Seed dispersal function of the brown bear Ursus arctos on Hokkaido Island in northern Japan: gut passage time, dispersal distance, germination, and effects of remaining pulp.

Megafauna are important seed dispersers because they can disperse large quantities of seeds over long distances. In Hokkaido, Japan, the largest terrestrial animal is the brown bear (Ursus arctos) and other megafauna seed dispersers are lacking. Thus, brown bears are expected to have an important function as seed dispersers in Hokkaido. In this study, we, for the first time, evaluated the seed dispersal function of brown bears in Hokkaido using three fleshy-fruited trees and studied: (1) gut passage time (GPT) in feeding experiments, (2) seed dispersal distance using tracking data of wild bears, and (3) the effect of gut passage and pulp removal on germination rate. Most seeds were defecated intact, and less than 6% were broken. The average GPT without pulp was 3 h and 56 min to 6 h and 13 min, depending on the plant and trial. Each plant's average simulated seed dispersal distance was 202-512 m. The dispersal distance of Actinidia arguta seeds with pulp was significantly longer than those without pulp because of their longer GPT. The germination rate of defecated seeds without pulp was 19-51%, depending on the plant, and was significantly higher or not different comparing with that of seeds with pulp. We concluded that brown bears in Hokkaido are effective seed dispersers. In managing brown bears in Hokkaido, such ecological functions should be considered along with conserving the bear population and reducing human-bear conflicts.

Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced.

Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300-400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.

Comparative analysis of spatial genetic structures in sympatric populations of two riparian plants, Saxifraga acerifolia and Saxifraga fortunei.

PREMISE: The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures. METHODS: To reveal genetic structures, we examined chloroplast microsatellite variations and genome-wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences. RESULTS: We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation. CONCLUSIONS: Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures.

Survival rate and environmental response of current-year seedlings of the temperate liana Wisteria floribunda across a heterogeneous environment.

Lianas have a huge influence on forest structure and function. However, it is unclear how the surrounding environment affects the establishment of liana seedlings in temperate forests. We addressed the following questions: (1) Can current-year seedlings persist under a closed canopy? (2) Do current-year seedlings form aggregated distribution and how has their spatial distribution varied over the years? (3) How does the light condition, soil moisture content, forest floor litter, understory vegetation, and the distance from the conspecific adults affect the establishment and survival of seedlings? We examined the distribution pattern and survivorship of current-year seedlings of the temperate liana species, Wisteria floribunda, across a heterogeneous environment for 6 years using 1 m2 sub-quadrats (n = 651) in a 6 ha plot within the Ogawa Forest Reserve, an old-growth, temperate, deciduous forest in central Japan. In total, 908 current-year seedlings were observed during the study period, 87% of which emerged in 2014. Over half (56%) of these seedlings survived until 1 year after germination, which was relatively high compared with other tree species in this forest. The seedlings formed significantly aggregated distribution, but the degree of aggregation decreased over time. The number of emerged seedlings was negatively associated with the presence of dwarf bamboo (Sasa borealis) and the distance from the nearest conspecific adult. However, the survival rate of the seedlings was negatively associated with the presence of dwarf bamboo and soil moisture content and was positively associated with the openness of the canopy and the distance from the nearest conspecific adult. An enhanced survival rate under more intense light conditions and the ability to persist within the shaded understory may be important for the survival of this species in the earlier stage of the life history.

Genetic consequences of plant edaphic specialization to solfatara fields: Phylogenetic and population genetic analysis of Carex angustisquama (Cyperaceae).

Edaphic specialization is one of the main drivers of plant diversification and has multifaceted effects on population dynamics. Carex angustisquama is a sedge plant growing only on heavily acidified soil in solfatara fields, where only extremophytes can survive. Because of the lack of closely related species in similar habitats and its disjunct distribution, the species offers ideal settings to investigate the effects of adaptation to solfatara fields and of historical biogeography on the genetic consequences of plant edaphic specialization to solfatara fields. Here, genome-wide single nucleotide polymorphisms were used to reveal the phylogenetic origin of C. angustisquama, and 16 expressed sequence tag-simple sequence repeat markers were employed to infer population demography of C angustisquama. Molecular phylogenetic analysis strongly indicated that C. angustisquama formed a monophyletic clade with Carex doenitzii, a species growing on nonacidified soil in the sympatric subalpine zone. The result of population genetic analysis showed that C. angustisquama has much lower genetic diversity than the sister species, and notably, all 16 loci were completely homozygous in most individuals of C. angustisquama. Approximate Bayesian computation analysis supported the model that assumed hierarchical declines of population size through its evolutionary sequence. We propose that the edaphic specialist in solfatara fields has newly attained the adaptation to solfatara fields in the process of speciation. Furthermore, we found evidence of a drastic reduction in genetic diversity in C. angustisquama, suggesting that the repeated founder effects associated with edaphic specialization and subsequent population demography lead to the loss of genetic diversity of this extremophyte in solfatara fields.

Role of ancient lakes in genetic and phenotypic diversification of freshwater snails.

Endemic organisms of ancient lakes have been studied as models to understand processes of speciation and adaptive radiation. However, it remains unclear how ancient lakes play roles in genetic and phenotypic diversity of freshwater mollusks. In the present study, we focus on viviparid freshwater snails in the ancient lakes of East and Southeast Asia (Japan and China) to address this question. Using molecular phylogenetic analyses based on mitochondrial (COI, 16S) and nuclear genes (18S, 28S, H3), we show that patterns of species diversification in viviparid lineages. Colonization to ancient lakes occurred independently in China and Japan at least four times, with subsequent diversification into more than two species within each lake group. Morphological analyses of fossil related viviparids suggest parallel phenotypic evolution occurred in the different lakes and ages. Each lake contained a single lineage which was phenotypically diversified relative to those from other sites. Using genome-wide SNPs obtained by MIG-seq, we also examined the genetic structure of three Japanese viviparids, including two endemic species of ancient Lake Biwa. The results suggest that these two species diversified from the population of the third species living in wetlands surrounding the lake. These findings suggest that rapid diversification of lineages and phenotypic divergence can occur in ancient lakes compared to other habitats. Formation of large lakes probably promotes speciation and phenotypic divergence as a result of adaptation into different microhabitats. High numbers of ancient lakes could be a driver of species diversity in Asian viviparid snails.

Enigmatic incongruence between mtDNA and nDNA revealed by multi-locus phylogenomic analyses in freshwater snails.

Phylogenetic incongruence has frequently been encountered among different molecular markers. Recent progress in molecular phylogenomics has provided detailed and important information for evolutionary biology and taxonomy. Here we focused on the freshwater viviparid snails (Cipangopaludina chinensis chinensis and C. c. laeta) of East Asia. We conducted phylogenetic analyses and divergence time estimation using two mitochondrial markers. We also performed population genetic analyses using genome-wide SNPs. We investigated how and which phylogenetic patterns reflect shell morphology. The results showed these two species could be separated into four major mitochondrial clades, whereas the nuclear clusters supported two groups. The phylogenetic patterns of both mtDNA and nDNA largely reflected the geographical distribution. Shell morphology reflected the phylogenetic clusters based on nDNA. The findings also showed these two species diversified in the Pliocene to early Pleistocene era, and occurred introgressive hybridisation. The results also raise the taxonomic issue of the two species.