Range expansion and lineage admixture of the Japanese evergreen tree Machilus thunbergii in central Japan

We investigated the range expansion histories of Machilus thunbergii populations in the Kinki region of central Japan on the basis of nuclear microsatellite data. In the Kinki region, M. thunbergii is typically found in the coastal area, with some fragmented populations inland, around Lake Biwa. Phylogenetic and Bayesian clustering analysis (STRUCTURE analysis) revealed that the inland populations have different genetic components between the west and east sides of Lake Biwa. The population located on the north side of the lake has an admixture of the two genetically differentiated lineages, contributing to an increase in the genetic diversity of the population. Populations around Lake Biwa had lost rare alleles and the F value obtained from STRUCTURE analysis was lower in the coastal populations than in the lake populations. These results suggest that populations around Lake Biwa experienced a bottleneck due to a founder effect during the initial migration to the lake and that glacial refugia of M. thunbergii in the Kinki region existed along the coast.     

Geographic variation in the molecular,morphological and reproductive characters of the ayuPlecoglossus altivelis (plecoglossidae) in the Japan-Ryukyu Archipelago

In an attempt to clarify geographic variation in the ayuPlecoglossus altivelis, the molecular, morphological and reproductive characters of populations from various localities in the Japan-Ryukyu Archipelago were examined. An electrophoretic analysis of enzymes encoded by 18–28 loci and univariate and multivariate analyses of 12 meristic and 17 morphometric characters indicated that there are two distinct groups of ayu in the archipelago: that of the Japan Islands and that of the Ryukyu Islands. Within the Japan Islands group, a landlocked population of Lake Biwa was found to diverge somewhat from other amphidromous populations genetically and morphologically. The Lake Biwa population was noted as being by far the most fecund, departing from a north-south cline of fecundity observed in amphidromous populations. Though no virtual divergence was observed among amphidromous populations in the Japan Islands in molecular data, divergence among these populations was considerable in morphological and fecundity data. Differences in geographic variation patterns are attributed to qualitative differences inherent in molecular and organismal characters: organismal characters are responsive to selection and also directly altered by environmental influences in part but molecular characters are hardly so. The evolution of different characters may have proceeded at different rates among geographic populations of ayu.     

Clines revisited: The timing of pupping in the harbour seal (Phoca vitulina)

The regional variation in the pupping season of the harbour seal ( Phoca vitulina ) was reviewed using the birth periods reported for 65 colony sites distributed over a range from 30.4 to 78.5 North latitude. The birth timing of P. v. vitulina was not related to latitude, but birthing in P. v. concolor along eastern North America exhibited a latitudinal cline. The timing of birth in P. v. richardsi varied in three distinct patterns: (1) a significant unidirectional latitudinal cline extending between Baja California and the west coast of Washington; (2) a cluster comprised of Puget Sound, Washington and Vancouver Island, British Columbia colonies in which birthing occurred an average of 65 days later than on the Washington coast; and (3) a cluster from northern British Columbia and Alaska which did not demonstrate a latitudinal cline. Insufficient data were available for the analysis of P. v. mellonae or P. v. stejnegeri .
We found great regional variation in the timing of birth among all colonies, with mean birth dates occurring as early as 15 March and as late as 3 September. Little variation existed north of 50. To the south of 50, however, most of the variation could be attributed to correlation with latitude or to affiliation with the Puget Sound, Washington-Vancouver Island, British Columbia geographic area.
Clinal variation in pupping could result from: (1) geographic variations in a selective factor with perhaps gene exchange between contiguous populations playing a role in smoothing the variation; or (2) for populations between Mexico and the west coast of Washington, regional variation in a non-selective environmental variable, such as photoperiod.     

