Genetic diversity and differentiation of Daphnia galeata in the middle and lower reaches of the Yangtze River,China

Mitochondrial 16S rDNA and CO I gene were used as molecular markers for the analysis of the genetic diversity and differentiation of Daphnia galeata populations in nine water bodies in the middle and lower reaches of the Yangtze River. In the combined 16S rDNA and CO I gene sequences, 54 variable sites and 44 haplotypes were observed among 219 individuals belonging to nine D. galeata populations. Average haplotype diversity and nucleotide diversity were, respectively, 0.72% and 0.56%. The F‐statistics (F_ST) value of the D. galeata populations was 0.149. According to the results of the neutral test, D. galeata in the middle and lower reaches of the Yangtze River had experienced a bottleneck effect in the history. Molecular variance analysis indicated that the genetic differentiation of the D. galeata populations mainly occurred within populations (85.09%). Greater genetic differentiations of D. galeata among individuals within populations appeared in the populations from the Huaihe River basin, whereas smaller genetic differentiations occurred in the populations from the middle reaches of the Yangtze River. Strong gene flows were all observed between Group I (four populations from the middle reaches of the Yangtze River) and Group ΙΙ (three populations from the middle and lower reaches of the Yangtze River), and Group ΙΙΙ (two populations from the Huaihe River basin). The effective migration rates (M) were 851.49 from Group I to Group ΙΙ and 685.96 from Group I to Group ΙΙΙ, respectively. However, no significant relationship was observed between the genetic differentiation and geographical distance of the nine populations (r = .137, p > .05). Results suggested that the genetic differentiation of D. galeata in the water bodies in the middle and lower reaches of the Yangtze River resulted mainly from geographical isolation.     

Bioclimatic regions influence genetic structure of four Jordanian Stipa species

Strong environmental gradients can affect the genetic structure of plant populations, but little is known as to whether closely related species respond similarly or idiosyncratically to ecogeographic variation. We analysed the extent to which gradients in temperature and rainfall shape the genetic structure of four Stipa species in four bioclimatic regions in Jordan. Genetic diversity, differentiation and structure of Stipa species were investigated using amplified fragment length polymorphism (AFLP) molecular markers. For each of the four study species, we sampled 120 individuals from ten populations situated in distinct bioclimatic regions and assessed the degree of genetic diversity and genetic differentiation within and among populations. The widespread ruderals Stipa capensis and S. parviflora had higher genetic diversity than the geographically restricted semi‐desert species S. arabica and S. lagascae. In three of the four species, genetic diversity strongly decreased with precipitation, while genetic diversity increased with temperature in S. capensis. Most genetic diversity resided among populations in the semi‐desert species (Φ_ST = 0.572/0.595 in S. arabica/lagascae) but within populations in the ruderal species (Φ_ST = 0.355/0.387 S. capensis/parviflora). Principal coordinate analysis ( PCoA) and STRUCTURE analysis showed that Stipa populations of all species clustered ecogeographically. A genome scan revealed that divergent selection at particular AFLP loci contributed to genetic differentiation. Irrespective of their different life histories, Stipa species responded similarly to the bioclimatic gradient in Jordan. We conclude that, in addition to predominant random processes, steep climatic gradients might shape the genetic structure of plant populations.     

A comparison of genetic structuring of Yellowcheek Darters (Etheostoma moorei) using AFLPs and allozymes

The goals of this study were to characterize the genetic structure of 6 populations of Etheostoma moorei (Yellowcheek Darter), endemic to the Little Red River watershed of central Arkansas, to estimate the levels of gene flow within isolated streams, and to compare AFLP genetic diversity and distance data to our previously published allozyme data. The Yellowcheek Darter is a candidate species for listing under the Endangered Species Act. This darter is found in previously connected headwater streams presently isolated and partially inundated downstream by Greers Ferry Reservoir. AFLP data for the Yellowcheek Darter was concordant with previous work utilizing allozymes (r_s = 0.682; p < 0.01), yet genetic differences among populations were greater in magnitude. Genetic diversity (polymorphism = 92.7; heterozygosity = 0.496) is higher for the Yellowcheek Darter than would be expected for a species in decline, and greater for AFLP versus allozyme data. Genetic structuring among streams was also more evident using AFLP data. Gene flow levels are indicative of a metapopulation structure within streams (F_ST = 0.003 − 0.010), with genetic structuring indicating distinct populations among streams.     

