Phylogeny of the cycads based on multiple single-copy nuclear genes: Congruence of concatenated parsimony, likelihood and species tree inference methods

Annals of Botany

Volumn 112, Issue 7, 2013, Pages 1263-1278

  Salas Leiva, Dayana E ^a,b   Meerow, Alan W ^b   Calonje, Michael ^a,c   Griffith, M Patrick ^c   Francisco Ortega, Javier ^a,d   Nakamura, Kyoko ^b   Stevenson, Dennis W ^e   Lewis, Carl E ^c   Namoff, Sandra ^f  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b U S DEPARTMENT OF AGRICULTURE   (United States)

^c MONTGOMERY BOTANICAL CENTER   (United States)

^d FAIRCHILD TROPICAL BOTANIC GARDEN   (United States)

^e NEW YORK BOTANICAL GARDEN   (United States)

^f RANCHO SANTA ANA BOTANIC GARDEN   (United States)

Author keywords

Biogeography; Bowenia; Cycadales; Dioon; Gymnosperms; Molecular systematics; Stangeria

Indexed keywords

ACCURACY ASSESSMENT; ANCESTRY; BAYESIAN ANALYSIS; CALIBRATION; CLADISTICS; CLASSIFICATION; DNA; ESTIMATION METHOD; GENE EXPRESSION; OPTIMIZATION; PARSIMONY ANALYSIS; PHYLOGENETICS; PHYLOGENY; SPECIES DIVERSITY; TREE;

ARTICLE; BIOGEOGRAPHY; BOWENIA; CELL NUCLEUS; CLASSIFICATION; CYCADOPHYTA; DIOON; GENE DOSAGE; GENETIC POLYMORPHISM; GENETICS; GYMNOSPERM; MOLECULAR SYSTEMATICS; PHYLOGENY; PHYLOGEOGRAPHY; PLANT GENE; SPECIES DIFFERENCE; STANGERIA; STATISTICAL MODEL; TIME; TREE;

BIOGEOGRAPHY; BOWENIA; CYCADALES; DIOON; GYMNOSPERMS; MOLECULAR SYSTEMATICS; STANGERIA;

CELL NUCLEUS; CYCADOPHYTA; GENE DOSAGE; GENES, PLANT; LIKELIHOOD FUNCTIONS; PHYLOGENY; PHYLOGEOGRAPHY; POLYMORPHISM, GENETIC; SPECIES SPECIFICITY; TIME FACTORS; TREES;

EID: 84889838350     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mct192     Document Type: Article

References (133)

