GENETIC DIFFERENTIATION AMONG POPULATIONS OF Chromobotia macracanthus BLEEKER FROM SUMATRA AND KALIMANTAN BASED ON SEQUENCING GENE OF MTDNA CYTOCHROME B AND NUCLEUS DNA RAG2

In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic diversity. Analyses of a 436 base pair fragment of the mtDNA control region revealed that the endemic C. joculator exhibited high haplotype (h > 0.98 at both locations) and nucleotide (Christmas p% = 3.63, Cocos p% = 9.99) diversity. Similarly, isolated populations of widespread angelfishes (C. bispinosa and C. flavicauda) had high haplotype (h > 0.98) and nucleotide (p% = 2.81 and p% = 5.78%, respectively) diversity. Therefore, in contrast to terrestrial patterns, endemic and isolated populations of widespread angelfishes do not have low genetic diversity, rather their haplotype and nucleotide diversities were among the highest reported for marine fishes. High genetic diversity should reduce extinction risk in these species as it could provide the evolutionary potential to adapt to the rapidly changing environmental conditions forecast for coral reefs.

Odontobutis potamophila is a Chinese endemic species and an economically important fishery resource in the Yangtze River. The genetic variability of O. potamophila was studied based on the sequence analysis of mitochondrial DNA control region from 150 individuals of five geographical populations including from Dangtu (n = 30), Sheyang (n = 30), Yuyao (n = 30), Tai Lake nearby Dongxishan (n = 30) and Minjiang (n = 30). Among five populations, the genetic distance between Minjiang population and other populations (0.1186–0.1223) was larger than that among four populations except for Minjiang (0.0015–0.0198). In addition, 23 haplotypes were obtained and each population had special haplotypes. The samples from five sites had high haplotype diversity (0.80510) and low nucleotide diversity (0.04028). Through Tajima’s D and Fu’s F neutral testing and mismatch distribution test among all geographical populations, O. potamophila did not undergo recent population expansion. During the population evolution, O. potamophila experienced a balanced selection function and maintained a stable state and population size. Moreover, the haplotype Neighbor-Joining (NJ) tree was separated two haplotype groups. The NJ tree, TCS network and median-joining network could clearly separate the haplotypes of the specimens from different areas. Analysis of molecular variance and pairwise FST revealed an obvious genetic differentiation among different geographical populations, suggesting that O. potamophila in different geographical populations should be managed and conserved separately.

In order to analyze the genetic diversity and genetic differentiation of Gymnocypris chilianensis, D-loop region of the mitochondrial DNA was sequenced in 50 individuals of G. chilianensis obtained from 2 geographic locations (Heihe River and Shule River) and 25 individuals of G. przewalskii (Qinghai Lake). Twenty-five homologous sequences of another G. eckloni (Yellow River) downloaded from GenBank were analyzed together. The sequences were analyzed by using the MEGA (version 7.0) and DnaSP (version 6.0) software. The results revealed that 82 haplotypes were detected among 100 individuals. The haplotype diversity (Hd) and nucleotide diversity (Pi) of G. chilianensis of the Shule River were 0.963 ± 0.029 and 0.00414 ± 0.00069, which were lower than those of 3 other populations. The genetic distance of G. chilianensis in both Heihe River and Shule River was 0.0013. The genetic distances between the 2 G. chilianensis populations and the G. eckloni were 0.0148 and 0.0141, respectively. Population differentiation values (Fst) and gene flow (Nm) showed that 4 population had occurred obvious genetic differentiation (Fst: 0.20811 ∼ 0.98863. p < 0.01; Nm < 1). Compared with G. przewalskii and G. eckloni, the differentiation degree was more significant between Heihe River G. chilianensis and Shule River G. chilianensis (Fst = 0.98863, p < 0.01; Nm = 0.00287). Maximum Likelihood (ML) phylogenetic tree showed that G. chilianensis had further genetic distance with G. eckloni and G. przewalskii. In conclution, G. chilianensis (HH&SL) had lower genetic diversity and further genetic distance than G. przewalskii (QH) and G. eckloni (YL). We suggest strengthen the protection of genetic resources of G. chilianensis.

