Genetic structure and phylogeography of Pyrus pashia L. (Rosaceae) in Yunnan Province, China, revealed by chloroplast DNA analyses

Tree Genetics and Genomes

Volumn 9, Issue 2, 2013, Pages 433-441

  Liu, Jing ^a   Sun, Ping ^a   Zheng, Xiaoyan ^a,b   Potter, Daniel ^c   Li, Kunming ^d   Hu, Chunyun ^a   Teng, Yuanwen ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b LISHUI UNIVERSITY   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d INSTITUTE OF MEDICINAL PLANTS   (China)

Author keywords

accD psaI; Genetic structure; Phylogeography; Pyrus pashia; trnL trnF; Yunnan Province

Indexed keywords

PYRUS; PYRUS PASHIA; ROSACEAE;

EID: 84875211579     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-012-0564-x     Document Type: Article

References (53)

1. Avise JC (1994) Molecular markers, natural history, and evolution. Chapman & Hall, New York.
2. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge.
3. Bailey LH (1917) Pyrus. In: Standard cyclopedia of horticulture, vol V. Macmillan, New York, pp 2865-2878.
4. Bao L, Chen KS, Zhang D, Cao YF, Yamamoto T, Teng YW (2007) Genetic diversity and similarity of pear cultivars native to East Asia revealed by SSR (simple sequence repeat) markers. Genet Resour Crop Evol 54: 959-971.
5. Bao L, Chen KS, Zhang D, Li XG, Teng YW (2008) An assessment of genetic variability and relationships within Asian pears based on AFLP (amplified fragment length polymorphism) markers. Sci Hortic 116: 374-380.
6. Chiang TY, Chiang YC, Chen YJ, Chou CH, Havanond S, Hong TN, Huang S (2001) Phylogeography of Kandelia candel in East Asiatic mangroves based on nucleotide variation of chloroplast and mitochondrial DNAs. Mol Ecol 10: 2697-2710.
7. Clegg MT, Zurawski G (1992) Chloroplast DNA and the study of plant phylogeny: present status and future prospects. Chapman & Hall, New York.
8. Clement M, Posda D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9: 1657-1659.
9. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
10. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferblack from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
11. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3. 0 An integrated software package for population genetics data analysis. Evol Bioinformatics Online 1: 47-50.
12. Ferris C, King RA, Vainola R, Hewitt GM (1998) Chloroplast DNA recognizes three refugia sources of European oaks and suggests independent eastern and western immigrations to Finland. Heredity 80: 584-593.
13. Gong X, LuanSS HKH, Hwang CC, Lin CJ, Chiang YC, Chiang TY (2011) Population structure of Nouelia insignis (Asteraceae), an endangered species in southwestern China, based on chloroplast DNA sequences: recent demographic shrinking. J Plant Res 124: 221-230.
14. Graur D, Li WH (1999) Fundamentals of molecular evolution. Sinauer Associates, Sunderland.
15. Harpending HC (1994) Signature of ancient population-growth in a low-resolution mitochondrial-DNA mismatch distribution. Hum Biol 66: 591-600.
16. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc 58: 247-276.
17. Hewitt GM (2001) Speciation, hybrid zones and phylogeography-or seeing genes in space and time. Mol Ecol 10: 537-549.
18. Hu CY, Zheng XY, Teng YW (2011) Characterization and phylogenetic utility of non-coding chloroplast regions trnL-trnF and accD-psaI in Pyrus. Acta Hortic Sina 38: 2261-2272 (in Chinese).
19. Huang S, Chiang YC, Schaal BA, Chou CH, Chiang TY (2001) Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Mol Ecol 10: 2669-2681.
20. Iketani H, Manabe T, Matsuta N, Akihama T, Hayashi Y (1998) Incongruence between RFLPs of chloroplast DNA and morphological classification in east Asian pear (Pyrus spp.). Genet Resour Crop Evol 45: 533-539.
21. Katayama H, Tachibana M, Iketani H, Zhang SL, Uematsu C (2012) Phylogenetic utility of structural alterations found in the chloroplast genome of pear: hypervariable regions in a highly conserved genome. Tree Genet Genomes 8: 313-326.
22. Kimura T, Iketani H, Kotobuki K, Matsuta N, Ban Y, Hayashi T, Yamamoto T (2003) Genetic characterization of pear varieties revealed by chloroplast DNA sequences. J Hortic Sci Biotechnol 78: 241-247.