Mitochondrial DNA analysis reveals hidden genetic diversity in captive populations of the threatened American crocodile (Crocodylus acutus) in Colombia

Identification of units within species worthy of separate management consideration is an important area within conservation. Mitochondrial DNA (mtDNA) surveys can potentially contribute to this by identifying phylogenetic and population structure below the species level. The American crocodile (Crocodylus acutus) is broadly distributed throughout the Neotropics. Its numbers have been reduced severely with the species threatened throughout much of its distribution. In Colombia, the release of individuals from commercial captive populations has emerged as a possible conservation strategy that could contribute to species recovery. However, no studies have addressed levels of genetic differentiation or diversity within C. acutus in Colombia, thus complicating conservation and management decisions. Here, sequence variation was studied in mtDNA cytochrome b and cytochrome oxidase I gene sequences in three Colombian captive populations of C. acutus. Two distinct lineages were identified: C. acutus‐I, corresponding to haplotypes from Colombia and closely related Central American haplotypes; and C. acutus‐II, corresponding to all remaining haplotypes from Colombia. Comparison with findings from other studies indicates the presence of a single “northern” lineage (corresponding to C. acutus‐I) distributed from North America (southern Florida), through Central America and into northern South America. The absence of C. acutus‐II haplotypes from North and Central America indicates that the C. acutus‐II lineage probably represents a separate South American lineage. There appears to be sufficient divergence between lineages to suggest that they could represent two distinct evolutionary units. We suggest that this differentiation needs to be recognized for conservation purposes because it clearly contributes to the overall genetic diversity of the species. All Colombian captive populations included in this study contained a mixture of representatives of both lineages. As such, we recommend against the use of captive‐bred individuals for conservation strategies until further genetic information is available.     

Aggressiveness and Genetic Diversity of Hemileia vastatrix During an Epidemic in Colombia

Since 2008, Colombia has been experiencing an epidemic of the coffee rust Hemileia vastatrix. The altitude range of the disease has expanded, and nursery and young plants that were usually not attacked by the disease are now significantly affected. To determine whether this new epidemic has been caused by a new pathogenic isolate, the molecular diversity of the pathogen causing the epidemic in different regions of the country was assessed, using AFLP molecular markers on isolates collected from coffee fields prior and after the year 2008. We also evaluated the aggressiveness of isolates collected from diverse coffee‐producing areas and from different coffee genotypes. Isolates collected before and during the present epidemic were quite similar both genetically and with regard to their aggressiveness. Out of a total of 349 fragments amplified from 6 AFLP primer combinations, 48 (13.2%) were polymorphic and only 18 were unique among H. vastatrix isolates representative of pre‐2008 and post‐2008 epidemic populations. We conclude that the epidemic was caused by the excessive rainfall that has occurred in Colombia since 2006 and that extended to 2011 and not by the arrival of a new isolate of the pathogen or a change in virulence of the species present in the country.     

Genetic insights into the historical distribution of <Emphasis Type="Italic">Polylepis pauta</Emphasis> (Rosaceae) in the northeastern Cordillera Oriental of Ecuador

Scattered patches of Polylepis forest that occur within the 3,000–4,500 m altitudinal belt of the Andean Cordillera from Venezuela to Argentina have been hypothesized to be remnants of once continuous forests whose range became fragmented through anthropogenic activities that probably preceded the Spanish conquest. Allozyme variation of Polylepis pauta from 12 forest populations in three adjacent watersheds in Northeastern Ecuador was investigated to assess whether observed patterns of gene diversity were consistent with a more continuous historical range of the species and to evaluate the populations’ potential for restoration. Genetic diversity and polymorphism in P. pauta populations were higher than mean values for most wind pollinated and dispersed temperate and tropical tree species with regional distributions. Genetic differentiation among watersheds was lower than among populations within each watershed. Isolation by distance was not evident and several populations from different watersheds were more genetically similar than populations from the same watershed. Larger forest patches with broader altitudinal ranges had more alleles. Forest patches on steeper slopes and at higher elevations supported populations with less genetic diversity; this might have resulted from the predominance of vegetative reproduction in these landslide prone areas. The amount of genetic diversity maintained by P. pauta, coupled with low genetic differentiation among populations within and among watersheds, is consistent with a more continuous historical range of the species in Northeastern Ecuador and point to the Oyacachi basin as having the highest levels of genetic diversity.     

Genetic variation and conservation assessment of Chinese populations of Magnolia cathcartii (Magnoliaceae), a rare evergreen tree from the South-Central China hotspot in the Eastern Himalayas

Nine natural populations of the rare evergreen tree Magnolia cathcartii (Magnoliaceae) were sampled across its natural range, and amplified fragment length polymorphism (AFLP) markers were used to assess genetic variation within and among populations. Three ex situ populations were also surveyed to determine whether conservation plantings include the entire genetic diversity of the species. Genetic diversity within the natural populations was very low (0.122 for Nei’s gene diversity), and the southeast populations had the highest diversity. The ex situ populations had a lower diversity than the mean diversity for all populations, and none of the ex situ populations reached the levels of diversity found in their source populations. Genetic differentiation was high among natural populations (G _st = 0.247), and an isolation-by-distance pattern was detected. Habitat fragmentation, restricted gene flow, and geitonogamy are proposed to be the primary reasons for the low genetic diversity and high genetic differentiation. More protection is needed, especially for the southeast populations, which possess the highest numbers of unique alleles according to AFLP fragment analyses. The ex situ program was a good first step towards preserving this species, but the current ex situ populations preserve only a limited portion of its genetic diversity. Future ex situ efforts should focus on enhancing the plantings with individuals from southeastern Yunnan.     