1. Albach DC, Meudt HM. 2010. Phylogeny of Veronica in the Southern and Northern Hemispheres based on plastid, nuclear ribosomal and nuclear low-copy DNA. Molecular Phylogenetics and Evolution 54: 457-471.
2. A ́ lvarez I,Wendel JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
3. Anderson JM, Anderson HM. 1989. Palaeoflora of southern Africa, Molteno Formation (Triassic), volume 2: Gymnosperms (excluding Dicroidium). Rotterdam: A.A. Balkema
4. Anderson J, Anderson H, Cleal C. 2007. Brief history of the gymnosperms: classification, biodiversity, phytogeography and ecology. Strelitzia 20: 1-280.
5. Ané C, Larget B, Baum DA, Smith SD,Rokas A. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24: 412-426.
6. Artabe AE, Stevenson DW. 1999. Fossil Cycadales of Argentina. Botanical Review 65: 219-238.
7. Artabe AE, Zamuner AB, Stevenson DW. 2004. Two new petrified cycad stems, Brunoa gen. nov. and Worsdellia gen. nov., from the Cretaceous of Patagonia (Bajo de Santa Rosa, Río Negro Province), Argentina. Botanical Review 70: 121-133.
8. Artabe AE, Zamuner AB, Stevenson DW. 2005. A new genus of Late Cretaceous cycad stem from Argentina, with reappraisal of known forms. Alcheringa 29: 87-100.
9. Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge, MA: Harvard University Press.
10. Avise JC, Wollenberg K. 1997. Phylogenetics and the origin of species. Proceedings of the National Academy of Sciences, USA 94: 7748-7755.
11. BaumDA. 2007.Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56: 417-426.
12. Bogler DJ, Francisco-Ortega J. 2004. Molecular systematic studies in cycads: evidence from trnL intron and ITS2 rDNA sequences. Botanical Review 70: 260-273.
13. Braun H, Czihal A, Shutov AD, Baumlein H. 1996. Avicilin-like seed protein of cycads: similarity to sucrose-binding proteins. Plant Molecular Biology 31: 35-44.
14. Brenner ED, StevensonDW, TwiggRW. 2003a. Cycads: evolutionary innovations and the role of plant-derived neurotoxins. Trends in Plant Science 8: 446-452.
15. Brenner ED, Stevenson DW, McCombie RW, et aL. 2003b. Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biology 4: R78.
16. Butler RJ, Barrett PM, Kenrick P, Penn MG. 2009. Testing co-evolutionary hypothesis over geological timescales: interactions between Mesozoic nonavian dinosaurs and cycads. Biological Reviews 84: 73-89.
17. Cantrill DJ. 2000.Apetrified cycad trunk fromtheLate Cretaceous of the Larsen Basin, Antarctica. Alcheringa 24: 307-318.
18. Caputo P, Cozzolino S, De Luca P, Moretti A. 2004. Molecular phylogeny of Zamia (Zamiaceae). In: Walters T, Osborene R. eds. Cycad classification. Concepts and recommendations. Wallingford, UK: CABI Publishing, 149-157.
19. Chaw S-M,WaltersTW, Chang C-C, Hu S-H, Chen S-H. 2005. A phylogeny of cycads (Cycadales) inferred fromchloroplastmatK gene, trnK intron, and nuclear rDNA ITS region. Molecular Phylogenetics and Evolution 37: 214-234.
20. Chiang Y-C, Hung K-H, Moore S-J, et aL. 2009. Paraphyly of organelle DNAs in Cycas sect. Asiorientalis due to ancient ancestral polymorphisms. BMC Evolutionary Biology 9: 161.
21. Christenhusz MJM, Reveal JL, Farjon A, Gardner MF, Mill RR, Chase MW. 2011. A new classification and linear sequence of extant gymnosperms. Phytotaxa 19: 5570.
22. CrispMD,CookLG.2011.Cenozoic extinctions account for the lowdiversity of extant gymnosperms compared with angiosperms. New Phytologist 192: 997-1009.
23. DeCastro O,Vazquez-TorresM,DeLucaP. 2006. Utility ofAFLPmarkers for the assessment of molecular relationships in Ceratozamia Brongn. (Zamiaceae). Plant Biosystems 140: 221-228.
24. Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genetics 2: e68.
25. Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology and Evolution 24: 332-340.
26. Dehgan B, SchutzmanBA, AlmiraF. 1993. Utilization of scanning electron microscopy on the study of surface features in Cycadales. In: Stevenson DW, Norstog KJ. eds. The biology, structure and systematics of the Cycadales. Proceedings of the Second International Conference on Cycad Biology. Palm & Cycad Societies of Australia, Milton, Queensland, 228-235.
