Phylogenetic relationships, possible ancient hybridization, and biogeographic history of Abies (Pinaceae) based on data from nuclear, plastid, and mitochondrial genomes

Molecular Phylogenetics and Evolution

Volumn 82, Issue PA, 2015, Pages 1-14

  Xiang, Qiao Ping ^a   Wei, Ran ^a,b   Shao, Yi Zhen ^a,b   Yang, Zu Yu ^a,b   Wang, Xiao Quan ^a   Zhang, Xian Chun ^a  

^a INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Ancient hybridization; Genome conflict; Northern hemisphere disjunction; Out of western North America; Section Balsamea

Indexed keywords

ABIES; PINACEAE;

PLANT DNA; RIBOSOMAL SPACER DNA;

ABIES; ASIA; BAYES THEOREM; BIOLOGICAL MODEL; CHLOROPLAST GENOME; CLASSIFICATION; DNA SEQUENCE; EUROPE; EVOLUTION; FOSSIL; GENETICS; HYBRIDIZATION; MITOCHONDRIAL GENOME; NORTH AMERICA; PHYLOGENY; PLANT GENOME; STATISTICAL MODEL;

ABIES; ASIA; BAYES THEOREM; BIOLOGICAL EVOLUTION; DNA, PLANT; DNA, RIBOSOMAL SPACER; EUROPE; FOSSILS; GENOME, CHLOROPLAST; GENOME, MITOCHONDRIAL; GENOME, PLANT; HYBRIDIZATION, GENETIC; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; NORTH AMERICA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84909642160     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.10.008     Document Type: Article

References (100)

