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Coldwater‐adapted freshwater fishes, especially their populations along warm‐range margins, are most vulnerable to the climate oscillations associated with global warming. Stocking is a major strategy for avoiding the extinction of these species. However, while stocking can reverse the decline of isolated populations, it may also result in a loss of genetic diversity in the native local population due to the introgressive replacement of hatchery genes. To plan an adequate strategy for conserving locally adapted populations, the genetic impacts of stocking on native lineages should be evaluated from small river branches to wide‐ranging drainage areas. We investigated the population genetic structure of white‐spotted charr (Salvelinus leucomaenis) within its southern range (Lake Biwa basin, Japan). By applying genome‐wide SNP analysis to the population's genetic structure, we assessed the extent of genetic introgression resulting from stocking. White‐spotted charr in the Lake Biwa watershed constitutes a distinctive genetic group, within which apparent genetic differentiation was observed. The hatchery‐reared fish line commonly used for supplementation stocking in the catchment was discernable from the native population, enabling us to analyze genetic introgression across the entire drainage area. Admixed individuals resulting from hatchery introgression were observed in most of the stocked sites that showed relatively high heterozygosity and nucleotide diversity. However, their genetic differentiation was much lower than that of native populations. The supplementation history as well as the road availability contributed substantially to the introgression of hatchery genes. Populations with the native genetic structure remained in the upstream regions of the tested rivers. However, their heterozygosity and nucleotide diversity were low when compared with that of the populations with hatchery supplementation. Our results shed light on the genetic impacts of stocking on isolated native populations and suggest that conventional supplementation methods cannot preserve a unique biodiversity in the distribution margin. [ABSTRACT FROM AUTHOR]

Estimating the role of specific processes in the spread of alien species necessitates the determination of introduction pathways and source populations of invaded areas. Alien grasses in the genus Lolium that have extensively invaded Japan provide a unique opportunity to estimate the expansion process through direct comparison between source and naturalised populations because the introduction pathways, contaminants in grain commodities and commercial cultivars for fodder crops or revegetation materials are well‐known. Therefore, by directly comparing source and naturalised populations, we estimated the introduction pathways and whether adaptative evolution occurred in Lolium species on sandy coasts in Japan.Lolium individuals sampled from naturalised populations in croplands, seaports, and sandy coasts were compared with those from two introduction sources for morphological and genetic variations based on a genome‐wide single nucleotide polymorphism analysis and a common garden experiment. Furthermore, we conducted a reciprocal transplant experiment between cropland and sandy coast.Populations naturalised in croplands were closely related to the cultivars, whereas those naturalised in seaports and sandy coasts were associated with contaminants. These results indicate that the cropland and sandy coast populations are derived from cultivars and contaminants, respectively. In addition, asymmetric gene flow from cropland populations to sandy coast populations was observed. The reciprocal transplant experiment clearly demonstrated the home site advantage; populations derived from croplands yielded higher floret numbers than those derived from other habitats at the cropland site; sandy coast populations had higher survival rates than those from croplands at the coastal site. Port populations exhibited a similar tendency as sandy coast populations, indicating that contaminants may be originally adapted to salty and dry environments, such as that in sandy coasts. The flowering phenology in the sandy coast populations evolved in the late flowering; therefore, late flowering alleles may have been transferred from cropland populations to sandy coast populations.Synthesis. We demonstrated that two congeneric species with different ecological characteristics were introduced through multiple introduction pathways and spread across different habitats. A direct comparison between source and naturalised populations can considerably elucidate the patterns and processes of biological invasions. [ABSTRACT FROM AUTHOR]