GEOGRAPHIC VARIATION WITHIN AN ISLAND: UNIVARIATE AND MULTIVARIATE CONTOURING OF SCALATION,SIZE, AND SHAPE OF THE LIZARD GALLOTIA GALLOTI

Microgeographic variation of the vegetarian lizard Gallotia galloti within the island of Tenerife is described using univariate analysis, correlation, multiple group principal component analysis, canonical analysis, transects, and contours. The size varies locally in a mosaic pattern while head shape shows a WNW–ESE cline in the south. The scalation (scale and femoral pore counts) has two facets to its geographic variation, both of which are incongruent with the primary variation in the size and shape. The scalation shows categorical variation (stepped cline) between northern and southern populations and also a strong clinal relationship with altitude. The possible causes of this variation are considered and adaptation to current ecological conditions appears to be implicated for at least the altitudinal variation, although the pertinent factors are not obvious. It is apparent that vertebrate populations distributed across small islands do not necessarily offer the advantage of a discrete homogeneous unit for evolutionary studies but can offer the opportunity for studying microgeographic variation.     

Long‐term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa,Japan

Lake Biwa is an ancient freshwater lake that was formed approximately 4 Mya and harbours many coastal plants that commonly inhabit the seashore. We used chloroplast DNA haplotype analysis using two spacer sequences and simple sequence repeat (SSR) analysis using eight nuclear microsatellite markers to detect genomic signatures indicating long‐term isolation of inland populations of Calystegia soldanella in Lake Biwa from coastal populations. We used 348 samples from 63 populations for haplotype analysis and 478 samples from 27 populations for SSR analysis covering the inland and coastal distribution of the species. We detected seven haplotypes, and the distribution pattern of these haplotypes was geographically highly structured between Lake Biwa and the coast. Nuclear SSR analysis also supported genetic differentiation between Lake Biwa and coastal populations (analyses of molecular variance, 43%), and the grouping of Lake Biwa and coastal populations by a Neighbour‐joining tree. In addition, genetic diversity of the inland populations (mean H_E = 0.153) was significantly lower than that of coastal populations (mean H_E = 0.328). These results suggested that inland populations at Lake Biwa have been isolated from coastal populations for a very long time. The inland populations most likely experienced a bottleneck effect, resulting in sufficient in situ genetic divergence to clearly distinguish them from coastal populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 51–66.     

Population Structure of Alaskan Shortraker Rockfish, Sebastes borealis, Inferred from Microsatellite Variation

Alaskan shortraker rockfish population structure was analyzed by examining allelic variation at eight microsatellite loci. Samples were collected along the continental shelf and upper slope from the south end of Baranof Island to the western Aleutian Islands, and collections were pooled into eight geographically distinct groups. An exact test of homogeneity indicated population structure (p < 0.0006) among groups. The proportion of the total variation that was attributable to divergence among populations (θ = 0.0014) was not statistically significant, and no evidence of a geographic cline of structure was detected. Finer scale analyses that compared adjacent collections indicated that the collection from the southern end of the range differed from all remaining collections at three loci. Structure related to geographic location was detected by partitioning the variation among populations. The size distributions of shortraker rockfish varied among collections from east to west. The size differences may reflect divergent oceanographic and biological factors acting on populations that have restricted migration and movement. Alternatively, if there is substantial movement accompanied by lengthy reverse migration to natal grounds, the size differences may be related to ages of cohorts that are differentially distributed along the Pacific Rim. Further biological information including size, age composition, and age of maturity data, as well as information on other life history characteristics will be required to explain shortraker rockfish population structure.     

Recent colonization by a coastal plant of inland habitats at an ancient freshwater lake,Lake Biwa: multilocus sequencing and a demographic history of Lathyrus japonicus (Fabaceae)

Ancient lakes have been recognized as “long‐term isolated islands” in terrestrial ecosystems. Lake Biwa, one of the few ancient lakes that formed around 4 million years ago, harbors many coastal species that commonly inhabit seashores. The beach pea, Lathyrus japonicus, is a typical coastal species of this freshwater lake, where morphological, physiological, and genetic differentiations have been reported between Biwa and coastal populations. Whether Biwa populations were isolated for long periods throughout Pleistocene climatic oscillations and subsequent range shifts is unclear. We assessed population genetic structure and demography of beach pea in this ancient freshwater lake using the sequences of eight nuclear loci. The results of STRUCTURE analyses showed evidence of admixture between Biwa and coastal populations, reflecting recent gene flow. The estimated demographic parameters implemented by the isolation with migration model (IM model) revealed a recent divergence (postglacial period) of Biwa populations, with some gene flow from Biwa to coastal populations. In addition, Biwa populations were significantly smaller in size than the ancestral or coastal populations. Our study suggests that a Holocene thermal maximum, when transgression could allow seeds from coastal plants to access Lake Biwa, was involved in the origin of the Biwa populations and their genetic divergence. Thus, coastal populations might have migrated to Lake Biwa relatively recently. Our study concluded that ancestral migrants in Lake Biwa were derived from small founding populations and accelerated genetic isolation of Biwa populations during short‐term isolation.     

