Fu's Fs Research Articles

Genetic Diversity and Sex Identification of Pelicans (Pelecanus conspicillatus Temminck, 1824) in the Captivity of Ragunan Zoo, Jakarta

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

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.

Mitochondrial DNA analysis reveals spatial genetic structure and high genetic diversity of Massicus raddei (Blessig) (Coleoptera: Cerambycidae) in China.

The oak longhorned beetle (OLB), Massicus raddei (Blessig, 1872) (Coleoptera: Cerambycidae), is widely distributed in Asia (China, the Korean Peninsula, Japan, Vietnam and the Russian Far‐East), but pest outbreaks have occurred only in Liaoning Province and Jilin Province of China. In order to explore possible mechanisms of local population outbreaks and characterize the genetic diversity and genetic structure of M. raddei across its range in China, three mitochondrial genes (COI, Cytb, and COII) were sequenced and analyzed for seven M. raddei populations collected from six provinces in China. From these different populations, we found a high haplotype and nucleotide diversity. Haplotype networks and phylogenetic analyses both demonstrate apparent genetic diversification between SC (southern China) and NC (northern China) population groups. A set of 21 pairwise comparisons for Fst (pairwise fixation indices) and Nm (genetic flow index) showed significant genetic differentiation and limited gene flow except for two pairs, Shandong (SD) and Liaoning (LN), and Anhui (AH) and Henan (HN). This pattern suggested that the periodic outbreak of the LN population could not be attributed to the absence of genetic flow with other spatial populations and that regional environmental factors might be responsible. AMOVA (Analysis of molecular variance) showed that the greater molecular genetic variation was among populations. Based on Tajima's D statistic, Fu's Fs, and the mismatch distribution test, we determined that the seven populations sampled were stable and had not experienced any recent population expansion. The fact that all the sampled populations showed only unique haplotypes and lacked shared or ancestral haplotypes, as well as the nonstar‐like distribution of haplotype network for concatenated genes, collectively provided powerful evidence of the stable and isolated nature of most populations. The high genetic differentiation and spatial genetic structuring among populations are both likely related to the beetle's moderate flight capacity, regional variation in host tree species and microclimate, as well as the geographic distance between sampling sites.

Low Genetic Diversity in Turkish Populations of Wels Catfish Silurus glanis L., 1758 (Siluridae, Pisces) Revealed by Mitochondrial Control Region Sequences

This study aimed to investigate the genetic diversity and population structure of Wels catfish Silurus glanis L. 1758 in Turkey using squences of the mitochondrial DNA control region The 887-bp fragment of D-loop was aligned for 112 S. glanis individuals from ten wild populations in Turkey, defined by 29 polymorphic sites comprising 16 haplotypes. The low haplotype diversity and nucleotide diversity within each population ranged from 0.000 to 0.378 and from 0.0000 to 0.0045, respectively. Analysis of molecular variance showed significant genetic differentiation among ten populations (FST =0.940; P<0.01). AMOVA revealed that the most of genetic variation was found between Thrace and Anatolia clades (74,07 %). The phylogenetic trees and haplotype network topologies were consistent with the results of AMOVA analysis. The non-significant negative Tajima's D (-0.875 P<0.05) and Fu's Fs (-0.381, P<0.02) values and mismatch distribution for S. glanis populations indicated no evidence for changes in population size. Furthermore, goodness-of-fit of the observed versus the theoretical mismatch distribution tested the sum of squared deviation (SSD; 0.00308, P>0.05), Harpending’s raggedness index (Hri; 0,300, P>0.05) and Ramos-Onsins & Rozas (R2; 0,0771, P>0.05), supporting population neutrality.

