scholarly journals Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water

2019 ◽  
Vol 2 (1) ◽  
pp. 42-52 ◽  
Author(s):  
Satsuki Tsuji ◽  
Masaki Miya ◽  
Masayuki Ushio ◽  
Hirotoshi Sato ◽  
Toshifumi Minamoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Environmental Dna ◽  
Intraspecific Genetic Diversity ◽  
Tank Water

scholarly journals Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

2019 ◽  
Author(s):  
Satsuki Tsuji ◽  
Atsushi Maruyama ◽  
Masaki Miya ◽  
Masayuki Ushio ◽  
Hirotoshi Sato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Sample ◽  
Sanger Sequencing ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Environmental Dna ◽  
Intraspecific Diversity ◽  
Survey Method ◽  
Intraspecific Genetic Diversity

AbstractEnvironmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, UNOISE3 and DADA2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (UNOISE3) and 41 (DADA2) haplotypes were detected by eDNA analysis. When DADA2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. This study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods, suggesting that it could become a more efficient survey method for investigating intraspecific genetic diversity in the field.

scholarly journals Evaluating intraspecific genetic diversity of a fish population using environmental DNA: An approach to distinguish true haplotypes from erroneous sequences

2018 ◽  
Author(s):  
Satsuki Tsuji ◽  
Masaki Miya ◽  
Masayuki Ushio ◽  
Hirotoshi Sato ◽  
Toshifumi Minamoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
False Positive ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Detection Accuracy ◽  
Sequence Variant ◽  
Plecoglossus Altivelis ◽  
Detection Rates ◽  
Loop Region ◽  
Intraspecific Genetic Diversity

AbstractRecent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) provide a non-invasive way to evaluate the intraspecific genetic diversity of aquatic macroorganisms. However, erroneous sequences present in HTS data can result in false positive haplotypes; therefore, reliable strategies are necessary to eliminate such erroneous sequences when evaluating intraspecific genetic diversity using eDNA metabarcoding. In this study, we propose an approach combining denoising using amplicon sequence variant (ASV) method and the removal of haplotypes with low detection rates. A mixture of rearing water of Ayu (Plecoglossus altivelis altivelis) was used as an eDNA sample. In total, nine haplotypes of Ayu mitochondrial D-loop region were contained in the sample and amplified by two-step tailed PCR. The 15 PCR replicates indexed different tags were prepared from the eDNA sample to compare the detection rates between true haplotypes and false positive haplotypes. All PCR replications were sequenced by HTS, and the total number of detected true haplotypes and false positive haplotypes were compared with and without denoising using the two types of ASV methods, Divisive Amplicon Denoising Algorithm 2 (DADA2) and UNOISE3. The use of both ASV methods considerably reduced the number of false positive haplotypes. Moreover, all true haplotypes were detected in all 15 PCR, whereas false positive haplotypes had detection rates varying from 1/15 to 15/15. Thus, by removing haplotypes with lower detection rates than 15/15, the number of false positive haplotypes were further reduced. The approach proposed in this study successfully eliminated most of false positive haplotypes in the HTS data obtained from eDNA samples, which allowed us to improve the detection accuracy for evaluating intraspecific genetic diversity using eDNA analysis.

scholarly journals Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

2020 ◽  
Vol 20 (5) ◽  
pp. 1248-1258 ◽  
Author(s):  
Satsuki Tsuji ◽  
Atsushi Maruyama ◽  
Masaki Miya ◽  
Masayuki Ushio ◽  
Hirotoshi Sato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Environmental Dna ◽  
Fish Population ◽  
High Potential ◽  
Wild Fish ◽  
Intraspecific Genetic Diversity

Thinning in mature eastern white pine: 43-year case study

2002 ◽  
Vol 78 (4) ◽  
pp. 539-549 ◽  
Author(s):  
Paul D Anderson ◽  
John C Zasada ◽  
Glen W Erickson ◽  
Zigmond A Zasada
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Large Diameter ◽  
White Pine ◽  
Thinning Intensity ◽  
Pine Regeneration ◽  
Volume Production ◽  
Pine Stands ◽  
Over Time

A white pine (Pinus strobus L.) stand at the western margin of the species range, approximately 125 years of age at present, was thinned in 1953 from 33.5 m2 ha-1 to target residual basal areas of 18.4, 23.0, 27.5, and 32.1 m2 ha-1 . Repeated measurement over the following 43-years indicated that the greatest total volume production and the greatest number of large diameter trees occurred in the unit of highest residual density. Over time, the distribution of stems was predominantly random although mortality between 1979 and 1996 resulted in a tendency for clumping in the 23.0 and 27.5 m2 ha-1 treatments. DNA analysis indicated that thinning intensity had little effect on the genetic diversity of residual white pine. This study suggests that mature white pine stands in northern Minnesota may be managed at relatively high densities without loss of productivity. However, regardless of overstory density, there was little or no white pine regeneration occurring in this stand. Key words: thinning, growth, genetic diversity, molecular markers, spatial pattern, regeneration

scholarly journals Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0149786 ◽  
Author(s):  
Satoshi Yamamoto ◽  
Kenji Minami ◽  
Keiichi Fukaya ◽  
Kohji Takahashi ◽  
Hideki Sawada ◽  
...  
Keyword(s):  
Sea Of Japan ◽  
Environmental Dna ◽  
Fish Distribution ◽  
Jack Mackerel ◽  
Japanese Jack Mackerel

Coppice forests and genetic diversity: A case study in Quercus pyrenaica Willd. from Central Spain

2008 ◽  
Vol 254 (2) ◽  
pp. 225-232 ◽  
Author(s):  
M. Valbuena-Carabaña ◽  
S.C. González-Martínez ◽  
L. Gil
Keyword(s):  
Genetic Diversity ◽  
Quercus Pyrenaica ◽  
Central Spain

scholarly journals Real-Time Hydraulic Interval State Estimation for Water Transport Networks: a Case Study

2017 ◽  
Author(s):  
Stelios G. Vrachimis ◽  
Demetrios G. Eliades ◽  
Marios M. Polycarpou
Keyword(s):  
State Estimation ◽  
Real Time ◽  
Water Distribution ◽  
Estimation Error ◽  
Distribution Networks ◽  
Water Levels ◽  
Water Distribution Networks ◽  
Unaccounted For Water ◽  
Tank Water

Abstract. Hydraulic state estimation in water distribution networks is the task of estimating water flows and pressures in the pipes and nodes of the network based on some sensor measurements. This requires a model of the network, as well as knowledge of demand outflow and tank water levels. Due to modeling and measurement uncertainty, standard state-estimation may result in inaccurate hydraulic estimates without any measure of the estimation error. This paper describes a methodology for generating hydraulic state bounding estimates based on interval bounds on the parametric and measurement uncertainties. The estimation error bounds provided by this method can be applied to estimate the unaccounted-for water in water distribution networks. As a case study, the method is applied to a transport network in Cyprus, using actual data in real-time.

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