Genetic differentiation of piscivorous chub (genus Opsariichthys) in Japan,Korea and Russia

A comparison of allozyme variation, restriction fragment length polymorphisms in the mitochondrial DNA and partial sequences of the ND II gene (496 bp) was made among two lacustrine populations of the piscivorous chub (Opsariichthys uncirostris uncirostris) in Japan, four fluvial populations in Korea, one lacustrine population in Russia and one specimen from the Amur River (O. u. amurensis). All analyses indicate that the Japanese populations of piscivorous chub are separable from the Asian mainland populations of Korea and Russia. The latter populations were further divided into the Korean and Russian fish. Although opinions are divided on the phylogenetic position of the population in Lake Mikata, Japan, which shows unique morphological traits intermediate between those of the population in Lake Biwa and the mainland populations, the current analysis indicates a closer relationship to the population in Lake Biwa.     

Mitochondrial DNA population structure of the white-spotted Charr (Salvelinus leucomaenis) in the Lake Biwa water system

A phylogeographic analysis of mitochondrial DNA sequences was performed in order to elucidate the origin, dispersal process, and genetic structure of white-spotted charr in the Lake Biwa water system. Two haplotypes were most common in the Lake Biwa water system, and were also common in the adjacent inlet rivers of the Sea of Japan. These results suggest that in the glacial periods of the Pleistocene, white-spotted charr dispersed into the northern inlet rivers of Lake Biwa from adjacent inlet rivers of the Sea of Japan by watershed exchanges, colonizing the whole of the Lake Biwa water system. Mitochondrial DNA diversity contrasted sharply between the western and eastern parts of the system, suggesting that the populations in the western part might be more reduced than those in the eastern part in relation to the smaller habitat size. The high overall FST estimate (0.50), together with pairwise comparisons of FST, indicated significant genetic divergence between populations due to isolation and small population size. Hierarchical analysis (AMOVA) also showed that genetic variation was more pronounced among regions (28.39%) and among populations within regions (47.24%) than within populations (24.37%). This suggests that each population in and around the Lake Biwa water system should be treated as a significant unit for conservation and management.     

The physical mechanism of cuticular color in Phelotrupes auratus (Coleoptera,Geotrupidae)

The physical mechanism of cuticular color in Phelotrupes auratus was investigated by polarized inspection, spectrophotometry and transmission electron microscopy (TEM). No color change was observed when viewed through either a right‐ or left‐handed circular polarizer. Further, under the incidence of linearly polarized light, the reflected intensity was markedly reduced when observed through a linear polarizer set with its optical axis perpendicular to that of the incident light. These results indicate that P. auratus does not possess any circularly polarizing reflectors. TEM observations revealed a total of ten or twelve thin layers (about 60–120 nm in thickness) of two types of material (electron‐dense and electron‐lucent) alternately stacked in the epicuticle. The thickness of the layers in the different color forms of the beetle corresponded to the peak wavelengths in the reflectance spectra, λmax(α), with thicker layers found in beetles exhibiting reflectance peaks at longer wavelengths and vice versa. Based on these findings, we concluded that all the cuticular color forms of P. auratus were not produced by a circularly polarizing reflector but by a simple multilayer reflector.     

Chromosomal and allelic variation in Drosophila americana: selective maintenance of a chromosomal cline.