Preliminary information on the prevalence and molecular description of Taenia hydatigena isolates in Pakistan based on mitochondrial cox1 gene

Taenia hydatigena is a cestode of veterinary importance. Infection with the metacestode larval stage results in cysticercosis, which poses a serious challenge to the livestock industry worldwide. Globally, there are numerous reports on cysticercosis caused by T. hydatigena in sheep and goat but a lack of data on the prevalence and genetic diversity exists for Pakistan. We designed this study to provide an insight into the disease status as well as investigate the genetic variation among the recovered isolates based on the mitochondrial cox1 gene. In this study, we examined small ruminants (sheep and goats) slaughtered in Faisalabad in eastern Punjab province of Pakistan for T. hydatigena metacestodes and described the population structure and genetic variation using the cytochrome c oxidase subunit 1 (cox1) mitochondrial gene. Overall, a prevalence of 4.40% (goat =4.67% sheep = 4.07%) from a total of 2225 small ruminant carcasses (sheep = 983, goats = 1242) was observed. Based on the NCBI BLAST search and Bayesian phylogeny, the identity of all isolates was confirmed via their nucleotide sequences. The diversity indices indicated a high haplotype and a low nucleotide diversity with 43 haplotypes from 98 isolates. The results also show the existence of unique haplotypes of T. hydatigena in Pakistan as demonstrated by the significant negative values of Tajima's D and Fu's Fs neutrality test suggesting a recent population expansion. The median-joining network of the partial cox1 sequence dataset showed the existence of two main haplotypes detected in both sheep and goat populations. This study shows that the prevalence of cycticercosis due to T. hydatigena is below 5% in sheep and goats in Faisalabad, Punjab, Pakistan. The molecular analysis of the partial cox1 gene also indicates a high degree of genetic variation with the existence of rare haplotypes. These findings represent a preliminary report on the prevalence and genetic variation of T. hydatigena in Pakistan and serve as baseline information for future studies on the prevalence and population structure of T. hydatigena in the country.

Hepatitis C virus genotype/subtype distribution and evolution among Chineseblood donors: Revealing recent viral expansion.

Hepatitis C virus (HCV) genotype (GT) distribution in China shows significant geographical and demographic difference. As a routinely tested virus in Chinese blood bank systems, rare molecular epidemiology research in blood donors is reported. Our purpose is to investigate the HCV GT/subtypes distribution, phylogenetic analysis and population genetics in Chinese blood donors. Anti-HCV screen positive samples and donor demographics were collected. HCV Core and E1 gene fragments were amplified by RT-PCR, followed by sequencing and phylogenetic analysis to determine HCV GTs/subtypes using MEGA 7.0. The population genetics were performed using Arlequin v3.0 and Beast v1.10.4. SPSS Statistics 17.0 software was used to analyze the correlation between HCV GTs/subtypes distribution and demographic characteristics. 419 and 293 samples based on Core and E1 gene respectively were successfully amplified. HCV la, lb, 2a, 3a, 3b, 6a, 6e and 6n were found, and the corresponding proportions were 0.66% (3/455), 58.68% (267/455), 17.80% (81/455) and 5.05% (23/455), 3.52% (16/455), 12.31% (56/455), 0.88% (4/455) and 0.66% (3/455). Samples from Guangxi showed the most abundant genetic diversity with 8 subtypes were found. The number of haplotypes in HCV-1b is higher than 2a and 6a. The negative Tajima's D and Fu's Fs values of HCV-1b, 2a and 6a suggested the population expansion of those HCV subtypes. The distribution of HCV GT showed significant statistical difference by age and ethnicity. Conclusion: An abundance of HCV genetic diversity was found in Chinese blood donors with mainly 1b and then 2a subtype. There were significant geographical and demographic differences in HCV GTs/subtypes among Chinese blood donors. HCV subtype 1b has stronger viability and HCV subtype 6a has experienced significant expansion.

Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation.

Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The “southerly refugia model” has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star‐like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice‐free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range‐wide patterns and identifies unique genetic units that can likely be used to inform conservation of at‐risk populations at the northern periphery.

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.

