Genetic variation and structure of Ubame oak (Quercus phillyraeoides A. Gray), a shrub tree on the Pacific coast of Japan, were examined to elucidate historical population dynamics using five chloroplast DNA (cpDNA) marker regions and 11 nuclear microsatellite loci. Three cpDNA haplotypes (A, B and C) were identified in a screen of 41 populations across the entire distribution range in Japan. Haplotype A was the most prevalent and was found in the entire range. Haplotype B was locally restricted to the Kii Peninsula, while haplotype C was restricted to the southwestern part of Japan. These haplotypes corresponded with the nuclear genetic constitution revealed by microsatellite markers. Two genetically differentiated major groups were identified by STRUCTURE analysis applied to 536 individuals from 28 populations, and they mostly corresponded with the two major cpDNA haplotypes, A and C. These populations were further divided into three geographically identified groups: group 1 in the area including Kanto and Tokai regions, the Kii Peninsula and the Muroto-misaki Cape on the Pacific coast; group 2 in the Bungo-suido Channel area; and group 3 in southern Kyushu and Okinawa. Populations in the Seto Inland Sea were divided into two groups: one was included in group 1 and appears to have originated from last glacial maximum (LGM) refugia located in the Kii Peninsula, while the other was included in group 2 and appears to have originated from LGM refugia located in southern Kyushu. These groups can be considered as conservation units for the preservation of unique seashore ecosystems, or as a seed source to foster coastal protection forests and next-generation production forests. Considerable care should be taken to protect isolated populations that may be specialized to unique local environments, such as those on the islands of Koshikijima and Izenajima.

对5种常见的丁香及2种新发现的金叶丁香叶绿体DNA的3个保守序列进行测序,共获得1 722 bp,发现多态性位点18个,atpB-rbcL区域的多态性位点最多,trnL-trnF区域次之.分析七种丁香的核苷酸多样性为0.004 72,每个位点的突变率为0.004 55.3个保守区域中,trnL-trnF区域的核苷酸多样性和突变率都高于其他2个区域,说明在这几种丁香中,trnL-trnF区域变异性最大,核酸多样性和突变率最高.

In order to investigate the historical expansion of common oaks (Quercus sect. Prinus) in the northeastern part of Japan, the relation between the chloroplast haplotypes (I and II) in Quercus mongolica var. crispula and the chloroplast types (T- and C-type) were examined. Complete linkage between haplotype II and chloroplast C-type was found. The chloroplasts examined in the oak species collected from Sakhalin and Primorski Krai, Russia, and Harbin, China were all T-type. This suggests that the T to C mutation had occurred in haplotype II in Japan. Neither of haplotype I nor haplotype II was found outside Japan, suggesting both occurred in Japan independently from an ancestral haplotype VI. Haplotype I, which has been known only in Mount Hayachine within Honshu, is distributed southward to the Kanto district, where refugia might have occurred during glaciations.

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.