Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual tree S ciadopitys verticillata ( C oniferales: S ciadopityaceae)

S ciadopitys verticillata is amongst the most relictual of all plants, being the last living member of an ancient conifer lineage, the S ciadopityaceae, and is distributed in small and disjunct populations in high rainfall regions of J apan. Although mega‐fossils indicate the persistence of the species within J apan through the P leistocene glacial–interglacial cycles, how the species withstood the colder and drier climates of the glacials is not well known. The present study utilized phylogeography and palaeodistribution modelling to test whether the species survived within pollen‐based coastal temperate forest glacial refugia or within previously unidentified refugia close to its current range. Sixteen chloroplast haplotypes were found that displayed significant geographical structuring. Unexpectedly, northern populations in central H onshu most distant from coastal refugia had the highest chloroplast diversity and were differentiated from the south, a legacy of glacial populations possibly in inland river valleys close to its current northern range. By contrast, populations near putative coastal refugia in southern J apan, harboured the lower chloroplast diversity and were dominated by a single haplotype. Fragment size polymorphism at a highly variable and homoplasious mononucleotide repeat region in the trn T ‐ trn L intergenic spacer reinforced the contrasting patterns of diversity observed between northern and southern populations. The divergent histories of northern and southern populations revealed in the present study will inform the management of this globally significant conifer. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society , 2012, 108 , 263–277.