Aim: River system rearrangements such as stream capture play a crucial role in determining range expansion and gene flow of stream organisms between different watersheds. However, it is challenging to clarify the role of stream capture in dynamic landscapes where frequent connections and disconnections occur in stream networks. We hypothesized that fine‐scale sampling with genome‐wide analysis could reveal the effect of stream capture on the range expansion of stream fish and detect unidentified river rearrangement of headwater streams in a highly heterogeneous landscape. Location: Honshu Island, Japan. Taxon: Salvelinus leucomaenis. Methods: To identify stream capture events from biological evidence, a sampling strategy was designed with fish collected from multiple pairs of adjacent headwater streams. This included a 'typical site' where the occurrence of a stream capture event has been confirmed with geological evidence. The genetic population structure was analysed using genome‐wide single nucleotide polymorphism (SNP) data using MIG‐seq, followed by a Bayesian clustering approach. Results: Evidence was found for historical dispersal across watersheds, including a typical stream capture site. This cross‐drainage dispersal promoted gene flow among the three genetic groups of focal fish inhabiting western Honshu Island. The likelihood of past stream capture increased substantially when the inter‐headwater distance was less than 2000 m, or the altitudinal difference was less than 200 m in the current topography. Main Conclusions: In highly dynamic areas, such as the study site, which is surrounded by active faults, stream capture may be frequent, and aids inter‐drainage dispersal of freshwater organisms, where large‐scale range expansions would otherwise be impossible. Systematic pairwise headwater sampling, together with genome‐wide SNP analysis, provides biological evidence for the history of water system rearrangements and enables the identification of geological events. [ABSTRACT FROM AUTHOR]

Although revegetation activities are often accompanied by extensive release of translocated or cultivated individuals into natural communities, their potential effects on native populations are relatively unclear. Understanding the original genetic structures in natural habitats and how the patterns have been maintained in populations at revegetation sites is a critical first step in assessing current revegetation efforts. Artemisia indica var. maximowiczii is a native species commonly used for revegetation in Japan. We assessed the genetic and morphological variations in individuals collected from natural habitats and revegetation sites across Japan, as well as individuals have grown from two types of commercial seeds from China used for revegetation: imported seeds that originated from Chinese populations and reimported seeds that originated from Japanese populations but were cultivated in China. Genome‐wide single nucleotide polymorphism (SNP) data revealed that individuals collected from natural habitats were genetically differentiated between northeastern and southwestern regions in Japan. Individuals grown from the reimported seeds were genetically similar to the northeastern populations in Japan, suggesting their original sources were areas in the northeast. Most individuals collected from revegetation sites were genetically similar to individuals from the reimported seeds, even though the revegetation sites were in southwestern Japan, suggesting that seeds derived from the northeastern populations were used for revegetation throughout Japan. Individuals grown from the imported seeds that originated from China were genetically and morphologically differentiated from native individuals in Japan. Careful consideration should be given to the extensive use of non‐local seeds for revegetation that is sourced only from northeastern Japan or foreign countries. [ABSTRACT FROM AUTHOR]

Miscanthus sinensis Andersson is a dominant perennial grass in East Asia, where it is a pioneer species in disturbed habitats. To obtain basic information about the genetic structure of this pioneer species, we investigated chloroplast DNA (cpDNA) variation in M. sinensis within and among native populations across Japan. We detected nine haplotypes in 636 individuals from 30 populations. Two distinct haplotypes had a wide geographical distribution and coexisted within most of the populations. The degree of genetic differentiation among the populations was relatively low. Two putative ancestral lineages were distributed in the Ryukyu Islands. Therefore, it is possible that lineages that originated in subtropical areas of mainland China migrated into the Ryukyu Islands via Taiwan. Another possible migration route is the Korean Peninsula. Two major haplotypes may have migrated from the Eurasian continent to the northern coast in Kyushu via the Korean Peninsula and then expanded throughout Japan. There was no clear genetic boundary among the populations north of Kyushu. The enhanced immigration ability and high rate of gene flow of Miscanthus may have modulated the genetic structure created during previous glacial periods. Alternatively, the shortage of unique haplotypes north of Kyushu may indicate the recent expansion of this species to northern Japan. Key words: genetic structure, haplotype distribution, Miscanthus sinensis, pioneer plant, silver grass. Le Miscanthus sinensis Andersson constitue une espece herbacee perenne et dominante se comportant en espece pionniere dans les habitats perturbes. Pour reunir l'information de base sur la structure genetique de cette espece pionniere, les auteurs ont etudie la variation de l'ADN chloroplastique (cpADN) chez le M. sinensis, dans et entre les populations indigenes au Japon. Ils ont detecte neuf haplotypes chez 636 individus provenant de 30 populations. Deux haplotypes affichent une large distribution geographique et coexistent a l'interieur de la plupart des populations. Le degre de variation genetique entre les populations s'avere relativement faible. On retrouve deux lignees ancestrales presumees dans les iles Ryukyu. Consequemment, il est possible que les lignees originaires des regions subtropicales de la Chine aient emigre dans les iles Ryukyu. La peninsule coreenne serait une autre route de migration possible. Deux haplotypes majeurs pourraient avoir migre du continent eurasien vers la cote nordique dans le Kyushu via la peninsule coreenne, pour s'etendre par la suite sur l'ensemble du Japon. Il n'y a pas de frontiere genetique bien delimitee entre les populations nordiques du Kyushu. La capacite migratoire accrue et le fort taux de flux genetique du Miscanthus pourrait avoir module la structure genetique generee au cours de periodes glaciaires antecedentes. Alternativement, l'absence d'haplotypes au nord du Kyushu pourrait indiquer la recente expansion de cette espece vers le nord du Japon. [Traduit par la Redaction] Mots-cles: structure genetique, distribution d'halotypes, Miscanthus sinensis, plante pionniere, herbe argentee., Introduction Phylogeographic studies based on chloroplast DNA (cpDNA) markers are used to gain understanding of the historical colonization process of a species (Avise 2000). Large-scale phylogeographic studies have shown that [...]

