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...h the diversification of the reef organisms themselves, this would still suggest that coral reefs have played a significant role in shaping patterns of standing tetraodontiform diversity. Recent methodological developments in the area of statistical phylogenetics facilitate the kinds of temporally explicit analyses necessary to understand reef fish evolution and test for the role of reefs in driving diversification. Relaxed-clock methods in conjunction with fossil information improve divergence time estimation by allowing rates to vary across the tree (Thorne and Kishino 2002; Sanderson 2003; Drummond et al. 2006). In turn, chronograms provide the ages of stem and crown groups necessary to quantify patterns of diversification and test for unexpectedly rich or poor levels of standing species diversity (Magallon and Sanderson 2001). Here we demonstrate the utility of this approach by adopting a statistical phylogenetic framework to test whether (1) tetraodontiform evolutionary history extends back to the Jurassic, (2) diversification within reef-associated families coincides with the first appearance of scleractinian reefs or with later episodes of reef diversification, and (3) whether reef-associated fa...

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...her in the program Tracer v1.3 (Drummond et al. 2003) to assess convergence. Tree and parameter samplings from the latter 500,000 generations of each run were pooled and used as an estimate of the posterior distribution. A Bayesian concordance analysis was performed to assess concordance in gene trees across loci following the method of Ane et al. (2007). Full details of this method are given in the Supplementary materials. Divergence time estimation A rate-smoothed tree with divergence times was estimated from our 18 locus nuclear data set using a Bayesian relaxed clock method in BEAST v1.4 (Drummond et al. 2006). BEAST analyses used a relaxed lognormal model of lineage rate variation, a GTR+I+ model of nucleotide substitution, and a Yule prior for branching rates. No fossil-based time calibrations are currently available for the Lemuriformes (Simons et al. 1995). However, two calibrations are available that are relevant to our data set: (1) The split between slow lorises (Loris and Nycticebus) and galagos (Galago and Otolemur) has been dated at 38–42 Mya (Seiffert et al. 2003), and we used this date as a normal-distribution prior on this node with a mean of 40 Mya and a SD of 1.2 Myr. (2) The split ...

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...mber of substitutions along branches (the product of rate and time) and a set of fossil calibrations on the tree (Ft), from which the set of rates and times comprising the sum total of branch lengths are calculated. This yields an ultrametric tree (T), with branch lengths equal to time, yielding divergence time estimates for every node in the phylogeny. Various algorithms have been implemented for these calculations, allowing rates of evolution to be constant (i.e., a strict clock, Zuckerkandl and Pauling 1962), autocorrelated through time (Thorne et al. 1998; Sanderson 2002) or uncorrelated (Drummond et al. 2006). In addition to nodes on which fossil constraints have been placed, a set of additional nodes from the Tree of Life for which a temporal scale is known (sensu Benton and Donoghue 2007) will be present in the phylogeny or can be added through the inclusion of more taxa. These nodes, here dubbed “likelihood checkpoints,” will be denoted Nt, consisting of V nodes, Nt(i). The actual location of these nodes (i.e., in the ingroup or as outgroups) is irrelevant, provided that their age bracketing can be robustly justified. If the ages of the nodes comprising Nt encompass a range of possible dates, t...

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...y influenced by the methods used, particularly the assumptions required to make evolution clocklike. Thus, we compared 3 methods of estimating branch lengths: 2 versions of a relaxed lognormal clock (=-=Drummond et al. 2006-=-) and a simple clock-constrained maximum likelihood search (see below). The 2 relaxed lognormal clock analyses were conducted with Bayesian analysis as implemented in BEAST version 1.4.7 (Drummond and...

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... major lineages within clades. The two most divergent terminals (Bungowannah and Antelope) were not included in the final analysis as isolated long branches confound phylogenetic analyses in general (Bergsten, 2005), and their effect on times of divergence analyses is unknown. The dates for all sampled pestiviruses were specified as years from some time in the past. The best-fit models “General Time Reversible (GTR)” for nucleotide substitution and “Gamma+Invariant sites” for site heterogeneity were used. The selection of the relaxed uncorrelatedexponential distribution molecular clock model (Drummond et al., 2006) and tree prior coalescent (exponential growth) was based on several initial tests, in which the MCMC chain was run for 50 to 150 million generations. “Auto optimise” was used in an attempt to tune the operators to maximum efficiency. In the final four independent BEAST analyses, the MCMC chains were run for 150 to 200 million generations and the ESS values (except “coefficient of variation) were greater than 100, as analysed by software Tracer v1.4 (Rambaut and Drummond, 2007). The analysis with maximum log tree likelihood value of −3.107×104 was selected and presented in this 357L. Liu et al...

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...sic ‘Gondwana’ paradigm and a more complicated history of the Southern Hemisphere is emerging, involving not only general drivers such as continental drift and niche conservatism, but also drowning and re-emergence of landmasses, biotic turnover and long-distance colonization. What is biogeography? Biogeography is the study of the distribution and evolution of organisms through space and time [1]. New methods have given impetus to the discipline: for example, geographic information systems (GIS) for spatial analysis [2]; Bayesian molecular phylogenetics for dating divergences between lineages [3]; and integrative models for reconstructing distributional change through evolutionary time, using either maximum likelihood [4] or Bayesian inference [5]. Above all, renewed recognition that ecological factors (e.g. climatic tolerance and dispersal limitation) underlie deep historical events (i.e. speciation, extinction and distributional change) [6,7] has rekindled interest in old questions, such as ‘how do ecological factors influence the processes of vicariance and long-distance dispersal and establishment (LDDE)?’ (see Glossary) [6–8]. It has also stimulated new questions, such as ‘what i...