Phylogenomics of polyploid Fothergilla (Hamamelidaceae) by RAD-tag based GBS - Insights into species origin and effects of software pipelines

Journal of Systematics and Evolution

Volumn 53, Issue 5, 2015, Pages 432-447

  Qi, Zhe Chen ^a,b   Yu, Yi ^a,c   Liu, Xiang ^a   Pais, Andrew ^a   Ranney, Thomas ^a   Whetten, Ross ^a   Xiang, Qiu Yun ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b ZHEJIANG SCI TECH UNIVERSITY   (China)

^c Guangzhou Zhongyi Pharmaceutical Co Ltd   (China)

Author keywords

Fothergilla; hybridization; illumina sequencing; phylogenomics; polyploidy; RAD tag based GBS

Indexed keywords

EID: 84941941628     PISSN: 16744918     EISSN: 17596831     Source Type: Journal    
DOI: 10.1111/jse.12176     Document Type: Article

References (63)

1. Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH., 2011. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics 188: 799-808.
2. Andersen EC, Gerke JP, Shapiro JA, Crissman JR, Ghosh R, Bloom JS, Félix M-A, Kruglyak L., 2012. Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nature Genetics 44: 285-290.
3. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA., 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
4. Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blaxter ML., 2011. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS ONE 6: e19315.
5. Buerkle CA, Gompert Z., 2013. Population genomics based on low coverage sequencing: How low should we go? Molecular Ecology 22: 3028-3035.
6. Cariou M, Duret L, Charlat S., 2013. Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecology and Evolution 3: 846-852.
7. Casazza G, Granato L, Minuto L, Conti E., 2012. Polyploid evolution and Pleistocene glacial cycles: A case study from the alpine primrose Primula marginata (Primulaceae). BMC Evolutionary Biology 12: 56.
8. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH., 2011. Stacks: Building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics 1: 171-182.
9. Chu ND, Kaluziak ST, Trussell GC, Vollmer SV., 2014. Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snail Nucella lapillus. Molecular Ecology 23: 1863-1873.
10. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM., 2011. Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 12: 4.
11. Clement M, Posada D, Crandall KA., 2000. TCS: A computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1660.
12. Davey JW, Blaxter ML., 2010. RADSeq: Next-generation population genetics. Briefings in Functional Genomics 9: 416-423.
13. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML., 2013. Special features of RAD sequencing data: Implications for genotyping. Molecular Ecology 22: 3151-3164.
14. Dufresne F, Hebert PD., 1997. Pleistocene glaciations and polyphyletic origins of polyploidy in an arctic cladoceran. Proceedings of the Royal Society B: Biological Sciences 264: 201-206.
15. Earl DA, vonHoldt BM., 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359-361.
16. Eaton DA, Ree RH., 2013. Inferring phylogeny and introgression using RAD-seq data: An example from flowering plants (Pedicularis: Orobanchaceae). Systematic Biology 62: 689-706.
17. Edgar RC., 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
18. Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM., 2010. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences USA 107: 16196-16200.
19. Gagnaire PA, Pavey SA, Normandeau E, Bernatchez L., 2013. The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing. Evolution 67: 2483-2497.
20. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES., 2014. TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9: E90346.
21. Goldblatt P, Endress PK., 1977. Cytology and evolution in Hamamelidaceae. Journal of the Arnold Arboretum 58: 67-71.
22. Gompert Z, Parchman TL, Buerkle CA., 2012. Genomics of isolation in hybrids. Philosophical Transactions of the Royal Society B: Biological Sciences 367: 439-450.
23. Greilhuber J, Temsch EM, Loureiro JCM., 2007. Nuclear DNA content measurement. In:, Doležel J, Greilhuber J, Suda J, eds. Flow cytometry with plant cells: Analysis of genes, chromosomes and genomes. Weinheim, Germany: Wiley-VCH. 67-101.
24. Griffin PC, Robin C, Hoffmann AA., 2011. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biology 9: 1-18.
25. Hijmans RJ, Guarino L, Bussink C, Mathur P, Cruz M, Barrentes I, Rojas E., 2012. DIVA-GIS 7.5. A geographic information system for the analysis of species distribution data [online]. Manual available from http://www.diva-gis.org (accessed 22 July 2015).
26. Hohenlohe PA, Bassham S, Currey M, Cresko WA., 2012a. Extensive linkage disequilibrium and parallel adaptive divergence across three spine stickleback genomes. Philosophical Transactions of the Royal Society B: Biological Sciences 367: 395-408.
27. Hohenlohe PA, Catchen J, Cresko WA., 2012b. Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. In:, Pompanon F, Bonin A, eds. Data production and analysis in population genomics. New York: Humana Press. 235-260.
28. Hu HH, Chaney RW., 1940. Miocene flora from Shantung province, China. Part I. Carnegie Institution of Washington. Contributions to Paleontology Publication 507: 1-147.
29. Huson DH, Bryant D., 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
