Abstract
Molecular evolutionary rate and dating studies have been carried out on nuclear ribosomal DNA (nrDNA ITS I and II) and non-coding plastid DNA (rps16 intron) nucleotide sequences from Corydalis and other related genera in the poppy family Papaveraceae s. l. Strict, relaxed, and local clock models have been compared. Although it has been suggested that the nrDNA ITS I and II regions evolved in concert, they may have evolved at different evolutionary rates under differential constraints. Based on random local clock and uncorrelated relaxed lognormal clock Bayesian analyses using BEAST v.1.6.2, the ITS II region may have evolved in a clock-like fashion.
Highlights
It has been suggested that the nrDNA ITS I and II regions evolved in concert, they may have evolved at different evolutionary rates under differential constraints
The results of the strict molecular clock analysis show that mean rates of change of nrDNA ITS I, ITS II, and cpDNA rps16 intron sequences of Corydalis were 1.70 x 10-8, 9.24 x 10-8, and 2.52 x 10-8 substitutions per site per million years (Myr), respectively (Table 2)
Based on the results reported here, nuclear ribosomal DNA ITS I and II regions may undergo rather independent evolutionary pathways, which is in contrast to a previous report (Baldwin et al, 1995) that these two non-coding regions of nrDNA evolved in concert in flowering plants
Summary
1.1 Molecular Evolutionary Rate ModelsMethodologies for estimating molecular evolutionary rates and for dating have been developed rapidly through the use of improved statistical tools as well as the introduction of relaxed (Drummond, Nicholls, Rodrigo, & Solomon, 2002; Bromham & Penny, 2003; Drummond, Pybus, Rambaut, Forsberg, & Rodrigo, 2003; Knapp, Stöckler, Havell, Delsuc, Sebastiani, & Lockhart, 2005; Drummond, Ho, Phillips, & Rambaut, 2006; Dornburg, Brandley, McGowen, & Near, 2012) and random local clock analytical methods (Douzery, Delsuc, Stanhope, & Huchon, 2002; Aris-Brosou, 2007; Drummond & Suchard, 2010; Battistuzzi, Filipski, & Kumar, 2011; Dornburg et al, 2012) as refinements of strict molecular clock approaches (Drummond et al, 2006; Drummond & Rambaut, 2007; Heled & Drummond, 2010; Hong & Jury, 2011). Random local molecular clock (LMC) theory has been developed, allowing variable branches in lineages as well as constant rates in shared clades (Drummond & Suchard, 2010; Drummond, Suchard, Xie, & Rambaut, 2012). This has depended on the introduction of sophisticated statistical parameter testing approaches (Drummond & Suchard, 2010; Drummond, Rambaut, & Suchard, 2011a; Drummond et al, 2012). The nrDNA ITS I and II regions (less than 300 bp each) have been considered to evolve in concert in flowering plants (Baldwin et al, 1995), and the cpDNA rps region is expected to evolve faster than coding gene regions such as the rbcL gene (Couvreur et al, 2011)
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