Advertisement

Russian Journal of Genetics

, Volume 52, Issue 11, pp 1164–1175 | Cite as

Phylogeny of firs (genus Abies, Pinaceae) based on multilocus nuclear markers (AFLP)

  • S. A. SemerikovaEmail author
  • V. L. Semerikov
Plant Genetics

Abstract

To study the phylogenetic relationships, evolutionary history, and molecular systematics of firs (genus Abies), the phylogenetic reconstruction, based on nuclear multilocus markers—amplified fragment length polymorphism (AFLP)—was conducted. Using seven combinations of selective primers, 84 samples of 39 taxa were genotyped for 553 polymorphic AFLP loci. A comparison with our earlier chloroplast and mitochondrial phylogenies of the genus (in 2014) shows that the nuclear phylogeny generally is more congruent to the chloroplast tree. Most of the clades resolved by the chloroplast phylogeny were supported also in the AFLP tree. Employing the nuclear DNA-based tree, we revealed the presence of new groups and the differences in the topology of several clades. AFLP confirmed the monophyly of Asian species of section Balsamea and their sister position in relation to the American group of species of this section. As shown by the tree of chloroplast DNA, Asian species of section Balsamea do not form a monophyletic group, but belong to the clade comprising the majority of Asian species. Phylogenetically mitochondrial DNA data to a large extent are not congruent to the nuclear and chloroplast DNA trees, and are more in line with geographical distribution of species. Conflicts between nuclear and cytoplasmic phylogeny were analyzed. Taking them into account, we consider the hypothesis of a hybrid origin of particular groups of firs, including ancient hybridization in section Balsamea. A comparison of molecular data with traditional taxonomy of the genus is discussed.

