BIOLOGICAL MODEL; CAPSELLA; DNA SEQUENCE; EUROPE; EVOLUTION; GENETICS; GENOTYPE; HYBRIDIZATION; MIDDLE EAST; POLYPLOIDY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; SPATIAL ANALYSIS; WEED;

ASIA; BAYES THEOREM; BIOLOGICAL EVOLUTION; CAPSELLA; EUROPE; GENETICS, POPULATION; GENOTYPE; HYBRIDIZATION, GENETIC; MIDDLE EAST; MODELS, GENETIC; PLANT WEEDS; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY; SEQUENCE ANALYSIS, DNA; SPATIAL ANALYSIS;

EID: 84957434082     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13491     Document Type: Article

References (64)

1. Aksoy A, Dixon JM, Hale WHG, (1998) Capsella bursa-pastoris (L.) Medikus (Thlaspi bursa pastoris L., Bursa bursa pastoris L. Shull, Bursa pastoris (L) Weber). Journal of Ecology, 86, 171-186.
2. Alexander DH, Novembre J, Lange K, (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19, 1655-1664.
3. Balfourier F, Imbert C, Charmet G, (2000) Evidence for phylogeographic structure in Lolium species related to the spread of agriculture in Europe. A cpDNA study. Theoretical and Applied Genetics, 101, 131-138.
4. Beaumont MA, (2010) Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology, Evolution, and Systematics, 41, 379-406.
5. Bertorelle G, Benazzo A, Mona S, (2010) ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Molecular Ecology, 19, 2609-2625.
6. Blum MB, François O, (2010) Non-linear regression models for Approximate Bayesian Computation. Statistics and Computing, 20, 63-73.
7. Bock DG, Caseys C, Cousens RD, et al,. (2015) What we still don't know about invasion genetics. Molecular Ecology, 24, 2277-2297.
8. Bombarely A, Coate JE, Doyle JJ, (2014) Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ, 2, e391.
9. Bradbury PJ, Zhang Z, Kroon DE, et al,. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633-2635.
10. Ceplitis A, Su Y, Lascoux M, (2005) Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae). Molecular Ecology, 14, 4221-4233.
11. Csillery K, Blum M, Francois O, (2012) Tools for Approximate Bayesian Computation (ABC). Available from http://cran.r-project.org/web/packages/abc/index.html.
12. Csilléry K, François O, Blum MGB, (2012) abc: an R package for approximate Bayesian computation (ABC). Methods in Ecology and Evolution, 3, 475-479.
13. Danecek P, Auton A, Abecasis G, et al,. (2011) The variant call format and VCFtools. Bioinformatics (Oxford, UK), 27, 2156-2158.
14. Davey JW, Hohenlohe PA, Etter PD, et al,. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews. Genetics, 12, 499-510.
15. De Wet JMJ, Harlan JR, (1975) Weeds and domesticates: evolution in the man-made habitat. Economic Botany, 29, 99-108.
16. Douglas G, Gos G, Steige K, et al,. (2015) Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. PNAS, 12, 2806-2811.
17. Doyle JJ, Doyle JL, Brown AHD, (1999) Origins, colonization, and lineage recombination in a widespread perennial soybean polyploid complex. Proceedings of the National Academy of Sciences of the United States of America, 96, 10741-10745.
18. Dufresne F, Stift M, Vergilino R, Mable BK, (2014) Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Molecular Ecology, 23, 40-69.
19. Elshire RJ, Glaubitz JC, Sun Q, et al,. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379.
20. Excoffier L, Lischer HEL, (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
21. Excoffier L, Foll M, Petit RJ, (2009) Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics, 40, 481-501.
22. Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M, (2013) Robust demographic inference from genomic and SNP data. PLoS Genetics, 9, e1003905.
23. François O, Blum MGB, Jakobsson M, Rosenberg NA, (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics, 4, e1000075.
24. Guo H, Wang X, Gundlach H, et al,. (2014) Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (Cotton). Genetics, 197, 1153-1163.
25. Hamrick JL, Godt MJW, (1996) Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society B: Biological Sciences, 351, 1291-1298.
26. Han T-S, Wu Q, Hou X-H, et al,. (2015) Frequent Introgressions from Diploid species contribute to the adaptation of the Tetraploid Shepherd's Purse (Capsella bursa-pastoris). Molecular Plant, 8, 427-438.
27. Hohenlohe P, Amish SJ, Catchen JM, Allendorf FW, Luikart G, (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11, 117-122.
28. Hurka H, Neuffer B, (1997) Evolutionary processes in the genus Capsella (Brassicaceae). Plant Systematics and Evolution, 206, 295-316.
29. Hurka H, Friesen N, German DA, Franzke A, Neuffer B, (2012) "Missing link" species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae). Molecular Ecology, 21, 1223-1238.
30. Husband BC, Barrett SC, (1991) Colonization history and population genetic structure of Eichhornia paniculata in Jamaica. Heredity, 66, 287-296.
