Phylogeography of Quercus phillyraeoides (Fagaceae) in Japan as revealed by chloroplast DNA variation

Abstract

In order to elucidate the phylogeographical relationships and to find the past colonization routes of evergreen oak (Quercus phillyraeoides), we collected samples from 19 populations from the central to western part of Japan and examined chloroplast DNA sequence variation. We analyzed the genetic variation for four non-coding and one coding region and examined a total of 3,665 bp. Total nucleotide diversity (π) was 0.00017 ± 0.00001, and the scaled mutation rate (θw) was 0.00021 ± 0.00011. These values were relatively smaller than those formerly reported for Japanese deciduous oak species (Q. mongolica var. crispula). A total of five haplotypes, two of which included two subtypes (A1, A2, B, C, D1, D2, E), were identified, with types A1 and D2 the most frequent. A large degree of genetic differentiation had occurred across the populations (GST = 0.833 for haplotype data and FST = 0.858 for sequence data). The data suggested several possible refugia populations on the Pacific Ocean coast and the East China Sea coast, nearly identical to those previously suggested for the lucidophyllus forest refugia. We could not find any evidence showing that any part of the Seto Inland Sea populations could be possible refugia. Largest genetic differentiation across the populations in the Seto Inland Sea region suggests that these areas have been recently colonized following the last glacial maximum from the refugia in the Pacific coast or in southern Kyushu.