Fluctuating asymmetry in the insular population of ayu, Plecoglossus altivelis ryukyuensis, estimating its genetic diversity at extinction

2021 ◽  
Author(s):  
Linh Manh Ha ◽  
Shin-ichiro Oka ◽  
Kei’ichiro Iguchi
Keyword(s):  
Genetic Diversity ◽  
Fluctuating Asymmetry ◽  
Plecoglossus Altivelis ◽  
Plecoglossus Altivelis Ryukyuensis ◽  
Insular Population

scholarly journals Does construction in the spawning ground improve the riverbed conditions making it suitable for spawning of the Ryukyu-ayu Plecoglossus altivelis ryukyuensis?

2020 ◽  
Vol 67 (4) ◽  
pp. 493-501
Author(s):  
Satoshi Awata ◽  
Tetsuya Tsuruta ◽  
Shin-ichiro Abe ◽  
Toshihiko Yonezawa ◽  
Kei’ichiro Iguchi
Keyword(s):  
Spawning Ground ◽  
Plecoglossus Altivelis ◽  
Plecoglossus Altivelis Ryukyuensis

scholarly journals AFLP Analysis of Genetic Diversity in Three Populations of Ayu Plecoglossus altivelis

1999 ◽  
Vol 65 (6) ◽  
pp. 888-892 ◽  
Author(s):  
Shingo Seki ◽  
Jeremy J. Agresti ◽  
G. A. E. Gall ◽  
Nobuhiko Taniguchi ◽  
Bernie May
Keyword(s):  
Genetic Diversity ◽  
Aflp Analysis ◽  
Plecoglossus Altivelis

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 Using environmental DNA analyses to assess the occurrence and abundance of the endangered amphidromous fish Plecoglossus altivelis ryukyuensis

2020 ◽  
Vol 8 ◽  
Author(s):  
Yoshihisa Akamatsu ◽  
Gen Kume ◽  
Masuji Gotou ◽  
Takanori Kono ◽  
Takuma Fujii ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Dna Fragments ◽  
Plecoglossus Altivelis ◽  
Endangered Fish ◽  
Non Invasive ◽  
Plecoglossus Altivelis Ryukyuensis ◽  
Natural Monument ◽  
Conservation Plans ◽  
Three Rivers ◽  
Probe Set

The Ryukyu ayu Plecoglossus altivelis ryukyuensis is an endangered amphidromous fish that inhabits rivers in the Ryukyu Archipelago (Japan). Populations of the species have declined dramatically. Consequently, the Ryukyu ayu has been registered as a natural monument in Japan and monitoring surveys with direct catching are restricted legally. This restriction, unfortunately, makes monitoring of population abundances difficult and creates a barrier to both advancing understanding of the species’ status and the development of appropriate conservation plans. We developed a non-invasive monitoring methodology using eDNA analyses. We designed a specific quantitative PCR assay for the Ryukyu ayu using the mitochondrial ND4 region. Using this primer/probe set, we conducted eDNA analyses in three rivers on Amami-Ohshima Island. The DNA fragments were amplified from the eDNA extracted from natural water in each river. The numbers of DNA fragments detected were positively correlated with individual counts of fish obtained by visual snorkelling surveys. Our method does not contravene restrictions and facilitates abundance monitoring of this endangered fish species.

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