scholarly journals Identification of Main Oyster Species and Comparison of Their Genetic Diversity in Zhejiang Coast, South of Yangtze River Estuary

2021 ◽  
Vol 8 ◽  
Author(s):  
Sheng Liu ◽  
Qinggang Xue ◽  
Hongqiang Xu ◽  
Zhihua Lin
Keyword(s):  
Genetic Diversity ◽  
River Estuary ◽  
Population Expansion ◽  
Fixation Index ◽  
Yangtze River Estuary ◽  
Indigenous Species ◽  
Molecular Variance ◽  
Introduction History ◽  
Oyster Species ◽  
C Subunit

Oysters are an important aquaculture species distributed worldwide, including in Zhejiang Province, located on the east coast of China. Because of the high diversity and complicated introduction history of oysters and their seedlings, there has been much disagreement regarding the origin of each species, and the dominant and indigenous species remain unclear. We sampled 16 batches of oysters from seven sites in three aquaculture bays and found two main oyster species, Crassostrea sikamea and Crassostrea angulata. The former occupied the higher intertidal zone and comprised more than 70% of the cultured oysters. Based on the cytochrome oxidase C subunit I (COI) and mitochondrial noncoding region (MNR), C. sikamea showed higher genetic diversity than C. angulata. The analysis of molecular variance among COI sequences of these species from the Xiangshan Bay populations were comparable to those of other populations and showed that most of the molecular variance was within groups, which was consistent with the low pairwise fixation index FST values. The neutrality test revealed that C. sikamea experienced population expansion events, whereas for C. angulata, the significant Fu’s Fs and non-significant Tajima’s D test results may indicate a possible population expansion event, implying that C. sikamea is likely an indigenous species. The method established based on internal transcribed spacer 1 digestion by the HindIII restriction enzyme is useful for identifying C. sikamea and C. angulata in the local region. The specific primers on the MNR sequence show potential for distinguishing C. sikamea from four other important Crassostrea oysters. These results highlight the abundance of C. sikamea on the Zhejiang coast and lay the foundation for protecting and utilizing the local oyster germplasm resources and for the sustainable development of the oyster industry.

scholarly journals Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Antonio Acini Vásquez-Aguilar ◽  
Arturo Barbachano-Guerrero ◽  
Diego F. Angulo ◽  
Víctor Hugo Jarquín-Díaz
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Expansion ◽  
Fixation Index ◽  
Hepatozoon Canis ◽  
Pairwise Comparisons ◽  
Distribution Analysis ◽  
Population Genetic Analysis ◽  
Molecular Variance ◽  
The World

Abstract Background Hepatozoon canis is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of H. canis from various geographical areas around the world. Methods We used 550 publicly available sequences of H. canis from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index (FST) values between groups and pairwise comparisons of FST values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed. Results The dataset of H. canis yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure (GST = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant FST was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups (FCT, p > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant FCT values for groups K = 5. The Tajima’s D and Fu’s Fs show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution). Conclusions The current molecular data confirmed that H. canis does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite. Graphical abstract

scholarly journals Spatial and Temporal Variability of Soil Salinity in the Yangtze River Estuary Using Electromagnetic Induction

2021 ◽  
Vol 13 (10) ◽  
pp. 1875
Author(s):  
Wenping Xie ◽  
Jingsong Yang ◽  
Rongjiang Yao ◽  
Xiangping Wang
Keyword(s):  
Electrical Conductivity ◽  
Spatial Distribution ◽  
Soil Salinity ◽  
Yangtze River ◽  
Laboratory Data ◽  
River Estuary ◽  
Yangtze River Estuary ◽  
Soil Electrical Conductivity ◽  
The Yangtze River ◽  
The Yangtze River Estuary