Aim: To investigate genetic diversity, gene flow and demographic history of frigate tuna (Auxis thazard) populations found in Tanzanian marine waters.&#x0D; Study Design: The study used a descriptive research design whereby fish samples were randomly collected from four locations and the genetic variation within and among the four populations analyzed using mitochondrial DNA (mtDNA) control region.&#x0D; Place and Duration of the Study: Fish samples were collected from landing sites in Tanga, Dar es Salaam, Mtwara and Zanzibar, Tanzania. The study was conducted between July 2020 and June 2021.&#x0D; Methodology: A total of 100 frigate tuna were randomly sampled from small-scale fishermen at the landing sites of Dar-es-Salaam (20), Tanga (30), Mtwara (30), and Zanzibar (20). For each fish, 50 g muscle tissue was obtained and put in a vial containing 95% ethanol. DNA was extracted from the muscle using a commercial DNA Kit (Quick-DNATM Miniprep Plus Kit, Zymo Research Corp.) according to the instructions of the manufacturer and a fragment of 432 bp of the mtDNA control region was amplified and sequenced using ABI PRISIM™ 3100 Genetic Analyzer (Applied Biosystems). Haplotype and nucleotide diversity, gene flow and historic demographic were estimated from 92 fish samples.&#x0D; Results: A total of 88 haplotypes were identified in all fish samples. The highest haplotype diversity was found in Zanzibar (1.000 ± 0.017) and Mtwara (1.000 ± 0.010) populations while the lowest was observed in Tanga population (0.992 ± 0.012). Tanga population had the highest nucleotide diversity (0.078 ± 0.018) while Dar es Salaam had the lowest (0.016 ± 0.009). The highest genetic differentiation (FST) was found between Tanga and Dar-es-Salaam (0.178) and the lowest was observed between Mtwara and Zanzibar (0.016). The genetic distances between pairs of populations were small. The phylogenetic tree revealed two main clusters. Cluster 1 which consisted of nine haplotypes was dominated by Tanga population with seven haplotypes while the remaining two haplotypes were from Mtwara and the reference sequences of Euthynnus affinis (Kawakawa tuna). Cluster II had 84 haplotypes of individuals from all four populations, with no population specific subcluster. The number of immigrants per generation was highest between Mtwara and Zanzibar (Nm=18.310) and lowest between Tanga and Dar-es-Salaam (Nm=1.180). The neutrality test indicated negative values, suggesting a recent population expansion.&#x0D; Conclusion: There is high genetic diversity within the populations, but there is no significant genetic differentiation among the four frigate tuna populations, suggesting that the four populations comprise a single panmictic population.

Native to tropical America, the charru mussel, Mytella strigata, has been spreading rapidly in the West Pacific Ocean, including the South China Sea. In order to study the adaptive evolution of M. strigata and examine the present status of invasion in China, the mitochondrial nad2 gene fragment was employed to analyze the genetic variations of seven populations sampled in both spring and autumn 2023. Results showed that all the populations had high haplotype diversity (>0.5) and low nucleotide diversity (<0.005), suggesting the ongoing rapid expansion following a genetic bottleneck. The Zhanjiang population had the highest genetic diversity in spring with 22 haplotypes, 37 polymorphic sites, and haplotype diversity, nucleotide diversity, and the average number of nucleotide differences being 0.911, 0.00623, and 4.341, respectively. However, in autumn, the Shanwei population had the most haplotypes (11) and polymorphic sites (19), with the highest haplotype diversity value of 0.891, while the Qunjian population had the highest nucleotide diversity (0.00392) and average number of nucleotide differences (2.809). Combining geographic populations by seasons confirmed lower genetic diversity in autumn compared to spring, evidenced by fewer haplotypes and polymorphic sites, reduced haplotype diversity and nucleotide diversity, and lower genetic distance within populations. These findings provided evidence for understanding the molecular characteristics of M. strigata population expansion in China.

