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jpy12027-sup-0001-FigureS1.tifimage/tif3066KFigure S1. Results of the GMYC species delimitation based on cox3 sequence data. (A) Ultrametric tree based on a Bayesian analysis with divergences estimated under a relaxed molecular clock using an uncorrelated lognormal (ULLN) model in BEAST and coalescent tree prior.
jpy12027-sup-0002-FigureS2.tifimage/tif3346KFigure S2. Results of the GMYC species delimitation based on rbcL sequence data. (A) Ultrametric tree based on a Bayesian analysis with divergences estimated under a relaxed molecular clock using an uncorrelated lognormal (ULLN) model in BEAST and coalescent tree prior. (B) The corresponding lineage-through-time plot. The red vertical line indicates the ML transition point of the switch in branching rates, as estimated by a GMYC model. (C) Single-threshold likelihood solutions to the GMYC model.
jpy12027-sup-0003-TableS1.xlsxapplication/msexcel19KTable S1. The distribution of Padina species based on literature data in Algaebase (Guiry and Guiry 2012).
jpy12027-sup-0004-TableS2.xlsxapplication/msexcel46KTable S2. Collection and publication details, provisional morphospecies names, voucher numbers, Genbank accession numbers and main morphoanatomical features for the Padina specimens included in this study. In the morphological matrix, states of the the eight characters (A–H) were encoded following the code provided as attached comments in the first row. Character states written in red refer to specimens that were examined by us. Character states written in black refer to specimens that were encoded based on literature.
jpy12027-sup-0005-TableS3.docxWord document82KTable S3. List of the PCR and sequencing primers used in this study, with indication of annealing temperature and source of each primer.
jpy12027-sup-0006-TableS4.xlsxapplication/msexcel20KTable S4. Summary of the data set built for divergence time inference analysis. A single concatenated sequence was built for each ESU. Details of each concatenated sequence (Genbank accession, voucher number, length).
jpy12027-sup-0007-TableS5.docxWord document75KTable S5. Basic properties and model parameters values as estimated with ModelTest for cox3, rbcL and psaA alignments. L: alignment length (nt); CS: number of constant sites (nt); PI: number of parsimony-informative sites (nt); α: gamma-shape heterogeneity parameter; I: estimated proportion of invariant sites.
jpy12027-sup-0008-TableS6.xlsxapplication/msexcel13KTable S6. Occurrence over ten Spalding's marine realms of the 60 ESUs (see Fig. 1 for geographic range of each realm) recognized with DNA-based algorithmic species delineation methods.

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