The genetic characteristics of invasive Largemouth Bass in southern Brazil

Largemouth Bass (Micropterus salmoides) have been introduced on a global scale for sport fishing but represent a conservation concern given their documented negative impacts on native faunal diversity and abundance. Recent research using molecular data to characterize invasive Largemouth Bass populations elsewhere has demonstrated that populations are typically characterized by limited genetic diversity, or represent a combination of Largemouth Bass and Florida Bass (Micropterus floridanus). To test whether these traits were consistent with invasive populations in Brazil, we generated mitochondrial sequence data from four established populations of Largemouth Bass collected in southern Brazil as well as a local aquaculture facility to confirm species identity and quantify levels of genetic diversity. We identified the exclusive presence of Largemouth Bass in the region and observed limited levels of haplotype (haplotype diversity = 0.0684, SE = 0.038) and nucleotide diversity (0.0003, SE = 0.0002) which suggested the presence of a founder effect associated with introduction. Each of the four populations were dominated by a single haplotype that was identical to one recovered from a nearby aquaculture facility, which identified this facility as a potential introduction source.     

Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation

Brachyplatystoma platynemum is a catfish species widely distributed in the Amazon basin. Despite being considered of little commercial interest, the decline in other fish populations has contributed to the increase in the catches of this species. The structure, population genetic variability, and evolutionary process that have driven the diversification of this species are presently unknown. Considering that, in order to better understand the genetic structure of this species, we analyzed individuals from seven locations of the Amazon basin using eight molecular markers: control region and cytochrome b mtDNA sequences, and a set of six nuclear microsatellite loci. The results show high levels of haplotype diversity and point to the occurrence of two structured populations (Amazon River and the Madeira River) with high values for F_ST. Divergence time estimates based on mtDNA indicated that these populations diverged about 1.0 Mya (0.2–2.5 Mya 95% HPD) using cytochrome b and 1.4 Mya (0.2–2.7 Mya 95% HPD) using control region. During that time, the influence of climate changes and hydrological events such as sea level oscillations and drainage isolation as a result of geological processes in the Pleistocene may have contributed to the current structure of B. platynemum populations, as well as of differences in water chemistry in Madeira River. The strong genetic structure and the time of genetic divergence estimated for the groups may indicate the existence of strong structure populations of B. platynemum in the Amazon basin.     

Genetic diversity,population structure,and traditional culture of Camellia reticulata

Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio‐economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi‐structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material (n = 190 individuals) from five populations at study sites using single‐dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species (H_sp = 0.3397, I_sp = 0.5236) and population (percentage of polymorphic loci = 85.63%, H_pop = 0.2937, I_pop = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio‐economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.     

No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola,Violaceae)

• Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations.
• For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH‐psbA.
• Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species‐specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among‐population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana.
• The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana.

     

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.     

Genetic diversity and population structure of a cyprinid fish (Ancherythroculter nigrocauda) in a highly fragmented river

In this study, samples of Ancherythroculter nigrocauda, an endemic fish in the upper Yangtze River, were collected above and below dams in the Longxi River, a tributary of the upper Yangtze River, China, to investigate the genetic impacts of dams. The mitochondrial cytochrome b gene (cyt b) and 13 microsatellite (SSR) loci were used to analyze whether dams have resulted in loss of genetic diversity of the two fragmented populations or caused genetic differentiation between them. The results showed that the haplotype diversity (0.488; 0.486), nucleotide diversity (0.084%; 0.082%) and average expected heterozygosity (0.652; 0.676) of the two populations were all at a low level, and recent bottlenecks were detected. However, there was no genetic differentiation detected by the low genetic differentiation index (F_st, cyt b: ?0.1677, p = 0.99707; SSR: 0.00259, p = 0.81427). Besides, 11 pairs of half‐sibling relationship were found between the two populations indicating that there were individual movements and gene flow between them. This could be the larvae moving from upstream to downstream when water spilled over dams in flooding season. Therefore, our analysis showed that the dams have caused a loss of genetic diversity of the populations of A. nigrocauda in the Longxi River, blocked the active upstream movement but allowing passive downstream drift of larvae.     

