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Genetica

, Volume 139, Issue 2, pp 221–232 | Cite as

High chloroplast haplotype diversity in the endemic legume Oxytropis chankaensis may result from independent polyploidization events

  • E. V. ArtyukovaEmail author
  • M. M. Kozyrenko
  • A. B. Kholina
  • Y. N. Zhuravlev
Article

Abstract

Oxytropis chankaensis Jurtz. (Fabaceae) is an endangered perennial tetraploid species endemic to the Khanka Lake coast. In Russia, O. chankaensis is distributed across a very restricted zone along the western shore of this lake. To characterise all known populations of this species, we assessed the genetic diversity of four noncoding regions of chloroplast DNA (cpDNA). Variable sites detected within the trnLtrnF, the petGtrnP, and the trnStrnG regions allowed the identification of seven haplotypes. On the other hand, no variation was found in the trnHpsbA region. O. chankaensis exhibited an overall low level of nucleotide diversity (π = 0.00052) but a marked haplotype diversity (h = 0.718). A combination of three or four haplotypes was found in each population, and most of the cpDNA variation (above 90%) was distributed within populations. The level of genetic structure that we detected in O. chankaensis using maternal plastid DNA markers was much lower (GST = 0.037) than the average that is estimated for angiosperms. We found no evidence for isolation by distance or for phylogeographic structuring in O. chankaensis. Our data suggest that autopolyploidy has arisen more than once in the evolutionary history of this species. Repetitive expansion and contraction during past and ongoing demographic events both seem to be involved in shaping the current genetic structure of O. chankaensis. This study provides valuable information for developing the most appropriate strategy for conserving this endemic species with a narrow habitat range.

Keywords

Oxytropis chankaensis Endemic species Autotetraploid Plastid DNA Genetic diversity 

Notes

Acknowledgments

This work was supported by Grant of Russian Academy of Sciences № 09-I-P23-06 and partly by the Program “Molecular and Cell Biology” of the Presidium of the Russian Academy of Sciences (project no. 09-1-P22-03). The authors thank two anonymous reviewers for their helpful comments on the paper.

