Population Structure and Historical Demography of the Oriental River Prawn (Macrobrachium nipponense) in Taiwan

Genetic Variations and Expansion of the Blue Swimmer Crab (Portunus pelagicus) in Southeast Asia

Blue swimmer crabs (Portunus pelagicus) primarily inhabit the coastal regions of Southeast Asia. This study aimed to examine their population genetic structure, phylogeography, and historical demography by applying partial sequences to the control region in the mitochondrial DNA. The analysis focused on 6 populations comprising 166 individual samples collected from Taiwan (Kezailiao Kaohsiung (KK) and Penghu (PH)), mainland China (Xiamen (XM) and Hong Kong (HK)), Vietnam (Hanoi (VN)), and Singapore (SGP). The estimated nucleotide diversity (π) for all of the samples was 0.062, with values ranging between 0.018 (PH) and 0.045 (HK). Our study collected 116 haplotypes and classified them into lineages A and B. The XM, HK, VN, and SGP populations made up lineage A, and the PH and KK populations comprised lineage B. For each lineage, the results highlighted indications of demographic expansion. Lineage A can be traced back to the second-to-last interglacial period, while lineage B possibly originated in the last glacial period. There were significant differences in the FST values among the six populations, except for the pairs HK–XM and PH–KK. In conclusion, the phylogeography and genetic structure of P. pelagicus in Southeast Asia were potentially affected by the Pleistocene glacial cycles and human introduction. These findings further highlight the possible dispersal routes of P. pelagicus throughout Southeast Asia.

Phylogeography and Genetic Structure of the Swimming Crabs Portunus sanguinolentus (Herbst, 1783) in East Asia

The three-spot swimming crab (Portunus sanguinolentus) is mainly distributed in South East Asia. An analysis of mitochondrial control region partial sequences allows us to determine the population genetic structure, phylogeography and historical demography of this species in East Asia. The seven populations, which included 110 individuals, were collected from mainland China (Shanghai, SH, Xiamen, XM and Hong Kong, HK), Taiwan (Yilan, YL, Taichung, TC, Donggang, DG) and Singapore (Singapore, SGP). The nucleotide diversity (π) of all individuals was 0.01149, with values ranging from 0.00372 (SGP) to 0.01345 (YL). In total, 90 haplotypes have been identified, which can be divided into two major lineages: lineage A consists of specimens from SH, YL, XM, TC and DG, and lineage B corresponds to specimen from SGP. From the second to the most recent interglacial period, population expansion was observed in each lineage. However, a low level of genetic differentiation was also observed in the three-spotted swimming crab, P. sanguinolentus, according to FST values. Our results suggest that several past and present habitat configurations have shaped the genetic patterns of P. sanguinolentus until now. During Pleistocene glaciations, when sea levels were low, this species may have moved along the coast from Southeast Asia to China. It first colonized the Hong Kong area during this era. After sea levels rose and shorelines receded, it subsequently spread to the coast of mainland China.

Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene

BACKGROUND

Chinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding.

METHODS

Palaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package.

RESULTS

Our study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (H_d) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (F_CT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and F_ST between the population pairs indicated that the JN population was distinctive from the others.

CONCLUSIONS

Our study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.

Comparison of morphology and genetic diversity between broodstock and hybrid offspring of oriental river prawn, Macrobrachium nipponense based on morphological analysis and SNP markers

Hybridization is an effective method for the genetic improvement of farmed species. In this study, three broodstock populations (Changjiang, CJ, Dongting, DT, and Dianshan, DS) of oriental river prawn, Macrobrachium nipponense were used, and DS was used as the female broodstock. Through three-line hybridization, two hybrid populations were finally obtained. The F3 generation of the broodstock population and the F1 generation of the hybrid population were cultured indoors for 3 months. Through morphological analysis (cluster analysis, discriminant analysis and path analysis) it was found that the hybrid population and the broodstock had some differences, but not enough to reach the subspecies level, and the dominant traits exhibited differentiation and reorganization. This study identified SNP genetic markers, carried out systematic evolution analysis and genetic diversity analysis and found that the nucleotide diversity π and heterozygosity Het of the hybrid population were higher than those of the broodstock. Among broodstocks, the differentiation index (F_st ) of SCD and SDC was smallest (0.055). This research provides some valuable reference for genetic breeding.

Trace metal pollution risk assessment in urban mangrove patches: Potential linkage with the spectral characteristics of chromophoric dissolved organic matter

Mangroves are inter-tidal ecosystems with important global ecological roles. Today, mangroves around the world are at risk of fragmentation, especially in areas with rapid urbanization. Mangroves experiencing habitat fragmentation may be more intensely affected by human activities and a scenario that might have been ignored by previous studies on trace metal (TM) environmental geochemistry. Here, we investigated the typically fragmented habitats in a subtropical mangrove estuary (the Danshuei Basin in Taiwan Strait) to evaluate how human activities affect the geochemical behaviors of TMs. Ni, Sb, Zn, Cr, Cu, and Cd were the primary contaminants found in the mangrove patches. Metal sequestration from the riverine (Ni, Cr) and in-patch activity (Sb, Zn, Cu, Cd) are primary sources of TM's risk. Using the synthesized pollution risk assessment, we showed that most of the mangrove patches are under moderate pollution risk. A significant relationship between the TMs pollution indicators and the absorption coefficient at 254 nm (a₂₅₄), implying that the a₂₅₄ could be a potential convenient parameter in the TMs risk assessment, which might be partly explained by the bio-remediation of sulfate-reduction microorganism. This study demonstrates the ecological risks posed by TM pollution on urban mangrove patches and emphasizes the importance of a more comprehensive survey for estuarine mangrove patch environments to achieve Sustainable Development Goals.

