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Shota Murakami

Bio: Shota Murakami is an academic researcher from Hokkaido University. The author has contributed to research in topics: Combustion & Premixed flame. The author has an hindex of 3, co-authored 3 publications receiving 37 citations.

Papers
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Journal ArticleDOI
TL;DR: Snow track surveys in combination with eDNA techniques could dramatically improve the efficiency of monitoring and conservation of mammals.
Abstract: Noninvasive genetic analysis is being used increasingly in field surveys. However, detecting large and middle-sized mammals, such as Carnivora species, using noninvasive samples, such as scat or hair, is time- and labor-intensive due to their low densities and elusive behaviors. As snow tracks are the most frequently encountered natural signs of terrestrial mammals in winter, we employed several methods to recover environmental DNA (eDNA) from snow tracks. We performed both DNA metabarcoding and Sanger sequence analyses, in combination with universal primers on the mitochondrial 12S rRNA gene for mammals and taxon-specific primers on the mitochondrial NADH dehydrogenase subunit 2 gene for Martes species (martens and sables in Mustelidae). Snow samples of four Martes melampus tracks, one Cervus nippon track, one Vulpes vulpes track, and the track of an unidentified Carnivora species were collected from a snowfall area in Kyoto, Japan, in February 2018. Regarding DNA metabarcoding analyses, the sequences of three Carnivora species (M. melampus, V. vulpes, and Canis lupus familiaris) and a deer (C. nippon) were obtained from their respective snow tracks. Using Sanger sequencing, eDNA on snow tracks was recovered at the species level except for M. melampus using universal primers, while eDNA of M. melampus was sequenced using Martes-specific primers. Snow track surveys in combination with eDNA techniques could dramatically improve the efficiency of monitoring and conservation of mammals.

25 citations

Journal ArticleDOI
TL;DR: In this paper, a new concept based on the Damkohler number (Da) was proposed to describe the complete transition behavior found in a flame spread in a solid combustible tube.

18 citations

Journal ArticleDOI
TL;DR: The time-dependent evolutionary rates of the mitochondrial Cytb presented here would provide a possible way for assessing population dynamics of cricetid rodents responding to the late Pleistocene environmental fluctuation.
Abstract: The Japanese archipelago is comprised of four main islands-Hokkaido, Honshu, Shikoku, and Kyushu-which contain high mountainous areas that likely allowed for lineage differentiation and population genetic structuring during the climatic changes of the late Pleistocene. Here, we assess the historical background of the evolutionary dynamics of herbivorous red-backed voles (Myodes) in Japan, examining the evolutionary trends of mitochondrial cytochrome b gene (Cytb) sequence variation. Four apparent signals from rapid expansion events were detected in three species, M. rufocanus and M. rutilus from Hokkaido and M. smithii from central Honshu. Taken together with results from previous studies on Japanese wood mice (Apodemus spp.), three of the expansion events were considered to be associated with predicted bottleneck events at the marine isotope stage (MIS) 4 period, in which glaciers are thought to have expanded extensively, especially at higher elevations. In the late Pleistocene, the possible candidates are transitions MIS 6/5, MIS 4/3, and MIS 2/1, which can be characterized by the cold periods of the penultimate glacial maximum, MIS 4, and the last glacial maximum, respectively. Our data further reveal the genetic footprints of repeated range expansion and contraction in the northern and southern lineages of the vole species currently found in central Honshu, namely M. andersoni and M. smithii, in response to climatic oscillation during the late Pleistocene. The time-dependent evolutionary rates of the mitochondrial Cytb presented here would provide a possible way for assessing population dynamics of cricetid rodents responding to the late Pleistocene environmental fluctuation.

14 citations


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Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations

Journal ArticleDOI
TL;DR: The primary areas in which population genomics approaches can be applied to wildlife conservation and management are reviewed, examples of how they have been used are highlighted, and recommendations for building on the progress that has been made are provided.
Abstract: Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

174 citations

Journal ArticleDOI
TL;DR: It is argued that the MiFish eDNA metabarcoding method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.
Abstract: We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.

94 citations

Journal ArticleDOI
TL;DR: In this article, the authors evaluated eDNA metabarcoding for monitoring semi-aquatic and terrestrial mammals, specifically nine species of conservation or management concern, and examined spatiotemporal variation in mammal eDNA signals.

67 citations

Journal ArticleDOI
TL;DR: In freshwater systems with fewer than 100 species, eDNA metabarcoding detected more species than conventional methods; however, more studies are needed in these environments to better evaluate relative performance.
Abstract: The ability to properly identify species present in a landscape is foundational to ecology and essential for natural resource management and conservation. However, many species are often unaccounted for due to ineffective direct capture and visual surveys, especially in aquatic environments. Environmental DNA metabarcoding is an approach that overcomes low detection probabilities and should consequently enhance estimates of biodiversity and its proxy, species richness. Here, we synthesize 37 studies in natural aquatic systems to compare species richness estimates for bony fish between eDNA metabarcoding and conventional methods, such as nets, visual census, and electrofishing. In freshwater systems with fewer than 100 species, we found eDNA metabarcoding detected more species than conventional methods. Using multiple genetic markers further increased species richness estimates with eDNA metabarcoding. For more diverse freshwater systems and across marine systems, eDNA metabarcoding reported similar values of species richness to conventional methods; however, more studies are needed in these environments to better evaluate relative performance. In systems with greater biodiversity, eDNA metabarcoding will require more populated reference databases, increased sampling effort, and multi-marker assays to ensure robust species richness estimates to further validate the approach. eDNA metabarcoding is reliable and provides a path for broader biodiversity assessments that can outperform conventional methods for estimating species richness.

55 citations