References

  1. Agapova ND, Arharova KB, Vahtina LI et al (1990) Chromosome numbers of flowering plants of the flora of the USSR: families Aceraceae–Menyanthaceae. In: Takhtajan A (ed) Numeri Chromosomatum Magnoliophytorum florae USSR. Nauka, Leningrad, pp 398–410Google Scholar
  2. Artyukova EV, Kholina AB, Kozyrenko MM, Zhuravlev YN (2004) Analysis of genetic variation in rare endemic species Oxytropis chankaensis Jurtz. (Fabaceae) using RAPD markers. Russ J Genet 40:710–716CrossRefGoogle Scholar
  3. Artyukova EV, Kozyrenko MM, Gorovoy PG, Zhuravlev YN (2009) Plastid DNA variation in highly fragmented populations of Microbiota decussata Kom. (Cupressaceae), an endemic to Sikhote Alin Mountains. Genetica 137:201–212CrossRefPubMedGoogle Scholar
  4. Ayele TB, Gailing O, Umer M, Finkeldey R (2009) Chloroplast DNA haplotype diversity and postglacial recolonization of Hagenia abyssinica (Bruce) J.F. Gmel. in Ethiopia. Plant Syst Evol 280:175–185CrossRefGoogle Scholar
  5. Barkalov VY, Kharkevich SS (1996) The vascular plants of the Khankaysky reservation. Bot Zhurn (Leningrad) 81:104–116Google Scholar
  6. Bazarova VB, Mokhova LM, Orlova LA, Belyanin PS (2008) Variation of the Lake Khanka level in the late Holocene, Primorye. Russ J Pac Geol 2:272–276CrossRefGoogle Scholar
  7. Bisby FA, Roskov YR, Orrell TM et al., (eds) (2009) Species 2000 & ITIS Catalogue of Life: 2009 Annual checklist. Digital resource at www.catalogueoflife.org/annual-checklist/2009/. Species 2000: reading, UK
  8. Bonfield JK, Smith KF, Staden R (1995) A new DNA sequence assembly program. Nucleic Acids Res 23:4992–4999CrossRefPubMedGoogle Scholar
  9. Byrne M, Macdonald B, Coates D (2002) Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia. J Evol Biol 15:576–587CrossRefGoogle Scholar
  10. Clement M, Posada D, Crandall K (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1660CrossRefPubMedGoogle Scholar
  11. Czerepanov SK (1995) Vascular plants of Russia and adjacent states (the former USSR). Cambridge University Press, New YorkGoogle Scholar
  12. Desplanqe B, Viard F, Bernard J et al (2000) The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies. Mol Ecol 9:141–154CrossRefGoogle Scholar
  13. Doyle JJ, Doyle JL, Rauscher JT, Brown AHD (2004) Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine). New Phytol 161:121–132CrossRefGoogle Scholar
  14. Ellstrand NC, Elam DR (1993) Population genetic consequences of small population size: implication for plant conservation. Ann Rev Ecol Syst 24:217–242CrossRefGoogle Scholar
  15. Ennos RA (1994) Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72:250–259CrossRefGoogle Scholar
  16. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform Online 1:47–50PubMedGoogle Scholar
  17. Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925PubMedGoogle Scholar
  18. Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709PubMedGoogle Scholar
  19. Galtier N, Gouy M, Gautier C (1996) Seaview and phylo-win: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548PubMedGoogle Scholar
  20. Gauthier P, Lumaret R, Bedecarrats A (1997) Chloroplast-DNA variation in the genus Lotus (Fabaceae) and further evidence regarding the maternal parentage of Lotus corniculatus L. Theor Appl Genet 95:629–636CrossRefGoogle Scholar
  21. Godt MJW, Johnson BR, Hamrick JL (1996) Genetic diversity and population size in four rare southern Appalachian plant species. Conserv Biol 10:796–805CrossRefGoogle Scholar
  22. Guo Y-P, Vogl C, Van Loo M, Ehrendorfer F (2006) Hybrid origin and differentiation of two tetraploid Achillea species in East Asia: molecular, morphological and ecogeographical evidence. Mol Ecol 15:133–144CrossRefPubMedGoogle Scholar
  23. Gurzenkov NN, Pavlova NS (1984) Chromosome numbers of the representatives of the genera Astragalus and Oxytropis (Fabaceae) from the Far East of the USSR. Bot Zhurn (Leningrad) 69:1569–1570Google Scholar
  24. Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc Lond B Biol Sci 351:1291–1298CrossRefGoogle Scholar
  25. Harpending HC, Batzer MA, Gruven MA et al (1998) Genetic traces of ancient demography. Proc Natl Acad Sci USA 95:1961–1967CrossRefPubMedGoogle Scholar
  26. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59(8):1633–1638PubMedGoogle Scholar
  27. Huang SSF, Hwang S-Y, Lin T-P (2002) Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia. Mol Ecol 11:2349–2358CrossRefPubMedGoogle Scholar