Genetic diversity analysis of the oriental river prawn (Macrobrachium nipponense) in Huaihe River

The oriental river prawn (Macrobrachium nipponense) is an economically and nutritionally important species of decapod crustaceans in China. Genetic structure and demographic history of Macrobrachium nipponense were examined using sequence data from portions of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Samples of 191 individuals were collected from 10 localities in the upper to middle reaches of the Huaihe River. Variability was detected at a total of 42 nucleotide sites along 684 bp length of homologous sequence (6.14%), and base substitutions occurred mostly at the second codon position. Haplotype diversity (h) and nucleotide diversity (π) of all populations were 0.9136 ± 0.0116 and 0.0078 ± 0.0042, respectively. Phylogenetic tree constructed using the maximum-likelihood (ML) method showed that the 44 haplotypes were assigned to two obvious clades associated with geographic regions. Moreover, the median-joining network was similar to the topology of the phylogenetic tree with 44 haplotypes. The pairwise F_ST values between the populations varied from -0.0298 to 0.2994. Generally, moderate genetic differentiation (F_ST = 0.1598, p = .0000) among different geographic populations was detected, with the significant differentiation between the Huaibin (HB) and other Macrobrachium nipponense populations. Both mismatch distribution analyses and neutrality tests suggested the early stage of Late Pleistocene population expansion 85,500 years before present for the species, which was consistent with the palaeoclimatic condition of the Huaihe River Basin.

Epidemiological risk factors of knowledge and preventive practice regarding avian influenza among poultry farmers and live bird traders in Ikorodu, Lagos State, Nigeria

Avian Influenza (AI) is an infectious disease of birds caused by type A influenza virus. The disease has a pandemic risk leading to death or depopulation of millions of birds. This study determined the risk factors that predict adequate knowledge and good preventive practice measures towards AI, among poultry farmers and live bird traders in Ikorodu, Lagos State, South-western Nigeria. A descriptive cross sectional survey was conducted with questionnaire on socio- demographics, knowledge of definition, and transmission of avian influenza administered to 244 respondents at interview. Descriptive, Chi-square and logistic regression analysis were carried out to explore associations between demographic characteristics, knowledge and preventive practice scores. All levels of significance were set at p < 0.05. The total knowledge score computed on a 25-item scale revealed a mean total knowledge of 9.9 (SD ± 6.6). Respondents aged <20 years, live bird traders and those with no formal education had the poorest knowledge. The total preventive practice score regarding avian influenza on a 9-item scale revealed a mean of 5.3 (SD ± 2.1). Younger respondents, live bird traders; those with no tertiary education and those spent <24 months in their profession had the poorest preventive practice score. Logistic regression analysis showed that increasing education (p < 0.05) significantly predicted adequate knowledge of avian influenza and good preventive practice among respondents. Poultry farmers and live bird traders, specially those with no formal education, should be aware of the transmission, seriousness and preventive measures of AI that will be reflected in the prevention and control of the disease in Nigeria.

Phylogeography and genetic structure of the oriental river prawn Macrobrachium nipponense (Crustacea: Decapoda: Palaemonidae) in East Asia

The oriental river prawn (Macrobrachium nipponense) is mainly distributed in East Asia. The phylogeography, population genetic structure and historical demography of this species in the East Asia were examined by using partial sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA in mitochondrial DNA. Ten populations that included 239 individuals were collected from Taiwan (Shihmen Reservoir, SMR, Mingte Reservoir, MTR and Chengching Lake Reservoir, CLR), mainland China (Taihu Lake, TLC, Min River, MRC, Jiulong River, JRC and Shenzhen Reservoir, SRC), Japan (Biwa Lake, BLJ and Kasumigaura Lake, KLJ) and Korea (Han River, HRK). The nucleotide diversity (π) of all individuals was 0.01134, with values ranging from 0.0089 (BLJ, Japan) to 0.01425 (MTR, Taiwan). A total of 83 haplotypes were obtained, and the haplotypes were divided into 2 main lineages: lineage A included the specimens from BLJ, KLJ, CLR, MTR, TLC, MRC and JRC, and lineage B comprised the ones from HRK, SRC, SMR, MTR, TLC, MRC and JRC. Lineage A could be further divided two sub-lineages (A₁ and A₂). Individuals of lineage A₂ were only from TLC. Demographic expansion was observed in each lineage, starting within the second-to-latest interglacial period for lineage A and within the last glacial period for lineage B. All F_ST values among the ten populations were significantly different, except for the values between MRC and JRC, and SMR and SRC. The phylogeography and genetic structure of M. nipponense in East Asia might be influenced by Pleistocene glacial cycles, lake isolation and human introduction. The possible dispersal routes of M. nipponense in the East Asia were also discussed.