cox1 MrBayes tree file

The mitochondrial cox1 MrBayes output tre

PEPCK pos3-intron *BEAST tree file

The nuclear PEPCK *BEAST output tree for codon position 3 and intro

CorSiM R script

the R script of the CorSiM analyses for simulation of missing specie

wg MrBayes tree file

The nuclear wg MrBayes output tre

species tree *BEAST output file

The *BEAST output species tree including the five genes (cox1 + 16S + PEPCK + EF-1α + wg

nuclear Garli tree file

The concatenated nuclear (PEPCK + EF-1α + wg) Garli output tre

cox1 pos3 *BEAST tree file

The mitochondrial cox1 *BEAST output tree for codon position

nuclear MrBayes tree file

The concatenated nuclear (PEPCK + EF-1α + wg) MrBayes output tre

AFLP data of 4 stream insects and environment data in Japan

AFLP data of 4 stream insects and environment data in Japa

Clock-constrained Bayesian maximum clade credibility tree of the complete <i>cox1</i> data set obtained using BEAST.

<p>The tree (upper panel), obtained under a relaxed lognormal molecular clock, is presented with its corresponding lineage-through-time plot (lower panel). The broken vertical line indicates the point of maximum likelihood fit of the single-threshold GMYC model, i.e. the point of transition from interspecies (Yule) to intraspecies (coalescent) branching events. The grey shading corresponds to the confidence interval of the transition point. The bars indicate significant clusters (arrows: significant singletons) that are inferred to be species. The five species groups are specified on subtending branches. All GMYC clusters were well supported (PP≥0.99).</p