23. Li N, Fu L (1997) Notes on gymnosperms I. Taxonomic treatment of some Chinese conifers. Novon 7: 261-264.
24. Liu J, Zheng XY, Potter D, Hu CY, Teng YW (2012) Genetic diversity and population structure of Pyrus calleryana (Rosaceae) in Zhejiang province, China. Biochem Syst Ecol 45: 69-78.
25. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
26. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York.
27. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269-5273.
28. Newton AC, Allnutt AR, Gillies ACM, Lowe AJ, Ennos RA (1999) Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends Ecol Evol 14: 140-145.
29. Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S et al (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300: 1563-1565.
30. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14: 689-701.
31. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237-1245.
32. Posada D, Crandall KA (2001) Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol 16: 37-45.
33. Posada D, Crandall KA, Templeton AR (2000) GeoDis: a program for the cladistic nested analysis of geographical distribution of genetic haplotypes. Mol Ecol 9: 487-488.
34. Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson TA, Campbell CS (2007) Phylogeny and classification of Rosaceae. Plant Syst Evol 266: 5-43.
35. Rozas J, Sanchez-Delbarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
36. Rubtsov GA (1944) Geographic distribution of the genus Pyrus and trends and factors in its evolution. Am Soc Nat 78: 358-366.
37. Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith W (1998) Phylogeography studies in plants: problems and prospects. Mol Ecol 7: 465-474.
38. Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in recently diverged plant group. Am J Bot 85: 1301-1345.
39. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonisation routes in Europe. Mol Ecol 7: 453-464.
40. Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140: 767-782.
41. Teng YW, Tanabe K, Tamura F, Itai A (2001) Genetic relationships of pear cultivars in Xinjiang, China as measublack by RAPD markers. J Hortic Sci Biotech 76: 771-779.
42. Teng YW, Tanabe K, Tamura F, Itai A (2002) Genetic relationship of Pyrus species and cultivars native to east Asia revealed by randomly amplified polymorphic DNA makers. J Am Soc Hortic Sci 127: 262-270.
43. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL X: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
44. Wang ZJ, Guan KY (2011) Genetic structure and phylogeography of a relict tree fern, Sphaeropteris brunoniana (Cyatheaceae) from China and Laos inferred from cpDNA sequence variations: implication for conservation. J Syst Evol 49: 71-79.
45. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondria, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84: 9054-9058.
46. Xue WQ, Zhang XS (2011) Geographic distribution of Coenosia Meigen (Diptera, Muscidae) of Yunnan, China, with descriptions of four new species. Dtsch Entomol Z 58: 155-164.
47. Yamamoto T, Kimura T, Sawamura Y, Kotobuki K, Ban Y, Hayashi T, Matsuta N (2001) SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theor Appl Genet 102: 865-887.
48. Yamamoto T, Kimura T, Sawamura Y, Manabe T, Kotobuki K, Hayashi T, Ban Y, Matsuta N (2002a) Simple sequence repeats for genetic analysis in pear. Euphytica 124: 129-137.
49. Yamamoto T, Kimura T, Sawamura Y, Manabe T, Kotobuki K, Hayashi T, Ban Y, Matsuta N (2002b) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet 106: 9-18.
50. Yao LH, Zheng XY, Cai DY, Gao Y, Wang K, Cao YF, Teng YW (2010) Exploitation of Malus EST-NSSRs and the utility in evaluation of genetic diversity in Malus and Pyrus. Genet Resour Crop Evol 57: 841-851.
51. Yu DJ, Lu LD, Gu CZ, Guan KJ, Jiang WF (1986) Flora Republicae Popularis Sinicae 38: 367-370.
52. Zhang Q, Chiang TY, George M, Liu JQ, Abbott RJ (2005) Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Mol Ecol 14: 3513-3524.
53. Zheng XY, Hu CY, Spooner D, Liu J, Cao JS, Teng YW (2011) Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae). BMC Evol Biol 11: 255.