1. Aguirre-Planter E., Jaramillo-Correa J.P., Gomez-Acevedo S., Khasa D.P., Bousquet J., Eguiarte L.E. Phylogeny, diversification rates and species boundaries of mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Mol. Phylogenet. Evol. 2012, 62:263-274.
2. Akhmetiev M.A. Ecological crises of the Paleogene and Neogene in extratropical Eurasia and their putative causes. Paleontol. J. 1996, 30:738-748.
3. Axelrod D.I. The Oligocene Haynes Creek flora of eastern Idaho. Univ. Calif. Publ. Geol. Sci. 1998, 143:1-99.
4. Biffin E., Hill R.S., Lowe A.J. Did kauri (Agathis: Araucariaceae) really survive the Oligocene drowning of New Zealand?. Syst. Biol. 2010, 59:594-602.
5. Campbell C.S., Wright W.A., Cox M., Vining T.F., Major C.S., Arsenault M.P. Nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in Picea (Pinaceae): sequence divergence and structure. Mol. Phylogenet. Evol. 2005, 35:165-185.
6. Clair S.J.B., Critchfield W.B. Hybridization of a Rocky Mountain fir (Abies concolor) and a Mexican fir (Abies religiosa). Can. J. For. Res. 1988, 18:640-643.
7. Cook L.G., Crisp M.D. Not so ancient: the extant crown group of Nothofagus represents a post-Gondwanan radiation. Proc. Roy. Soc. B 2005, 272:2535-2544.
8. Critchfield W.B. Hybridization of the California firs. For. Sci. 1988, 34:139-151.
9. Cronn R., Wendel J.F. Cryptic trysts, genomic mergers, and plant speciation. New Phytol. 2004, 161:33-142.
10. Cullings K.W. Design and testing of a plant-specific PCR primer for ecological and evolutionary studies. Mol. Ecol. 1992, 1:233-240.
11. Cunningham C.W. Can three incongruence tests predict when data should be combined?. Mol. Biol. Evol. 1997, 14:733-740.
12. Donoghue M.J., Smith S.A. Patterns in the assembly of temperate forests around the Northern Hemisphere. Philos. Trans. Roy. Soc. Lond. B 2004, 359:1633-1644.
13. Doyle J.J., Doyle J.S. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987, 19:11-15.
14. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214-221.
15. Drummond A.J., Ho S.Y.W., Philips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:699-710.
16. Dzhabarova, K.S., 1980. Developmental stages of upper Paleogene and Neogene floras of Azerbaijan according to palynological data. In: Fourth International Palynology Conference, Lucknow, India, vol. 2, pp. 747-749.
17. Farjon A. A Handbook of the World's Conifers 2010, vols. 1-2. EJ Brill, Leiden.
18. Farjon A., Rushforth K.D. A classification of Abies Miller (Pinaceae). Notes Roy. Bot. Gard. Edinburgh 1989, 46:59-77.
19. Farris J.S., Kallersjo M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1994, 10:315-319.
20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981, 17:368-376.
21. Ferguson S.K. On the phytogeography of Coniferales in the European Cenozoic. Palaeogeogr. Paleoclimatol. Palaeoecol. 1967, 3:73-110.
22. Fu L.G., Li N., Mill R.R. Pinaceae. Flora of China 1999, vol. 4. Science Press/Missouri Botanical Garden Press, Beijing/St. Louis.
23. Gernandt D.S., Liston A. Internal transcribed spacer region evolution in Larix and Pseudotsuga (Pinaceae). Am. J. Bot. 1999, 86:711-723.
24. Goldman N., Anderson J.P., Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 2000, 49:652-670.
25. González F., Wagner S.T., Salomo K., Symmank L., Samain M., Isnard S., Rowe N.P., Neinhuis C., Wanke S. Present trans-Pacific disjunct distribution of Aristolochia subgenus Isotrema (Aristolochiaceae) was shaped by dispersal, vicariance and extinction. J. Biogeogr. 2014, 41:380-391.
26. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
27. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
28. Harris A.J., Wen J., Xiang Q.Y. Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA approach. J. Syst. Evol. 2013, 51:117-133.
29. Havill N.P., Campbell C.S., Vining T.F., LePage B., Bayer R.J., Donoghue M.J. Phylogeny and biogeography of Tsuga (Pinaceae) inferred from nuclear ribosomal ITS and chloroplast DNA sequence data. Syst. Bot. 2008, 33:478-489.
30. He T.H., Pausas J.G., Belcher C.M., Schwilk D.W., Lamont B.B. Fire-adapted traits of Pinus arose in the fiery Cretaceous. New Phytol. 2012, 194:751-759.
31. Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
32. Huson D.H. Splits Tree: analyzing and visualizing evolutionary data. Bioinformatics 1998, 14:68-73.
33. Isoda K., Shiraishi S., Kisanuki H. Classifying Abies species (Pinaceae) based on the sequence variation of a tandemly repeated array found in the chloroplast DNA trnL and trnF intergenic spacer. Silvae Genet. 2000, 49:161-165.
34. Isoda K., Shiraishi S., Watanabe S., 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, 9:1965-1974.
35. Jaramillo-Correa J.P., Bousquet J., Beaulieu J., Isabel N., Perron M., Bouillé M. Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: the nature of polymorphism and variation within and among species in Picea. Theor. Appl. Genet. 2003, 106:1353-1367.
36. Jaramillo-Correa J.P., Aguirre-Planter E., Khasa D.P., Eguiarte L.E., Piñero D., Furnier G.R., Bousquet A. Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala. Evolution 2008, 17:2476-2490.