Soil salt-water dynamics in the Yangtze River Estuary (YRE) is complex and soil salinity is an obstacle to regional agricultural production and the ecological environment in the YRE. Runoff into the sea is reduced during the impoundment period as the result of the water-storing process of the Three Gorges Reservoir (TGR) in the upper reaches of the Yangtze River, which causes serious seawater intrusion. Soil salinity is a problem due to shallow and saline groundwater under serious seawater intrusion in the YRE. In this research, we focused on the temporal variation and spatial distribution characteristics of soil salinity in the YRE using geostatistics combined with proximally sensed information obtained by an electromagnetic induction (EM) survey method in typical years under the impoundment of the TGR. The EM survey with proximal sensing method was applied to perform soil salinity survey in field in the Yangtze River Estuary, allowing quick determination and quantitative assessment of spatial and temporal variation of soil salinity from 2006 to 2017. We developed regional soil salinity survey and mapping by coupling limited laboratory data with proximal sensed data obtained from EM. We interpreted the soil electrical conductivity by constructing a linear model between the apparent electrical conductivity data measured by an EM 38 device and the soil electrical conductivity (EC) of soil samples measured in laboratory. Then, soil electrical conductivity was converted to soil salt content (soil salinity g kg−1) through established linear regression model based on the laboratory data of soil salinity and soil EC. Semivariograms of regional soil salinity in the survey years were fitted and ordinary kriging interpolation was applied in interpolation and mapping of regional soil salinity. The cross-validation results showed that the prediction results were acceptable. The soil salinity distribution under different survey years was presented and the area of salt affected soil was calculated using geostatistics method. The results of spatial distribution of soil salinity showed that soil salinity near the riverbanks and coastlines was higher than that of inland. The spatial distribution of groundwater depth and salinity revealed that shallow groundwater and high groundwater salinity influenced the spatial distribution characteristics of soil salinity. Under long-term impoundment of the Three Gorges Reservoir, the variation of soil salinity in different hydrological years was analyzed. Results showed that the area affected by soil salinity gradually increased in different hydrological year types under the impoundment of the TGR.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Numerical Study on the Expansion and Variation of Changjiang Diluted Water in Summer and Autumn

2021 ◽  
Vol 9 (3) ◽  
pp. 317
Author(s):  
Wanli Hou ◽  
Menglin Ba ◽  
Jie Bai ◽  
Jianghua Yu
Keyword(s):  
Yangtze River ◽  
Sea Water ◽  
Numerical Study ◽  
River Estuary ◽  
Ocean Model ◽  
Theoretical Research ◽  
Yangtze River Estuary ◽  
Hydrodynamic Characteristics ◽  
Changjiang Diluted Water ◽  
Transportation Route

In view of the expansion and directional change mechanisms of Yangtze River water diluted with sea water in the shelf region (also known as Changjiang diluted water [CDW]) during summer and autumn, a three-dimensional hydrodynamic model of the Yangtze River Estuary (YRE) and its adjacent waters was established based on the Finite Volume Community Ocean Model (FVCOM). Compared with the measured data, the model accurately simulates the hydrodynamic characteristics of the YRE. On that basis, the influence of the expansion patterns of the CDW in both summer and autumn was studied. It was found that, in 2019, the CDW expanded to the northeast in the summer and to the southeast in the autumn, and that the route of the CDW is mainly controlled by the wind, not the runoff. Current seasonal winds also change the transportation route of the CDW by affecting its hydrodynamic field. Typhoons are frequent in both summer and autumn, causing abnormalities in both the transportation route and expansion of the CDW. During a typhoon, a large amount of the CDW is transported in a continuous and abnormal manner, accelerating the path turning of the CDW. This paper enhances the existing theoretical research of the CDW and provides a reference with respect to the expansion of diluted water all over the world.

scholarly journals Effect of social structure and introduction history on genetic diversity and differentiation

2021 ◽  
Author(s):  
Sylvia M. Flucher ◽  
Patrick Krapf ◽  
Wolfgang Arthofer ◽  
Andrew V. Suarez ◽  
Ross H. Crozier ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Social Structure ◽  
Introduction History

scholarly journals Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Population Expansion ◽  
Prunus Armeniaca ◽  
River Valley ◽  
Nuclear Ribosomal Dna ◽  
Glacial Refugium ◽  
Ili River Valley ◽  
Wild Apricot

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

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