31. Ilut DC, Coate JE, Luciano AK, et al,. (2012) A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. American Journal of Botany, 99, 383-396.
32. Kryvokhyzha D, Holm K, Chen J, et al,. (2016) The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). Molecular Ecology. accepted.
33. Langmead B, Trapnell C, Pop M, Salzberg S, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.
34. Meirmans PG, (2015) Seven common mistakes in population genetics and how to avoid them. Molecular Ecology, 24, 3223-3231.
35. Nathan R, (2006) Long-distance dispersal of plants. Science, 313, 786-788.
36. Nei M, (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.
37. Neuffer B, (2011) Native range variation in Capsella bursa-pastoris (Brassicaceae) along a 2500 km latitudinal transect. Flora-Morphology, Distribution, Functional Ecology of Plants, 206, 107-119.
38. Neuffer B, Bartelheim S, (1989) Gen-ecology of Capsella bursa-pastoris from an altitudinal transsect in the Alps. Oecologia, 81, 521-527.
39. Neuffer B, Hoffrogge R, (1999) Ecotypic and allozyme variation of Capsella bursa-pastoris and C. rubella (Brassicaceae) along latitude and altitude gradients on the Iberian Peninsula. Anales del Jardín Botánico de Madrid, 57, 239-315.
40. Neuffer B, Hurka H, (1986) Variation of development time until flowering in natural populations of Capsella bursa-pastoris. Plant Systematics and Evolution, 152, 277-296.
41. Neuffer B, Hurka H, (1999) Colonization history and introduction dynamics of Capsella bursa-pastoris (Brassicaceae) in North America: isozymes and quantitative traits. Molecular Ecology, 8, 1667-1681.
42. Pannell JR, (2015) Evolution of the mating system in colonizing plants. Molecular Ecology, 24, 2018-2037.
43. Parisod C, (2012) Polyploids integrate genomic changes and ecological shifts. New Phytologist, 193, 297-300.
44. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE, (2012) Double digest RADseq: an inexpensive method for de novo SNP Discovery and genotyping in model and non-model species. PLoS ONE, 7, e37135.
45. Platt A, Horton M, Huang YS, et al,. (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genetics, 6, e1000843.
46. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
47. Ramsey J, Schemske DW, (2002) Neopolyploidy in flowering plants. Annual Review of Ecology and Systematics, 33, 589-639.
48. Rousset F, (1997) Genetic differentiation and estimation of gene flow from f-statistics under isolation by distance. Genetics, 145, 1219-1228.
49. Roux C, Pannell JR, (2015) Inferring the mode of origin of polyploid species from next-generation sequence data. Molecular Ecology, 24, 1047-1059.
50. Senn H, Ogden R, Cezard T, et al,. (2013) Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data. Molecular Ecology, 22, 3141-3150.
51. Shull G, (1929) Species hybridization among old and new species of Shepherd's Purse. International Congress of Plant Science, 1, 837-888.
52. Slotte T, Huang H, Lascoux M, Ceplitis A, (2008) Polyploid speciation did not confer instant reproductive isolation in Capsella (Brassicaceae). Molecular Biology and Evolution, 25, 1472-1481.
53. Slotte T, Hazzouri KM, Ågren JA, et al,. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics, 45, 831-835.
54. Soltis PS, Liu X, Marchant DB, Visger CJ, Soltis DE, (2014) Polyploidy and novelty: Gottlieb's legacy. Philosophical Transactions of the Royal Society B Biological Sciences, 369, pii: 20130351.
55. Sousa V, Peischl S, Excoffier L, (2014) Impact of range expansions on current human genomic diversity. Genetics of Human Evolution, 29, 22-30.
56. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
57. Tiffin P, Ross-Ibarra J, (2014) Advances and limits of using population genetics to understand local adaptation. Trends in Ecology & Evolution, 29, 673-680.
58. Wakeley J, Hey J, (1997) Estimating ancestral population parameters. Genetics, 145, 847-855.
59. Watterson GA, (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276.
60. Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L, (2010) ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics, 11, 116.
61. Weir BS, Cockerham CC, (1984) Estimating F-Statistics for the analysis of population structure. Evolution, 38, 1358-1370.
62. White TA, Perkins SE, Heckel G, Searle JB, (2013) Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland. Molecular Ecology, 22, 2971-2985.
63. Xu P, Xu S, Wu X, et al,. (2014) Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd. The Plant Journal, 77, 430-442.
64. Yang W-Y, Novembre J, Eskin E, Halperin E, (2012) A model-based approach for analysis of spatial structure in genetic data. Nature Genetics, 44, 725-731.