Genetic disturbance is propagated by artificial reinforcement or reintroduction of organisms from populations whose genetic structure is sufficiently different from the original populations. Many ...cultivars were produced from wild plant species, and fears exist that genetic disturbance of wild populations occurred by the human migration of cultivars. In this study, we detected genetic disturbance in
Pecteilis radiata
=
Habenaria radiata
(Orchidaceae) in the Hyogo Prefecture of Japan using multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). Also, we estimated the risk of the spread of genetically disturbed individuals based on the results of spatial genetic structure and gene flow. In five out of 33 examined sites, we detected genetically disturbed individuals that possessed the same genetic cluster as cultivar samples. No spatial genetic structure was found among the sites within a 0.64 km radius, which indicated that pollen or seeds of
P. radiata
freely migrated among these populations. Consequently, we demonstrated that a risk exists of spreading genetic disturbances by gene flow within a radius of 0.64 km from the site where genetic disturbance was found. Raised public awareness of the risk of genetic disturbance would be necessary to prevent additional spread of genetic disturbances by human activities.
Eleven native
Geranium
species have been reported in Japan, several of which include infraspecific taxa. Although phylogenetic analyses have been conducted using conventional methods (i.e., ...chloroplast fragment and ribosomal DNA sequencing), relationships at the infraspecific level have not been elucidated due to a lack of genetic polymorphisms. We collected specimens of 22
Geranium
taxa from Japan and peripheral areas (e.g., mainland China, South Korea, Russia, and Taiwan), and performed detailed phylogenetic analyses using chloroplast genome sequencing and genome-wide single-nucleotide polymorphisms. Some discrepancies were observed between the current taxonomy and the phylogenetic relationships elucidated in our analyses. The
Geranium tripartitum
complex was found to be paraphyletic, and
Geranium onoei
f.
yezoense
, which is synonym of
Geranium reinii
, was found to be more closely related to
Geranium erianthum
than to
G. reinii
. In particular,
G. tripartitum
var.
hastatum
located at intermediate position between
Geranium thunbergii
and
Geranium wilfordii
in the network analysis. Therefore, we suggest that
G. tripartitum
var.
hastatum
should be treated as an independent species, and that
G. onoei
f.
yezoense
should be transferred to
G. erianthum
.
Geranium erianthum
is an alpine plant growing in dry habitats, which is distributed from East Asia to northern coastal regions of the northern Pacific. The ice-free area around the current Bering ...Strait (i.e., Beringia) had played an important role in range expansion into neighboring regions such as East Asia and North America for some alpine plants. However, recent studies suggest that some alpine plants in snowbed environment spread from East Asia to northern coastal regions of the northern Pacific. In this study, we investigated phylogenetic relationships and genetic differentiations among populations of
G. erianthum
and the related species using the chloroplast genome and single-nucleotide polymorphisms, to evaluate the alternative biogeographic hypotheses in which region of Beringia, British Columbia or East Asia is probable for its distributional origin. Range reconstruction based on phylogenetic tree of chloroplast genome indicated
G. erianthum
and related species originated in East Asia, from where
G. erianthum
migrated eastward into Beringia and British Columbia. In addition, nuclear genome-wide SNPs indicated that no significant genetic differentiation was detected between Japanese and Beringian populations. The lack of genetic differentiation suggests that the current range of
G. erianthum
resulted from rapid range expansion during the latter period of the last glacial era. Overall, the East Asian refugium hypothesis was applicable to the alpine plant
G. erianthum
in dry habitat, indicating that range expansion pattern from East Asia into the northern Pacific may be more common rather than limited for snowbed species.
Using Japanese literature, we created a consolidated list of host records of butterflies in Japan. The list used the host records described in eight major illustrated reference books, two checklists, ...and 14 other pieces of literature. The presence of larvae on plants, the observation of larvae eating plants or insects in the field were considered as host records. We collected all species recorded in Japan. Scientific, family, and Japanese names of butterflies were consolidated using the BINRAN database (
http://binran.lepimages.jp/
). Scientific and Japanese names of host plants were based on the YList database (
http://ylist.info/
). If scientific names of host plants were not found in YList, we used scientific names based on The Plant List (
http://www.theplantlist.org/
). Family names of host plants were based on the Catalogue of Life database (
http://www.catalogueoflife.org/
). Scientific, family, and Japanese names of host insects were based on the MOKUROKU database (
http://konchudb.agr.agr.kyushu-u.ac.jp/mokuroku/
) for Hymenoptera and the catalogue of the Paraneoptera of Japan published by the Entomological Society of Japan for Hemiptera. We also provided the references of each host record and the original names described in the referred literature. Two datasets, HostDB and ReferenceDB, were created to include 3600 records of butterfly larval hosts in Japan, along with scientific and Japanese names of each species and a literature list. These datasets will be useful for basic and applied biological studies of butterflies. Data files are stored in the Ecological Research Data Archives (
http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/
) and available from
http://hostbj.lepumus.net/
. These datasets are published under the Creative Commons License Attribution-ShareAlike 4.0 (CC BY-SA,
https://creativecommons.org/licenses/by-sa/4.0/
).