Silver carp’s (Hypophthalmichthys molitrix) traits and genetic structure are being impacted by artificial proliferation and restocking enhancement. A clear genetic background of cultured silver carp is helpful for exploitation and utilization. Limited research reported the germplasm resources of cultured silver carp. This study was conducted to investigate the genetic diversity of cultured silver carp. Two hundred thirty‐three silver carps were sampled from eight cultured populations in Hubei province, and their population structures were analyzed by mitochondrial COI gene. Average contents of bases T, C, A, and G in the 659 bp COI gene sequence were 30.03%, 26.62%, 26.08% and 17.32%, respectively. And 18 haplotypes were defined from 77 variable nucleotides in COI gene. The haplotypes and nucleotide diversities were 0.604 and 0.00325, respectively. Meanwhile, the highest genetic diversity and lowest genetic diversity were detected in cultured populations from Jianli population (Hd: 0.883 and π: 0.00699) and Yaowan population (Hd: 0.186 and π: 0.00085), respectively. Pairwise fixation index (Fst) analysis revealed that the level of genetic diversity was moderate (Fst: 0.06). The genetic distance between and within populations were 0.00353 and 0.00329, respectively. And the genetic variation occurred mainly within populations (93.42%), but genetic variation between the population was only 6.58%. Therefore, moderate‐level genetic diversity was observed with high haplotype diversity and low nucleotide diversity, suggesting that inbreeding should be avoided among the eight cultured populations in Hubei.

The ricebean genome provides insight into Vigna genome evolution and facilitates genetic enhancement.

Nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P < 0.001) and among regions (PhiCT = 0.368, P < 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.

AimThe coqui frog (Eleutherodactylus coqui) was introduced to the Hawai'ian archipelago in the late 1980s and became established as a widespread species on Hawai'i Island over a short timespan, suggesting that humans are facilitating their movement. To determine the importance of human facilitation, we assessed dispersal patterns and genetic structure of coqui populations using microsatellite data.LocationHawai'i Island.MethodsWe obtained genotype data using seven microsatellites from coqui specimens collected from 25 populations on Hawai'i Island. The dispersal mechanism was examined using a Mantel test in GenAlEx and a genetic distance tree analysis in Phylip. Allelic diversity, measures of equilibrium, and genetic structure were analysed in GenAlEx and Arlequin. The correlation between genetic distance and geographical distance was used to distinguish between diffusion dispersal (positive correlation) and jump dispersal (zero or negative correlation).ResultsThe Mantel test for isolation by distance found no significant correlation between genetic and geographical distance (r2 = 0.002, P = 0.4401). The genetic distance tree topology is consistent with this result and exhibited a pattern expected if population establishment occurred through jump dispersal. Migration rates were high (NM = 4.228), inbreeding was high, genetic differentiation between populations was low, and significant genetic structure was detected among populations (4% of total variation, P &lt; 0.002).Main conclusionsGenetic distance is not correlated with geographical distance, suggesting that humans are important facilitators of coqui dispersal. Migration rate was high, indicating that the rapid expansion of coquies on Hawai'i Island was human‐facilitated, while high levels of inbreeding and significant genetic structure suggest low post‐establishment dispersal. If this is the case, early detection of coqui populations will be crucial for management due to their propensity to be spread through human‐facilitated jump dispersal, followed by slow rates of diffusion dispersal from these newly established populations.

This noble research provides information on the genetic differentiation between black-skinned and white-skinned ectotypes of giant African land snails (Archachatina marginata). Ten (10) snails consisting of five (5) black-skinned and five (5) white-skinned ectotypes were examined by using the random amplified polymorphic DNA (RAPD) technique. Five (5) primers (OPAD-09, OPAE-04, OPAE-05, OPAF-07 and OPAF-09) were screened and selected to amplify DNA from the ten (10) samples of snails. A total of 31 bands were generated from the two snail types, out of which 14 bands were generated from the black-skinned ectotype, while 17 bands were from the whiteskinned ectotype. The DNA banding between the two ectotypes showed no statistical difference (P &gt; 0.05) between the black-skinned and the white-skinned ectotypes of Archachatina marginata. There were however, relative high genetic differences in numerical number of bands between the two ectotypes. This implied that the genetic similarities are relatively low. The high genetic differences between the two ectotypes of Archachatina marginata snails studied signaled high level of genetic diversity and heterogeneity among the giant African land snails (GALS).Keywords: DNA, Banding, Differentiation, Black-skinned, White-skinned

