The genetic structure of <Emphasis Type="Italic">Quercus crispula</Emphasis> in northeastern Japan as revealed by nuclear simple sequence repeat loci

Previous studies have reached different discussions about the genetic variation and genetic structure of Quercus crispula populations in northeastern Japan. This is a common oak species in Eastern Asia. Some studies have suggested that the populations in northeastern Japan were derived from those remaining in the southwest after the last glacial maximum (LGM), whilst other studies have found evidence that populations persisted in northeastern Japan during the LGM. Using seven highly polymorphic nuclear simple sequence repeat loci, we investigated the genetic structure of 16 Q. crispula populations along a latitudinal gradient in northeastern Japan (northern Honshu and Hokkaido), spanning about half of the species’ biogeographic range in the country. Although the level of population differentiation was low (F _ST = 0.021; G^￠_\textST G^{\prime}_{\text{ST}}  = 0.090), two geographically differentiated clusters were detected by STRUCTURE analysis. The first cluster included most of the populations in Hokkaido, and may indicate continued survival throughout past glacial periods. We found a significant decrease in allelic richness with latitude, so the second cluster may represent an expansion of the lineage from Honshu during the post-glacial period. These results should enhance our understanding of historical north–south migrations of this species in northeastern Japan.     

Lineage admixture during postglacial range expansion is responsible for the increased gene diversity of Kalopanax septemlobus in a recently colonised territory

We aimed to reveal the effects of range expansion and subsequent lineage admixture from separated glacial refugia on genetic diversity of Kalopanax septemlobus in Japan, by combining nuclear microsatellite data and ecological niche modelling. Allelic richness and gene diversity were compared at the population and regional level. We also statistically examined these indices as a function of population accessibility to the last glacial maximum (LGM) palaeodistribution reconstructed by ecological niche modelling to test a simple range expansion scenario from glacial refugia. Genetic diversity was highest in the populations of southern Japan and gradually decreased towards the north. However, an additional centre of genetic diversity, when measured as gene diversity, was found in northern Honshu Island, where distinct lineages were shown to be in contact. Positive effects of population accessibility to the LGM range were detected in both diversity indices at different spatial scales. The combined data support independent postglacial range expansions towards the north from the edge populations on the exposed coastal shelf of Pacific and Sea of Japan in northern Honshu during the LGM, which subsequently resulted in markedly low genetic diversity in the northernmost extant range, Hokkaido. The regional increase in gene diversity in northern Honshu is likely to be the result of postglacial lineage admixture. Relative difference in the spatial scales best relating population genetic diversity with the LGM distribution can be explained by a higher rate of allelic richness diversity loss during range expansions and stronger effects of lineage admixture on gene diversity.     

Phylogeography of a northeast Asian spruce, Picea jezoensis, inferred from genetic variation observed in organelle DNA markers

Range-wide genetic variation of the widespread cold-temperate spruce Picea jezoensis was studied throughout northeast Asia using maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA markers. This study assessed 33 natural populations including three varieties of the species in Japan, Russia, China, and South Korea. We depicted sharp suture zones in straits around Japan in the geographical distribution pattern of mitochondrial haplotypes (GST=0.901; NST=0.934). In contrast, we detected possible extensive pollen flow without seed flow across the straits around Japan during the past population history in the distribution pattern of chloroplast haplotypes (GST=0.233; NST=0.333). The analysis of isolation by distance of the species implied that by acting as a barrier for the movement of seeds and pollen, the sharp suture zones contributed considerably to the level of genetic differentiation between populations. Constructed networks of mitochondrial haplotypes allowed inference of the phylogeographical history of the species. We deduced that the disjunction with Kamchatka populations reflects range expansion and contraction to the north of the current distribution. Within Japan, we detected phylogeographically different types of P. jezoensis between Hokkaido and Honshu islands; P. jezoensis in Honshu Island may have colonized this region from the Asian continent via the Korean peninsula and the species in Hokkaido Island is likely to have spread from the Asian continent via Sakhalin through land bridges. Japanese endemism of mitochondrial haplotypes in Hokkaido and Honshu islands might have been promoted by separation of these islands from each other and from the Asian continent by the straits during the late Quaternary.     

