Fu's Fs Tests Research Articles

Seasonal distribution and population genetic structure of Psenopsis anomala (Japanese butterfish) inferred from otolith oxygen isotope ratios and mitochondrial DNA

Psenopsis anomala (Japanese butterfish) is a commercially important fish species with a wide distribution in the Northwest Pacific Ocean, but its catch in Taiwanese waters has been declining for decades. This study aims to elucidate the migration pattern and population structure of P. anomala by analyzing otolith δ18O values, mitochondrial COI and cyt b sequences, respectively. The results reveal a seasonal migration pattern between the northern South China Sea and the Yellow Sea. Analysis of the haplotype network reveals that most P. anomala collected from each location share the haplotypes Hap1 and Hap5, while each population also has its own unique haplotypes. Analysis of molecular variance reveals that the primary variation (92.98%) is observed among individuals within the populations. Fu's FS test conducted for all populations showed no significant differences, and the mismatch distribution aligns with recent population expansion. Both the maximum likelihood tree and the median-joining network show no geographic population structuring in P. anomala samples from Japan and Taiwan. The combined findings from otolith microchemistry and genetic analysis suggests that P. anomala distributed in east Asia shall be managed as a single stock.

Integrating wing morphometrics and mitochondrial DNA analysis to assess the filaria vector Mansonia uniformis (Diptera: Culicidae) populations in Thailand.

Mansonia uniformis (Diptera: Culicidae) is recognized as a vector of Brugia malayi and has been reported to transmit Wuchereria bancrofti, both causing lymphatic filariasis in humans. This study employed geometric morphometrics (GM) to investigate wing shape variation and analyzed genetic diversity through cytochrome c oxidase subunit 1 (COI) gene analyses in Ma. uniformis populations across Thailand. Wing GM analyses indicated significant differences in wing shape based on Mahalanobis distances among nearly all population pairs (p < 0.05), with no significant correlation between wing shape and geographic distance (r = 0.210, p > 0.05). Genetic analyses identified 63 haplotypes and 49 polymorphic sites, with the overall population exhibiting a nucleotide diversity of 0.006 (± 0.001) and a haplotype diversity of 0.912 (± 0.017). Deviations from neutrality, as indicated by Tajima's D and Fu's FS tests for the overall Ma. uniformis populations in Thailand, were statistically significant and negative, suggesting population expansion (both p < 0.05). Analysis of molecular variance revealed no significant genetic structure when all populations were categorized based on collection sites and geographic regions. However, significant differences in FST values were observed between some populations. These findings enhance our understanding of the geographical and genetic factors influencing Ma. uniformis populations, which are crucial for developing effective control strategies in Thailand.

Phylogeography, Genetic Diversity and Population Structure of Echinococcus granulosus Sensu Stricto Inferred by Mitochondrial DNA Markers between Southeast of Iran and Pakistan.

Current study was designed to provide a better insight into the circulating genotypes, genetic diversity, and population structure of Echinococcus spp. between southeast of Iran and Pakistan. From Jun 2020 to Dec 2020, 46 hydatid cysts were taken from human (n: 6), camel (n: 10), goat (n: 10), cattle (n: 10) and sheep (n: 10) in various cities of Sistan and Baluchestan Province of Iran, located at the neighborhood of Pakistan. DNA samples were extracted, amplified, and subjected to sequence analysis of cox1 and nad1 genes. The phylogeny inferred by the Maximum Likelihood algorithm indicated that G1 genotype (n: 19), G3 genotype (n: 14) and G6 genotype (n: 13) assigned into their specific clades. The diversity indices showed a moderate (nad1: Hd: 0.485) to high haplotype diversity (cox1: Hd: 0.867) of E. granulosus s.s. (G1/G3) and low nucleotide diversity. The negative value of Tajima's D and Fu's Fs test displayed deviation from neutrality indicating a recent population expansion. A parsimonious network of the haplotypes of cox1 displayed star-like features in the overall population containing IR9/PAK1/G1, IR2/PAK2/G3 and IR18/G6 as the most common haplotypes. A pairwise fixation index (Fst) indicated that E. granulosus s.s. populations are genetically moderate differentiated between southeast of Iran and Pakistan. The extension of haplotypes PAK18/G1 (sheep) and PAK26/G1 (cattle) toward Iranian haplogroup revealed that there is dawn of Echinococcus flow due to a transfer of alleles between mentioned populations through transport of livestock or their domestication. The current findings strengthen our knowledge concerning the evolutionary paradigms of E. granulosus in southeastern borders of Iran and is effective in controlling of hydatidosis.

