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The phylogeographic structure of Japanese coniferous species as revealed by genetic markers

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Abstract:

The phylogeography of Japanese conifers studied using polymorphic allozyme and organelle (chloroplast and mitochondrial) DNA markers is reviewed. Three Abies species showed a clear geographical cline based on mtDNA polymorphisms. Allozyme markers revealed a clear genetic cline in A. mariesii, with no mtDNA polymorphism. Refugia of these species during the last glaciation were probably located along the southwestern Pacific side of Japan. Based on allozyme analysis, Pinus pumila may have migrated from Siberia southward from Hokkaido to higher mountains in central Japan. Mitochondrial DNA polymorphisms clearly differentiated the pentaphylla and parviflora varieties of Pinus parviflora and suggest that refugia of the latter species were located south of the central mountains of Chubu district during the last glaciation. Current populations in the Chubu highlands, Tohoku, and Hokkaido presumably became established by colonization from these refugia. Phylogeographic analysis of Cryptomeria japonica using allozymes and DNA markers did not reveal distinct patterns. However, microsatellite analysis revealed highest allelic diversity in putative refugia of the last glaciation. Allozyme analysis of Chamaecyparis obtusa revealed a clear cline. Recently, substantial numbers of loci based on expressed sequence tags for population and genome mapping were developed. Cryptomeria japonica and Chamaecyparis obtusa belong to different families, but molecular phylogeny based on chloroplast sequence data revealed that they are closely related and that sequence tag site markers of C. japonica are highly applicable to C. obtusa. Using such markers, researchers have attempted to clarify the genetic structure of the two species. This paper also discusses the most successful approaches (to date) for elucidating the genetic structure of the above-mentioned species and other phylogeographic issues related to Japanese conifers.

Keywords: ALLOZYMES; CONIFERS; CPDNA; GLACIAL REFUGIA; MICROSATELLITES; MTDNA

Document Type: Research Article

Affiliations: Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan

Publication date: February 1, 2006

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