Phylogeography and genetic structure of disjunct Salix arbutifolia populations in Japan

Disjunct geographic distributions of boreal plant species at the southern edges of their ranges are expected to result in low genetic diversity and high genetic differentiation in the disjunct populations. This prediction was tested in a riparian willow, Salix arbutifolia, distributed in the northeastern Eurasian continent and the Sakhalin, Hokkaido, and Honshu Islands, using chloroplast DNA haplotypes and nuclear microsatellite genotypes. Hokkaido and Honshu populations shared a chloroplast haplotype identical to a closely related species, S. cardiophylla. This haplotype was divergent from haplotypes in the Eurasian continent (Primorsky) and the Sakhalin Island. In the nuclear microsatellites, most Hokkaido populations were genetically closer to Primorsky populations than to Sakhalin populations in spite of the geographical vicinity between Sakhalin and Hokkaido. The unexpected genetic divergence between Sakhalin and Hokkaido implies a complicated history of migration and colonization. The most peripheral populations in Honshu had the lowest genetic diversity and were most differentiated from the others. Thus, low genetic diversity and high genetic differentiation at the range periphery suggest substantial effects of genetic drift on genetic structure in the disjunct populations of Salix arbutifolia at the southern edge of its range.     

Genetic structure of Japanese populations of an ambrosia beetle,Xylosandrus germanus (Curculionidae: Scolytinae)

We examined the genetic structures of 13 Japanese populations of an ambrosia beetle, Xylosandrus germanus (Curculionidae: Scolytinae), to understand the effects of geographical barriers on the colonization dynamics of this species. The genetic structure was studied using portions of the mitochondrial cytochrome oxidase I (COI) gene. A phylogenetic analysis revealed three distinct lineages (clades A, B and C) within X. germanus. Clade A contained 21 haplotypes from all 13 populations; whereas clade B contained eight haplotypes from Hokkaido (Sapporo and Furano), Iwate and Nagano populations; and clade C contained only a single a haplotype from the Hokkaido (Furano) population. In the analysis of molecular variance (amova ), the greatest amount of genetic variation was detected between populations in Hokkaido and those in Honshu and other southern islands. Between these two groups of populations, all the values of the coefficient of gene differentiation were significantly larger than zero, except for the Hokkaido (Sapporo) versus Nagano comparison. Our results confirm that for X. germanus, gene flow has been interrupted between Hokkaido and Honshu since the last glacial maximum.     

Further Analysis of Intraspecific Sequence Variation of Chloroplast DNA in Primula cuneifolia Ledeb. (Primulaceae): Implications for Biogeography of the Japanese Alpine Flora

Primula cuneifolia Ledeb. (Primulaceae), we analyzed intraspecific variation of the nucleotide sequences of non-coding regions of chloroplast DNA: the intergenic spacers between trnT (UGU) and the trnL (UAA) 5′exon, the trnL (UAA) 3′exon and trnF (GAA), and atpB and rbcL. In 20 populations of P. cuneifolia, 22 nucleotide substitutions and five insertions/deletions were inferred, and their genetic distances ranged from 0.001 to 0.008. Eight distinct haplotypes could be recognized and each haplotype was found to be geographically structured. Three major clades (the Northern, Hokkaido and Southern clades) were revealed in phylogenetic analyses of the haplotypes. The haplotypes of the Northern clade had a wider distribution area in the populations of Mt. Rausu and Rishiri Island of eastern and northern Hokkaido in Japan, northward to Unalaska Island in the Aleutians, and those of the Hokkaido clade were distributed in the populations of central Hokkaido and Mt. Iwaki of the northern Honshu in Japan; in addition, those of the Southern clade were observed only in the populations of the central Honshu. It was shown that the genetic diversifications of the Southern clade were higher than those of the Northern and Hokkaido clades. Furthermore, it was shown that the topology within the Southern clade was hierarchical, and the haplotypes of the Southern populations in the clade were derivative. From these results, we concluded that the cpDNA haplotypes of the three clades in P. cuneifolia arose and assumed the present distribution areas through several cycles of glacial advance and retreat in the Pleistocene. Received 24 June 1998/ Accepted in revised form 28 December 1998     

