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

Abstract

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 (Hd) 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 (FCT), 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 FST 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.

Genetic Variability of Wild Populations of Invasive Redclaw Crayfish (Cherax quadricarinatus) von Martens 1868 Across Peninsular Malaysia

“…The low pairwise distance value (0.002 -0.014) further reinforce the grouping of all haplotypes into one clade due to high sequence similarity (Azhar & Azmir, 2019;Azmi et al, 2022). In addition, it is also believed that all the haplotypes from this study came from the native area of this crayfish as the pairwise distance between the haplotypes and C. quadricarinatus from Papua New Guinea and Australia was 0.000 to 0.009, respectively (Zhao et al, 2021;Azmi et al, 2022). Although, it has been widely believed that redclaws were introduce through aquarium trade in Malaysia (Naqiuddin et al, 2016).…”

Genetic variation and population structure of a widely distributed damselfly (Ischnura senegalensis)

“…Low dispersal ability might also block the genetic exchanges between insular populations. Additionally, the existence of rear haplotypes might also be attributed to population expansion events (population expansion was also detected in RKI in Table 3), which might enhance the retention of rear mutations (Zhao et al, 2021). Previous researches indicate that female color polymorphism of I. senegalensis in the Ryukyu Islands might be another factor inducing divergent selection and thus promoted genetic diversification (Inomata et al, 2015).…”