Genetic homogenization of the nuclear ITS loci across two morphologically distinct gentians in their overlapping distributions in the Qinghai-Tibet Plateau

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Hu, Quanjun ^a   Peng, Huichao ^b   Bi, Hao ^a   Lu, Zhiqiang ^c   Wan, Dongshi ^c   Wang, Qian ^a,d   Mao, Kangshan ^a  

^a SICHUAN UNIVERSITY   (China)

^b NORTHWEST INSTITUTE OF PLATEAU BIOLOGY   (China)

^c LANZHOU UNIVERSITY   (China)

^d ZUNYI MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84989862733     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep34244     Document Type: Article

References (53)

1. Roberts, H. F., & Mendel, G. Plant hybridization before Mendel. (Princeton University Press, 1929
2. Comes, H. P., & Kadereit, J. W. The effect of Quaternary climatic changes on plant distribution and evolution. Trends Plant Sci. 3, 432-438 (1998
3. Hewitt, G. M. Genetic consequences of climatic oscillations in the Quaternary. Philos. Trans. R. Soc. London B Biol. Sci. 359, 183-195 (2004
4. Rieseberg, L. H., Archer, M. A., & Wayne, R. K. Transgressive segregation, adaptation and speciation. Heredity. 83, 363-372 (1999
5. Arnold, M. L. Evolution through Genetic Exchange. (Oxford University Press, 2007
6. Abbott, R., et al. Hybridization and speciation. J. Evol. Biol. 26, 229-246 (2013
7. Rieseberg, L. H., et al. Hybridization and the colonization of novel habitats by annual sunflowers. Genetica 129, 149-165 (2006
8. Kim, M., et al. Regulatory genes control a key morphological and ecological trait transferred between species. Science. 322, 1116-1119 (2008
9. Chan, K. M. A., & Levin, S. A. Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evolution. 59, 720-729 (2005
10. Currat, M., Ruedi, M., Petit, R. J., & Excoffier, L. The hidden side of invasions: massive introgression by local genes. Evolution. 62, 1908-1920 (2008
11. Du, F. K., et al. Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau. New Phytol. 192, 1024-1033 (2011
12. Wang, L., et al. History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Mol. Ecol. 18, 709-721 (2009
13. Zhang, Q., Chiang, T. Y., George, M., Liu, J. Q., & Abbott, R. J. Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Mol. Ecol. 14, 3513-3524 (2005
14. Zhang, X. L., et al. Molecular phylogeny and biogeography of Gentiana sect. Cruciata (Gentianaceae) based on four chloroplast DNA datasets. Taxon 58, 862-870 (2009
15. Ho, T., & Liu, S A worldwide monograph of ?Gentiana?. (Science Press, 2001
16. Hou, Q., Meng, L. H., & Yang, H. L. Pollination ecology of Gentiana siphonantha (Gentianaceae) and a further comparison with its sympatric congener species. J. Syst. Evol. 46, 554-562 (2008
17. Li, X., Wang, L., Yang, H., & Liu, J. Q. Confirmation of natural hybrids between Gentiana straminea and G. siphonantha (Gentianaceae) based on molecular evidence. Front. Biol. China 3, 470-476 (2008
18. Koch, M. A., Dobeš, C., & Mitchell-Olds, T. Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae). Mol. Biol. Evol. 20, 338-350 (2003
19. Liu, J. Q., Gao, T. G., Chen, Z. D., & Lu, A. M. Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae). Mol. Phylogenet. Evol. 23, 307-325 (2002
20. Liu, J. Q., Wang, Y. J., Wang, A. L., Hideaki, O., & Abbott, R. J. Radiation and diversification within the Ligularia-Cremanthodium- Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau. Mol. Phylogenet. Evol. 38, 31-49 (2006
21. Álvarez, I., & Wendel, J. F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29, 417-434 (2003
22. Wang, Q., Yu, Q. S., & Liu, J. Q. Are nuclear loci ideal for barcoding plants?. A case study of genetic delimitation of two sister species using multiple loci and multiple intraspecific individuals. J. Syst. Evol. 49, 182-188 (2011
23. China Plant BOL Group et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc. Natl. Acad. Sci. USA 108, 19641-19646 (2011