Biogeographical consequences of Cenozoic tectonic events within East Asian margins: a case study of Hynobius biogeography

Few studies have explored the role of Cenozoic tectonic evolution in shaping patterns and processes of extant animal distributions within East Asian margins. We select Hynobius salamanders (Amphibia: Hynobiidae) as a model to examine biogeographical consequences of Cenozoic tectonic events within East Asian margins. First, we use GenBank molecular data to reconstruct phylogenetic interrelationships of Hynobius by bayesian and maximum likelihood analyses. Second, we estimate the divergence time using the bayesian relaxed clock approach and infer dispersal/vicariance histories under the 'dispersal-extinction-cladogenesis' model. Finally, we test whether evolutionary history and biogeographical processes of Hynobius should coincide with the predictions of two major hypotheses (the 'vicariance'/'out of southwestern Japan' hypothesis). The resulting phylogeny confirmed Hynobius as a monophyletic group, which could be divided into nine major clades associated with six geographical areas. Our results show that: (1) the most recent common ancestor of Hynobius was distributed in southwestern Japan and Hokkaido Island, (2) a sister taxon relationship between Hynobius retardatus and all remaining species was the results of a vicariance event between Hokkaido Island and southwestern Japan in the Middle Eocene, (3) ancestral Hynobius in southwestern Japan dispersed into the Taiwan Island, central China, 'Korean Peninsula and northeastern China' as well as northeastern Honshu during the Late Eocene-Late Miocene. Our findings suggest that Cenozoic tectonic evolution plays an important role in shaping disjunctive distributions of extant Hynobius within East Asian margins.     

Multiple origins of Locusta migratoria (Orthoptera: Acrididae) in the Japanese Archipelago and the presence of two major clades in the world: evidence from a molecular approach

Phylogenetic relationships among migratory locust (Locusta migratoria) populations in different climatic regions were analysed by sequencing four mitochondrial DNA regions, with special reference to the origin of Japanese populations. The populations are clearly separated into two clades: one consists of individuals from temperate and cold‐temperate areas of Japan and the Chinese continent, and the other comprises those from subtropical islands of Japan, Hainan Island in China, Timol Leste, Australia, Ethiopia, France, and some individuals from Tsushima Island and Honshu of Japan. The divergence time between the two clades is estimated to be 0.86–1.89 Mya. The phylogenetic analysis revealed that Japanese L. migratoria populations were composed of individuals of six different origins: (1) Hokkaido populations possibly from the Russian continent; (2) Honshu–Kyushu populations from the Chinese continent; (3) Southwest Island populations from Hainan Island or adjacent areas; (4) Ogasawara populations that might have originated from Micronesia; (5) part of the Tsushima population that originated from somewhere in the Asian tropics; and (6) a possible relict population of ancient southern haplotypes that exists in western areas of northern Honshu. The Tsugaru Straits and Tokara Straits have acted as effective geographical barriers, as in other organisms, isolating locust populations for a few thousand years. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 570–581.     