Geographically structured genetic variation, as represented by clines and hybrid zones, offers unique opportunities to study adaptation and speciation in natural populations. A hybrid zone has been reported between Drosophila americana americana and Drosophila americana texana, two taxa that are distinguished solely by the arrangement of their X and 4th chromosomes. In this study, samples of D. americana were collected along a latitudinal transect across the inferred hybrid zone, and the frequency of the alternative chromosomal arrangements is reported. These data illustrate that the alternative chromosomal arrangements are distributed along a shallow cline over a broad geographic region, and that the frequency of the arrangements is tightly correlated with latitude. Allelic variants at 13 RFLP loci in three genes on chromosome 4 exhibit no evidence of association with the cline. Presence of a cline for the chromosomal arrangements, as well as a general absence of geographic structure for variation at these genes, is interpreted as evidence that natural selection is responsible for the maintenance of this chromosomal cline. Furthermore, these results demonstrate that taxonomic subdivision of D. americana is unwarranted, because it exists as a cohesive species that is segregating a chromosomal fusion.     

Genetic diversity and reproductive biology in Warea carteri (Brassicaceae), a narrowly endemic Florida scrub annual

Carter's mustard (Warea carteri) is an endangered, fire-stimulated annual endemic of the Lake Wales Ridge, Florida, USA. This species is characterized by seed banks and large fluctuations in plant numbers, with increases occurring in postdisturbance habitat. We investigated the mating system, patterns of isozyme variation, and effective population sizes of W. carteri to better understand its population biology and to comment on reserve designs and management proposals relevant to this species. Warea carteri is self-compatible and autogamous, and probably largely selfing. Measures of genetic variation in W. carteri were lower than values reported for species with similar ecological and life history traits (6.6% of loci polymorphic within populations, 1.87 alleles per polymorphic locus, and 0.026 and 0.018 expected and observed heterozygosity, respectively). The high average value for Nei's genetic identity (0.989) reflects the paucity of genetic diversity. Genetic variation within populations was not correlated with aboveground population size, effective population size estimates (N(e)), or recent disturbance history. Much of the diversity detected was found among populations (F(ST) = 0.304). A significant cline in allele frequencies at one locus and a significant negative correlation between geographic distance and Nei's genetic identity also point to spatial organization of genetic diversity. As a result we propose that reserve design should include the entire geographic range of W. carteri. We also recommend that the natural fire regime be mimicked.     

Biogeography of the Indonesian archipelago: mitochondrial DNA variation in the fruit bat, Eonycteris spelaea

The fruit bat, Eonycteris spelaea , occurs from India through the Philippines to the southeast limit of its distribution in the Lesser Sunda islands of Indonesia. Mitochondrial DNA (mtDNA) variation was examined in Indonesian E. spelaea island populations by amplification of the D-loop and digestion with restriction endonucleases. In addition, microgeographic variation was assessed by investigation of three cave populations within one island. A total of 24 genotypes, comprising two broad clades, was detected. The pattern of mtDNA variation reflects the colonization history of E. spelaea with estimates of haplotype and sequence diversity highest in the older western populations and lowest at the eastern periphery of the species' distribution. These findings may also be associated with an environmental cline from west to east. There is also evidence that genetic distance between populations reflects geographic relationships, especially historical connectedness, as measured by Pleistocene sea-crossing distances. At the microgeographic level, cave populations were heterogeneous and composed of diverse lineages suggesting restricted local interchange.     

中国栗疫病菌群体遗传结构的空间自相关性分析

应用空间自相关分析方法对中国栗疫病菌17个居群RAPD遗传变异的空间结构进行研究,以探讨栗疫病菌居群遗传变异的分布特征及其形成机制。结果表明：中国栗疫病菌居群缺乏空间结构,绝大多数RAPD位点变异为随机分布的空间模式,但部分位点表现出渐变、斑块和双向渐变的非随机分布模式,又显示了一定的空间结构。推测其形成原因可能是长距离的基因流、人类活动、地理隔离以及栗疫病菌本身的繁殖特性综合作用的结果,并依据部分位点呈单向渐变的模式推测西南地区为中国栗疫病菌的起源中心。     

A quantitative analysis of geographic color variation in two Geotrupes dung beetles