PDF HTML阅读 XML下载 导出引用 引用提醒 南海鸢乌贼的遗传差异: 种群分化还是种间分化 DOI: 作者: 作者单位: 中国水产科学研究院南海水产研究所, 农业农村部外海渔业开发重点实验室, 广东 广州 510300 作者简介: 李敏(1984-),男,博士,副研究员,从事海洋生物多样性和保护研究.E-mail:limin@scsfri.ac.cn 通讯作者: 中图分类号: S931 基金项目: 国家重点研发计划项目（2018YFC1406500）；农业农村部财政专项（NFZX2018）；广东省自然科学基金项目（2014A030310177）；国家重点基础研究发展计划项目（2014CB441500）. Genetic differentiation of the purpleback flying squid, Sthenoteuthis oualaniensis, in the South China Sea:population or species divergence Author: Affiliation: Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs;South China Sea Fisher-ies Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:利用线粒体ND2、COI和16S rDNA序列，对2012年9月至2015年9月采自南海的鸢乌贼（）样本进行了种群遗传结构的分析。系统发育关系显示鸢乌贼中型群和微型群各自形成了单系群分支，而分支内没有形成与地理群体或季节群体对应的支系。分子方差分析同样表明，地理群体或季节群体之间不存在明显的遗传分化，而中型群和微型群之间具有极显著的遗传分化（<0.0001）。遗传多样性分析显示，鸢乌贼中型群和微型群均呈现出较高的单倍型多样性（0.9465和0.8545）和较低的核苷酸多样性（0.0051和0.0021），中型群的遗传多样性指数要高于微型群。基于ND2、COI和16S rDNA序列计算的中型群和微型群之间的遗传距离分别达到了14.0%、9.6%和8.8%，远大于类群内的遗传分化（平均<1%）。研究结果表明，南海鸢乌贼存在分布高度重合且有显著遗传分化的两个种群，即中型群和微型群。中型群和微型群之间的遗传差异达到了种间分化的水平，提示体型较大、具有背部发光器的中型群鸢乌贼（典型鸢乌贼）与体型较小、背部发光器缺失的微型群鸢乌贼可能是两个相互独立的种类。 Abstract:In the present study, the population differentiation of the purpleback flying squid () in the South China Sea was examined based on mitochondrial ND2, COI, and 16S rDNA sequences, using samples collected between September 2012 and September 2015. Phylogenetic analysis revealed two significantly divergent monophyletic groups corresponding to the "medium form" and the "dwarf form, " but no geographical lineages corresponding to the sampling localities or seasonal groups were found. The Analysis of Molecular Variance also revealed significant genetic differentiation between the "medium form" and the "dwarf form" (<0.0001), while no genetic variance between either geographic populations or seasonal groups was found. The genetic diversity analysis showed that both the "medium form" and the "dwarf form" of in the South China Sea were characterized by high haplotype diversity (0.9465 and 0.8545) and low nucleotide diversity (0.0051 and 0.0021). The genetic distance between the ‘medium form’ and the "dwarf form" based on ND2, COI, and 16S sequences were 14.0%, 9.6%, and 8.8%, respectively. The genetic distances between the two forms were considerably larger than the genetic distances within each of the two forms (<1%). It was demonstrated that two divergent populations of were sympatrically distributed in the South China Sea, i.e. the "medium form" and the "dwarf form." The genetic differentiation between these two populations was similar to that among separate species within Ommastrephidae, which indicated that the two morphologically distinct forms of the purpleback flying squid, namely the "medium form" (middle sized, with a photophore) and the "dwarf form" (small sized, without a photophore), are two distinct species. 参考文献 相似文献 引证文献

When species are introduced to a new environment, they can quickly adapt to the environment and may differ from the indigenous species. The indigenous population of Protosalanx chinensis has a high level of genetic diversity, but it is unclear on the genetic diversity of the introduced populations in northeast China, which supports the major production of P. chinensis in the world. A total of 556 individuals of P. chinensis were collected during 2016-2021, from Lianhuan Lake (LHL), Xingkai Lake (XK), and Shuifeng Reservoir (SF), and one population was collected from the indigenous Taihu Lake (TH). Overall, 36 haplotypes were detected, and the genetic differences in P. chinensis populations within and between river basins were investigated. The nucleotide diversity (π) of the populations ranged from 0.0005 to 0.0032, and the haplotype diversity (Hd) ranged from 0.455 to 0.890, with the highest genetic diversity in the TH population, followed by the SF population, and lower genetic diversity in the XK and LHL populations. The analysis of the genetic differentiation index (Fst) and the genetic distance between populations showed that there was significant genetic differentiation between the TH population and the other populations. More sampling points have been set up in LHL for further analysis; the Dalong Lake (DL) and the Xiaolong Lake (XL) populations were far from the other populations within the LHL population. In this study, we didn't find a correlation between population size, stability, and genetic diversity, and the ecological measures of management should be decisive to the population dynamics. These results provide a basis for the rational utilization and effective management of P. chinensis.