Imprint of post-glacial history in a narrowly distributed endemic spruce, Picea alcoquiana, in central Japan observed in nuclear microsatellites and organelle DNA markers

Aim We aim to infer the post‐glacial history of the narrowly distributed endemic spruce Picea alcoquiana in Japan, and to assess the hypothesis that the existing narrow natural range of the species has resulted from the diminution of the past natural range since the last glacial period. Location Mountainous forests in central Honshu Island in Japan. Methods We assessed the geographical patterns of genetic variation across nine populations of P. alcoquiana across its natural range using five nuclear microsatellites and polymerase chain reaction–restriction fragment length polymorphism markers for chloroplast (cp) and mitochondrial (mt) DNA. This study focuses on the genetic differentiation between northern peripherally isolated and southern core populations within the natural range of the species in central Honshu. In addition, based on diagnostic morphological traits of the cone, we used reliable macrofossil evidence to gain further insight into the past natural range of the species. Results Picea alcoquiana shows a level of genetic differentiation among populations (Φ_ST = 0.082) that was higher than the levels observed in nuclear microsatellites for other anemophilous and widespread tree species in Japan. A notable finding for the nuclear microsatellites was the loss of rare alleles and strong evidence of a recent bottleneck in the peripherally isolated populations. Analysis of molecular variance in cpDNA and mtDNA markers showed an absence of genetic differentiation between the peripherally isolated and core populations. Macrofossil evidence indicated that the past natural range of the species extended to a lower elevation and c. 135 km north of the existing peripherally isolated populations during the last glacial period (c. 28,000 yr bp ). Main conclusions During the last glacial period, P. alcoquiana had a wider natural range in which the peripherally isolated and core populations could have been geographically continuous with each other, and effective gene flow by means of pollen and seeds might have occurred. The recent bottleneck and consequent loss of rare alleles in the peripherally isolated populations might have evolved during the diminution and retreat of the northern part of the past natural range southwards to the core area and during the subsequent separation of the peripherally isolated populations from the core area since the last glacial period.     

Management units of the endangered herb Primula sieboldii based on microsatellite variation among and within populations throughout Japan

To promote programs for the conservation and restoration of the endangered species Primula sieboldii, we examined genetic variation at eight microsatellite loci among and within 32 remnant wild populations throughout Japan. Total allelic diversity within a population was higher in larger populations, but not so after rarefaction adjustment. The positive relationship between population size and the inbreeding coefficient may suggest that more heterozygous genets tend to survive the habitat contraction possibly because of the higher fitness associated with heterozygosity. By principal coordinate analysis and Bayesian analysis, we detected four genetic groups (Hokkaido, northern Honshu, central Honshu, and western Japan), which could be recognized as management units of P. sieboldii. If supplementation with plants from other populations were planned, it should be conducted among populations which belong to the same management unit and which are likely to represent the same adaptive variation.     

Genetic structure of <Emphasis Type="Italic">Cerasus jamasakura</Emphasis>, a Japanese flowering cherry,revealed by nuclear SSRs: implications for conservation

The genetic resources of a particular species of flowering cherry, Cerasus jamasakura, have high conservation priority because of its cultural, ecological and economic value in Japan. Therefore, the genetic structures of 12 natural populations of C. jamasakura were assessed using ten nuclear SSR loci. The population differentiation was relatively low (F _ST, 0.043), reflecting long-distance dispersal of seeds by animals and historical human activities. However, a neighbor-joining tree derived from the acquired data, spatial analysis of molecular variance and STRUCTURE analysis revealed that the populations could be divided into two groups: one located on Kyusyu Island and one on Honshu Island. Genetic diversity parameters such as allelic richness and gene diversity were significantly lower in the Kyushu group than the Honshu group. Furthermore, STRUCTURE analysis revealed that the two lineages were admixed in the western part of Honshu Island. Thus, although the phylogeographical structure of the species and hybridization dynamics among related species need to be evaluated in detail using several marker systems, the Kyusyu Island and Honshu Island populations should be considered as different conservation units, and the islands should be regarded as distinct seed transfer zones for C. jamasakura, especially when rapid assessments are required.     