Hybridization is a major source of phenotypic variation and a driving force for evolution. Although novel hybrid traits can often disrupt adaptive relationships between the parental phenotypes and their environments, how new hybrid traits disrupt local adaptation remains unclear. Here, we report how a new phenotype of hybrids between two Imperata cylindrica ecotypes contributes to rapid reproductive isolation from their parents and affects hybrid fitness.We analysed 350 accessions of I. cylindrica collected from the 1980s to the 2010s throughout Japan to explore the genetic population structure of the hybrids. We surveyed the flowering periods, seed set, and germination of two ecotypes and their hybrids in both natural habitats and common gardens.Genetic analyses of population structure revealed that the hybrid populations consisted of only F1 individuals, without advanced generation hybrids. The flowering phenology of the F1 plants was delayed until autumn, 5–6 months later than the parental ecotypes. The drastic shift in flowering phenology prevents F1s from backcrossing. In addition, it changes their seed dispersal time to winter. Germination is inhibited by low temperatures, and the seeds likely decay before the next spring, resulting in the absence of an F2 generation. We identified the environmental mismatch of the F1 population as a specific mechanism for the maintenance of an only F1 population.Synthesis. We have demonstrated that this flowering phenology mismatch promotes reproductive isolation between the parents and F1s and affects various temporal components of the hybrids, resulting in a unique hybrid population consisting only of F1s. This system sheds light on the importance of hybrid traits in driving rapid reproductive isolation. [ABSTRACT FROM AUTHOR]

Summary: The evolution of herbicide resistance in weeds is an example of parallel evolution, through which genes encoding herbicide target proteins are repeatedly represented as evolutionary targets. The number of herbicide target‐site genes differs among species, and little is known regarding the effects of duplicate gene copies on the evolution of herbicide resistance.We investigated the evolution of herbicide resistance in Monochoria vaginalis, which carries five copies of sulfonylurea target‐site acetolactate synthase (ALS) genes. Suspected resistant populations collected across Japan were investigated for herbicide sensitivity and ALS gene sequences, followed by functional characterization and ALS gene expression analysis.We identified over 60 resistant populations, all of which carried resistance‐conferring amino acid substitutions exclusively in MvALS1 or MvALS3. All MvALS4 alleles carried a loss‐of‐function mutation. Although the enzymatic properties of ALS encoded by these genes were not markedly different, the expression of MvALS1 and MvALS3 was prominently higher among all ALS genes.The higher expression of MvALS1 and MvALS3 is the driving force of the biased representation of genes during the evolution of herbicide resistance in M. vaginalis. Our findings highlight that gene expression is a key factor in creating evolutionary hotspots. [ABSTRACT FROM AUTHOR]

