Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of central Asia

Canadian Journal of Forest Research

Volumn 42, Issue 12, 2012, Pages 2142-2152

  Semerikova, Svetlana A ^a   Lascoux, Martin ^b   Semerikov, Vladimir L ^a  

^a INSTITUTE OF PLANT AND ANIMAL ECOLOGY   (Russian Federation)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ABIES SIBIRICA; ALLOZYMES; CENTRAL ASIA; CONSERVATION POLICY; EFFECTIVE POPULATION SIZE; GENE FLOWS; GENETIC DIVERSITY; HAPLOTYPES; KAMCHATKA; NUCLEAR MARKERS; POPULATION BOTTLENECKS; POPULATION DECLINE; POPULATION EXPANSION;

BIODIVERSITY; FORESTRY;

POPULATION STATISTICS;

CONIFEROUS TREE; CONSERVATION GENETICS; CYTOPLASM; EFFECTIVE POPULATION SIZE; ENDEMIC SPECIES; GENE FLOW; GENETIC MARKER; GENETIC VARIATION; PALYNOLOGY; POPULATION BOTTLENECK; POPULATION DECLINE; RANGE EXPANSION;

CENTRAL ASIA;

ABIES; ABIES SIBIRICA; CONIFEROPHYTA;

EID: 84870909579     PISSN: 00455067     EISSN: 12086037     Source Type: Journal    
DOI: 10.1139/cjfr-2012-0158     Document Type: Article

References (51)