Investigation and genetic polymorphism analysis of rodents infected with Echinococcus in Ili Prefecture, Xinjiang Uygur Autonomous Region, China.

Alveolar echinococcosis (AE) is a life-threatening disease in humans caused by the larval stage of Echinococcus multilocularis. Domestic animals, dogs, foxes, and small mammals constitute the circular chain of AE. To evaluate the infection, distribution, and genetic polymorphism of AE in the Ili Prefecture (Nilka, Xinyuan and Zhaosu), we conducted this survey. In June and July 2018, 267 small mammals were captured using water-infusion and mousetrap methods. Combined pathogenic and molecular biological methods were used to observe the histopathology of Echinococcus carried by rodents, amplify the mitochondrial nad1 gene of the pathogen, and investigate the genotype and haplotype diversity of Echinococcus in rodents in Ili Prefecture. Morphological identification revealed that these captured small mammals belonged to three species, with Microtus gregalis being the dominant species (183/267). Pathological and molecular biological results confirmed that E. multilocularis was the pathogen of echinococcosis in small mammals, with an infection rate of 15.73% (42/267). Among the three areas sampled, the highest infection rate of rodents was 25.45% (14/55) in Nilka County. However, there was no significant difference in the infection rates between regions (χ2 = 5.119, p > 0.05). Of the three captured rodent species, M. gregalis had the highest infection rate of 17.49% (32/183), but there was no significant difference in infection rates between the rodent species (χ2 = 1.364, p > 0.05). Phylogenetic analyses showed that the nad1 gene sequences obtained in this study clustered in the same clade as isolates from China. These isolates contained 21 haplotypes (Hap_1-21); Hap_2 was the most common haplotype (9/42). Furthermore, haplotype diversity (0.925 ± 0.027) and nucleotide diversity (0.01139 ± 0.00119) were higher in the Ili Prefecture than in other regions, indicating that population differentiation was high. Tajima's D and Fu's Fs tests were negative (p > 0.10), indicating that the population had expanded. The low fixation index (Fst) ranged from 0.00000 to 0.16945, indicating that the degree of genetic differentiation was different among different populations. In summary, Ili Prefecture is a high incidence area of AE, and Microtus spp. may play an important role in the transmission of AE in this area. The results of this study provide basic data for further study of the molecular epidemiology, genetic differences, and control of E. multilocularis in the Ili Prefecture, Xinjiang.

Genetic Diversity and Population Structure of Brown Croaker (Miichthys miiuy) in Korea and China Inferred from mtDNA Control Region.

Brown croaker (Miichthys miiuy), a species of fish with significant commercial value, is found in the coastal seas of Korea, China, and Japan. The genetic diversity and population structure of a representative sample of brown croaker specimens were assessed based on the control region of their mitochondrial DNA (mtDNA). Samples from a total of 115 individuals were collected from three separate locations, one in China (Lianyungang) and two in Korea (Mokpo and Gyeongnyeolbiyeoldo Island). Analysis of the 436-base-pair mtDNA control region revealed that the haplotype diversity ranged from 0.973 ± 0.025 to 0.988 ± 0.008, while the nucleotide diversity ranged from 0.012 ± 0.006 to 0.017 ± 0.009. The level of genetic diversity, star-shaped haplotype network, significant Fu's Fs test, and analysis of the mismatch distribution all suggested that this species has experienced population expansion. Fixation index analysis indicated that the population collected at the site in China differed significantly from the two populations obtained in Korea. The findings of this study extend the general understanding of the population structure of M. miiuy and can be used to develop strategies for effective resource management.

Genetic diversity of tick (Acari: Ixodidae) populations and molecular detection of Anaplasma and Ehrlichia infesting beef cattle from upper-northeastern Thailand.