37. Jiang Z.Y., Peng Y.L., Hu X.X., Zhou Y.F., Liu J.Q. Cytoplasmic DNA variation in and genetic delimitation of Abies nephrolepis and Abies holophylla in northeastern China. Can. J. For. Res. 2011, 41:1555-1561.
38. Kremp G.O.W. Catalog of Fossil Spores and Pollen 1958, vol. 4. The Pennsylvania State University, Pennsylvania, USA.
39. Kremp G.O.W. Catalog of Fossil Spores and Pollen 1967, vol. 26. The Pennsylvania State University, Pennsylvania, USA.
40. Leopold E.B., Liu G., Clay-Poole S. Eocene-Oligocene Climatic and Biotic Evolution 1992, 399-420. Princeton University Press, Princeton, N.J. D.R. Prothero, W.A. Berggren (Eds.).
41. LePage B.A., Basinger J.F. Evolutionary history of the genus Pseudolarix Gordon (Pinaceae). Int. J. Plant Sci. 1995, 156:910-950.
42. Liepelt S., Mayland-Quellhorst E., Lahme M., Ziegenhagen B. Contrasting geographical patterns of ancient and modern genetic lineages in Mediterranean Abies species. Plant Syst. Evol. 2010, 284:141-151.
43. Liu T.S. A Monograph of the Genus Abies 1971, Department of Forestry, College of Agriculture, National Taiwan University, Taiwan.
44. Lo E.Y.Y., Stefanović S., Christensen K.I., Dickinson T.A. Evidence for genetic association between East Asian and western North American Crataegus L. (Rosaceae) and rapid divergence of the eastern North American lineages based on multiple DNA sequences. Mol. Phylogenet. Evol. 2009, 51:157-168.
45. Manos P.S., Donoghue M.J. Progress in northern hemisphere phytogeography: an introduction. Int. J. Plant Sci. 2001, 162:S1-S2.
46. Martin D.P., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26:2462-2463.
47. Milne R.I. Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a tertiary relict distribution. Mol. Phylogenet. Evol. 2004, 33:389-401.
48. Milne R.I., Abbott R.J. The origin and evolution of Tertiary relict floras. Adv. Bot. Res. 2002, 38:281-314.
49. Neale D.B., Sederoff R.R. Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. Theor. Appl. Genet. 1989, 77:212-216.
50. Nylander J.A.A. MrModeltest v. 3.7. Program Distributed by the Author 2004, Evolutionary Biology Centre, Uppsala University.
51. Peng Y., Yin S., Wang J., Tian B., Ren G.P., Guo Q.H., Liu J.Q. Phylogeographic analysis of the fir species in southern China suggests complex origin and genetic admixture. Ann. For. Sci. 2012, 69:409-416.
52. Rambaut, A., Drummond, A., 2002. TREEANNOTATOR v.1.4. Part of the BEAST Package. http://evolve.zoo.ox.ac.uk/.
53. Rambaut, A., Drummond, A., 2003. TRACER v.1.4.http://evolve.zoo.ox.ac.uk/.
54. Rambaut A., Grass N.C. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1997, 13:235-238.
55. Ran J.H., Wei X.X., Wang X.Q. Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes. Mol. Phylogenet. Evol. 2006, 41:405-419.
56. Raven P.H., Axelrod D.I. Angiosperm biogeography and past continental movement. Ann. Mo. Bot. Gard. 1974, 61:539-673.
57. Ree R.H., Moore B.R., Webb C.O., Donoghue M.J. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 2005, 59:2299-2311.
58. Rieseberg L.H., Raymond O., Rosenthal D.M., Lai Z., Livingstone K., Nakazato T., Durphy J.L., Schwarzbach A.E., Donovan L.A., Lexer C. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 2003, 301:1211-1216.
59. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:572-1574.
60. Sanmartín I., Enghoff H., Ronquist F. Patterns of animal dispersal, vicariance and diversification in the Holarctic. Biol. J. Linn. Soc. 2001, 73:345-390.
61. Schilling E.E. Hybrid genera in Liatrinae (Asteraceae: Eupatorieae). Mol. Phylogenet. Evol. 2011, 59:158-167.
62. Schnabel A., Wendel J.F. Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences. Am. J. Bot. 1998, 85:1753-1765.
63. Schorn H.E., Wehr W.C. Abies milleri sp. nov. from the middle Eocene Klondike Mountain Formation, Republic Ferry County, Washington. Burke Museum Contrib. Anthropol. Nat. Hist. 1986, 1:1-7.
64. Schultheis L.M., Donoghue M.J. Molecular phylogeny and biogeography of Ribes (Grossulariaceae), with an emphasis on gooseberries (subg. Grossularia). Syst. Bot. 2004, 29:77-96.
65. Seehausen O. Hybridization and adaptive radiation. Trends Ecol. Evol. 2004, 19:198-207.
66. Semerikova S.A., Semerikov V.L. Molecular phylogenetic analysis of the genus Abies (Pinaceae) based on the nucleotide sequence of chloroplast DNA. Russ. J. Genet. 2014, 50:7-19.
67. Semerikova S.A., Semerikov V.L., 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, 8:326-340.
68. Shaw J., Lickey E.B., Beck J.T., Farmer S.B., Liu W. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 2005, 92:142-166.
69. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
70. Suyama Y., Yoshimaru H., Tsumura Y. Molecular phylogenetic position of Japanese Abies (Pinaceae) based on chloroplast DNA sequences. Mol. Phylogenet. Evol. 2000, 16:271-277.
71. Swofford D.L. PAUP*: Phylogenetic Analysis using Parsimony (*and Other Methods), version 4.0b10 2002, Sinauer, Sunderland.