We conducted a quantitative analysis of geographic color variation in two species of dung beetles: Geotrupes auratus and G. laevistriatus. The reflectance of the dorsal surfaces was measured from 300 to 700 nm using a spectrophotometer. The reflectance curves for both beetles were bimodal; there were two distinct peaks, namely, the a peak, between 400 and 700 nm, and the beta peak at around 300 nm. A stepwise discriminant analysis indicated that geographic color variation in Geotrupes beetles was primarily characterized by a shift of the a peak. Using beetles from three locations, we compared the wavelength (nm) of the a peak (lambdamax(alpha)) and its reflectance intensity (R(a)) to investigate sex and population differences. Intraspecific geographic variation in coloration was effectively detected by discriminant analysis of spectral reflectance curves. Our results showed that G. auratus and G. laevistriatus had similar coloration within each sampling location. Our study also revealed hidden sex differences in R(a); R(a) of males were significantly higher than those of females in both species. Since the dorsal surface of the beetles shows remarkable color variation, and coloration can be assessed objectively using reflectance spectra, Geotrupes beetles may be good model organisms to investigate geographic color variation.     

Genetic diversity and population structure of white-spotted charr, Salvelinus leucomaenis, in the Lake Biwa water system inferred from AFLP analysis

The genetic variations—and the time dependence of such variations—of natural populations of the white-spotted charr ,Salvelinus leucomaenis, in the Lake Biwa water system as well as those of a hatchery-reared population were inferred from AFLP. Upon the application of principal coordinate analysis using 118 polymorphic AFLP fragments based on the Jaccard similarity index, specimens of each of six natural local populations from the inlet rivers of Lake Biwa grouped roughly together, suggesting that each local population was genetically differentiated. The hatchery-reared population was shown to be closely related to the local population in the Seri River, suggesting that the Seri River population originated from hatchery-reared charr due to extensive stocking. Furthermore, specimens of the Yasu River grouped in a somewhat different position from the other natural populations, agreeing well with its geographic distance from the other populations. The nucleotide diversities of six natural populations (Harihata River, Ishida River, two reaches of the Takatoki River, Ane River, and Yasu River) in 2002 or 2003 were relatively low (π = 0.067–0.146%) compared with that of the Seri River (0.278%) and the hatchery-reared charr (0.316%). The nucleotide diversity in the five local populations (Ishida River, two reaches of the Takatoki River, Ane River, and Yasu River) remained at a low level from 1994 to 2002/2003, but only the nucleotide diversity in the Harihata River actually decreased. From 1994 to 2002/2003, the nucleotide diversity in the Seri River remained at a higher level among the natural populations from 1994 to 2002/2003; it was enhanced by the artificial release of hatchery-reared charr before 1994. In order to conserve the genetic diversity of the white-spotted charr in the Lake Biwa water system, it is necessary to prevent the stocking of hatchery-reared charr in reaches where hatchery-reared charr have not previously been stocked.     

The ZZ/ZW sex-determining mechanism originated twice and independently during evolution of the frog, Rana rugosa

The Japanese frog, Rana rugosa, has two distinct sex chromosome types, XX/XY and ZZ/ZW. These two types are found in localized groups, separated geographically by a boundary area predicted to lie somewhere around Lake Biwa in central Japan. To determine this precise boundary, the heterogametic sex of 18 populations around Lake Biwa was examined by genotyping sex-linked genes. Phylogenetic relationships between the populations were also analyzed using mitochondrial 12S rRNA gene. Results showed that the Suzuka-Kii mountain range located east of Lake Biwa separated the XX/XY populations from the ZZ/ZW populations. Unexpectedly, from a phylogenetic perspective, the ZZ/ZW populations around Lake Biwa belonged not to the main ZW group but to the XY group. The authors propose that the ZZ/ZW populations around Lake Biwa diverged secondarily from the XX/XY group through a change of heterogametic sex, eventually forming a new group. This group was thus named the 'Neo-ZW group'. As the main ZW group inhabiting northwestern Japan is known to have a different male heterogametic origin, this finding shows that change of heterogametic sex from male to female may have occurred twice, and independently, during the frog speciation.     