1. Aguirre-Planter, E., Jaramillo-Correa, J.P., Gomez-Acevedo, S., Khasa, D.P., Bousquet, J., and Eguiarte, L.E. 2012 Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Mol. Phylogenet. Evol. 62(1): 263-274. doi:10.1016/j.ympev.2011.09.021 PMID:22019929
2. Beer, R., Kaiser, F., Schmidt, K., Ammann, B., Carraro, G., Grisa, E., and Tinner, W. 2008 Vegetation history of the walnut forests in Kyrgyzstan (Central Asia): natural or anthropogenic origin? Quat. Sci. Rev. 27(5-6): 621-632. doi:10.1016/j.quascirev.2007.11.012
3. Bikirov, S.B. 2009 Taxonomy of Semenovii fir, and its introduction in the Kyrgyzstan. In Proceedings of the International Scientific Conference dedicated to the centenary of P.I. Lapin, corresponding member of Academy of Science of the USSR: The Problems of Modern Dendrology, Moscow, 30 June -2 July 2009 Edited by A.S. Demidov (Editor -in -Chef) et al. KMK Scientific Press Ltd., Moscow. pp. 545-547. [In Russian.]
4. Devey, M.E., Bell, J.S., Smith, D.N., Neale, D.B., and Moran, G.F. 1996 A genetic linkage map for Pinus radiata based on RFLP, RAPD and microsatellite markers. Theor. Appl. Genet. 92(6): 673-679. doi:10.1007/BF00226088
5. Dodonov, A.E. 2002 Quaternary of Middle Asia: stratigraphy, correlation, paleogeography. Transactions of GIN RAS, V. 546 Geos, Moscow, Russia. [In Russian.]
6. El Mousadik, A., and Petit, R.J. 1996 High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Sceels] endemic to Morocco. Theor. Appl. Genet. 92(7): 832-839. doi:10.1007/BF00221895
7. Farjon, A. 2001 World checklist and bibliography of Conifers. Royal Botanical Gardens at Kew, U.K.
8. Farjon, A., and Rushforth, K.D. 1989 A classification of Abies Miller (Pinaceae). Notes R. Bot. Gard. 46: 59-79
9. Fu, Y.X. 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147(2): 915-925. PMID:9335623
10. Goldstein, D.B., Ruiz Linares, A., Cavalli-Sforza, L.L., and Feldman, M.W. 1995 An evaluation of genetic distances for use with microsatellite loci. Genetics, 139(1): 463-471 PMID:7705647
11. Goncharenko, G.G., and Padutov, A.E. 1995 Genetic structure, taxonomic and phylogenetic relationships in firs occurring in the CIS (former Soviet Union). Dokl. Akad. Nauk, 342: 122-126. [In Russian.]
12. Goudet, J. 1995 FSTAT (vers. 1.2): a computer program to calculate F-statistics. J. Hered. 86(6): 485-486
13. Hamrick, J.L., Godt, J.W., and Sherman-Broyles, S.L. 1992 Factors influencing levels of genetic diversity in woody plant species. New For. 6(1-4): 95-124. doi:10.1007/BF00120641
14. Hubisz, M.J., Falush, D., Stephens, M., and Pritchard, J.K. 2009 Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9(5): 1322-1332. doi: 10.1111/j.1755-0998.2009.02591.x. PMID:21564903
15. Huff, D.R., Peakall, R., and Smouse, P.E. 1993 RAPD variation within and among natural populations of outcrossing buffalograss Buchloe dactyloides (Nutt) Engelm. Theor. Appl. Genet. 86(8): 927-934
16. Jaramillo-Correa, J.P., Aguirre-Planter, E., Khasa, D.P., Eguiarte, L.E., Pinero, D., Furnier, G., and Bousquet, J. 2008 Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern Mexico and Guatemala. Mol. Ecol. 17(10): 2476-2490. doi:10.1111/j.1365- 294X.2008.03762.x. PMID:18422927
17. Kropf, M., Comes, H.P., and Kadereit, J.W. 2009 An AFLP clock for the absolute dating of shallow-time evolutionary history based on the intraspecific divergence of southwestern European alpine plant species. Mol. Ecol. 18(4): 697-708. doi:10.1111/j.1365-294X. 2008.04053.x. PMID:19175503
18. Krylov, G.V., Maradudin, I.I., Mikheev, N.I., and Kozakova, N.F. 1986 Fir (Pikhta). Agropromizdat, Moscow. [In Russian.]
19. Ledig, F.T., Conkle, M.T., Bermejo-Velázquez, B., Eguiluz-Piedra, T., Hodgskiss, P.D., Johnson, D.R., and Dvorak, W.S. 1999 Evidence for an extreme bottleneck in a rare Mexican pinyon: genetic diversity, disequilibrium, and the mating system in Pinus maximartinezii. Evolution, 53(1): 91-99. doi:10.2307/2640922
20. Ledig, F.T., Hodgskiss, P.D., and Johnson, D.R. 2006 Genetic diversity and seed production in Santa Lucia fir (Abies bracteata), a relict of the Miocene broadleaved evergreen forest. Conserv. Genet. 7(3): 383-398. doi:10.1007/s10592-005-9049-x
21. Li, Y., Stocks, M., Hemmila, S., Kallman, T., Zhu, H., Zhou, Y., Chen, J., Liu, J., and Lascoux, M. 2010 Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci. Mol. Biol. Evol. 27(5): 1001-1014. doi:10.1093/molbev/msp301 PMID: 20031927
22. Liepelt, S., Mayland-Quellhorst, E., Lahme, M., and Ziegenhagen, B. 2010 Contrasting geographical patterns of ancient and modern genetic lineages in Mediterranean Abies species. Plant Syst. Evol. 284(3-4): 141-151. doi:10.1007/s00606-009-0247-8
23. Liu, T.S. A monograph of the genus Abies. 1971 Department of Forestry, College of Agriculture, National Taiwan University, Taipei, Taiwan, China.
24. Matzenko, A.E. 1956 About the species status of Tien Shan fir. Bot. Z. 41(10): 1504-1509. [In Russian.]
25. Matzenko, A.E. 1964 Firs of the Eastern Hemisphere. In Flora and systematics of the higher plants. Edited by B.K. Schishkin. Nauka, Leningrad. pp. 3-103. [In Russian.]
