Advertisement

Russian Journal of Genetics

, Volume 54, Issue 1, pp 64–74 | Cite as

Polymorphism of Chloroplast DNA and Phylogeography of Green Alder (Alnus alnobetula (Ehrh.) K. Koch s. l.) in Asiatic Russia

  • E. V. HantemirovaEmail author
  • E. A. Pimenova
  • O. S. Korchagina
Plant Genetics
  • 49 Downloads

Abstract

This paper studies the phylogeography of Alnus alnobetula s. l. in the Asian part of the Russian range with the use of chloroplast DNA (cpDNA) sequences (intergenic spacers trnH-psbA, trnS-trnG, and psaA-trnS). Nine haplotypes were identified as a result of a combination of polymorphism of all sites in 241 plants in 20 populations of A. alnobetula. High interpopulation differentiation (GST = 0.914, NST = 0.928) and a significant phylogeographic structure (NST > GST, p < 0.05) were found. Reconstruction of genealogical relationships of green alder haplotypes revealed five highly divergent genetic lineages: one geographically widespread throughout Siberia and the Urals and several allopatric lines in the Far East of Russia, namely, the Chukotka Peninsula and the mouth of the Yana River, Magadan oblast, Primorye and the central part of Sakhalin Island, and the southern part of Sakhalin Island. Our data confirm that in the past the range of this species in the Far East was fragmented in several refugia that were isolated for a long time in various ice-free regions. This could have contributed to a high level of intraspecific polymorphism of green alder as a result of the divergence of endemic haplotypes, with almost non-overlapping distribution. However, the level of their molecular divergence does not correspond to the level of morphological differences.