27. De Luca P, Moretti A, Sabato S, Gigliano GS. 1982. A comparative study of cycad mucilages. Phytochemistry 21: 1609-1611.
28. Delevoryas T. 1975. Mesozoic cycadophytes. In: Campbell KSW. ed. Papers presented at the 3rd Gondwana symposium. Australian National University Press, Canberra. Doyle JJ. 1992. Gene trees and species trees -molecular systematics as onecharacter taxonomy. Systematic Botany 17: 144-163.
29. Doyle JJ. 1997. Trees within trees: genes and species, molecules and morphology. Systematic Biology 46: 537-553.
30. Drummond A,HoS, PhillipsM,RambautA. 2006.Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88.
31. Drummond A, Suchard M, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
32. Edwards SV. 2008. Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.
33. EdwardsSV, Liu L, Pearl DK. 2007. High-resolution species trees without concatenation. Proceedings of the National Academy of Sciences, USA 104: 5936-5941.
34. Erdei B, Argun F, Barone Lumaga MR. 2010. Pseudodioon akyoli gen. et sp. nov., an extinct member of Cycadales from Turkish Miocene. Plant Systematics and Evolution 285: 33-49.
35. Erdei B, Manchester SR, Kvacek Z. 2012. Dioonopsis Horiuchi et Kimura leaves from the Eocene of Western North America: A cycad shared with thePaleogene of Japan. International Journal of Plant Sciences173: 81-95.
36. FrohlichMW, Parker DS. 2000. The mostly male theory of flower evolutionary origins: from genes to fossils. Systematic Botany 25: 155-170.
37. González D, Vovides AP. 2002. Low intralineage divergence in Ceratozamia (Zamiaceae) detected with nuclear ribosomal DNA ITS and chloroplast DNA trnL-F non-coding region. Systematic Botany 27: 654-661.
38. González D, Vovides AP, Bárcenas C. 2008. Phylogenetic relationships of the neotropical genus Dioon (Cycadales, Zamiaceae) based on nuclear and chloroplast DNA sequence data. Systematic Botany 33: 229-236.
39. Graham A. 2003a. Historical phytogeography of the Greater Antilles. Brittonia 55: 357-383.
40. Graham A. 2003b. Geohistorical models and Cenozoic paleoenvironments of the Caribbean region. Systematic Botany 28: 378-386.
41. GriffithMP, Calonje MA, StevensonDW, Husby CE, Little DP. 2012. Time, place, and relationships: cycad phenology in a phylogenetic and biogeographic context. Memoirs of the New York Botanical Garden 106: 59-81.
42. Heled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27: 570-580.
43. HendyMD,Penny D. 1982. Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59: 277-290.
44. Hermsen EJ, Taylor TN, Taylor EL, Stevenson DW. 2006. Cataphylls of the Middle Triassic cycad Antarcticycas schopfii and new insights into cycad evolution. American Journal of Botany 93: 724-738.
45. Hermsen EJ, Taylor EL, Taylor TN. 2009. Morphology and ecology of the Antarcticycas plant. Review of Palaeobotany and Palynology 153: 108-123.
46. Hill KD. 1999. Cycas -an evolutionary perspective. In: Chen CJ. ed. Biology and conservation of cycads. Proceedings of the Fourth International Conference on Cycad Biology. International Academic Publishers, Beijing, 98-115.
47. Hill KD, ChaseMW, StevensonDW, Hills HG, Schutzman B. 2003. The families and genera of cycads: A molecular phylogenetic analysis of Cycadophyta based on nuclear and plastid DNA sequences. International Journal of Plant Sciences 164: 933-948.
48. Hummel J, Gee CT, Sudekum K-H, Sander PM, Nogge G, Clauss M. 2008. In vitro digestibility of fern and gymnosperm foliage: implications for sauropod feeding ecology and diet selection. Proceedings of the Royal Society B: Biological Sciences 275: 1015-1021.
49. Jaramillo C, Rueda MJ, Mora G. 2006. Cenozoic plant diversity in the Neotropics. Science 311: 1893-1896.
50. Jobb G. TREEFINDER version of March 2011. 2011. Munich, Germany. Distributed by the author at www.treefinder.de.
51. Kluge AG. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38: 7-25.
