DOI: 10.5061/dryad.jv4nd82
title: Data from: Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago

description: The generation of the high species diversity of insects in Japan was
 profoundly influenced by the formation of the Japanese Archipelago. We
 explored the species diversification and biogeographical history of the
 Nemouridae Billberg, 1820 family in the Japanese Archipelago using
 mitochondrial DNA and nuclear DNA markers. We collected 49 species among
 four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898;
 Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South
 Korea and North America. We estimated their divergence times—based on
 three molecular clock node calibrations—using Bayesian phylogeography
 approaches. Our results suggested that Japanese Archipelago formation
 events resulted in diversification events in the middle of the Cretaceous
 (&lt;120 Ma), speciation in the Paleogene (&lt;50 Ma) and
 intra-species diversification segregated into eastern and western Japan of
 the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples
 were genetically separated into two clades—that of Mainland China and that
 of Japan. The Japanese clade clustered with the Nemouridae species from
 North America, suggesting the possibility of a colonisation event prior to
 the formation of the Japanese Archipelago. We believe that our results
 enhanced the understanding both of the origin of the species and of local
 species distribution in the Japanese Archipelago.
description: Alignment file of cox1
 used for molecular clock analysisAlignment file for cox1
 molecular marker used for node calibration analysiscox1.calibrated.alnPhylogenetic tree file of cox1 with node calibrationPhylogenetic tree file of cox1 molecular marker obtained as the output file of pooling fossil calibration and biogeographical calibration analysis using Log Combiner software in BEAST package.cox1.Fos-Bio.treesPhylogenetic tree file of cox1 rates node calibrationPhylogenetic tree file of cox1 molecular marker using the time of the most recent common ancestor. This is the output file of pooling cox1 rates using Log Combiner software in BEAST package.cox1rates.treesCox1 alignment file of Japan and North America speciesCox1 alignment file of Japan and North America stoneflies species.cox1-All-America.alnCox1 phylogenetic file of Japan and North America speciesCox1 phylogenetic tree file of Japan and North America stoneflies species.cox1-All-America.txtGMYC scriptGMYC script used in R for delimitation of putative DNA speciesGMYC-script.txtAlignment file of H3 used for molecular clock analysisAlignment file for H3 molecular marker used for node calibration analysis.H3.calibrated.alnPhylogenetic tree file of H3 with node calibrationPhylogenetic tree file H3 molecular marker obtained as the output file of pooling fossil calibration and biogeographical calibration analysis using Log Combiner software in BEAST package.H3.Fos-Bio.treesH3 alignment file of Japan and North America speciesH3 alignment file of Japan and North America stoneflies species.H3-All-America.alnH3 phylogenetic file of Japan and North America speciesH3 phylogenetic tree file of Japan and North America stoneflies species.H3-All-America.txt