Recent studies revealed that green spaces in urban areas are critical for conservation of native biodiversity and that assessment of the present flora of green spaces in urban areas is critical for ...protection of the native biodiversity. The Komaba Campus of the University of Tokyo embraces a relevant green area, located in a highly urbanised area in Tokyo Metropolis (35.66 N 139.68 E, Japan). The total area of this Campus is 25.4 ha, from which, 4.5 ha are covered by vegetation. Although intense urbanisation can be observed around the Campus, new insect species had been reported for the Campus area, suggesting that the biodiversity on the Campus still demands some attention. Differently from fauna surveys, no flora survey has been done for more than 30 years on the Campus. In this study, we have extensively surveyed the plants diversity on the Komaba Campus of the University of Tokyo, aiming for an update of the plants list on this green urban area in Tokyo.
The survey covered all herbaceous and arboreous plants growing wild on the Campus. Garden plants were excluded in this survey because these plants were supposed to be cultivated. The final dataset contained, in total, 324 taxa, from which 234 were herbaceous plants and 90 were arboreous plants. The top three taxa are as follows: Poaceae (38 taxa), Asteraceae (34 taxa) and Rosaceae (14 taxa), respectively. This is the first update to the Flora of the Komaba Campus of the University of Tokyo in 30 years and represent an important contribution to conservation of native species in the Tokyo metropolis.
We analyzed whether the relationship between population density and urban land use rate differs depending on the region by the third mesh unit. When calculating the number of urban meshes based on ...population density and land use criteria, the number of urban meshes based on population density criteria was slightly larger than the number based on criteria of land use in many prefectures. However, in Hokkaido, there was atendency that the number of urban mesh is small with criteria based on population density. Pearsonʼs correlation coefficients between population density and urban land use rate were calculated for each prefecture, and as a result, a high value of 0.82 on average wasobtained, but relatively low values of around 0.6 were obtained in Hokkaido and Iwateprefecture. We analyzed whether these differences influence the prediction model of the number of woody plants in Kanto district and Hokkaido. Population density was estimated as a significant variable in the prediction model of Kanto district, but in the Hokkaido the opposite result to the Kanto model was obtained. When population density and urban land use rate are used as an index of urbanization, it will be necessary to recognize that therelationship has regional differences.
Background : All human land use (LU) affects the distribution of plant species; however, the impacts vary with the type/intensity of LU. For managing ecosystems, it is therefore essential to ...understand the effects of LU types on the distribution of plant species on a macroscale. Aims : The objectives of our study were to quantify the effects of various LU types on the distribution of vascular plant species in Japan and to determine in particular the extent to which LU was an important factor for the distribution of common species. Methods : Based on a logistic regression model and variation partitioning being applied to each plant species, we evaluated the partial deviance by six LU types, four climatic types and three topographic and geological factors for 647 plant species at 14,412 sites in Japan. Results : The effect of LU was significant for species present at multiple sites. Of the six LU types, secondary vegetation and plantation were the most important factors determining species distribution for many species. Conclusions : Our results suggest that distribution of the common species is largely affected by LU on macroscale. The design of LU relating to secondary vegetation and plantations will thus be important in determining changes in the vegetation composition within Japan.
Abstract
Recent phylogeographical studies have revealed that refugia sometimes retain high levels of genetic heterogeneity due to multiple colonization events, a phenomenon defined as ‘refugia within ...refugium’. In previous research, we reported a complex genetic structure within the Geranium yesoense complex, an alpine plant found in an interglacial refugium at high elevation in Central Japan, probably resulting from multiple colonization and hybridization events. However, we were unable to evaluate instances of introgression due to limited sample size. In the present study, we performed additional chloroplast genome sequencing, along with Sanger sequencing of selected chloroplast DNA regions, to elucidate the phylogenetic relationships among the refugial populations. The chloroplast genome sequence of a sample from Mt. Asama (an important refugium) was nested within the northern lineage (i.e. var. yesoense and var. pseudopratense), and haplotypes from Mt. Asama and Mt. Ibuki were also grouped with those of the northern lineage. Although our previous study suggested hybridization events between northern and southern lineages (i.e. var. nipponicum) at Mt. Asama, haplotypes from the southern lineage were not detected at range margins. This suggests that directional introgression occurred in these regions. Overall, our results further support that genetic heterogeneity within these refugia was amplified by recolonization and hybridization during past climate oscillations.
The Heteroptera, or true bugs, forms one of the major insect groups with respect to the very diverse habitat preferences, including both aquatic and terrestrial species, as well as a variety of ...feeding types. The first comprehensive inventory of the Heteroptera at Komaba Campus of the University of Tokyo, or an urban green space in the center of the Tokyo Metropolis, Japan, was conducted.
A total of 115 species in 29 families of the suborder Heteroptera were identified. The area had a high species richness compared with other urbanized and suburbanized localities in Tokyo. The campus is found to show a substantial difference in heteropteran species compositions, despite being close to the other localities surrounded by highly urbanized zones in central Tokyo.
PDF