Genetic diversity, genetic structure and demographic history of the ticks infesting beef cattle in Thailand were examined based on mitochondrial cytochrome c oxidase I (cox1) sequences. Tick samples were collected in 12 provinces in upper-northeastern Thailand. Three species were found; Rhipicephalus microplus, R. sanguineus, and Haemaphysalis bispinosa. Of these, R. microplus was by far the most abundant species in beef cattle and was widely distributed throughout the area. No cox1 sequence variation was found in the R. sanguineus or H. bispinosa specimens collected. Low nucleotide diversity but high haplotype diversity was observed in R. microplus. All collected R. microplus specimens belonged to lineage A. Mismatch-distribution analysis, as well as Tajima's D and Fu's Fs tests, provided evidence of recent demographic expansion. A subsample of tick specimens was investigated for presence of Anaplasma and Ehrlichia using a fragment of the 16S rRNA gene. Three species of Anaplasma were detected from R. microplus; Anaplasma marginale (19.08%), Anaplasma platys (1.97%) and unidentified Anaplasma strain (0.66%). The infection rate of Ehrlichia was 7.24% (two ticks were infected with E. minasensis (1.97%) and eight with an unidentified Ehrlichia strain (5.26%). No infections were found in R. sanguineus or H. bispinosa. This is the first report of A. platys and E. minasensis in cattle ticks in Thailand, providing information for future epidemiological surveys and control strategies in this region.

The polymorphic analysis of cox1 and cob genes of Echinococcus granulosus in the Ngari region of Tibet in China

Cystic echinococcosis (CE) is an important zoonotic parasitic disease caused by Echinococcus granulosus (E. granulosus). CE seriously threatens human health and the development of animal husbandry. The Ngari region is one of the world's highest endemic regions for CE, while genetic polymorphisms of E. granulosus were unclear. Paraffin slices of liver Cyst were collected from seventy-nine surgical patients with echinococcosis in the Ngari region. DNA was extracted from samples. The cox1 and cob genes of mitochondrial DNA of E. granulosus were simultaneously amplified and sequenced. The sequencing results were compared with the standard sequence (KU925397.1and HF947574.1). Phylogenetic trees and the haplotype network of cob and cox1 genes were constructed and analyzed genotypes of E. granulosus isolated from humans in the Ngari Region of Tibet. Out of 79 hydatid cyst samples collected from surgery patients, 60 isolates were identified as G1/ G3, and two isolates were identified as G6/ G7. Analysis of the cob/ cox1 genes revealed 9/7 mutations resulting in 8/6 haplotypes, respectively. The cob and cox1 neutrality indices computed by Tajima's D and Fu's Fs tests showed high negative values in Echinococcus granulosus sensu stricto (E. granulosus s. s.). The result suggested that E. granulosus in the Ngari region experienced population expansion or a negative selection. We found that G1/ G3 was still the main genotype, and G6/ G7 was found occasionally in humans of the Ngari region. Therefore, we recommend future surveys and control efforts to investigate G1/ G3 and G6/ G7 transmission in the Ngari region.

Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses.

The present‐day population structure of a species reflects the combination of oceanographic currents, life‐history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here, we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star‐shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species’ response to future climate change.

Molecular diversity, haplotype distribution and genetic variation flow of Bipolaris sorokiniana fungus causing spot blotch disease in different wheat-growing zones.