  28. Ikeda H, Setoguchi H (2007) Phylogeography and refugia of the Japanese endemic alpine plant Phyllodoce nipponica Makino (Ericaceae). J Biogeogr 34:169–176CrossRefGoogle Scholar
  29. Ikeda H, Senni K, Fujuu N, Setoguchi H (2008) Consistent geographic structure among multiple nuclear sequences and cpDNA polymorphisms of Cardamine nipponica Franch. et Savat, (Brassucaceae). Mol Ecol 17:3178–3188CrossRefPubMedGoogle Scholar
  30. Jorgensen JL, Stehlik I, Brochmann C, Conti E (2003) Implication of ITS sequences and RAPD markers for the taxonomy and biogeography of the Oxytropis campestris and O. arctica (Fabaceae) complexes in Alaska. Am J Bot 90:1470–1480CrossRefGoogle Scholar
  31. Kao RH (2008) Origins and widespread distribution of co-existing polyploids in Arnica cordifolia (Asteraceae). Ann Bot 101:145–152CrossRefPubMedGoogle Scholar
  32. Kharkevich SS, Kachura NN (1981) Rare plant species of the soviet Far East and their conservation. Nauka, Moscow, pp 156–161Google Scholar
  33. Kholina AB, Kholin SK (2006) Population age structure of rare plant Oxytropis chankaensis. In: Problems of preservation of wetlands of international meaning: Khanka Lake: Proceedings of the 2 Inter. Conf. Idea, Vladivostok, pp 26–35Google Scholar
  34. Kholina AB, Kholin SK (2008) Intraspecific variation of Oxytropis chankaensis, Far Eastern endemic. Russ J Ecol 39:14–20. doi: 10.1007/s11184-008-1003-y CrossRefGoogle Scholar
  35. Kholina AB, Markelova OV, Kholin SK (2003) Population structure and reproduction biology of the rare endemic species Oxytropis chankaensis Jurtz. In: Botanical researches in Asian Russia: proceedings of the XI congress of the Russian Botanical Society (18–22 August 2003, Novosibirsk–Barnaul), vol 3. Azbuka, Barnaul, pp 369–370Google Scholar
  36. Kholina AB, Koren OG, Zhuravlev YN (2004) High polymorphism and autotetraploid origin of the rare endemic species Oxytropis chankaensis Jurtz. (Fabaceae) inferred from allozyme data. Russ J Genet 40:393–400CrossRefGoogle Scholar
  37. Kholina AB, Koren OG, Artyukova EV et al. (2007) High level of polymorphism in a narrow endemic Oxytropis chankaensis (Fabaceae) inferred from molecular markers. In: Kartavtsev YP and Kryukov AP (eds) Modern achievements in population, evolutionary and ecological genetics (MAPEEG–2007) Reg Found Dev Gen, Vladivostok, p 19Google Scholar
  38. Kholina AB, Koren OG, Zhuravlev YN (2009) Genetic structure and differentiation of populations of the tetraploid species Oxytropis chankaensis (Fabaceae). Russ J Genet 45:70–80CrossRefGoogle Scholar
  39. Kitagawa M (1979) Neo-Lineamenta florae Manshuricae. J Cramer, Vaduz, pp 409–410Google Scholar
  40. Korotkii AM, Grebennikova TA, Karaulova LP, Belyanina NI (2007) Lacustrine transgressions in the late Cenozoic Ussuri-Khanka depression (Primor’e). Russ J Pac Geol 1:352–365CrossRefGoogle Scholar
  41. Korpelainen H (2004) The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes. Naturwissenschaften 91:505–518CrossRefPubMedGoogle Scholar
  42. Lorenz-Lemke AP, Mäder G, Muschner VC, Stehmann JR et al (2006) Diversity and natural hybridization in a highly endemic species of Petunia (Solanaceae): a molecular and ecological analysis. Mol Ecol 15:4487–4497CrossRefPubMedGoogle Scholar
  43. Lu H-P, Cai Y-W, Chen X-Y et al (2006) High RAPD but no cpDNA sequence variation in the endemic and endangered plant, Heptacodium miconioides Rehd. (Caprifoliaceae). Genetica 128:409–417CrossRefPubMedGoogle Scholar
  44. Mokhova L, Tarasov P, Bazarova V, Klimin M (2009) Quantitative biome reconstruction using modern and late quaternary pollen data from the southern part of the Russian Far East. Quat Sci Rev 28:2913–2926CrossRefGoogle Scholar
  45. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 137:1143–1155CrossRefGoogle Scholar
  46. Parisod C, Holderegger R, Brochmann C (2010) Evolutionary consequences of autopolyploidy. New Phytol 186:5–17CrossRefPubMedGoogle Scholar
  47. Pavlova NS (1989) Family Fabaceae. In: Kharkevich SS (ed) The vascular plants of the Soviet Far East, vol 4. Nauka, Leningrad, pp 191–339Google Scholar
  48. Petit RJ, Duminil E, Fineschi S et al (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701CrossRefPubMedGoogle Scholar
  49. Pleines T, Jakob SS, Blattner FR (2009) Application of non-coding DNA regions in intraspecific analyses. Plant Syst Evol 282:281–294CrossRefGoogle Scholar
  50. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144:1237–1245PubMedGoogle Scholar