24. Wendel, J. F., Schnabel, A., & Seelanan, T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA 92, 280-284 (1995
25. Fuertes Aguilar, J., Rosselló, J. A., & Nieto Feliner, G. Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plumbaginaceae). Mol. Ecol. 8, 1341-1346 (1999
26. Hillis, D. M., & Dixon, M. T. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 66, 411-453 (1991
27. Widmer, A., Lexer, C., & Cozzolino, S. Evolution of reproductive isolation in plants. Heredity. 102, 31-38 (2008
28. Gay, L., et al. Molecular and morphological patterns of introgression between two large white-headed gull species in a zone of recent secondary contact. Mol. Ecol. 16, 3215-3227 (2007
29. McGuire, J. A., et al. Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution. 61, 2879-2897 (2007
30. Du, F. K., Petit, R. J., & Liu, J. Q. More introgression with less gene flow: chloroplast vs. mitochondrial DNA in the Picea asperata complex in China, and comparison with other Conifers. Mol. Ecol. 18, 1396-1407 (2009
31. Zhou, Y. F., et al. Gene flow and species delimitation: a case study of two pine species with overlapping distributions in southeast China. Evolution 64, 2342-2352 (2010
32. Lu, Z., et al. Initial diversification, glacial survival, and continuous range expansion of Gentiana straminea (Gentianaceae) in the Qinghai-Tibet Plateau. Biochem. Syst. Ecol. 62, 219-228 (2015
33. Liu, J. Q., Duan, Y. W., Hao, G., Ge, X. J., & Sun, H. Evolutionary history and underlying adaptation of alpine plants on the Qinghai-Tibet Plateau. J. Syst. Evol. 52, 241-249 (2014
34. Doyle, J. J., & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15 (1987
35. Hamilton, M. B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol. Ecol. 8, 521-523 (1999
36. White, T. J., Bruns, T., Lee, S., & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications 18, 315-322 (1990
37. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., & Higgins, D. G. The CLUSTAL-X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882 (1997
38. Clement, M., Posada, D., & Crandall, K. A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9, 1657-1659 (2000
39. Swofford, D. L. PAUP: phylogenetic analyses using parsimony (and other methods), Version 4. (Sinauer Associates, Sunderland, 2003
40. Huelsenbeck, J. P., & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755 (2001
41. Ronquist, F., & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003
42. Posada, D., & Crandall, K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818 (1998
43. Pons, O., & Petit, R. J. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144, 1237-1245 (1996
44. Excoffier, L., Smouse, P. E., & Quattro, J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479-491 (1992
45. Excoffier, L., Laval, G., & Schneider, S. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47-50 (2005
46. Rousset, F. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145, 1219-1228 (1997
47. Pease, J. B., & Hahn, M. W. Detection and polarization of introgression in a five-Taxon phylogeny. Syst. Biol. 64, 651-662 (2015
48. Kay, K. M., et al. A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evol. Biol. 6, 1-9 (2006
49. Phillips, S. J., Anderson, R. P., & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231-259 (2006
50. Hasumi, H., & Emori, S. K-1 Coupled GCM (MIROC) description (Center for climate System Research, University of Tokyo, 2004
51. Collins, W., et al. The community climate system model version 3 (CCSM3). J. Clim. 19, 2122-2143 (2006
52. Alan, H. F., & John, F. B. A review of methods for the assessment of prediction errors in conservation presence/absence models. Environ. Conserv. 1, 38-49 (1997
53. Amante, C., & Eakins, B. W. ETOPO1 1 Arc-minute global relief model: Procedures, data sources and analysis. NOAA Technical Memorandum NESDIS NGDC-24. (National Geophysical Data Center, NOAA, 2009), doi: 10.7289/V5C8276M [Access date: Jan 29] (2016