The role of propagule pressure in the invasion success of bluegill sunfish, Lepomis macrochirus, in Japan

The bluegill sunfish, Lepomis macrochirus, is a widespread exotic species in Japan that is considered to have originated from 15 fish introduced from Guttenberg, Iowa, in 1960. Here, the genetic and phenotypic traits of Japanese populations were examined, together with 11 native populations of the USA using 10 microsatellite markers and six meristic traits. Phylogenetic analysis reconfirmed a single origin of Japanese populations, among which populations established in the 1960s were genetically close to Guttenberg population, keeping high genetic diversity comparable to the ancestral population. In contrast, genetic diversity of later-established populations significantly declined with genetic divergence from the ancestral population. Among the 1960s established populations, that from Lake Biwa showed a significant isolation-by-distance pattern with surrounding populations in which genetic bottlenecks increased with geographical distance from Lake Biwa. Although phenotypic divergence among populations was recognized in both neutral and adaptive traits, P(ST)-F(ST) comparisons showed that it is independent of neutral genetic divergence. Divergent selection was suggested in some populations from reservoirs with unstable habitats, while stabilizing selection was dominant. Accordingly, many Japanese populations of L. macrochirus appear to have derived from Lake Biwa population, expanding their distribution with population bottlenecks. Despite low propagule pressure, the invasion success of L. macrochirus is probably because of its drastic population growth in Lake Biwa shortly after its introduction, together with artificial transplantations. It not only enabled the avoidance of a loss in genetic diversity but also formed a major gene pool that supported local adaptation with high phenotypic plasticity.     

Occurrence of the endangered species Nitellopsis obtusa (Charales,Charophyceae) in western Japan and the genetic differences within and among Japanese populations

Nitellopsis obtusa (Charales, Charophyceae) are widely distributed from Europe to Asia; however, this species has been recorded in only the five lakes in central Honshu in Japan. This species was thought to be extinct in Japan, but was rediscovered in limited areas of Lake Kawaguchi in central Honshu. More recently, we discovered more Japanese populations of N. obtusa in Lake Biwa in western Honshu, and it became clear that the species had a broader distribution in Japan than originally believed. In addition, although only male or female thalli have been collected at each lake, both male and female thalli were found from Lake Biwa. This is the first report of a potentially sexual population of N. obtusa in Japan. The DNA sequences of three chloroplast DNA markers, including both coding and non‐coding regions, were identical in all specimens from Lake Kawaguchi and Lake Nojiri (Central Honshu), and differed from those of Lake Biwa and German specimens. Although Japanese and German specimens were genetically similar, Japanese specimens displayed considerable genetic diversity according to locality.     

Distribution of dissolved organic carbon and dissolved fulvic acid in mesotrophic Lake Biwa, Japan

The dissolved organic carbon (DOC) concentrations in mesotrophic Lake Biwa were determined by a total organic carbon (TOC) analyzer, and DOC molecular size distributions were determined by size exclusion chromatography (SEC) using a fluorescence detector at excitation/emission (Ex/Em) levels of 300/425 nm with the eluent at pH 9.7. The fluorescence wavelengths for detection were chosen from the result of excitation–emission matrix spectrometry (EEM) analysis for dissolved fulvic acid (DFA) extracted from Ado River (peak A, Ex/Em = 260–270/430–440 nm; peak B, Ex/Em = 300–310/420–430 nm). Ado River DFA was eluted with a retention time (RT) of 7.4–8.9 min and the apparent molecular weight was estimated at 22–87 kDa based on the elution curve for the spherical protein molecular weight standard. A DFA peak eluted at the same retention time as Ado River DFA also appeared in all the samples of Lake Biwa water. From the linear relationship between the peak areas with an RT of 7.4–8.9 min by SEC analysis and DOC values of DFA by TOC analysis of a series of DFA samples (r² = 0.9995), the concentrations of DFA in the lake water were roughly calculated. DFA was distributed within the range 0.25–0.43 mg C l⁻¹ and accounted for 15%–41% of DOC, with the highest ratios observed at a depth of 70 m in August and the lowest at 2.5 m in May.