30. Li J, Bogle AL., 2001. A new suprageneric classification system of the Hamamelidoideae based on morphology and sequences of nuclear and chloroplast DNA. Harvard Papers in Botany 5: 499-515.
31. Librado P, Rozas J., 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
32. Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE., 2013. Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol. PLoS Geneticx 9: e1003215.
33. McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT., 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution 66: 526-538.
34. Meyer FG., 1997. Fothergilla. In: Flora of North America Editorial Committee eds. Flora of North America North of Mexico. New York: Oxford University Press. 3: 365-366.
35. Meyer HW, Manchester SR., 1997. The Oligocene Bridge Creek Flora of the John Day Formation. Oregon: University of California Press.
36. Miller MA, Pfeiffer W, Schwartz T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans (USA), November 2010. 1-8. doi: 10.1109/GCE2010.5676129
37. Nadeau NJ, Martin SH, Kozak KM, Salazar C, Dasmahapatra KK, Davey JW, Baxter SW, Blaxter ML, Mallet J, Jiggins CD., 2013. Genome-wide patterns of divergence and gene flow across a butterfly radiation. Molecular Ecology 22: 814-826.
38. Pante E, Abdelkrim J, Viricel A, Gey D, France S, Boisselier M-C, Samadi S., 2015. Use of RAD sequencing for delimiting species. Heredity 114: 450-459.
39. Paun O, Stuessy TF, Hörandl E., 2006. The role of hybridization, polyploidization and glaciation in the origin and evolution of the apomictic Ranunculus cassubicus complex. New Phytologist 171: 223-236.
40. Peirson JA, Dick CW, Reznicek AA., 2013. Phylogeography and polyploid evolution of North American goldenrods (Solidago subsect. Humiles, Asteraceae). Journal of Biogeography 40: 1887-1898.
41. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE., 2012. Double digest RAD-seq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7: e37135.
42. Pfender W, Saha M, Johnson E, Slabaugh M., 2011. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theoretical and Applied Genetics 122: 1467-1480.
43. Posada D., 2008. jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
44. Pritchard JK, Stephens M, Donnelly P., 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
45. Radtke MG, Pigg KB, Wehr WC., 2005. Fossil Corylopsis and Fothergilla leaves (Hamamelidaceae) from the Lower Eocene flora of Republic, Washington, USA, and their evolutionary and biogeographic significance. International Journal of Plant Sciences 166: 347-356.
46. Raj A, Stephens M, Pritchard JK., 2014. fastSTRUCTURE: Variational inference of population structure in large SNP data sets. Genetics 197: 573-589.
47. Ranney TG, Lynch NP, Fantz PR, Cappiello P., 2007. Clarifying taxonomy and nomenclature of Fothergilla (Hamamelidaceae) cultivars and hybrids. HortScience 42: 470-473.
48. Ranney TG, Miller R, Lewandowski R, Xiang J., 2012. Discovery of a new diploid cytotype of Fothergilla. HortScience 47: S367.
49. Recknagel H, Elmer KR, Meyer A., 2013. A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq). G3: Genes, Genomes, Genetics 3: 65-74.
50. Ronquist F, Huelsenbeck JP., 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
51. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP., 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
52. Rowe H, Renaut S, Guggisberg A., 2011. RAD in the realm of next-generation sequencing technologies. Molecular Ecology 20: 3499-3502.
53. Rubin BE, Ree RH, Moreau CS., 2012. Inferring phylogenies from RAD sequence data. PLoS ONE 7: e33394.
54. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Wall PK, Soltis PS., 2009. Polyploidy and angiosperm diversification. American Journal of Botany 96: 336-348.
55. Soltis PS, Soltis DE., 2009. The role of hybridization in plant speciation. Annual Review of Plant Biology 60: 561-588.
56. Stamatakis A, Hoover P, Rougemont J., 2008. A rapid bootstrap algorithm for the raxml web servers. Systematic Biology 57: 758-771.
57. Stebbins GL., 1985. Polyploidy, hybridization, and the invasion of new habitats. Annals of the Missouri Botanical Garden 72: 824-832.
58. Suzuki K., 1961. The important and characteristic Pliocene and Miocene species of plants from the southern part of the Tohoku district, Japan. Science Reports of the Faculty of Arts and Science, Fukushima University 10: 1-95.
59. Swofford DL., 2003. PAUP∗: Phylogenetic analysis using parsimony (and other methods), Version 4. Sunderland: Sinauer Associates.
60. Vorsa N, Jelenkovic G, Draper A, Welker W., 1987. Fertility of 4x x 5x and 5x x 4x progenies derived from Vaccinium ashei/corymbosum pentaploid hybrids. Journal of the American Society for Horticultural Science (USA) 112: 993-997.
61. Weakley A., 2008. Flora of the Carolinas, Virginia, and Georgia, and surrounding areas. Chapel Hill: UNC Herbarium, North Carolina Botanical Garden, University of North Carolina at Chapel Hill.
62. Weaver RE Jr., 1969. Studies in the North American genus Fothergilla (Hamamelidaceae). Journal of the Arnold Arboretum 50: 599-619.
63. Xie L, Yi T-S, Li R, Li D-Z, Wen J., 2010. Evolution and biogeographic diversification of the witch-hazel genus (Hamamelis L., Hamamelidaceae) in the Northern Hemisphere. Molecular Phylogenetics and Evolution 56: 675-689.