Premise: Divergent selection due to environmental heterogeneity can lead to local adaptation. However, the ecological and evolutionary processes of local adaptation that occurs across multiple regions are often unknown. Our previous studies reported on the ecotypic divergence within a local area of variation of Potentilla matsumurae, an alpine herb adapted to the fellfield–snowbed environment. Here we investigated large‐scale geographic patterns of ecotypic differentiation in this species to infer local adaptation and selective forces across multiple regions. Methods: We compiled information on the overall distributions of fellfield and snowbed habitats on the mountains in Japan across the distribution of the species. Next, we conducted common garden experiments to test the adaptive divergence of the fellfield–snowbed plants derived from multiple regions. Finally, we evaluated phylogeographic structures based on cpDNA and allozyme variations and inferred the evolutionary history of ecotype differentiation. Results: The mosaic distribution of the fellfield–snowbed ecotypes across isolated mountaintops constitutes indirect evidence for habitat‐specific natural selection. The significant difference in survivorship between the ecotypes observed in a controlled snow environment provides more substantial evidence of local selection. Phylogeographic structures support the hypothesis that ecotypic divergence events from fellfield to snowbed populations occurred independently in at least two distinct regions. Conclusions: Ecotypic divergence of P. matsumurae has occurred across a series of mountain sky islands. Local selection in snowy environments is a driving force that maintains the divergent ecotypes across multiple mountain regions and can contribute to the diversification of plants in heavy‐snow regions. [ABSTRACT FROM AUTHOR]

Understanding the characteristics of alien species is a prerequisite for any biological study or anti‐invasion management strategy. Lolium rigidum (Poaceae) is an alien species that has become naturalized on the sandy coasts of Japan; however, it exhibits extensive morphological variation, leading to speculation that several taxa of Lolium have become naturalized. Here, we compared the morphology, reproductive biology and genetic structure of this Lolium species by growing individuals from different locations in the same environment to clarify whether the observed morphological variation is genetically based or is caused by intraspecific variation as a result of environmental differences. Principle component analyses of 11 morphological traits separated the study species into two types. Bagging experiments showed that one type exhibited an outcrossing life history, whereas the other type selfed exclusively. Nuclear DNA microsatellite analyses supported this distinction between these morphological types, with no intermediate individuals being found. The outcrossing type exhibited high genetic diversity, whereas the selfing type exhibited almost no polymorphism, reflecting the differences in their breeding systems. Moreover, both types differed from the economically important outcrossing species Lolium multiflorum and Lolium perenne. These two types of Lolium are expected to have different introduction histories and invasive potential on the coasts of Japan. In conclusion, it is important to distinguish between these types through additional biological studies to design effective control measures. [ABSTRACT FROM AUTHOR]

Sagittaria trifolia is a noxious paddy weed in East Asia. This weed propagates both sexually and asexually. Information on the role of sexual reproduction in the spread of herbicide‐resistant gene(s) and control of S. trifolia is important. Therefore, effects of oxygen, light, and temperature on the germination; germination percentages of fresh and stored seeds; and seed dormancy cycles were clarified. Seeds of S. trifolia require hypoxia and light with temperatures above 30/20°C for germination. Germination percentages increased after 1 month of storage on the soil surface. Germination percentages at 35/25°C for seeds submerged in the summer (simulating a well‐drained paddy during winter) and year round (simulating a poorly drained paddy) for 5 months and exhumed on April 7 were 84.7 and 94.4%, respectively, and decreased gradually to 41.3 and 40.0%, respectively, on June 2 (7 months burial). Germination percentages increased again and reached 63.7 and 94.0%, respectively, on July 25 (9 months burial). Seeds that form in summer germinate quickly at high temperatures, and the seedlings form tubers before winter. Thus, once herbicide‐resistant individuals emerge, the resistant gene or genes is/are easily distributed and fixed in the next generation. Autumn plowing and/or the spraying of herbicides is/are effective for controlling this weed. [ABSTRACT FROM AUTHOR]

