Data from: Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific

A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from one another in the early Pliocene–late Miocene (c. 4.5–7.7 Ma). The remarkably deep divergences, both within and between lineages, appear to have resulted from ancient isolations, accelerated by random drift and limited genetic exchange between regions. The disjunct distributions of lineages A and C along the coasts of Japan may reflect divergence during isolation in scattered refugia. The distribution of lineage B, from the South China Sea to the Korean Peninsula, appears to reflect postglacial recolonizations of coastal habitats. These three lineages do not coincide with the three documented morphological formae in C. ocellatus, suggesting that additional cryptic species may exist in this taxon. Our study illustrates the interaction of environmental variability and demographic processes in producing lineage diversification in an intertidal seaweed and highlights the importance of phylogeographic approaches for discovering cryptic marine biodiversity.Mec-15-0566 Archiving DataThis is a compressed file folder which includes five files. Of which three files contain sequences of 16 mtDNA haplotypes in Fasta format,and 33 nrDNA ribotypes in both Fasta and Mega format. The fourth file (table 1) contains the information of geographic locality, coordinates and collector for each sampling population. The fifth file (Table 2) indicates the geographic distribution of each mtDNA haplotype and nrDNA ribotypes in every sampling locality.Mec-15-0566 Archiving Tree filesThis compressed package contains mtDNA Cox1 and nrDNA ITS1+2 sequences with Fasta format, using for underlying phylogenetic construction.Mec-15-0566 Arching Data for each sample's mtDNA Cox1 and nuclear ITS1+2This is a compressed file which contains 452 aligned mitochondrial Cox1 sequences and 370 aligned nuclear ITS1+2 sequences for the red alga Chondrus ocellatus. For each sequence, we provide the identification information with sampling code (e.g. KJ) + specimen number + the name of marker