Bipolaris sorokiniana (BS) is an economically important fungal pathogen causing spot blotch of wheat (Trtiticum aestivum) and found in all wheat-growing zones of India. Very scanty and fragmentary information is available on its genetic diversity. The current research is the first detailed report on the geographic distribution and evolution of BS population in five geographically distinct wheat-growing zones (North Western Plain Zone (NWPZ), North Eastern Plain zone (NEPZ), North Hill Zone (NHZ), Southern Hill Zone (SHZ) and Peninsular Zone (PZ)) of India, studied by performing nucleotide sequence comparison of internal transcribed spacer region of 528 isolates. A moderate to low levels of haplotypic diversity was noticed in different wheat-growing zones. Phylogenetic analysis suggests that B. sorokiniana exist in two distinct lineages as all isolates under study were grouped in two different clades and found analogous to the findings of haplotypic and TCS network analysis. The genetic parameters revealed the existence of 40 haplotypes with three major haplotypes (H-1, H-2 and H-3) which showed star-like structure network surrounded by several single haplotypes, revealing high frequency of the mutations (Eta = 2 - 158) in total analyzed population. H-1 was observed as a predominant haplotype and prevalent in all the five zones. Moderate level of genetic differentiation was found between NHZ and other zones like NWPZ (Fst = 0.332) and SHZ (Fst = 0.382) and PZ (Fst = 0.299), whereas it was low between NEPZ and PZ (Fst = 0.034). Higher transfer rate of genetic variation was noticed between NEPZ and PZ (Nm = 7.06), while it was found minimum between NHZ and SHZ (Nm = 0.40). Moreover, negative score of neutrality statistics (Tajima's D and Fu's FS test) for NWPZ population suggested recent population expansion. However, positive score for both the neutrality tests observed in NEPZ indicated the dominance of balancing selection in structuring their population. Recombination events were observed in the NWPZ and NHZ population, while it was absent in SHZ, NEPZ and PZ population. Thus, the lack of any specific genetic population structure in all the zones indicates for the expansion history only from one common source population, i.e. NWPZ, a mega zone of wheat production in India. Overall, it seems that the predominance of individual haplotypes with a moderate level of genetic variation and human-mediated movement of contaminated seed and dispersal of inoculum, mutations and recombination as prime evolutionary processes play essential role in defining the genetic structure of BS population.

Genetic structure, population diversity and ancestry of Nicobari fowl based on mtDNA complete D-loop sequences

Nicobari fowl constitute an endemic poultry germplasm of Andaman and Nicobar Islands, India. Genetic diversity, population structure and ancestry of Nicobari fowl were analysed with mitochondrial D-loop sequences. Analysis of complete D-loop sequences (1231-1232 bp) showed 46 polymorphic sites resulting in 26 haplotypes with overall haplotype diversity of 0.895 and nucleotide diversity of 0.0064. Analysis of molecular variance of spatial populations (sampling sites) of Nicobari fowl revealed that the estimated FST value as 0.229 among the populations. Tajima's D and Fu's FS tests indicated nonsignificant deviation from neutrality and the multimodal pattern of mismatch distribution in demographic expansion suggested that Nicobari fowl populations are in equilibrium. The median-joining (MJ) network of D-loop sequences with reference haplogroup sequences identifies the presence of haplogroups A, B, E1, E2, F and I in Nicobari fowl. The major haplogroup in Nicobari fowl was E (60%), which is otherwise found mainly in the Indian subcontinent. Phylogenetic analysis of Nicobari fowl with junglefowl by maximum likelihood method showed Gallus gallus murghi and G. g. spadiceus as maternal progenitors. Grouping of Nicobari fowl with their primary ancestor, Indian red Junglefowl (G. g. murghi) and the presence of Indian subcontinent-specific haplogroups (E2 and I) support the independent domestication of chickens in India. This study will help to design breeding strategy for conservation of Nicobari fowl in its island habitat.

Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide

Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, and the haplotype diversity (Hd) was 0.9983. Phylogenetic analysis revealed that 98.92% of haplotypes were divided into six obvious clusters, consistent with the classification of the known mitochondrial haplogroups of goats. Haplogroup A accounted for the largest proportion (86%). Interestingly, two unknown divisions (Unknown I and Unknown II) were discovered from goats in Southwest China, suggesting that Southwest China has unique maternal haplogroups. Analysis of molecular variance (AMOVA) and the average number of pairwise differences between populations (PiXY) indicated that geographical variation was small but significant. Neutrality tests (Tajima's D and Fu's FS tests) and mismatch distribution showed that haplogroups B, C, and G had expansion histories. In addition, the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A, B, C, and F haplogroups. A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’ genetic diversity, population structure, and matrilineal system evolution worldwide. The results may help further understand the domestication history and gene flow of goats worldwide.

Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo.

This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d‐loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d‐loop region (1169 bp d‐loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor‐joining (NJ) tree and median‐joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (FST ) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p‐value <.05) values for Fu's Fs (−20.418) and Tajima's (−2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long‐term conservation of indigenous goats in DRC.

Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine.

Fluoroquinolones are important antimicrobial agents for the treatment of Pseudomonas infections. A total of 11 isolates of P. aeruginosa were collected from different clinical samples from different medical centers in the North West Bank-Palestine during 2017. In this study, resistance to fluoroquinolones and secretions of β-lactamases were detected by phenotypic methods, while presence of β-lactamase gene sequences and other virulence factors were detected by PCR technique. PCR product for gyrA, parC and parE genes were sequenced for further analyses. The phylogenetic analyses, population diversity indices and haplotypes determination were conducted using computer programs MEGA version 6, DnaSP 5.1001 and median-joining algorithm in the program Network 5, respectively. Results of this study showed that the MIC for ciprofloxacin and norfloxacin had a range of 32-256 µg/ml. In addition, all isolates carried either exoT or exoT and exoY genes, different β-lactamase genes and 82% of these isolates harbored class 1 integrons. Analyses of the gyrA, parC and parE sequences were found to be polymorphic, had high haplotype diversity (0.945-0.982), low nucleotide diversity (0.01225-0.02001) and number of haplotypes were 9 for each gyrA and parE genes and 10 haplotypes for parC gene. The founder haplotypes being Hap-1 (18%), Hap-2 (27.3%) and Hap-6 (9.1%) for gyrA, parC and parE genes, respectively. Two of ParE haplotypes were detected as indel haplotypes. The Median-joining- (MJ) networks constructed from haplotypes of these genes showed a star-like expansion. The neutrality tests (Tajima's D test and Fu's Fs test) for these genes showed negative values. Palestinian fluoroquinolone resistant P. aeruginosa strains showed high MIC level for fluoroquinolones, β-lactamase producers, carried type III secretion exotoxin-encoding genes, most of them had integrase I gene and had high level of mutations in QRDR regions in gyrA, parC and parE genes. All these factors may play an important role in the invasiveness of these strains and make them difficult to treat. Isolation of these strains from different medical centers, indicate the need for a strict application of infection control measures in Medical centers in the North West Bank-Palestine that aim to reduce expense and damage caused by P. aeruginosa infections. Molecular analyses showed that Palestinian fluoroquinolone resistant P. aeruginosa haplotypes are not genetically differentiated; however, more mutations may exist in these strains.

Evolutionary and phylogenetic analyses of the barcoding region suggest geographical relationships among Blastocystis sp., ST3 in humans.

Blastocystis sp., has 21 distinct subtypes of which ST3 thought to be the most prevalent subtype. This study aims to analyze the global variations of ST3. In total, 496 sequences with more than 400 nucleotides from Asia, Europe, Africa, and America were included in this study. Results show that allele 34 was the most prevalent allele in all continents. The lowest and highest allele diversity were observed in Europe and Africa, respectively. The nucleotide diversity ranged from 0.0077 in Europe to 0.02 in Africa, and haplotype diversity ranged from 0.461 in America to 0.6 in Africa. The haplotype network and Bayesian structure showed at least two major clusters including Asia and Europe-Africa-America. Tajima's D values for all continents were negative and statistically significant, indicating an excess of rare nucleotide variants. Similarly, the Fu's FS test showed negative values for all regions, indicating an excess of rare haplotypes. Pairwise FST exhibited a high genetic differentiation between Asia and other continents. Mismatch analysis for all populations showed a unimodal distribution. Our findings indicate that there are two probable major clusters of Blastocystis sp. ST3, a cluster which is shared between Europe, Africa, and America, and a cluster which is restricted to Asia.

Mosquito Diversity and Population Genetic Structure of Six Mosquito Species From Hainan Island.

