Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers

The razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations (Fst value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, monitoring the interbreeding status of the two genetically distinct populations and the genetic differentiation within each population is important for conserving the genetic diversity of S. constricta in Japan.

Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers

The razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations (Fst value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, the two genetically distinct populations need to be available as fishery resources, while taking into account their conservation and hybridization status.

Improved MODIS-Aqua Chlorophyll-a Retrievals in the Turbid Semi-Enclosed Ariake Bay, Japan

The accurate retrieval of chlorophyll-a concentration (Chl-a) from ocean color satellite data is extremely challenging in turbid, optically complex coastal waters. Ariake Bay in Japan is a turbid semi-enclosed bay of great socio-economic significance, but it suffers from serious water quality problems, particularly due to red tide events. Chl-a derived from the MODerate resolution Imaging Spectroradiometer (MODIS) sensor on satellite Aqua in Ariake Bay was investigated, and it was determined that the causes of the errors were from inaccurate atmospheric correction and inappropriate in-water algorithms. To improve the accuracy of MODIS remote sensing reflectance (Rrs) in the blue and green bands, a simple method was adopted using in situ Rrs data. This method assumes that the error in MODIS Rrs(547) is small, and MODIS Rrs(412) can be estimated from MODIS Rrs(547) using a linear relation between in situ Rrs(412) and Rrs(547). We also showed that the standard MODIS Chl-a algorithm, OC3M, underestimated Chl-a, which was mostly due to water column turbidity. A new empirical switching algorithm was generated based on the relationship between in situ Chl-a and the blue-to-green band ratio, max(Rrs(443), Rrs(448)/Rrs(547), which was the same as the OC3M algorithm. The criterion of Rrs(667) of 0.005 sr−1 was used to evaluate the extent of turbidity for the switching algorithm. The results showed that the switching algorithm performed better than OC3M, and the root mean square error (RMSE) of estimated Chl-a decreased from 0.414 to 0.326. The RMSE for MODIS Chl-a using the recalculated Rrs and the switching algorithm was 0.287, which was a significant improvement from the RMSE of 0.610, which was obtained using standard MODIS Chl-a. Finally, the accuracy of our method was tested with an independent dataset collected by the local Fisheries Research Institute, and the results revealed that the switching algorithm with the recalculated Rrs reduced the RMSE of MODIS Chl-a from 0.412 of the standard to 0.335.