26. Navascués, M., Vaxevanidou, Z., González-Martínez, S.C., Climent, J., Gil, L., and Emerson, B.C. 2006 Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine. Mol. Ecol. 15(10): 2691-2698. doi:10.1111/j.1365- 294X.2006.02960.x. PMID:16911194
27. Nei, M. 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3): 583-590 PMID:17248844
28. Nei, M. 1987 Molecular evolutionary genetics. Columbia University Press, New York.
29. Orlova, L.V., and Firsov, G.A. 2004 Mysterious silver fir of Kamchatka. The British Conifer Society J. 3: 38-42
30. Parducci, L., Szmidt, A.E., Madaghiele, A., Anzidei, M., and Vendramin, G.G. 2001 Genetic variation at chloroplast microsatellites (cpSSRs) in Abies nebrodensis (Lojac.) Mattei and three neighboring Abies species. Theor. Appl. Genet. 102(5): 733-740. doi:10.1007/ s001220051704
31. Peakall, R., and Smouse, P.E. 2006 Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes, 6(1): 288-295. doi:10.1111/j.1471-8286.2005.01155.x.
32. Provan, J., Soranzo, N., Wilson, N.J., Goldstein, D.B., and Powell, W. 1999 A low mutation rate for chloroplast microsatellites. Genetics, 153(2): 943-947 PMID:10511569
33. Raymond, M., and Rousset, F. 1995 GENEPOP (version 1.2): population genetics software for exact tests and ecumenism. J. Hered. 86: 248-249
34. Rogers, A.R., and Harpending, H. 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9(3): 552-569 PMID:1316531
35. Samils, B., Lagercrantz, U., Lascoux, M., and Gullberg, U. 2001 Genetic structure of Melampsora epitea populations in Swedish Salix viminalis plantations. Eur. J. Plant Pathol. 107(4): 399-409. doi:10.1023/A:1011270315251
36. Schneider, S., and 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(3): 1079-1089 PMID:10388826
37. Schneider, S., Roessli, D., and Excoffier, L. 2000 ARLEQUIN ver. 2.000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
38. Semerikova, S.A., and Semerikov, V.L. 2006 Genetic variation and population differentiation in Siberian fir Abies sibirica Ledeb. inferred from allozyme markers. Russ. J. Genet. 42(6): 636-644. doi:10.1134/S1022795406060081
39. Semerikova, S.A., and Semerikov, V.L. 2007 The diversity of chloroplast microsatellite loci in Siberian fir (Abies sibirica Ledeb.) and two Far East fir species A. nephrolepis (Trautv.) Maxim., and A. sachalinensis Fr. Schmidt. Russ. J. Genet. 43(12): 1373-1381. doi:10.1134/S102279540712006X
40. Semerikova, S.A., Semerikov, V.L., and Lascoux, M. 2011 Postglacial history and introgression in Abies (Pinaceae) species of the Russian Far East inferred from both nuclear and cytoplasmic markers. J. Biogeogr. 38(2): 326-340. doi:10.1111/j.1365- 2699.2010.02394.x
41. Sneath, P.H., and Sokal, R.R. 1973 Numerical taxonomy. W.H. Freeman and Company, San Francisco, Calif.
42. Sun, J.M., and Zhang, Z.Q. 2008 Palynological evidence for the Mid-Miocene Climatic Optimum recorded in Cenozoic sediments of the Tian Shan Range, northwestern China. Global Planet. Change, 64(1-2): 53-68. doi:10.1016/j.gloplacha.2008.09.001
43. Swofford, D.L., and Selander, R.B. 1981 BIOSYS-1: a FORTRAN program for the comprehensive analysis of electrophoretic data in population genetics and systematics. J. Hered. 72(4): 281-283
44. Tang, S., Dai, W., Li, M., Zhang, Y., Geng, Y., Wang, L., and Zhong, Y. 2008 Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers. Genetica, 133(1): 21-30. doi:10.1007/s10709-007-9178-x. PMID: 17661154
45. Vendramin, G.G., Lelli, L., Rossi, P., and Morgante, M. 1996 A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Mol. Ecol. 5(4): 595-598. doi:10.1111/j.1365- 294X.1996.tb00353.x. PMID:8794566
46. Vendramin, G.G., Degen, B., Petit, R.G., Anzidei, M., Madaghiele, A., and Ziegenhagen, B. 1999 High level of variation at Abies alba chloroplast microsatellite loci in Europe. Mol. Ecol. 8(7): 1117-1126. doi:10.1046/j.1365-294x.1999.00666.x. PMID: 10447853
47. Vendramin, G.G., Fady, B., Gonzalez-Martinez, S.C., Hu, F.S., Scotti, I., Sebastiani, F., Soto, A., and Petit, R.J. 2008 Genetically depauperate but widespread: The case of an emblematic mediterranean pine. Evolution, 62(3): 680-688. doi:10.1111/j.1558- 5646.2007.00294.x. PMID:17983461
48. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Vandelee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., and Zabeau, M. 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23(21): 4407-4414. doi:10.1093/nar/23.21.4407 PMID:7501463
49. Weir, B.S., and Cockerham, C.C. 1984 Estimating F-statistics for the analysis of population structure. Evolution, 38(6): 1358-1370. doi:10.2307/2408641
50. Xue, X., Wang, Y., Korpelainen, H., and Li, C. 2005 Assessment of AFLP-based Genetic variation in the populations of Picea asperata. Silvae Genet. 54(1): 24-30
51. Zhang, Z.Q., and Sun, J.M. 2011 Palynological evidence for Neogene environmental change in the foreland basin of the southern Tianshan range, northwestern China. Global Planet. Change, 75(1-2): 56-66. doi:10.1016/j.gloplacha.2010.10.006