Keywords

molecular phylogeny biogeography hybridization and introgression molecular systematics 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Brito, P. and Edwards, S.V., Multilocus phylogeography and phylogenetics using sequence-based markers, Genetica, 2009, vol. 135, no. 3, pp. 439–455.CrossRefPubMedGoogle Scholar
  2. 2.
    Estimating Species Trees: Practical and Theoretical Aspects, Knowles, L.L. and Kubatko, L.S., Eds., Wiley–Blackwell, 2010.Google Scholar
  3. 3.
    Tsutsui, K., Suwa, A., Sawada, K., et al., Incongruence among mitochondrial, chloroplast and nuclear gene trees in Pinus subgenus Strobus (Pinaceae), J. Plant Res., 2009, vol. 122, no. 5, pp. 509–521.PubMedGoogle Scholar
  4. 4.
    Bouillé, M., Senneville, S., and Bousquet, J., Discordant mtDNA and cpDNA phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea, Tree Genet. Genom., 2011, vol. 7, no. 3, pp. 469–484.CrossRefGoogle Scholar
  5. 5.
    Lockwood, J.D., Aleksic, J.M., Zou, J., et al., A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences, Mol. Phyl. Evol., 2013, vol. 69, no. 3, pp. 717–727.CrossRefGoogle Scholar
  6. 6.
    Semerikova, S.A. and Semerikov, V.L., Molecular phylogenetic analysis of the genus Abies Mill. (Pinaceae) based on the chloroplast DNA nucleotide sequences, Russ. J. Genet., 2014, vol. 50, no. 1, pp. 7–19.CrossRefGoogle Scholar
  7. 7.
    Semerikova, S.A. and Semerikov, V.L., Mitochondrial DNA variation and reticulate evolution of the genus Abies, Russ. J. Genet., 2014, vol. 50, no. 4, pp. 366–377.CrossRefGoogle Scholar
  8. 8.
    Wang, X.Q. and Ran, J.H., Evolution and biogeography of gymnosperms, Mol. Phylogenet. Evol., 2014, vol. 75, pp. 24–40.CrossRefPubMedGoogle Scholar
  9. 9.
    Wang, B.S. and Wang, X.R., Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus, Mol. Phylogenet. Evol., 2014, vol. 80, pp. 20–30.CrossRefPubMedGoogle Scholar
  10. 10.
    Ran, J.H., Shen, T.T., Liu, W.J., et al., Mitochondrial introgression and complex biogeographic history of the genus Picea, Mol. Phylogenet. Evol., 2015, vol. 93, pp. 63–76.CrossRefPubMedGoogle Scholar
  11. 11.
    Hao, Z.Z., Liu, Y.Y., Nazaire, M., et al., Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography, Mol. Phylogenet. Evol., 2015, vol. 87, pp. 65–79.CrossRefPubMedGoogle Scholar
  12. 12.
    Matsenko, A.E., Firs of the Eastern Hemisphere, in Flora i sistematika vysshikh rastenii, (Flora and Taxonomy of Higher Plants), Trudy Botanicheskogo Instituta im. V.L. Komarova, (Proceedings of V.L. Komarov Botanical Institute), Moscow: Nauka, 1964, ser.1, issue 13, pp. 3–103.Google Scholar
  13. 13.
    Liu, T.S., A Monograph of the Genus Abies, Department of Forestry, College of Agriculture, Natl. Taiwan Univ.: Taipei, 1971.Google Scholar
  14. 14.
    Krylov, G.V., Maradudin, I.I., Mikheev, N.I., and Kozakova, N.F., Pikhta (Fir), Moscow: Agropromizdat, 1986.Google Scholar
  15. 15.
    Farjon, A. and Rushforth, K.D., A classification of Abies Miller. (Pinaceae), Not. R. Bot. Garden Edinburg, 1989, vol. 46, pp. 59–79.Google Scholar
  16. 16.
    Aguirre-Planter, E., Jaramillo-Correa, J.P., Gomez-Acevedo, S., et al., Phylogeny,diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context, Mol. Phylogenet. Evol., 2012, vol. 62, no. 1, pp. 263–274.CrossRefGoogle Scholar
  17. 17.
    Xiang, Q.P., Wei, R., Shao, Y.Z., et al., Phylogenetic relationships, possible ancient hybridization, and biogeographic history of Abies (Pinaceae) based on data from nuclear, plastid, and mitochondrial genomes, Mol. Phylogenet. Evol., 2015, vol. 82, pp. 1–14.PubMedGoogle Scholar
  18. 18.
    Peng, Y., Tian, B., Tian, X., et al., Range expansion during the Pleistocene drove morphological radiation of the fir genus (Abies, Pinaceae) in the Qinghai–Tibet Plateau and Himalayas, Bot. J. Linn. Soc., 2015, vol. 179, no. 3, pp. 444–453.CrossRefGoogle Scholar
  19. 19.
    Kormutak, A., Vookova, B., Camek, V., et al., Artificial hybridization of some Abies species, Plant Syst. Evol., 2013, vol. 299, no. 6, pp. 1175–1184.CrossRefGoogle Scholar
  20. 20.
    Tsumura, Y. and Suyama, Y., Differentiation of mitochondrial DNA polymorphisms in populations of five Japanese Abies species, Evolution, 1998, vol. 52, no. 4, pp. 1031–1042.CrossRefGoogle Scholar
  21. 21.
    Isoda, K., Shiraishi, S., Watanabe, S., and Kitamura, K., Molecular evidence of natural hybridization between Abies veitchii and A. homolepis (Pinaceae) revealed by chloroplast, mitochondrial and nuclear DNA markers, Mol. Ecol., 2000, vol. 9, no. 12, pp. 1965–1974.PubMedGoogle Scholar
  22. 22.
    Oline, D., Geographic variation in chloroplast haplotypes in the California red fir–noble fir species complex and the status of Shasta red fir, Canad. J. For. Res., 2008, vol. 38, no. 10, pp. 2705–2710.CrossRefGoogle Scholar
  23. 23.
    Liepelt, S., Mayland-Quellhorst, E., Lahme, M., and Ziegenhagen, B., Contrasting geographical patterns of ancient and modern genetic lineages in Mediterranean Abies species, Plant Syst. Evol., 2010, vol. 284, nos. 3–4, pp. 141–151.CrossRefGoogle Scholar
