title: Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica.
abstract: OBJECTIVE
  Distribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM).
  
  
  METHODS
  Genetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis.
  
  
  RESULTS
  STRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia.
  
  
  CONCLUSIONS
  The combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis.
authors.affiliation: Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan.
authors.forename: Megumi K
authors.initials: MK
authors.lastname: Kimura
authors.affiliation: Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Uchiyama
authors.affiliation: Department of Forest Vegetation, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan.
authors.forename: Katsuhiro
authors.initials: K
authors.lastname: Nakao
authors.affiliation: Graduate School of Science and Technology, Niigata University, 8050, Igarashi 2-Nocho, Nishi-ku Niigata 950-2181, Japan.
authors.forename: Yoshinari
authors.initials: Y
authors.lastname: Moriguchi
authors.affiliation: Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan.
authors.forename: Lerma
authors.initials: L
authors.lastname: San Jose-Maldia
authors.affiliation: Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan ytsumu@ffpri.affrc.go.jp.
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Tsumura
mesh_terms: D032485:Cryptomeria / Q000235:genetics*; D017753:Ecosystem; D014644:Genetic Variation; D005828:Genetics, Population; D005843:Geography; D046448:Ice Cover; D007564:Japan; D011157:Population Dynamics; D025341:Principal Component Analysis; D011336:Probability
keywords: Approximate Bayesian computation; Cryptomeria japonica; Taxodiaceae; cryptic refugia; genetic divergence time estimation; last glacial maximum; microrefugia; species distribution modelling; sugi