In Shizuoka Prefecture, Japan, glyphosate‐resistant Lolium multiflorum is a serious problem on the levees of rice paddies and in wheat fields. The mechanism of resistance of this biotype was analyzed. Based on LD50, the resistant population was 2.8–5.0 times more resistant to glyphosate than the susceptible population. The 5‐enolpyruvyl‐shikimate‐3‐phosphate synthase (EPSPS) gene sequence of the resistant biotype did not show a non‐synonymous substitution at Pro106, and amplification of the gene was not observed in the resistant biotype. The metabolism and translocation of glyphosate were examined 4 days after application through the direct detection of glyphosate and its metabolite aminomethylphosphonic acid (AMPA) using liquid chromatograph‐tandem mass spectrometer (LC‐MS/MS). AMPA was not detected in either biotype in glyphosate‐treated leaves or the other plant parts. The respective absorption rates of the susceptible and resistant biotypes were 37.90 ± 3.63% and 41.09 ± 3.36%, respectively, which were not significantly different. The resistant biotype retained more glyphosate in a glyphosate‐treated leaf (91.36 ± 1.56% of absorbed glyphosate) and less in the untreated parts of shoots (5.90 ± 1.17%) and roots (2.76 ± 0.44%) compared with the susceptible biotype, 79.58 ± 3.73%, 15.77 ± 3.06% and 4.65 ± 0.89%, respectively. The results indicate that the resistance mechanism is neither the acquisition of a metabolic system nor limiting the absorption of glyphosate but limited translocation of the herbicide in the resistant biotype of L. multiflorum in Shizuoka Prefecture. [ABSTRACT FROM AUTHOR]

Invasive alien plants have caused negative ecological and economic impacts and numerous studies have focused on determining which traits make these plants successful invaders. Although it is commonly believed that only a small proportion of introduced species can become invasive, it is unknown why many alien species fail to establish. In order to identify the alien species that are exhibiting a limited distribution in their new habitat, the vegetation in an international trading port, which is a primary site for the introduction of alien plants, and residential areas of Kobe, western Japan, were surveyed every month from April–October, 2014. A total of 167 species, of which 59.3% were annual and 61.2% were alien, was found. Species that originated in Mediterranean regions were the dominant alien species, followed by those from North America. A principal component analysis showed that the species compositions were different between the port and the residential areas, particularly in spring. The species from the port areas were major weeds from the cereal crop fields of North America and Australia, but were limited in distribution in Japan. The residence time might be too short to allow them to expand or climatic differences between the areas where these aliens are naturally dominant and Japan could serve as ecological barriers to the range expansion of such species. [ABSTRACT FROM AUTHOR]

Nucleotide sequence variations were investigated with respect to the geographical distribution patterns of Miscanthus sinensis populations that were sampled from 26 Japanese national parks and three populations of the Ryukyu Islands. Twelve homozygous sequences in the nuclear ribosomal DNA internal transcribed spacer region were detected. The populations of M. sinensis in mainland Japan mainly were composed of a monophyletic group with a symapomorphic character, whereas those in the Ryukyu Islands included a polyphyletic group. Only an internal transcribed spacer haplotype with a plesiomorphic character was found in both mainland Japan and the Ryukyu Islands. Thus, no clear geographical isolation was observed in this species. These facts might be caused by the ability of M. sinensis as a pioneer plant to have a high migration potential and high gene flow by outcrossing. On the basis of the results of this study (nuclear ribosomal DNA) and the previous study (chloroplast DNA), a phylogeographical history of M. sinensis was presumed where the ancestral and derived lineages were distributed in the southern and northern regions of Japan, respectively, without strict geographical isolation. [ABSTRACT FROM AUTHOR]

The rapid range expansion of naturalized Italian ryegrass ( Lolium multiflorum Lam.) in farmland is a serious problem in Fukuroi city in Shizuoka Prefecture, Japan. Glyphosate has been used to control Italian ryegrass in the levees of rice paddy fields and wheat fields for ∼20 years, but this weed in Fukuroi city is poorly controlled by glyphosate. In order to elucidate the level of resistance to glyphosate in Italian ryegrass populations, seed bioassays and a foliar application experiment, using seeds collected from 16 wild populations in and around Fukuroi city and from three susceptible cultivars, were conducted. For the susceptible cultivars and one population from a site where glyphosate had not been applied for >10 years, the shoot length in the seed bioassays was greatly suppressed at a glyphosate concentration of 10 mg ai L−1 and no seedling survived after the foliar application of glyphosate at a rate of 2.3 kg ai ha−1. Nine wild populations from levees in the southern part of Fukuroi city showed vigorous shoot growth at a glyphosate concentration of 10 mg ai L−1 and had at least a 78% survival rate after the application of glyphosate at 2.3 kg ai ha−1. Four wild populations from levees in the northern part of Fukuroi city showed a slight suppression of the shoot growth as a result of the glyphosate treatment and their survival rates ranged from 20 to 64%. The results suggested that resistance to glyphosate has evolved in the wild populations of Italian ryegrass that are growing on the levees. This is the first report of a glyphosate-resistant weed in Japan. [ABSTRACT FROM AUTHOR]