72. Syring J., Farrell K., Businský R., Cronn R., Liston A. Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus. Syst. Biol. 2007, 56:163-181.
73. Takenouchi M., Chien J.J. On Abies sibirica and a new hybrid of the genus Abies in Heilungkiang, China. Acta Phytotax. Sin. 1957, 6:145-152.
74. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
75. Tiffney B.H. Geographic and climatic influences on the Cretaceous and Tertiary history of Euramerican floristic similarity. Acta Univ. Carol. Geol. 2000, 44:5-16.
76. Tiffney B.H., Manchester S.R. The use of geological and paleontological evidence in evaluating plant phylogeographic hypotheses in the Northern Hemisphere Tertiary. Int. J. Plant Sci. 2001, 162(Suppl.):3-17.
77. Tsumura Y., Suyama Y. Differentiation of mitochondrial DNA polymorphisms in populations of five Japanese Abies species. Evolution 1998, 52:1031-1042.
78. Tsutsui K., Suwa A., Sawada K., Kato T., Ohsawa T.A., Watano Y. Incongruence among mitochondrial, chloroplast and nuclear gene trees in Pinus subgenus Strobus (Pinaceae). J. Plant. Res. 2009, 122:509-521.
79. Wang X.Q., Tank D.C., Sang T. Phylogeny and divergence time in Pinaceae: evidence from three genomes. Mol. Biol. Evol. 2000, 17:773-781.
80. Watano Y., Imazu M., Shimizu T. Chloroplast DNA typing by PCR-SSCP in the Pinus pumila-P. parviflora var. pentaphylla complex (Pinaceae). J. Plant. Res. 1995, 108:493-499.
81. Watano Y., Imazu M., Shimizu T. Spatial distribution of cpDNA and mtDNA haplotypes in a hybrid zone between Pinus pumila and P. parviflora var. pentaphylla (Pinaceae). J. Plant. Res. 1996, 109:403-408.
82. Watano Y., Kanai A., Tani N. Genetic structure of hybrid zones between Pinus pumila and P. parviflora var. pentaphylla (Pinaceae) revealed by molecular hybrid index analysis. Am. J. Bot. 2004, 91:65-72.
83. Wei R., Zhang X.C. Rediscovery of Cystoathyrium chinense Ching (Cystopteridaceae): phylogenetic placement of the critically endangered fern species endemic to China. J. Syst. Evol. 2014, 52:450-457.
84. Wen J. Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Ann. Rev. Ecol. Syst. 1999, 30:421-455.
85. Wen J., Jansen R.K. Morphological and molecular comparisons of Campsis grandiflora and C. radicans (Bignoniaceae), an eastern Asian and eastern North American vicariad species pair. Plant Syst. Evol. 1995, 196:73-83.
86. Wen J., Ickert-Bond S., Nie Z.L., Li R. Timing and modes of evolution of eastern Asian-North American biogeographic disjunctions in seed plants. Darwin's Heritage Today: Proceedings of the Darwin 200 Beijing International Conference 2010, 252-269. Higher Education Press, Beijing. M. Long, H.Y. Gu, Z. Zhou (Eds.).
87. Whitehead D.R. Fossil pine pollen and full-glacial vegetation in southeastern North Carolina. Ecology 1964, 45:767-777.
88. Wolfe J.A. Some aspects of plant geography of the Northern Hemisphere during the late Cretaceous and Tertiary. Ann. Mo. Bot. Gard. 1975, 62:264-279.
89. Wolfe J.A. Tertiary climates and floristic relationships at high latitudes in the Northern Hemisphere. Palaeogeogr. Paleoclimatol. Palaeoecol. 1980, 30:313-323.
90. Wolfe J.A. Tertiary climatic changes at middle latitudes of western North America. Palaeogeogr. Paleoclimatol. Palaeoecol. 1994, 108:195-205.
91. Xiang Q.Y., Soltis D.E. The eastern Asian and eastern and western North American floristic disjunction: congruent phylogenetic patterns in seven diverse genera. Mol. Phylogenet. Evol. 1998, 10:178-190.
92. Xiang Q.Y., Crawford D.J., Wolfe A.D., Tang Y.C., DePamphilis C.E. Origin and biogeography of Aesculus (Hippocastanaceae): a molecular phylogenetic perspective. Evolution 1998, 52:988-997.
93. Xiang Q.P., Xiang Q.Y., Liston A., Zhang X.C. Phylogenetic relationships in Abies (Pinaceae): evidence from PCR-RFLP of the nuclear ribosomal DNA internal transcribed spacer region. Bot. J. Linn. Soc. 2004, 145:425-435.
94. Xiang Q.Y., Zhang W.H., Ricklefs R.E., Qian H., Chen Z.D., Wen J., Li J.H. Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North America. Evolution 2004, 58:2175-2184.
95. Xiang X.G., Cao M., Zhou Z.K. Fossil history and modern distribution of the genus Abies (Pinaceae). Front. For. China 2007, 2:355-365.
96. Xiang Q.P., Xiang Q.Y., Guo Y.Y., Zhang X.C. Phylogeny of Abies (Pinaceae) inferred from nrITS sequence data. Taxon 2009, 58:141-152.
97. Yu Y., Harris A.J., He X. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Mol. Phylogenet. Evol. 2010, 56:848-850.
98. Yu, Y., Harris, A.J., He, X., 2011. RASP (Reconstruct Ancestral State in Phylogenies) 2.0 beta. http://mnh.scu.edu.cn/soft/blog/RASP.
99. Zachos J., Pagani M., Sloan L., Thomas E., Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to Present. Science 2001, 292:686-693.
100. Zhao Y.P., Qi Z.C., Ma W.W., Dai Q.Y., Li P., Cameron K.M., Lee J., Xiang Q.Y., Fu C.X. Comparative phylogeography of the Smilax hispida group (Smilacaceae) in eastern Asia and North America - implications for allopatric speciation, causes of diversity disparity, and origins of temperate elements in Mexico. Mol. Phylogenet. Evol. 2013, 68:300-311.