Genetic variations and phylogeography of the swallowtail butterfly Papilio machaon on the Japanese Islands

The swallowtail butterfly Papilio machaon Linnaeus, 1758 is widely distributed in the Holarctic region, including all of the main islands of Japan, as well as Sakhalin, and on other smaller islands south to Yakushima Island. The Japanese population is situated at the margin of the Eurasian distribution range of this species. It is morphologically different from other populations and has been classified as the subspecies hippocrates C. & R. Felder, 1864. The population of the Japanese Islands is considered to be genetically distinct from the continental populations in relation to the geographical history of the Japanese Islands. Therefore, we examined a part of the ND5 gene sequence of the mitochondrial DNA for P. machaon individuals of various localities in Japan and some nearby countries, and found 68 haplotypes in 400 individuals from the Japanese Islands and Sakhalin. A DNA polymorphism analysis revealed that the genetic structure of the Hokkaido population was significantly different from that of the southern populations on the main Japanese islands. These results imply that P. machaon expanded its range from the Amur region of Russia southward through Sakhalin to the Japanese Islands, and that the Tsugaru Strait between Hokkaido and Honshu may have subsequently limited their gene flow as a geographical barrier.     

Development of microsatellite markers for an extremely limited distributed rare diving beetle species,Acilius kishii,and a widely distributed species,Acilius japonicus (Coleoptera: Dytiscidae)

Acilius kishii Nakane, 1963 (Coleoptera: Dytiscidae) is an endangered diving beetle species distributed in only one location, Lake Yashaga‐Ike, Honshu Island, Japan. Acilius japonicus, which is related to A. kishii, is distributed widely in northern Honshu Island and Hokkaido Island in Japan. In this study, we identified 14 microsatellite loci for A. kishii and A. japonicus, including both polymorphic and monomorphic loci, using the next‐generation sequencing method. We observed that 5 and 10 loci showed polymorphisms in 31 and 32 individuals of A. kishii and A. japonicus, respectively. The observed and expected heterozygosities were 0.00–1.00 and 0.00–0.74, respectively. These microsatellite loci could be useful for future conservation genetic studies, including monitoring of genetic diversity and extinction risk of A. kishii.     

Ongoing localized extinctions of stream-dwelling white-spotted charr populations in small dammed-off habitats of Hokkaido Island,Japan

Habitat fragmentation caused by damming can greatly reduce the population viability of aquatic organisms, with smaller fragmented populations at higher risk of extinction due to increased demographic, genetic, and environmental stochasticity. However, empirical evidence demonstrating that smaller natural populations are more vulnerable to extinction is limited. We studied the vulnerability to extinction of white-spotted charr (Salvelinus leucomaenis) populations in 30 dammed-off streams in Oshima Peninsula, southwestern Hokkaido Island, Japan, by comparing the incidence of charr populations in streams between 1999 and 2014. Using electrofishing and environmental DNA surveys, we identified three localized extinctions, with the probability of extinction increasing with decreasing watershed area (our surrogate for habitat size). We also found a new population in one dammed-off stream in which white-spotted charr were previously unknown, after installation of a fish ladder, indicating the capacity of white-spotted charr to recolonize reconnected habitat in a short period. Our results suggest that localized extinction of white-spotted charr in small dammed-off streams is ongoing, but that appropriate fish migration corridors can reduce localized extinction risk and increase the probability of species persistence.

     

Allozyme Variation among Populations of Rana pirica (Amphibia: Anura)

Genetic variation of Rana pirica , an east Asian brown frog of the R. temporaria group, was elucidated by analysing 140 specimens from 11 populations from Hokkaido and Sakhalin, both locating near the eastern coasts of the Asian continent, and 12 specimens of R. ornativentris from Honshu, Japan mainland, as an outgroup, through horizontal starch gel electrophoresis. Rana pirica shows relatively low genetic differentiation, and high genetic affinities are found between Hokkaido and Sakhalin populations. Populations from these islands are morphologically somewhat differentiated but should be regarded as conspecific. Degree of genetic divergence among populations of amphibian species from Hokkaido, including R. pirica , is not so extensive as that reported for species from Japan mainland and relatively recent formation of amphibian fauna in Hokkaido is suggested.     

