Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation
CCMAR, CIMAR-Laboratório Associado, Universidade do Algarve, Gambelas 8005-139, Faro, Portugal
BMC Evolutionary Biology 2011, 11:371 doi:10.1186/1471-2148-11-371Published: 21 December 2011
Additional file 1:
Incorporated cDNA sequences. Annotations of coding region transcripts used in this study. Total and used length expressed in base pairs (bp) and amino acids (aa) as well as primer sequences are presented. As P, we indicate the partition number for each region used in mixed analyses.
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Additional file 2:
Sampling sites and GeneBank accession numbers of all incorporated cDNA sequences.
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Additional file 3:
Separate analyses of ribosomal nuclear DNA together with ITS regions (see Methods section: estimation of ancestral character states). Phylogenetic reconstructions using 5.8 S ribosomal nuclear DNA together with ITS-1 and ITS-2 regions (re-analysis of data from  after testing for best fit model). Values shown are the 50% majority rule percentage of support for clades given by Bayesian posterior probabilities from one million generation MCMC analysis (above) and the 50% majority rule consensus tree of maximum likelihood bootstraps (below). H. banskii was used as outgroup to root the phylogenetic reconstructions (as in ). These results were also used to root the multi-gene phylogenetic trees since the specificity of primers used to amplify transcriptomic regions in the Fucaceae did not allow amplification outside this group. Topology is based on maximum likelihood reconstruction.
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Additional file 4:
Bayesian dating of Fucaceae diversification using cDNA. Full tree showing the Bayesian dated phyloreconstruction using the 13 coding loci. Node ages in million years (Myr) correspond to the time scale at the bottom of the figure.
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Additional file 5:
Multi-gene phylogenetic reconstruction from cDNA (see Methods section: Multi-gene phylogenetic analyses of cDNA sequences) including introgressed sequences. Multi-gene phylogenetic relationships as shown in Figure 1 but adding sequences of F. guiryi from northern Portugal, where the species co-occurs in sympatry with F. vesiculosus and F. spiralis, creating an introgressed range for F. guiryi that continues northwards [11,25,26,47]. Methods are the same as described for Figure 1. Comparison of this tree with Figure 1 illustrates the effect of introgressed contact regions in preventing phylogenetic resolution, by confounding vertical lineage splitting with horizontal introgressive mixing.
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Additional file 6:
Bayesian dating of Fucaceae diversification using nuclear ribosomal DNA: the 5.8 S gene together with ITS-1 and ITS-2 regions. Bayesian dated phyloreconstruction using nuclear ribosomal DNA, the 5.8 S together with ITS-1 and ITS-2 regions. Node ages in million years (Myr) with their 95% HPD interval correspond to the time scale at the bottom of the figure. Node age estimates were obtained using an uncorrelated log-normal relaxed clock under GTR model of evolution. Tree priors were fixed on Yule speciation model of demographic history. One individual of Cystoseira neglecta, C. osmundacea and C. setchellii species were included as representatives of the family Sargassaceae for the inferences (; accession numbers: AY542816, AY542819 and AY542812). Monophyletic constraints were imposed for the nodes that were used to calibrate the evolutionary rates. Normal priors were used for the times to the most recent common ancestor (tmrca) of Fucaceae and Sargassaceae families (Medium Chattium to Aquitanium age from Miocene epoch: mean 22.5 million years (Myr); standard deviation 2.5 Myr ). Results were processed as described in the methods section.
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