Hainan is a tropical island in southern China with abundant mosquito species, putting Hainan at risk of mosquito-borne virus disease outbreaks. The population genetic diversity of most mosquito species on Hainan Island remains elusive. In this study, we report the diversity of mosquito species and the genetic diversity of the predominant species on Hainan. Field populations of adults or larvae were collected from 12 regions of Hainan Island in 2018 and 2019. A fragment of the mitochondrial cytochrome c oxidase subunit I (coxI) gene was sequenced from 1,228 mosquito samples and used for species identification and genetic diversity analysis. Twenty-three known mosquito species from the genera Aedes, Armigeres, Culex, Mansonia, and Anopheles and nine unconfirmed mosquito species were identified. Aedes albopictus, Armigeres subalbatus, and Culex pipiens quinquefasciatus were the most prevalent mosquito species on Hainan. The regions north of Danzhou, Tunchang, and Qionghai exhibited high mosquito diversity (26 species). The order of the total haplotype diversity and nucleotide diversity of the populations from high to low was as follows: Culex tritaeniorhynchus, Ar. subalbatus, Culex pallidothorax, Culex gelidus, Ae. albopictus, and C. p. quinquefasciatus. Tajima’s D and Fu’s Fs tests showed that Ae. albopictus, C. p. quinquefasciatus, C. tritaeniorhynchus, and C. gelidus had experienced population expansion, while the Ar. subalbatus and C. pallidothorax populations were in genetic equilibrium. Significant genetic differentiation existed in the overall populations of Ae. albopictus, Ar. subalbatus, C. p. quinquefasciatus, and C. pallidothorax. The Ae. albopictus populations on Hainan were characterized by frequent gene exchange with populations from Guangdong and four other tropical countries, raising the risk of viral disease outbreaks in these regions. Two subgroups were reported in the Ar. subalbatus populations for the first time. Our findings may have important implications for vector control on Hainan Island.

Population structure of leishmania major in southeastern morocco

Cutaneous leishmaniasis (CL) is an infectious disease caused by various Leishmania species. It is among the most neglected tropical diseases and has been considered a major health threat over the past decades in the country. Its zoonotic form caused by Leishmania (L) major is the most prevalent in Morocco. This study investigated the population structure of L. major in southeastern Morocco. Samples (n = 67) were collected from patients with CL in five different endemic areas located in three provinces (Ouarzazate, Tinghir, and Zagora). These samples were then sequenced using two nuclear markers: internal transcribed spacer 1 (ITS1) and a fragment of the virulence factor GP63. Next, the sequences were edited and analyzed. Molecular diversity indices showed a high population genetic diversity but an overall low haplotype diversity. Our results suggest small population differentiation, indicating a low geographic structure. Tajima's D and Fu's Fs tests both suggested recent population expansion based on the significant deviations from neutrality in both tests for all populations except Tinghir, which may be due to a small sample size. Based on our findings, the region is experiencing rapid population expansion caused by recent CL outbreaks, and one of them has been recently studied. In addition, analysis of molecular variance and FST suggested gene flow between Zagora and both Ouarzazate and Tinghir. Nonetheless, no gene flow was observed between Tinghir and Ouarzazate. To the best of our knowledge, this is the first analysis of the population structure of L. major in Morocco. The results of this study provide crucial background information for epidemiological studies by showing the presence of gene flow between populations and clonal expansion in cases of an outbreak. This will drive authorities to reconsider the implemented control strategies.

Genetic diversity of Echinococcus granulosus sensu stricto in Sardinia (Italy).

Cystic echinococcosis (CE) is a severe parasitic zoonosis caused by the metacestode of the tapeworm Echinococcus granulosus sensu lato (s.l.). The disease has a global distribution representing a significant public health concern. Based on mitochondrial DNA analysis E. granulosus s.l. has been subdivided into five species: E. granulosus sensu stricto (s.s.) (G1, G3 genotype), E. equinus (G4 genotype), E. ortleppi (G5 genotype), E. canadensis (G6-G8, G10 genotype) and E. felidis. E. granulosus s.s., and in particular G1, is the most widespread genotype and the major responsible of human CE cases worldwide. In Italy G1 genotype is higly represented with larger percentages in some hyperendemic areas such as Sardinia. Molecular studies represent a valuable tool to improve our understanding of the E. granulosus epidemiology and CE control strategies. In the present study we investigated genetic variability of E. granulosus s.s. in Sardinia. To this purpose 83 hydatid cysts were collected from different animal species including humans and the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was partially sequenced (720bp). Nucleotide sequences from Mediterranean basin were also analyzed for comparison. The phylogenetic network revealed 30 haplotypes grouped around a predominant isolate that had been already reported from other world regions. Haplotype diversity (0.8495±0.0336) and nucleotide diversity (0.003305±0.002014) were similar in Sardinia respect to other Mediterranean countries. Neutrality indices obtained by Tajima's D and Fu's Fs test were significantly negative (p≤.01) suggesting expansion of Sardinian population. Low Fixation indices (Fst), ranging from negative values (Algeria, Greece, Spain, other part of Italy) to 0.089 (Albania, France), indicated absence of genetic differentiation, and gene flow between Sardinia and other Mediterranean countries.