Keywords

green alder alder Alnus alnobetula cpDNA Far East Last Glacial Maximum phylogeography 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Krishtofovich, A.N., The main features of the development of the tertiary flora of Asia, Izv. Gl. Bot. Sada, 1930, vol. 29, nos. 3—4, pp. 391–401.Google Scholar
  2. 2.
    Lavrenko, E.M., The history of the flora and vegetation of the Soviet Union according to the current plant distribution, Rastitel’nost’ SSSR (Vegetation of the Soviet Union), Moscow: Akad. Nauk SSSR, 1938, vol. 1, pp. 235–296.Google Scholar
  3. 3.
    Hewitt, G., The genetic legacy of the Quaternary ice ages, Nature, 2000, vol. 405, pp. 907–913.CrossRefPubMedGoogle Scholar
  4. 4.
    Abbott, R.J., Smith, L.C., Milne, R.I., et al., Molecular analysis of plant migration and refugia in the Arctic, Science, 2000, vol. 289, no. 5483, pp. 1343–1346.CrossRefPubMedGoogle Scholar
  5. 5.
    Demesure, B., Comps, B., and Petit, R.J., Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe, Evolution, 1996, vol. 50, no. 6, pp. 2515–2520.CrossRefPubMedGoogle Scholar
  6. 6.
    Dumolin-Lapègue, S., Demesure, B., Fineschi, S., et al., Phylogeographic structure of white oaks throughout the European continent, Genetics, 1997, vol. 146, no. 4, pp. 1475–1487.PubMedPubMedCentralGoogle Scholar
  7. 7.
    King, R.A. and Ferris, C., Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn., Mol. Ecol., 1998, vol. 7, pp. 1151–1161.CrossRefGoogle Scholar
  8. 8.
    King, R.A. and Ferris, C., Chloroplast DNA and nuclear DNA variation in the sympatric alder species, Alnus cordata (Lois.) Duby and A. glutinosa (L.) Gaertn., Biol. J. Linn. Soc., 2000, vol. 70, no. 1, pp. 147–160.CrossRefGoogle Scholar
  9. 9.
    Havrdova, A., Douda, J., Krak, K., et al., Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture, Mol. Ecol., 2015, vol. 24, no. 18, pp. 4759–4777.CrossRefPubMedGoogle Scholar
  10. 10.
    Petit, R.J., Aguinagalde, I., de Beaulieu, J.L., et al., Glacial refugia: hotspot but not melting pots of genetic diversity, Science, 2003, vol. 300, pp. 1563–1565.CrossRefPubMedGoogle Scholar
  11. 11.
    Dering, M., Latałowa, M., Boratyńska, K., et al., Could clonality contribute to the northern survival of grey alder [Alnus incana (L.) Moench] during the Last Glacial Maximum?, Acta Soc. Bot. Pol., 2017, vol. 86, no. 1, p. 3523. doi 10.5586/asbp.3523Google Scholar
  12. 12.
    Mandak, B., Havrdova, A., Krak, K., et al., Recent similarity in distribution ranges does not mean a similar postglacial history: a phylogeographical study of the boreal tree species Alnus incana based on microsatellite and chloroplast DNA variation, New Phytol., 2016, vol. 210, no. 4, pp. 1395–1407.CrossRefPubMedGoogle Scholar
  13. 13.
    Semerikov, V.L., Semerikova, S.A., Polezhaeva, M.A., et al., Southern montane populations did not contribute to the recolonization of West Siberian Plain by Siberian larch (Larix sibirica): a range-wide analysis of cytoplasmic markers, Mol. Ecol., 2013, vol. 22, no. 19, pp. 4958–4971.CrossRefPubMedGoogle Scholar
  14. 14.
    Polezhaeva, M.A., Lascoux, M., and Semerikov, V.L., Cytoplasmic DNA variation and biogeography of Larix Mill. in Northeast Asia, Mol. Ecol., 2010, vol. 19, pp. 1239–1252.CrossRefPubMedGoogle Scholar
  15. 15.
    Tollefsrud, M.M., Kissling, R., Gugerli, F., et al., Genetic consequences of glacial survival and postglacial colonization in Norway spruce: combined analysis of mitochondrial DNA and fossil pollen, Mol. Ecol., 2008, vol. 17, pp. 4134–4150.CrossRefPubMedGoogle Scholar
  16. 16.
    Maliouchenko, O., Palme, A.E., Buonamici, A., et al., Comparative phylogeography and population structure of European Betula species, with particular focus on B. pendula and B. pubescens, J. Biogeogr., 2007, vol. 34, no. 9, pp. 1601–1610. doi 10.1111/j.13653-2699.2007. 01729.xCrossRefGoogle Scholar
  17. 17.
    Palme, A.E., Semerikov, V., and Lascoux, M., Absence of geographical structure of chloroplast DNA variation in sallow, Salix caprea L., Heredity, 2003, vol. 91, no. 5, pp. 465–474.CrossRefGoogle Scholar
