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Metabarcoding of feces and intestinal contents to determine carnivorous diets in red-crowned cranes in eastern Hokkaido, Japan
Get PDFjournal articleThe red-crowned crane Grus japonensis in Hokkaido, Japan forms a closed population as a residence that is independent of the mainland population. Based on observations of a limited number of individuals as well as cranes in captivity, red-crowned cranes are omnivores and eat fish, worms, insects and plants in their own territories except in winter, when they are fed with dent corn that is supplied in eastern Hokkaido. DNA metabarcoding based on high throughput sequencing was carried out using universal primer sets for cytochrome oxidase subunit I gene. Feces from 27 chicks collected in June and July in the period from 2016 to 2018 and intestinal contents from 33 adult and subadult cranes that were found dead almost throughout year in 2006–2013 in the field in eastern Hokkaido were used. Although compositions varied considerably in the cranes, both insects and fish were found in adults and subadults to the same extents, while insects were predominant in chicks. Both insects and fish were detected in all seasons for adults and subadults. Horse flies, scarab beetles and weevils accounted for the most of the insects regardless of the life stage. Dace, stickleback, flatfish and sculpin were the major fish species in adults, while chicks ate almost only stickleback. The results provide the first comprehensive data on carnivorous diets in wild red-crowned cranes in eastern Hokkaido as basis for conservation of red-crowned cranes, for which the life style and area continue to change.journal articl
Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo
Get PDFjournal articleCommunity phylogenetic analysis is an effective approach to understanding the process of community formation. The phylogenetic tree of the species pool is reconstructed in the first step, and the phylogenetic tree obtained in the second step is used to analyze phylogenetic diversity. Sythetic trees have often been used in the construction of phylogenentic trees; however, in tropical rainforests with many closely related species, synthetic trees contain many unresolved nodes, which may affect the results of phylogenetic structure analysis. Here, we constructed a phylogenetic tree using DNA barcode sequences (rbcL, matK, trnH-psbA) for 737 tree species from the rainforests of Borneo, which have a high-species diversity and many closely related species. The phylogenetic tree had fewer polytomies and more branch length variations than the Phylocom synthetic trees. Comparison of community phylogenetic analyses indicated that values of the standardized effect size of mean pairwise distance (SES–MPD) were highly correlated between Phylocom and DNA barcode trees, but less so for the standardized effect size of mean nearest taxon distance (SES–MNTD), suggesting that caution is needed when using synthetic trees for communities containing many congeneric species, especially when using SES–MNTD. Simulation analysis suggested that spatial dependence on phylogenetic diversity is related to the phylogenetic signal of the species' habitat niche and the spatial structure of habitat, indicating the importance of detailed phylogeny in understanding community assembly processes.journal articl
Tsunami deposits associated with the 1983 Nihonkai-Chubu earthquake tsunami in coastal forests near Happo Town, Akita Prefecture, Japan
Get PDFjournal articleOn 26 May 1983 the Nihonkai-Chubu earthquake occurred off the western coast of Noshiro City, Akita Prefecture, Japan. The tsunami associated with this earthquake caused widespread damage to the northeastern coastal region of the Sea of Japan, including Akita Prefecture, and left behind sand and mud deposits. These deposits were first described in the 1990s, but have not been studied further. During December 2019 and January 2020, we conducted geological surveys to investigate post-1948 soil thinning in the pine-based coastal protective forests planted near Happo Town. A sand layer that thinned inland was observed in the soil at depths greater than 10 cm. Because the sand layer contained well-preserved fossil brackish–marine diatoms and exhibited a high bulk density, it is likely that the sand was transported inland from the coast. The sand layer was distributed from the coast to 150–270 m inland, but only within the coastal protective forest. By reference to historical records, we concluded that this sand layer was deposited by the 1983 tsunami, because this region could not have been reached by any event other than the tsunami produced by the Nihonkai-Chubu earthquake. We also observed another sand layer above the tsunami deposits, which may have been formed by Typhoon 9119 on 28 September 1991.journal articl
Infiltration of hidden antimicrobial resistance among healthy people in a Japanese community
Get PDFjournal articleBackground: Under non-antimicrobial selective pressure, antimicrobial-resistant bacteria do not easily become dominant in the microbiota. Furthermore, their low levels prevent detection by isolation, resulting in an underestimation of the prevalence of antimicrobial-resistant bacteria. Objectives: We evaluated the infiltration of antimicrobial-resistant bacteria and their related β-lactamase genes among healthy people in non-clinical settings. Methods: Cephalosporin- and fluoroquinolone-resistant Escherichia coli and bla genes were quantified in 217 faecal samples from healthy people in non-clinical settings in Japan. E. coli colonies grown on deoxycholate hydrogen sulphide-lactose (DHL) agar, with and without antimicrobials (cefotaxime and ciprofloxacin), were quantified, and E. coli isolates were analysed for their susceptibility to antimicrobials and the presence of bla genes. DNA extracted from faecal samples was used to quantify bla genes using quantitative PCR (qPCR). Results: The isolation rates of cefotaxime- and ciprofloxacin-resistant E. coli were 6.9% and 12.4%, respectively, using agars without antimicrobials, and 12.0% and 24.4%, respectively, using agars with antimicrobials. For samples from which cefotaxime- and ciprofloxacin-resistant E. coli were isolated only using agars with antimicrobials, the ratios of cfu on DHL agars with and without antimicrobials were below −2 log. E. coli harbouring bla genes were isolated from 35.0% of the faecal samples using agars, and bla genes were detected in 65.0% of faecal DNA samples using qPCR. Conclusions: Among people carrying cefotaxime- and ciprofloxacin-resistant E. coli in non-clinical settings, cefotaxime- and ciprofloxacin-resistant E. coli were not dominant in half of the subjects. These individuals may play a role as reservoirs of antimicrobial-resistant bacteria.journal articl
A deregression method for a single-step SNP BLUP model using all genotype data
Get PDFjournal articleFor various applications in dairy cattle evaluation, pseudo-phenotype data are needed for cows with own records or bulls with daughters. The purpose of this paper was to develop a GEBV deregression method for the single-step model using all genotype data. A special single-step SNP BLUP model was assumed in this study to deregress GEBV. All animals with own phenotype data and all genotyped animals including young candidates were considered in the GEBV deregression. The same pedigree file as well as the same genotype data were used in the deregression process as the original single-step evaluation. Thanks to the efficient single-step SNP BLUP model, the proposed GEBV deregression should be feasible for analysing millions of genotyped animals. Methodological and technical issues were addressed, and a validation procedure was proposed for the GEBV deregression method. Analysis of real data will be required to verify the developed GEBV deregression method.journal articl
Expression of Indian hedgehog signaling in murine oviductal infundibulum and its relationship with epithelial homeostasis
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