The genetic diversity and population genetic structure of Onchidium “struma” were investigated using mitochondrial cytochrome c oxidase subunit I (CO I) gene sequences. A total of 240 individuals representing 10 collection sites from across a large portion of its known range were included in the analysis. Overall, 42 haplotypes were defined and 97 polymorphic sites were observed. The O. “struma” populations had high haplotype diversity (0.9280) and nucleotide diversity (0.0404). We inferred that the early maturity and extensive survival habitat led to high genetic diversity of O. “struma” populations in China. Bayesian analysis and SAMOVA analysis showed significant genetic differentiation among populations and all populations were divided into two groups, (HK and HN) versus (GY, DF, CX, CN, ND and XM). The Mantel test revealed no significant correlation between geographic distance and genetic distance (r = 0.251; p = 0.058). Restricted gene flow caused by a shorter term pelagic veliger stage and limited dispersal potential were inferred to result in genetic differentiation among populations based on nested analysis. HK population might be an invasive species by artificial transplantation.

Triatoma dimidiata is the second most important vector of Chagas disease in Colombia after Rhodnius prolixus. Population genetic studies are essential for the adequate design and implementation of vector control and surveillance strategies. The level of genetic variability and population differentiation was surveyed among three Colombian populations of T. dimidiata from different geographic locations and ecotopes, using ND4 mitochondrial gene. Genetic comparison was made between two wild populations from La Guajira (n=10) and Santander (n=10) provinces, and one intra (n=15) and one peridomiciliary (n=5) population from the Cesar province. The polymorphism frequencies of the ND4 mitochondrial gene sequence were analyzed to deduce population structure based on the 40 samples. Colombian T. dimidiata showed a high nucleotide (π: 0.034) and haplotype diversity (Hd: 0.863), as well as significant population subdivision (fST: 0.761) and a low migration rate (Nm: 0.157). Genetic distances and variability differences among populations indicate distinct population subdivision amongst the three provinces. ND4 proved useful in elucidating the significant genetic differentiation that has occurred among T. dimidiata populations from La Guajira, Cesar and Santander. The analysis suggested a relationship between population subdivision and some eco-epidemiological attributes of this vector from the central eastern and northwestern regions of Colombia.

Esox lucius is an economically important freshwater species. Mitochondrial cytb, 12SrRNA, and 16SrRNA gene sequences were used in order to clarify the genetic variation and population structure in three E. Lucius populations, i.e., one Wild population (W) and two hatchery populations (Hatchery Population I-HPI and Hatchery Population II-HPII). A total of 55 individuals, with 19 from wild and 18 from each hatchery population, were sequenced. The results are as follows: 1) cytb. Eleven variable sites defined eight distinct haplotypes, with 1137 base pairs (bp) complete cytb sequences. The nucleotide diversity (π) values were W 0.009%, HPI 0.075% and HPII 0.068%, respectively. Genetic distances within and between populations were both between 0 and 0.1%. Analysis of molecular variance (AMOVA) analysis revealed that variation within populations accounts for 98.49% of total variation. 2) 12SrRNA. We obtained 380 bp consensus 12SrRNA sequence and found little variation among the 55 sequences. 3) 16SrRNA. Twelve variable sites defined seven haplotypes, with 519 bp consensus 16SrRNA sequence. The π values were W 0.041%, HPI 0.310% and HPII 0.021%, respectively. Genetic distances were between 0 and 0.3% within populations and from 0 to 0.2% between populations. AMOVA disclosed that variation within populations accounts for 91.79% of total variation. Variation within populations is the main source of total variation. The results suggest that low genetic variation can be found in both wild and hatchery populations of E. lucius, and the effect of genetic drift and adaptation to culture conditions gradually emerged under only two generations’ artificial cultivation.