The historical differentiation process inHemerocallis middendorfii (Liliaceae) of Japan based on restriction site variations of chlorplast DNA

Chloroplast DNA restriction site variation inHemerocallis middendorfii Trautv. & Meyer was investigated to deduce the historical differentiation process that had taken place in populations among three districts Hokkaido, Honshu and the Island of Tobishima in Japan as distinct from the morphological data. The populations selected were eight in total, consisting of two populations from Honshu, one each from the Islands of Sado and Tobishima and four from Hokkaido. Twelve endonuclease restriction enzymes were used. Six restriction site mutations were found among the populations investigated. A single, most parsimonious phylogenetic tree is generated, and revealed that the four populations of Hokkaido and two populations of the Islands of Sado and Tobishima are monophyly, respectively.     

Different phylogeographic patterns in two Japanese Silpha species (Coleoptera: Silphidae) affected by climatic gradients and topography

To reveal differences in phylogeographic patterns of flightless insect species occurring in different regions of Japan, we studied the phylogeography and demographic history of Silpha beetles occurring in cool-temperate habitats of two major islands, Honshu and Hokkaido, using sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene. Honshu has a more mountainous topography, and cool-temperate habitats occur discontinuously, whereas Hokkaido, located to the north of Honshu, has more continuous cool-temperate habitats. A species endemic to Honshu, S. longicornis occurs on Honshu, whereas S. perforata occurs on Hokkaido and the East Asian continent. Our results indicate that the ancestors of S. longicornis colonized Honshu via a south-west route c . 0.7 Mya and the species has highly divergent populations in isolated mountainous areas of Honshu, whereas S. perforata colonized Hokkaido via a northern route less than 90 000 years ago and has less divergent geographic populations. During the last glacial period, S. perforata was probably restricted to refugia in southern Hokkaido and later expanded into northern Hokkaido, whereas S. longicornis populations existed in many isolated refugia, probably because of the complex topography of Honshu. Thus, our study demonstrates that, even between closely related species, interactions among biology, latitudinal climatic gradients and topography can produce different phylogeographic patterns.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 452–467.     

Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual tree Sciadopitys verticillata (Coniferales: Sciadopityaceae)

Sciadopitys verticillata is amongst the most relictual of all plants, being the last living member of an ancient conifer lineage, the Sciadopityaceae, and is distributed in small and disjunct populations in high rainfall regions of Japan. Although mega‐fossils indicate the persistence of the species within Japan through the Pleistocene 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 Honshu 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 Japan, 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 trnT‐trnL 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.     

Genetics of the Shimokita macaque population suggest an ancient bottleneck

The macaque population of the Shimokita Peninsula represents the northernmost distribution of this species and is isolated from other populations in the Tohoku region of Japan. A previous protein-based study revealed a high level of genetic variability in this population and considerable differentiation from other populations. In order to reassess the genetic features of the Shimokita macaques, we examined 11 autosomal microsatellite loci and three Y chromosomal microsatellite loci. We observed considerable differentiation from other Japanese populations of macaques, but in contrast to the previous results, we observed significantly lower genetic variability in this population. There was a weak indication of a population bottleneck, suggesting a decay over time from an excess of heterozygotes that might be expected in the initial stages of a bottleneck. This may indicate that an ancient bottleneck occurred during the warm period after the last glacial period rather than a recent bottleneck due to hunting in modern times. The frequencies of private alleles were exceptionally high in the Shimokita population, suggesting that the difference in variability as determined in various studies was due to accidental sampling of marker loci with low power to resolve genetic variations in the protein-based studies. The assessments of interpopulation differentiation as determined using autosomal and Y chromosomal markers were highly correlated, and using both types of markers the Shimokita population was found to be the most differentiated of the study populations, probably due to infrequent gene flow with surrounding populations.