As herbicide-resistant weeds have spread in the agricultural fields of grain-exporting countries, their seeds could be introduced into other countries as contaminants in imported grain. The spread of resistance genes through seed and pollen can cause significant economic loss. In order to assess the extent of the problem, we investigated the contamination by herbicide-resistant annual ryegrass ( Lolium rigidum) of wheat imported from Western Australia into Japan. Annual ryegrass seeds were recovered from wheat shipments and seed bioassays were conducted to identify resistance to the herbicides that are commonly used in Australia: diclofop-methyl, sethoxydim, chlorsulfuron, and glyphosate. Nearly 4500 ryegrass seeds were detected in 20 kg of wheat that was imported in both 2006 and 2007. About 35% and 15% of the seeds were resistant to diclofop-methyl, 5% and 6% were resistant to sethoxydim, and 56% and 60% were resistant to chlorsulfuron in 2006 and 2007, respectively. None was resistant to glyphosate in either year. As the contamination of crops by herbicide-resistant weeds is probably a common phenomenon, the monitoring of incoming grain shipments is necessary to stem the further spread of herbicide-resistant weeds into importing countries. [ABSTRACT FROM AUTHOR]

The great majority of studies on foundation species focused on a single dominant plant in a community, while more than one such species can often coexist and compete for space and limited resources. Morphologically different coexisting foundation species can create diverse niches occupied by different subsets of beneficiary species. To test this hypothesis, we sampled alpine plant communities at exposed fellfields in alpine zone, in the Taisetsu Mountains (Hokkaido, northern Japan), with coexisting putative foundation species Pinus pumila (evergreen shrub) and Diapensia lapponica (evergreen cushion‐forming shrub), and analyzed their spatial relationships with other plants. Preliminary vegetation survey indicated that fruticose lichens and Loiseleuria procumbens (evergreen mat‐forming shrub) might also act as a foundation species; thus, we included them in our analyses. The coexisting foundation species had both general as well as specific effects on plant community structure. Namely, almost all the members of the community aggregated spatially with lichens, while the other foundation species were spatially segregated from each other. These foundation plants associated with different members of the community, thus showing species‐specific effects on the community structure. Blooming species showed even stronger patterns of species‐specific spatial associations, suggesting that foundation species had beneficial effects on their associated species. We conclude that the focus on coexisting foundation species can reveal important details of community structure which would be hidden if we treated all species as equal members of the community. Studying the effects of coexisting foundation species could greatly advance our understanding of how species diversity functions in plant communities. [ABSTRACT FROM AUTHOR]

Severe infestations of Alopecurus aequalis (shortawn foxtail), a noxious weed in wheat and barley cropping systems in Japan, can occur even after application of thifensulfuron-methyl, a sulfonylurea (SU) herbicide. In the present study, nine accessions of A. aequalis growing in a single wheat field were tested for sensitivity to thifensulfuron-methyl. Seven of the nine accessions survived application of standard field rates of thifensulfuron-methyl, indicating that severe infestations likely result from herbicide resistance. Acetolactate synthase (ALS) is the target enzyme of SU herbicides. Full-length genes encoding ALS were therefore isolated to determine the mechanism of SU resistance. As a result, differences in ALS gene copy numbers among accessions were revealed. Two copies, ALS1 and ALS2 , were conserved in all accessions, while some carried two additional copies, ALS3 and ALS4 . A single-base deletion in ALS3 and ALS4 further indicated that they represent pseudogenes. No differences in ploidy level were observed between accessions with two or four copies of the ALS gene, suggesting that copy number varies. Resistant plants were found to carry a mutation in either the ALS1 or ALS2 gene, with all mutations causing an amino acid substitution at the Pro197 residue, which is known to confer SU resistance. Transcription of each ALS gene copy was confirmed by reverse transcription PCR, supporting involvement of these mutations in SU resistance. The information on the copy number and full-length sequences of ALS genes in A. aequalis will aid future analysis of the mechanism of resistance.