  18. 18.
    Skrede, I., Eidesen, P.B., Piñeiro Portela, R., and Brochmann, C., Refugia, differentiation and postglacial migration in arctic-alpine Eurasia, exemplified by the mountain avens (Dryas octopetala L.), Mol. Ecol., 2006, vol. 15, pp. 1827–1840.CrossRefPubMedGoogle Scholar
  19. 19.
    Eidesen, P.B., Alsos, I.G., Popp, M., et al., Nuclear vs. plastid data: complex Pleistocene history of a circumpolar key species, Mol. Ecol., 2007, vol. 16, pp. 3902–3925.CrossRefPubMedGoogle Scholar
  20. 20.
    Eidesen, P.B., Ehrich, D., Bakkestuen, V., et al., Genetic roadmap of the arctic: plant dispersal highways, traffic barriers and capitals of diversity, New Phytol., 2013, vol. 200, pp. 898–910.CrossRefPubMedGoogle Scholar
  21. 21.
    Hantemirova, E.V., Heinze, B., Knyazeva, S.G., et al., A new Eurasian phylogeographical paradigm? Limited contribution of southern populations of the recolonization of high latitude populations in Juniperus communis L. (Cupressaceae), J. Biogeogr., 2017, vol. 44, no. 2, pp. 271–282. doi 10.1111/jbi.12867CrossRefGoogle Scholar
  22. 22.
    The Plant List. http://www.theplantlist.org/.Google Scholar
  23. 23.
    The International Plant Name Index. http://www.ipni.org/.Google Scholar
  24. 24.
    Greuter, W. and Raab-Straube, Eds., Euro + Med Notulae, 5, Willdenowia, 2011, vol. 41, pp. 129–138. doi: doi 10.3372/wi.41.41117CrossRefGoogle Scholar
  25. 25.
    Chery, J., New nomenclature combinations in the green alder species complex (Betulaceae), PhytoKyes, 2015, vol. 56, pp. 1–6.CrossRefGoogle Scholar
  26. 26.
    Komarov, V.L., Genus 365: alder—Alnus Gaertn., Flora SSSR (Flora of the Soviet Union), Moscow: Akad. Nauk SSSR, 1936, vol. 5, pp. 306–319.Google Scholar
  27. 27.
    Myking, T., Evaluating genetic resources of forest trees by means of life history traits—a Norwegian example, Biodiv. Conserv., 2002, vol. 11, pp. 1681–1696.CrossRefGoogle Scholar
  28. 28.
    Bennett, K.D., Boreham, S., Sharp, M.J., et al., Holocene history of environment, vegetation and human settlement on Catta Ness, Lunnasting, Shetland, J. Ecol., 1992, vol. 80, pp. 241–273.CrossRefGoogle Scholar
  29. 29.
    Gajewski, K., Payette, S., and Ritchie, J.C., Holocene vegetation history at the boreal-forest—shrub-tundra transition in north-western Quebec, J. Ecol., 1993, vol. 81, no. 3, pp. 433–443. doi 10.2307/2261522CrossRefGoogle Scholar
  30. 30.
    Brubaker, L.B., Anderson, P.M., and Edwards, M.E., Beringia as a glacial refugium for boreal trees and shrubs: new perspectives from mapped pollen data, J. Biogeogr., 2005, vol. 32, pp. 833–848.CrossRefGoogle Scholar
  31. 31.
    Müller, S., Tarasov, P.E., Andreev, A.A., et al., Late Quaternary vegetation and environments in the Verkhoyansk Mountains region (NE Asia) reconstructed from a 50-kyr fossil pollen record from Lake Billyakh, Quat. Sci. Rev., 2010, vol. 29, pp. 2071–2086.CrossRefGoogle Scholar
  32. 32.
    Sturm, M., Racine, C., and Tape, K., Climate change: increasing shrub abundance in the Arctic, Nature, 2001, vol. 411, pp. 546–547.CrossRefPubMedGoogle Scholar
  33. 33.
    Tape, K.D., Hallinger, M., Welker, J.M., et al., Landscape heterogeneity of shrub expansion in Arctic Alaska, Ecosystems, 2012, vol. 15, no. 5, pp. 711–724.CrossRefGoogle Scholar
  34. 34.
    Wiedmer, E. and Senn-Irlet, B., Biomass and primary productivity of an Alnus viridis stand—a case study from the Schachental valley, Switzerland, Bot. Helv., 2006, vol. 116, no. 1, pp. 55–64.CrossRefGoogle Scholar
  35. 35.
    Buehlmann, T., Hiltbrunner, E., and Koerner, C., Alnus viridis expansion contributes to excess reactive nitrogen release, reduces biodiversity and constrains forest succession in the Alps, Alp. Bot., 2014, vol. 124, no. 2, pp. 187–191.CrossRefGoogle Scholar
  36. 36.
    Cherepanov, S.K., System of the genus Alnus Mill. s. str. and the related genera, in Botanicheskie materialy gerbariya Botanicheskogo Instituta Akademii Nauk SSSR (Botanical Materials of the Herbarium of Komarov Botanical Institute of the Academy of Sciences of the USSR), Moscow, 1955, vol. 17, pp. 90–105.Google Scholar