52. Kluge AG. 2004. On total evidence: for the record. Cladistics 20: 205-207.
53. Kono M, Hiroshi T. 2007. Is Cycas revoluta (Cycadaceae) wind-or insectpollinated? American Journal of Botany 94: 847-855.
54. Kubatko LS, Degnan JH. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56: 17-24.
55. Kunzig R. 2011.World without ice. National Geographic 220: 90-109.
56. Kvacek Z. 2002. A new Tertiary Ceratozamia (Zamiaceae, Cycadopsida) from the European Oligocene. Flora 197: 303-316.
57. Kvacek Z. 2004. A noteworthy cycad, Ceratozamia hofmannii Ettinghausen 1881, from the Lower Miocene of Austria re-examined. Neues Jahrbuch fur Geologie und Palaontologie, Monatshefte 240: 111-118.
58. Kvacek Z, Manchester S. 1999. Eostangeria barthel (extinct Cycadales) from the Paleogene of Western North America and Europe. International Journal of Plant Sciences 16: 621-629.
59. Larget BR, Kotha SK, Dewey CN, Ane C. 2010.BUCKy:gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26: 2910-2911.
60. Lindstrom AJ. 2009. Typification of some species names in Zamia L. (Zamiaceae), with an assessment of the status of Chigua D. Stev. Taxon 58: 265-270.
61. Liu L. 2008. BEST: Bayesian estimation of species trees under the coalescent modeL. Bioinformatics 24: 2542-2543.
62. Liu L, Pearl DK. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56: 504-514.
63. Liu L, Pearl DK, Brumfield RT, Edwards SV. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62: 2080-2091.
64. Liu L,YuL,Kubatko L,PearlDK,EdwardsSV. 2009.Coalescent methods for estimating phylogenetic trees. Molecular Phylogenetics and Evolution 53: 320-328.
65. Liu YS, Zhou ZY, Li HM. 1991. First discovery of Cycas fossil leaf in northeast China. Science Bulletin 22: 1758-1759.
66. Maddison WP. 1997. Gene trees in species trees. Systematic Biology 46: 523-536.
67. MaddisonWP, Maddison DR. 2011. Mesquite: A modular system for evolutionary analysis. Version 2.75. http://mesquiteproject.org.
68. Manchester SR. 1981. Fossil plants of the Eocene Clarno nut beds. Oregon Geology 43: 75-81.
69. Martínez LCA, Artabe AEE, Bodnar J. 2012. A new cycad stem from the Cretaceous in Argentina and its phylogenetic relationships with other Cycadales. Botanical Journal of the Linnean Society 170: 436-458.
70. Meerow AW, Noblick L, Borrone JW, et aL. 2009. Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Arecaceae) identifies Syagrus as sister group of the coconut. PLoS One 4: e7353.
71. Miyata KK, Kazuharu M, Kei-ichi K, Takashi M. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066.
72. Moretti A, Caputo P, Cozzolino S, et aL. 1993. A phylogenetic analysis of Dioon (Zamiaceae). American Journal of Botany 80: 204-214.
73. Mort ME, Crawford DJ. 2004. The continuing search: low-copy nuclear sequences for lower-level plant molecular phylogenetic studies. Taxon 53: 257-261.
74. Moynihan J, Stevenson DW, Lewis CE, Vovides AP, Caputo P, Francisco-Ortega J. 2012. A phylogenetic study of Dioon Lind. (Zamiaceae, Cycadales), based on morphology, nuclear ribosomal DNA, a low copy nuclear gene and plastid RFLPs. Memoirs of the New York Botanical Garden 106: 448-479.
75. Mustoe GE. 2008. Cycadophyte fossils from the Pacific Northwest. Cycad Newsletter 31(2/3): 28-32.
76. Nagalingum NS, Marshall CR, Quental TB, Rai HS, Little DP, Mathews S. 2011. Recent synchronous radiation of a living fossiL. Science 334: 796-799.
77. Nichols D, Johnson L. 2008. Plants and the K-T boundary. Cambridge: Cambridge University Press.
78. Nickerson J, Drouin G. 2004. The sequence of the largest subunit ofRNApolymerase II is a useful marker for inferring seed plant phylogeny. Molecular Phylogenetics and Evolution 31: 403-415.
79. Nicolalde-Morejón F, Vergara-Silva F, González-Astorga J, StevensonDW, Vovides AP, Sosa V. 2011. A character-based approach in the Mexican cycads supports diverse multigene combinations for DNA barcoding. Cladistics 27: 150-164.
80. Norstog KJ, Nicholls TJ. 1997. The biology of the cycads. Ithaca, NY: Cornell University Press.
81. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53: 47-67.
82. Osborne R. 2002. Cycad fossils. Encephalartos 69: 4-13.
83. Osborne R, Calonje M, Hill KD, Stanberg L, StevensonDW. 2012. The world list of cycads. Memoirs of the New York Botanical Garden 106: 480-510.
84. Oxelman B, Yoshikawa N, McConaughy BL, Luo J, Denton AL, Hall DB. 2004. RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids. Molecular Phylogenetics and Evolution 32: 462-479.
85. Passalia MG, Del Fueyo G, Archangelsky S. 2010. An Early Cretaceous zamiaceous cycad of South West Gondwana: Restrepophyllum nov. gen. from Patagonia, Argentina. Review of Palaeobotany and Palynology 161: 137-150.
86. Penalver E, Labandeira CC, Barrón E, et aL. 2012. Thrips pollination of Mesozoic gymnosperms. Proceedings of National Academy of Sciences, USA 22: 8623-8628.
87. Pindell J, Keenan K. 2009.Tectonic evolution of the Gulf ofMexico, Caribbean and northern South America in the mantle reference frame: An update. In: James K, Lorente M, Pindell J. eds. The origin and evolution of the Caribbean plate. London: Geological Society of London, 1-55.
88. Poczai P, Hyvonen J. 2010. Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Molecular BiologyReports 37: 1897-1912.
89. Popp M, Oxelman B. 2007. Origin and evolution of North American polyploid Silene (Caryophyllaceae). American Journal of Botany 94: 330-349.
90. Pott C, McLoughlin S, LindstromA. 2010. Late Palaeozoic foliage fromChina displays affinities to Cycadales rather than to Bennettitales necessitating reevaluation of the Paleozoic Pterophyllum species. Acta Palaeontologica Polonica 55: 157-168.
91. Rai HS, Obrien HE, Reeves PA, Olmstead RG, GrahamSW. 2003. Inference of higher-order relationships in the cycads from a large chloroplast data set. Molecular Phylogenetics and Evolution 29: 350-359.
92. Rambout A. 2012. FigTree v. 1.4. Available from http://tree.bio.ed.ac.uk/ software/figtree/
93. Raven PH, Axelrod DI. 1974. Angiosperm biogeography and past continental movements. Annals of the Missouri Botanical Garden 61: 539-673.
94. Ree RH, Smith SA. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 4-14.
95. Rokas A, Carroll AB. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Molecular Biology and Evolution 22: 1337-1344.
96. Roncal J,ZonaS,LewisCE.2008. Molecular phylogenetic studies of Caribbean palms (Arecaceae) and their relationships to biogeography and conservation. Botanical Review 74: 78-102.
97. Ronquist F, Teslenko M, van der BankMP, et aL. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-42.
98. Rosenberg MS,KumarS. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proceedings of the National Academy of Sciences, USA 98: 10751-10756.
99. RousseauP. 2012. Amolecular systematic study of the African endemic cycads. Unpublished Masters thesis, Department of Botany and Microbiology, University of Johannesburg.
100. Rousseau-Gueutin M, Gaston A, Ainouche A, et aL. 2009. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): newinsights from phylogenetic analyses of low-copy nuclear genes. Molecular Phylogenetics and Evolution 51: 515-530.
101. Sabato S. 1990. West Indian and South American cycads. Memoirs of the New York Botanical Garden 57: 173-185.
102. Samarakoon T,Wang SY, Alford MH. 2013. Enhancing PCR amplification of DNA from recalcitrant plant specimens using a trehalose-based additive. Applications in Plant Sciences 1: 1200236.
103. SanginP, LindstromA, Kokubugata G, ChaiprasongsukM, MingmuangM. 2010. Phylogenetic relationships within Cycadaceae inferred from noncoding regions of chloroplast DNA. Kasetsart Journal 44: 544-557
104. Sanmartin I,Ronquist F. 2004. Southern Hemisphere biogeography inferred by event-based models: plant versus animal patterns. Systematic Biology 53: 216-243.
105. Sass C, Little DP, Stevenson DW, Specht CD. 2007. DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS One 2: pe1154.
