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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]

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 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]