  37. 37.
    Cherepanov, S.K., Sosudistye rasteniya Rossii i sopredel’nykh gosudarstv (Vascular Plants of Russia and Neighboring Countries), St. Petersburg: Mir i Sem’ya, 1995.Google Scholar
  38. 38.
    Koropachinskii, I.Yu. and Vstovskaya, T.N., Drevesnye rasteniya Aziatskoi Rossii (Arboreal Plants of the Asian Part of Russia), Novosibirsk: Sib. Otd. Ross. Akad. Nauk, 2002.Google Scholar
  39. 39.
    Hultén, E., Flora of Kamtchatka and the Adjacent Islands, Stockholm, 1927.Google Scholar
  40. 40.
    Banaev, E.V. and Adel’shin, R.V., The structure of Alnus fruticosa Rupr. s. l. and the interrelations of the species with other taxa of the Alnobetula (Ehrhart) Peterman subgenus, Sib. Ekol. Zh., 2009, no. 6, pp. 927–939.Google Scholar
  41. 41.
    Chen, Z.D. and Li, J.H., Phylogenetics and biogeography of Alnus (Betulaceae) inferred from sequences of nuclear ribosomal DNA its region, Int. J. Plant Sci., 2004, vol. 165, no. 2, pp. 325–335.CrossRefGoogle Scholar
  42. 42.
    Ren, B., Xiang, X., and Chen, Z., Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers, Mol. Ecol. Resour., 2010, vol. 10, pp. 594–605.CrossRefPubMedGoogle Scholar
  43. 43.
    Banaev, E.V., Genus Alnus Mill. (Betulaceae) in the Asian Part of Russia: species population structure and the gene pool conservation, Extended Abstract of Doctoral Dissertation, Tomsk, 2010.Google Scholar
  44. 44.
    Devey, M.E., Bell, J.S., Smith, D.N., et al., A genetic linkage map for Pinus radiata based on RFLP, RAPD and microsatellite markers, Theor. Appl. Genet., 1996, vol. 92, pp. 673–679.CrossRefPubMedGoogle Scholar
  45. 45.
    Hamilton, M.B., Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation, Mol. Ecol., 1999, vol. 8, pp. 521–523.PubMedGoogle Scholar
  46. 46.
    Demesure, B., Sodzi, N., and Petit, R.J., A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants, Mol. Ecol., 1995, vol. 4, pp. 129–131.CrossRefPubMedGoogle Scholar
  47. 47.
    Taberlet, P.T., Geilly, L., Patou, G., and Bouvet, J., Universal primers for amplification of three non-coding regions of chloroplast DNA, Plant Mol. Biol., 1991, vol. 17, pp. 1105–1109.CrossRefPubMedGoogle Scholar
  48. 48.
    Dumolin-Lapègue, S., Pemonge, M.-H., and Petit, R.J., An enlarged set of consensus primers for the study of organelle DNA in plants, Mol. Ecol., 1997, vol. 6, pp. 393–397.CrossRefPubMedGoogle Scholar
  49. 49.
    Shaw, J., Lickey, E.B., Beck, J.T., et al., The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis, Am. J. Bot., 2005, vol. 92, pp. 142–166.CrossRefPubMedGoogle Scholar
  50. 50.
    Grivet, D., Heinze, B., Vendramin, G.G., and Petit, R.J., Genome walking with consensus primers: application to the large single copy region of chloroplast DNA, Mol. Ecol. Notes, 2001, vol. 1, no. 4, pp. 345–349.CrossRefGoogle Scholar
  51. 51.
    Hall, T.A., Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser., 1999, vol. 41, pp. 95–98.Google Scholar
  52. 52.
    Excoffier, L. and Lischer, H., Arlequin suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour., 2010, vol. 10, pp. 564–567.CrossRefPubMedGoogle Scholar
  53. 53.
    Rogest, A.R. and Harpending, H., Population growth makes waves in the distribution of pairwise genetic differences, Mol. Biol. Evol., 1992, vol. 9, pp. 552–569.Google Scholar
  54. 54.
    Bandelt, H.J., Forster, P., and Röhl, A., Median-joining networks for inferring intraspecific phylogenics, Mol. Biol. Evol., 1999, vol. 16, pp. 37–48.CrossRefPubMedGoogle Scholar
  55. 55.
    Huelsenbeck, J.P., MrBayes: Bayesian inference of phylogenetic trees, Bioinformatics, 2001, vol. 17, pp. 754–755.CrossRefPubMedGoogle Scholar
  56. 56.
    Pons, O. and Petit, R.J., Measuring and testing genetic differentiation with ordered versus unordered alleles, Genetics, 1996, vol. 144, pp. 1237–1245.PubMedPubMedCentralGoogle Scholar
  57. 57.
