title: Nuclear ribosomal ITS functional paralogs resolve the phylogenetic relationships of a late-Miocene radiation cycad Cycas (Cycadaceae).
abstract: Cycas is the most widespread and diverse genus among the ancient cycads, but the extant species could be the product of late Miocene rapid radiations. Taxonomic treatments to date for this genus are quite controversial, which makes it difficult to elucidate its evolutionary history. We cloned 161 genomic ITS sequences from 31 species representing all sections of Cycas. The divergent ITS paralogs were examined within each species and identified as putative pseudogenes, recombinants and functional paralogs. Functional paralogs were used to reconstruct phylogenetic relationships with pseudogene sequences as molecular outgroups, since an unambiguous ITS sequence alignment with their closest relatives, the Zamiaceae, is unachievable. A fully resolved and highly supported tree topology was obtained at the section level, with two major clades including six minor clades. The results fully supported the classification scheme proposed by Hill (2004) at the section level, with the minor clades representing his six sections. The two major clades could be recognised as two subgenera. The obtained pattern of phylogenetic relationships, combined with the different seed dispersal capabilities and paleogeography, allowed us to propose a late Miocene rapid radiation of Cycas that might have been promoted by vicariant events associated with the complex topography and orogeny of South China and adjacent regions. In contrast, transoceanic dispersals might have played an important role in the rapid diversification of sect. Cycas, whose members have evolved a spongy layer in their seeds aiding water dispersals.
authors: Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.
authors: Long-Qian
authors: LQ
authors: Xiao
authors: Science Division, Royal Botanic Garden Edinburgh, Edinburg, Scotland, United Kingdom.
authors: Michael
authors: M
authors: Möller
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics*; D029784:Cycas / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D058974:Phylogeography; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013997:Time Factors
chemical_list: D021903:DNA, Ribosomal Spacer
references: Syst Biol. 2005 Apr;54(2):241-53
references: 16012095
references: Mol Phylogenet Evol. 2005 Oct;37(1):214-34
references: 16182153
references: Ann Bot. 2013 Nov;112(7):1263-78
references: 23997230
references: Mol Phylogenet Evol. 2003 Nov;29(2):350-9
references: 13678689
references: Cladistics. 2005 Apr;21(2):163-193
references: 34892859
references: Genetics. 1997 Mar;145(3):821-32
references: 9055091
references: Trends Plant Sci. 2003 Sep;8(9):446-52
references: 13678912
references: Mol Phylogenet Evol. 2010 Apr;55(1):168-177
references: 19945537
references: Mol Ecol. 2004 Oct;13(10):3115-23
references: 15367124
references: Science. 2011 Nov 11;334(6057):796-9
references: 22021670
references: New Phytol. 2011 Dec;192(4):997-1009
references: 21895664
references: Mol Phylogenet Evol. 2007 Aug;44(2):503-20
references: 17611127
references: Syst Biol. 2000 Jun;49(2):369-81
references: 12118412
references: Evolution. 1992 Oct;46(5):1329-1346
references: 28569006
references: Mol Phylogenet Evol. 2003 Dec;29(3):417-34
references: 14615184
references: Mol Biol Evol. 2002 Oct;19(10):1769-81
references: 12270903
references: Naturwissenschaften. 2002 May;89(5):221-5
references: 12135087
references: Virology. 1999 Dec 20;265(2):218-25
references: 10600594
references: Mol Biol Evol. 1996 Apr;13(4):612-22
references: 8882504
references: Naturwissenschaften. 2002 Jul;89(7):281-94
references: 12216856
references: Bioinformatics. 2003 Aug 12;19(12):1572-4
references: 12912839
references: J Mol Evol. 1997 Mar;44(3):258-71
references: 9060392
references: Mol Phylogenet Evol. 2015 Jun;87:46-9
references: 25819445
references: Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13765-70
references: 20643945
references: Bioinformatics. 2006 Nov 1;22(21):2688-90
references: 16928733
references: Mol Phylogenet Evol. 2012 Jul;64(1):243-53
references: 22503758
references: Evolution. 1985 Jul;39(4):783-791
references: 28561359
references: J Hered. 2000 May-Jun;91(3):221-7
references: 10833048
references: Mol Phylogenet Evol. 2008 Sep;48(3):892-903
references: 18577457
references: Mol Phylogenet Evol. 2007 Aug;44(2):752-64
references: 17570687
references: Appl Bioinformatics. 2005;4(1):65-9
references: 16000015