  24. 24.
    Semerikova, S.A., Semerikov, V.L., and Lascoux, M., Post-glacial history and introgression in Abies (Pinaceae) species of the Russian Far East inferred from both nuclear and cytoplasmic markers, J. Biogeogr., 2011, vol. 38, no. 2, pp. 326–340.CrossRefGoogle Scholar
  25. 25.
    Peng, Y., Yin, S., Wang, J., et al., Phylogeographic analysis of the fir species in southern China suggests complex origin and genetic admixture, Ann. For. Sci., 2012, vol. 69, no. 3, pp. 409–416.CrossRefGoogle Scholar
  26. 26.
    Sanchez-Robles, J.M., Balao, F., Terrab, A., et al., Phylogeography of SW Mediterranean firs: different European origins for the North African Abies species, Mol. Phylogenet. Evol., 2014, vol. 79, pp. 42–53.CrossRefPubMedGoogle Scholar
  27. 27.
    Bella, E., Liepelt, S., Parducci, L., and Drouzas, A.D., Genetic insights into the hybrid origin of Abies × borisii-regis Mattf., Plant Syst. Evol., 2015, vol. 301, no. 2, pp. 749–759.CrossRefGoogle Scholar
  28. 28.
    Cinget, B., De Lafontaine, G., Gerardi, S., and Bousquet, J., Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs, Mol. Ecol., 2015, vol. 24, no. 11, pp. 2856–2870.CrossRefPubMedGoogle Scholar
  29. 29.
    Neale, D.B. and Sederoff, R.R., Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine, Theor. Appl. Genet., 1989, vol. 77, pp. 212–216.CrossRefPubMedGoogle Scholar
  30. 30.
    Gernandt, D.S., Liston, A., and Pinero, D., Variation in the nrDNA ITS of Pinus subsection Cembroides: Implications for molecular systematic studies of pine species complexes, Mol. Phylogenet. Evol., 2001, vol. 21, no. 3, pp. 449–467.CrossRefPubMedGoogle Scholar
  31. 31.
    Campbell, C.S., Wright, W.A., Cox, M., et al., Nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in Picea (Pinaceae): sequence divergence and structure, Mol. Phylogenet. Evol., 2005, vol. 35, no. 1, pp. 165–185.CrossRefPubMedGoogle Scholar
  32. 32.
    Vos, P., Hogers, R., Bleeker, M., et al., AFLP: a new technique for DNA fingerprinting, Nucleic Acids Res., 1995, vol. 23, no. 21, pp. 4407–4414.CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Meudt, H.M. and Clarke, A.C., Almost forgotten or latest practice? AFLP applications, analyses and advances, Trends Plant Sci., 2007, vol. 12, no. 3, pp. 106–117.PubMedGoogle Scholar
  34. 34.
    Aradhya, M., Wang, Y., Walker, M.A., et al., Genetic diversity, structure, and patterns of differentiation in the genus Vitis, Plant Syst. Evol., 2013, vol. 299, no. 2, pp. 317–330.CrossRefGoogle Scholar
  35. 35.
    Semerikova, S.A. and Semerikov, V.L., Genetic variability of Siberian fir Abies sibirica Ledeb. inferred from AFLP markers, Russ. J. Genet., 2011, vol. 47, no. 2, pp. 241–246.CrossRefGoogle Scholar
  36. 36.
    Semerikova, S.A., Lascoux, M., and Semerikov, V.L., Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of Central Asia, Canad. J. For. Res., 2012, vol. 42, no. 12, pp. 2142–2152.Google Scholar
  37. 37.
    Semerikov, V.L., Zhang, H., Sun, M., and Lascoux, M., Conflicting phylogenies of Larix (Pinaceae) based on cytoplasmic and nuclear DNA, Mol. Phylogenet. Evol., 2003, vol. 27, no. 2, pp. 173–184.CrossRefPubMedGoogle Scholar
  38. 38.
    Devey, M.E., Bell, J.C., 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, no. 6, pp. 673–679.CrossRefPubMedGoogle Scholar
  39. 39.
    Samils, B., Lagercrantz, U., Lascoux, M., and Gullberg, U., Genetic structure of Melampsora epitea populations in Swedish Salix viminalis plantations, Eur. J. Plant Pathol., 2001, vol. 107, no. 4, pp. 399–409.CrossRefGoogle Scholar
  40. 40.
    Van De Peer, Y. and De Wachter, R., TREECON for Windows–a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment, Comput. Appl. Biosci., 1994, vol. 10, no. 5, pp. 569–570.PubMedGoogle Scholar
  41. 41.
    Nei, M. and Li, W.H., Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc. Natl. Acad. Sci. U.S.A., 1979, vol. 76, no. 10, pp. 5269–5273.CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Koopman, W.J.M., Phylogenetic signal in AFLP data sets, Syst. Biol., 2005, vol. 54, no. 2, pp. 197–217.CrossRefPubMedGoogle Scholar
  43. 43.
    Currat, M., Ruedi, M., Petit, R.J., and Excoffier, L., The hidden side of invasions: massive introgression by local genes, Evolution, 2008, vol. 62, no. 8, pp. 1908–1920.PubMedGoogle Scholar
  44. 44.
    Zachos, J.C., Dickens, G.R., and Zeebe, R.E., An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics, Nature, 2008, vol. 451, pp. 279–283.CrossRefPubMedGoogle Scholar
  45. 45.
    Potter, K.M., Frampton, J., Josserand, S.A., and Nelson, C.D., Evolutionary history of two endemic Appalachian conifers revealed using microsatellite markers, Conserv. Genet., 2010, vol. 11, no. 4, pp. 1499–1513.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2016

Authors and Affiliations

  1. 1.Institute of Plant and Animal Ecology, Ural BranchRussian Academy of SciencesYekaterinburgRussia

Personalised recommendations