First author - Biology Letters
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Table S1. List of studies using autocorrelated relaxed-clock methods and published in Royal Society journals, complete as of 19 November, 2008. The studies are ranked by the approximate taxonomic level of the data being analysed. First author Emerson Papadopoulou Thorpe Matthee Monaghan Percy Ueda Fleischer Smith Day Kadereit Kozak Ribas Ronstedc Schneider Baker Brady Crisp Lavin Linder Miller Rabosky Richardson Schulte Warren Year Journala Program(s)b 2000 2008 2008 2004 2006 2008 2008 2006 2008 2006 2004 2006 2007 2005 2005 2006 2006 2004 2004 2004 2008 2007 2004 2003 2006 PRSB PTRS PTRS PRSB PRSB PRSB PRSB BL PRSB BL PTRS PRSB PRSB PRSB PRSB PRSB PRSB PTRS PTRS PTRS PRSB PRSB PTRS PRSB PRSB NPRS PL PL divtime PL PL NPRS PL PL PL NPRS PL PL, divtime NPRS, PL NPRS PL divtime, PL NPRS, PL PL NPRS NPRS PL NPRS, PL NPRS divtime Sequences Data Type Dominant Taxonomic Level DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA Proteins, RNA Proteins Proteins Proteins, RNA Proteins, RNA Introns Proteins Proteins, RNA Introns Proteins Introns Proteins, RNA Proteins Introns, Proteins Proteins, Introns Proteins Proteins, Introns Proteins, Introns Proteins, RNA, Introns Proteins, Introns Proteins Proteins, RNA, Introns Proteins, Introns Proteins, RNA Proteins, RNA, Introns Conspecifics Conspecifics Conspecifics Individuals to species Individuals to species Individuals to species Individuals to species Individuals to genera Individuals to families Congenerics Congenerics Congenerics Congenerics Congenerics Congenerics Species to genera Species to genera Species to genera Species to genera Species to genera Species to genera Species to genera Species to genera Species to genera Species to genera Wiens Cook Loader Davis Pena Ronstedc Beresford Nagy Pennington (2) Renner Vences Givnish Haddrath Merckx Smith Ericson Paton Wikstrom Cotton Roger Peterson Berney 2007 2005 2007 2005 2008 2005 2005 2003 2004 2004 2003 2005 2001 2008 2005 2006 2002 2001 2005 2006 2008 2006 PRSB PRSB BL PRSB BL PRSB PRSB PRSB PTRS PTRS PRSB PRSB PRSB PRSB PRSB BL PRSB PRSB PRSB PTRS PTRS PRSB PL NPRS, PL PL, divtime, BEAST PL PL NPRS, PL NPRS NPRS PL divtime NPRS PL NPRS PL, divtime NPRS PL, pathd8 NPRS, PL NPRS NPRS NPRS, PL, divtime divtime divtime DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA Protein Protein Protein DNA Proteins, RNA Proteins, RNA, Introns RNA Proteins Proteins Introns, Proteins Proteins Proteins, RNA Introns, RNA Proteins Proteins Proteins Proteins, RNA Proteins, RNA Proteins, RNA Proteins, Introns Proteins, RNA Proteins, RNA Proteins Proteins Proteins RNA Species to genera Species to families Species to families Species to phyla Genera to subfamilies Confamilials Genera to families Genera to families Genera to families Genera to families Genera to families Genera to orders Genera to orders Genera to orders Conordinals Families to orders Families to orders Conclass Orders to classes Orders to phyla Classes to phyla Phyla to kingdoms Journal names: PRSB – Proceedings of the Royal Society of London B; PTRS – Philosophical Transactions of the Royal Society B; BL – Biology Letters. b Relaxed-clock methods and programs: NPRS – non-parametric rate smoothing implemented in r8s; PL – penalized likelihood implemented in r8s; divtime – Bayesian autocorrelated relaxed-clock implemented in divtime; BEAST – Bayesian uncorrelated relaxed-clock implemented in BEAST; pathd8 – local clocks implemented in Pathd8. c Ronsted et al. (2005) performed separate analyses of two data sets in their paper; these are treated separately in this survey. a