  51. Posada D, Crandall KA (2001) Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol 16:37–45CrossRefPubMedGoogle Scholar
  52. Prentice HC, Malm JU, Mateu-Andres I, Segarra-Moragues JG (2003) Allozyme and chloroplast DNA variation in island and mainland populations of the rare Spanish endemic, Silene hifacensis (Caryophyllaceae). Conserv Genet 4:543–555CrossRefGoogle Scholar
  53. Probatova NS, Seledets VP, Rudyka EG (2008) Oxytropis chankaensis. In: Marhold K. (ed.), IAPT/IOPB chromosome data 5. Taxon 57:560, E20Google Scholar
  54. Ramos ACS, Lemos-Filho JP, Ribeiro RA et al (2007) Phylogeography of the tree Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae) and the influence of quaternary climate changes in the Brazilian Cerrado. Ann Bot 100:1219–1228CrossRefPubMedGoogle Scholar
  55. Rausch JH, Morgan MT (2005) Effect of salf-fertilizatiom, inbreeding depression, and population size on autopolyploid establishment. Evolution 59:1867–1875PubMedGoogle Scholar
  56. Red Data Book Primorsky Kray (2008) Plants. Rare and endangered species of plants and fungi. In: Kozhevnikov AE, Nedoluzhko VA, Barkalov VYu et al. (eds) AVK Apelsin, Vladivostok, pp 339–341Google Scholar
  57. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569PubMedGoogle Scholar
  58. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228PubMedGoogle Scholar
  59. Rozas J, Sanchez-DelBarrio JC, Messequer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497CrossRefPubMedGoogle Scholar
  60. Schaal BA, Gaskin JF, Caicedo AL (2003) Phylogeography, haplotype trees, and invasive plant species. J Hered 94:197–204CrossRefPubMedGoogle Scholar
  61. Schneider S, Excoffier L (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1079–1089PubMedGoogle Scholar
  62. Segraves KA, Thompson JN, Soltis PS, Soltis DE (1999) Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Mol Ecol 8:253–262CrossRefGoogle Scholar
  63. Shaw J, Lickey EB, Beck JT et al (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92:142–166CrossRefGoogle Scholar
  64. Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49:369–381CrossRefPubMedGoogle Scholar
  65. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555–562PubMedGoogle Scholar
  66. Soltis PS, Soltis DE (2000) The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci USA 97:7051–7057CrossRefPubMedGoogle Scholar
  67. Soltis PS, Soltis DE (2009) The role of hybridization in plant speciation. Annu Rev Plant Biol 60:561–588CrossRefPubMedGoogle Scholar
  68. Soltis DE, Soltis PS, Tate JA (2003) Advances in the study of polyploidy since plant speciation. New Phytol 161:173–191CrossRefGoogle Scholar
  69. Soltis DE, Soltis PS, Schemske DW et al (2007) Autopolyploidy in angiosperms: have we grossly underestimated the number of species? Taxon 56:13–30Google Scholar
  70. Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MassachusettsGoogle Scholar
  71. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109CrossRefPubMedGoogle Scholar
  72. Tajima F (1989) The effect of change in population size on DNA polymorphism. Genetics 123:597–601PubMedGoogle Scholar
  73. Tremetsberger K, UrtubeyY E, Terrab A (2009) Pleistocene refugia and polytopic replacement of diploids by tetraploids in the Patagonian and Subantarctic plant Hypochaeris incana (Asteraceae). Mol Ecol 18:3668–3682CrossRefPubMedGoogle Scholar
  74. Wang L, Abbott RJ, Zheng W et al (2009) History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateu: Aconitum gimnandrum (Ranunculaceae). Mol Ecol 18:709–721CrossRefPubMedGoogle Scholar
  75. Wojeiechowski MF (2005) Astragalus (Fabaceae): a molecular phylogenetic perspective. Brittonia 57:382–396CrossRefGoogle Scholar
  76. Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22:506–519CrossRefPubMedGoogle Scholar
  77. Yurtsev BA (1964) Conspectus of the system of section Baicalia Bge., genus Oxytropis DC. In: Linchevskii IA (ed) News in the systematics of higher plants. Nauka, Moscow-Leningrad, pp 191–218Google Scholar
  78. Zhu X, Welsh SL., Ohashi H (2010) Oxytropis. In: Wu Z-Y, Raven PH, Hong DY (eds) Flora of China, vol 10, pp 453–500. Published on the Internet http://www.efloras.org(accessed 31 January 2010)

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • E. V. Artyukova
    • 1
    Email author
  • M. M. Kozyrenko
    • 1
  • A. B. Kholina
    • 1
  • Y. N. Zhuravlev
    • 1
  1. 1.Institute of Biology and Soil ScienceFar East Branch of Russian Academy of SciencesVladivostokRussia

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