Genetic analysis and population structure of the Anopheles gambiae complex from different ecological zones of Burkina Faso

The Anopheles gambiae complex (Diptera: Culicidae) is the most important vector for malaria in Sub-Saharan Africa, besides other vectors such as Anopheles funestus. Malaria vector control should encompass specific identification, genetic diversity and population structure of An. gambiae to design vector control strategies.The aim of this study was to determine the distribution of sibling species of the An. gambiae complex according to climatic regions related to cotton-growing or cotton-free areas by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Then, variation in mitochondrial cytochrome c oxidase 1 (COI) was used to assess the genetic structure within and between populations from our selected ecological zones.At the sibling species level, the following proportions were found across all samples (n = 180): An. coluzzii 65.56%, An. gambiae stricto sensu (s.s). 21.11%, and An. arabiensis 3.33%. Hybrids between An. gambiae s.s. and An. coluzzii (7.78%) and hybrids between An. coluzzii and An. arabiensis (2.22%) were found. The phylogenetic tree and Integer Neighbour-Joining (IntNJ) haplotype network did not reveal any distinct genetic structure pattern related to climatic or agricultural conditions in Burkina Faso. The Fst (Wright's F-statistic) values close to zero showed a free gene flow and no differentiation in An. gambiae complex populations. Furthermore, neutrality indices calculated by Tajima's D, Fu and Li's D⁎, Fu and Li's F⁎, Fu's Fs tests suggested an excess of rare mutations in the populations.Overall, variation in the proportions of An. gambiae s.s., An. coluzzii and An. arabiensis was found according to climatic regions, but COI analysis did not evidence any population structuring of the An. gambiae complex. These scientific contributions can be used as a basis for further in-depth study of the genetic diversity of the An. gambiae complex for epidemiological risk assessment of malaria in Burkina Faso.

Molecular characterization and genetic diversity study of Vibrio parahaemolyticus isolated from aquaculture farms in India

Vibrio parahaemolyticus is known to cause disease and infection in humans. This study was conducted to understand the prevalence of V. parahaemolyticus and the presence of virulence factors in environmental isolates of V. parahaemolyticus, collected from three major shrimp producing states viz, West Bengal, Andhra Pradesh and Gujarat of India during February 2014 to June 2017. Total 183 V. parahaemolyticus were isolated from moribund shrimp and identified using toxR and 16S rRNA gene. Polymerase Chain Reaction (PCR) was performed to detect virulence genes under T3SS1 and T3SS2 along with AHPND. All the isolates showed presence of vcrD1, vp1680 and vopD1 gene under T3SS1 but negative for AHPND. Only 3% of isolates showed presence of all the virulence genes (vcrD2, vopD2, vopB2 and vopC) used in the present study under T3SS2. The isolates were also tested for the presence of tdh, trh or both the genes; 8% of the isolates had trh gene and 3% of the isolates had tdh gene. The genetic diversity within and between V. parahaemolyticus isolated from three different geographical locations, was analyzed by using 16S rRNA gene. Though the biotype diversity (h) was high for all three populations, phylogenetic study of V. phaemolyticus revealed an admixture of biotypes. Tajima's D (−2.59470; p < .001) test of selective neutrality and Fu's Fs (−32.422; p < .001) test were negative and significant, suggesting a sudden population expansion with limited time for population differentiation.

Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite.

Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB‐psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: h S = 0.330, h T = 0.866; ITS: h S = 0.458, h T = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions—Tarim Basin, the central regions—Hami Basin and Hexi Corridor, and the eastern regions—Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.