106. Schneider D, Wink M, Sporer F, Lounibos P. 2002. Cycads: their evolution, toxins, herbivores and insect pollinators. Naturwissenschaften 89: 281-294.
107. Schulte P, Alegret L, Arenillas I, et aL. 2010. The Chicxulub asteroid impact and mass extinction at the Cretaceous-Paleogene boundary. Science 327: 1214-1218.
108. Shigyo M, Hasebe M, Ito M. 2006. Molecular evolution of the AP2 subfamily. Gene 366: 256-265.
109. Small RL, Cronn RC, Wendel JF. 2004. LAS Johnson Review No. 2. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 17: 145-170.
110. Sorenson MD, Franzosa EA. 2007. TreeRot, version 3. Boston, MA: Boston University.
111. StevensonDW. 1990. Morphologyand systematics of the Cycadales. Memoirs of the New York Botanical Garden 57: 8-55.
112. StevensonDW. 1992. A formal classification of the extant cycads. Brittonia 44: 220-223.
113. Sugiura N. 1978. Further analysis of data by Akaikes information criterion and finite corrections. Communications in Statistics Part a -Theory and Method, 7: 13-26.
114. Swofford DL. 2004. PAUP phylogenetic analysis using parsimony (and other methods). v. 4.0 beta 10. Sunderland, MA: Sinauer Associates.
115. Tanabe AS. 2007.KAKUSAN:a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data. Molecular Ecology Notes 7: 962-964.
116. TangW. 2002.The greater Antilles and the cycads of Puerto Rico. Encephalartos 71: 16-22.
117. TangW. 2004.Continental drift and the evolution of Asian cycas. Encephalartos 80: 23-28.
118. Tang W. 2006. Continental drift and the evolution of South American cycads. Encephalartos 86: 26-31.
119. Tang W. 2012. The evolutionary history of North American cycads. Cycad Newsletter 35: 7-13.
120. Terry I, Gimme HW, Moore C, Roemer R, Hull C. 2007. Odor-mediated push-pull pollination in cycads. Science 318: 70.
121. Treutlein J, Vorster P, Wink M. 2005. Molecular relationships in Encephalartos (Zamiaceae, Cycadales) based on nucleotide sequences of nuclear ITS 1 and 2, rbcl, and genomic ISSR fingerprinting. Plant Biology 7: 79-90.
122. Uzunova K, Palamarev E, Kvaĉek Z. 2001. Eostangeria ruzinciniana (Zamiaceae) from the Middle Miocene of Bulgaria and its relationship to similar taxa of fossil Eostangeria, and extant Chigua and Stangeria (Cycadales). Acta Palaeobotanica 41: 177-193.
123. Wang D, Wu YW, Shih ACC, Wu CS,Wang YN, Chaw SM. 2007. Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 mya. Molecular Biology and Evolution 24: 2040-2048.
124. Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24: 1540-1541.
125. Xiao LQ, Moller M, Zhu H. 2010. High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: incomplete concerted evolution and the origin of pseudogenes. Molecular Phylogenetics and Evolution 55: 168-177.
126. Yu Y, Harris AJ, He X. 2010. S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories. Molecular Phylogenetics and Evolution 56: 848-50.
127. Yu Y, Harris AJ, He X-J. 2011. RASP (Reconstruct Ancestral State in Phylogenies) 2.0 beta. Available at http://mnh.scu.edu.cn/soft/blog/RASP. Last accessed 24 December 2012.
128. Zachos JC, Dickens GR, Zeebe RE. 2008. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451: 279-283.
129. Zgurski JM, Rai HS, Fai QM, Bogler DJ, Francisco-Ortega J, GrahamSW. 2008.Howwell dowe understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set. Molecular Phylogenetics and Evolution 47: 1232-1237.
130. Zhang N, Zeng L, Hongyan S,MaH. 2012. Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms. New Phytologist 195: 923-937.
131. Zhang PY, Tan HTW, Pwee KH, Kumar PP. 2004. Conservation of class C function of floral organ development during 300 million years of evolution from gymnosperms to angiosperms. The Plant Journal 37: 566-577.
132. Zhao L, Annie ASH, Amrita S, Yi SKF, Rudolf M. 2013. Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers. Molecular Phylogenetics and Evolution 69: 153-164.
133. Zimmer EA, Wen J. 2013. Using nuclear gene data for plant phylogenetics: progress and prospects. Molecular Phylogenetics and Evolution 66: 539-550.