Bat assemblage structure in two dry forests of Colombia: Composition, species richness, and relative abundance

We studied the composition, species richness, and relative abundance of bat assemblages in the Colombian dry forests of Chicamocha and Patía. In Chicamocha, 11 bats of the family Phyllostomidae were captured with mist-nets, corresponding to 85–100% of the potential phyllostomids species in the area. Two bats of the family Vespertilionidae were also captured in Chicamocha. In Patía, 12 species were captured with mist-nets, all Phyllostomidae, representing 72–100% of the estimated total number of species in the zone. Minor differences in number of species and composition were detected among sampling periods in Chicamocha. The most common species in this dry forest were Glossophaga longirostris and Sturnira lilium. In Patía, notable differences in the number of species and composition were observed among sampling periods, and the most common species were Artibeus jamaicensis, Carollia perspicillata and Phyllostomus discolor. Arid-zone dwelling bats were absent in Patía and we suggest that this absence may be associated with the isolation of Patía from other northern dry zones of Colombia since Quaternary times. There was also low abundance of bats in Patía, which appears to be related to human disturbance. The most abundant phyllostomid bat species in the two dry forests studied are those that include fruit and/or nectar-pollen from columnar cacti as an important proportion of their diets.     

Rapid genetic divergence in response to 15 years of simulated climate change

Genetic diversity may play an important role in allowing individual species to resist climate change, by permitting evolutionary responses. Our understanding of the potential for such responses to climate change remains limited, and very few experimental tests have been carried out within intact ecosystems. Here, we use amplified fragment length polymorphism (AFLP) data to assess genetic divergence and test for signatures of evolutionary change driven by long‐term simulated climate change applied to natural grassland at Buxton Climate Change Impacts Laboratory (BCCIL). Experimental climate treatments were applied to grassland plots for 15 years using a replicated and spatially blocked design and included warming, drought and precipitation treatments. We detected significant genetic differentiation between climate change treatments and control plots in two coexisting perennial plant study species (Festuca ovina and Plantago lanceolata). Outlier analyses revealed a consistent signature of selection associated with experimental climate treatments at individual AFLP loci in P. lanceolata, but not in F. ovina. Average background differentiation at putatively neutral AFLP loci was close to zero, and genomewide genetic structure was associated neither with species abundance changes (demography) nor with plant community‐level responses to long‐term climate treatments. Our results demonstrate genetic divergence in response to a suite of climatic environments in reproductively mature populations of two perennial plant species and are consistent with an evolutionary response to climatic selection in P. lanceolata. These genetic changes have occurred in parallel with impacts on plant community structure and may have contributed to the persistence of individual species through 15 years of simulated climate change at BCCIL.     

Genetic variation within the endangered mangrove species Sonneratia paracaseolaris (Sonneratiaceae) in China detected by inter-simple sequence repeats analysis

Sonneratia paracaseolaris, is a critically endangered mangrove species in China. Using inter-simple sequence repeats (ISSR) markers, we compared the genetic variation of introduced populations with that of natural populations to check whether the genetic diversity has been conserved. At the species level, genetic diversity was relatively high (P = 81.37%, He = 0.2241, and SI = 0.3501). Genetic variation in introduced populations (P = 75.78%, He = 0.2291, and SI = 0.3500) was more than that in natural populations (P = 70.81%, He = 0.1903, and SI = 0.2980). Based on Nei's G_ST value, more genetic differentiation among natural populations was detected (G_ST = 0.3591). Our data show that the genetic diversity of S. paracaseolaris was conserved in introduced populations to some extent, however, owing to the small natural populations and the threats they encountered, more plants should be planted to enlarge and restore the populations.     

The genetic diversity and spatial genetic structure of the Corso‐Sardinian endemic Ferula arrigonii Bocchieri (Apiaceae)

Corsica and Sardinia represent major hotspots of plant diversity in the Mediterranean area and are priority regions for conservation due to their high number of endemic plant species. However, information supporting human decision‐making on the conservation of these species is still scarce, especially at the genetic level. In this work, the first assessment is reported of the species‐wide spatial genetic structure and diversity of Ferula arrigonii Bocchieri, a Corso‐Sardinian endemic located in a few coastal sites and on small islands. Nine populations covering the entire natural range of the species were investigated by means of AFLP (amplified fragment length polymorphism) markers. Results indicate that this species is characterised by high levels of genetic polymorphism (92% polymorphic fragments) and of genetic diversity (H_w = 0.317) and by relatively low differentiation among populations (F_st = 0.057). PCoA, Bayesian analysis and neighbour‐joining clustering were also employed to investigate the genetic structure of this species. Three genetically distinct groups were detected, although with considerable overlap between populations.     

Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus F_ST = 0.32, F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) and F_IS increased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

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.