    Dupanloup, I., Schneider, S., and Excoffier, L., A simulated annealing approach to define the genetic structure of populations, Mol. Ecol., 2002, vol. 11, pp. 2571–2581.CrossRefPubMedGoogle Scholar
  58. 58.
    Herbarium them. D.P. Syreyschikov, Biological Faculty of Moscow State University. http://www.bio.msu. ru/doc/index.php?ID=146.Google Scholar
  59. 59.
    Nature Korea Biodiversity Information System. http://nature.go.kr/ekbi/plant/smpl/selectPlantSmplGnrlSrch1. do.Google Scholar
  60. 60.
    Vorob’ev, D.P., Voroshilov, V.N., Gorovoi, P.G., and Shreter, A.I., Opredelitel’ rastenii Primor’ya i Priamur’ya (Key to Plants of Primorye and the Amur Region), Moscow: Nauka, 1966.Google Scholar
  61. 61.
    Lee, T.B., Illustrated Flora of Korea, Seoul: Hyangmun, 1980 (in Korean).Google Scholar
  62. 62.
    Li, P. and Skvortsov, A.K., Betulaceae, Flora of China, Wu, Z.Y., Raven, P.H., and Hong, D.Y., Eds., Beijing: Science Press, 1999, vol. 4, pp. 286–313.Google Scholar
  63. 63.
    Ohba, H., Alnus, in Flora of Japan, vol. 2a: Angiospermae, Dicotyledoneae, Archichlamydea, Tokyo: Kodansha, 2006, pp. 26–31.Google Scholar
  64. 64.
    Voroshilov, V.N., Opredelitel’ rastenii sovetskogo Dal’nego Vostoka (Key to Plants of the Soviet Far East), Moscow: Nauka, 1982.Google Scholar
  65. 65.
    Nedoluzhko, V.A. and Skvortsov, A.K., Family 48: Betulaceae S.F. Gray, in Sosudistye rasteniya sovetskogo Dal’nego Vostoka (Vascular Plants of the Soviet Far East), St. Petersburg: Nauka, 1996, vol. 8. pp. 9–28.Google Scholar
  66. 66.
    Chang, C.-S., Kim, H., and Chang, K.S., Provisional Checklist of Vascular Plants for the Korea Peninsula Flora (Version 1.0), 2014.Google Scholar
  67. 67.
    Grichuk, V.P. and Borisova, O.K., Vegetation: late Pleistocene, in Paleoklimaty i paleolandshafty vnetropicheskogo prostranstva Severnogo polushariya: pozdnii pleistotsen-golotsen: atlas-monografiya (Paleoclimates and Paleolandscapes of the Extratropical Space of the Northern Hemisphere: Late Pleistocene—Holocene: Atlas—Monography), Moscow: GEOS, 2009, pp. 70–78.Google Scholar
  68. 68.
    Lozhkin, A.V., Modern pollen rain in the Arctic regions of Beringia and reconstruction of the vegetation of the glacial intervals of the Pleistocene, in Chetvertichnaya paleogeografiya Beringii (Quaternary Paleogeography of Beringia), Magadan: Severo-Vostochnyi Kompleksnyi Nauchno-Issledovatel’skii Institut, 2002, pp. 13–27.Google Scholar
  69. 69.
    Abbott, R.J. and Brochmann, C., History and evolution of the arctic flora: in the footsteps of Eric Hultén, Mol. Ecol., 2003, vol. 11, pp. 299–313.CrossRefGoogle Scholar
  70. 70.
    Korotkii, A.M., Volkov, V.G., Grebennikova, T.A., et al., The Far East, in Izmenenie klimata i landshaftov za poslednie 65 millionov let: kainozoi (ot paleotsena do golotsena) (Change in Climate and Landscapes during the Past 65 Million Years: Cenozoic (from Paleocene to Holocene)), Moscow: GEOS, 1999, pp. 146–164.Google Scholar
  71. 71.
    Aleksandrova, A.N., Pleistotsen Sakhalina (Pleistocene of Sakhalin), Moscow: Nauka, 1982.Google Scholar
  72. 72.
    Krestov, P.V., Barkalov, V.Yu., and Taran, A.A., Botanico-geographical regionalization of Sakhalin Island, Rastitel’nyi i zhivotnyi mir ostrova Sakhalin (Plant and Animal World of Sakhalin Island) (Proc. Int. Sakhalin Project), Vladivostok: Dal’nauka, 2004, part 1, pp. 67–92.Google Scholar
  73. 73.
    Pletnev, S.P., Geological development of Sakhalin Island, in Flora i fauna ostrova Sakhalin (Flora and Fauna of Sakhalin Island), Vladivostok, 2004, pp. 11–23.Google Scholar
  74. 74.
    Furlow, J.J., The systematics of American species of Alnus (Betulaceae), Rhodora, 1979, vol. 81, no. 825, pp. 1–69.Google Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  • E. V. Hantemirova
    • 1
    Email author
  • E. A. Pimenova
    • 2
  • O. S. Korchagina
    • 1
  1. 1.Institute of Plant and Animal Ecology, Ural BranchRussian Academy of SciencesYekaterinburgRussia
  2. 2.Botanical Garden Institute, Far Eastern BranchRussian Academy of SciencesVladivostokRussia

Personalised recommendations