Molecular identification of seven new Zygopteran genera from South China through partial cytochrome oxidase subunit I (COI) gene

The study was carried out in eight provinces of China, with 16 different localities. A total of 150 adult damselflies were collected for the study from the area. Mitochondrial (COI) was the target gene to sequence from all 51 representative samples of the entire collection. From the resulted sequences, ten species belonging to seven genera and four families were identified. The families are Calopterygidae, Coenagrinidae, Chlorocyphidae and Devadattiade. After alignment through BioEdit v6, MEGA7 was used for phylogenetic tree construction as well as the calculation of genetic divergence, whereas genetic diversity was calculated by DnaSP v5. All species from the respective families had clustered together within the groups, but divided into sub-groups. Maximum genetic divergence (9.31%) was found in the genus Rhinocypha, followed by Hetaerina with (8.23%), while, minimum divergence was observed for the genus Ceriagrion (0.32%) followed by Ischnura (0.48%). However, significant genetic diversity was found for all sequences at 346 mutations confirmed by two tests, Tajima's D and Fu's Fs. Maximum genetic diversity among genera was also observed, the genus Hetaerina has maximum genetic diversity (181 mutations) followed by Rhinocypha (68 mutations) while minimum genetic diversity was observed for the genus Ceriagrion followed by Ischnura. The presented results showed a higher diversity of damselflies in the south China regions.

Genetic variability and diversity of Echinococcus granulosus sensu lato in human isolates of Pakistan based on cox1 mt-DNA sequences (366bp)

Cystic echinococcosis (CE) is a cyclo-zoonotic disease endemic to Pakistan, however, phylogeography and etiology of Echinococcus granulosus from human host has remained unexplored so far. The current study was carried out to estimate population structure and appraise the genetic variability of E. granulosus in two major provinces of Pakistan, Sindh and Punjab. 94 isolates were subjected to sequence analysis from histopathologically confirmed CE patients using a fragment of mitochondrial cytochrome c oxidase subunit 1 gene (cox1; 366bp). Three genotypes of E. granulosus sensu lato, G1 (57.44%), G3 (41.48%) and G6 (1.06%), were inferred to exist in human patients. Molecular diversity indices for E. granulosus sensu stricto manifested the presence of 14 haplotypes among the regional populations forming distinct clades with sheep (G1) and buffalo (G3) strains. The haplotype network displayed a double clustered star like feature with PK-H1c (37.63%) and PK-H9c (32.25%) as most dominant haplotypes displaying low genetic differentiation between the two geographic regions. Neutrality indices (Tajima's D and Fu's Fs) were negative for all populations indicating population expansion across Pakistan. The sympatric presence of G1 and G3 genotypes among humans in endemic focus of Pakistan confirms the zoonotic potential of E. granulosus s.s. with special emphasis on the G3 strain which emerged as a dominant cause of CE in humans compared to other global studies, where only G1 is linked to the majority of CE cases. Data from this study will prove to be a keystone for devising robust regional control strategies for human hydatidosis and investigating potential pathogenicity of E. granulosus s.l. haplotypes and their clinical manifestations in Pakistan.

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.

Genetic diversity and differentiation in the blackflies Simulium cheongi, Simulium jeffreyi and Simulium vanluni (Diptera: Simuliidae) in Peninsular Malaysia

The population genetic structures of S. vanluni, S. cheongi and S. jeffreyi were determined from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) across different states in Peninsular Malaysia. High levels of genetic diversity and genetic differentiation were observed among three species. All three species revealed an intermediate level of gene flow among the populations. Negative values of Fu's Fs and low values of Raggedness index supported the hypothesis of population expansion in S. vanluni, S. cheongi and S. jeffreyi.

High genetic connectivity among pink shrimp Farfantepenaeus paulensis (Pérez-Farfante, 1967) groups along the south-southeastern coast of Brazil

The pink shrimp Farfantepenaeus paulensis is one of the most important fishing resources along the south-southeast coast of Brazil. Its fishing zone includes two main reproductive stocks, located at the coasts of Santa Catarina and São Paulo states. The species life cycle includes an offshore reproductive stage and juvenile recruitment to estuarine areas; therefore, adults are caught in oceanic areas by industrial fisheries and juveniles in estuarine areas by artisanal fisheries. The unrestricted growth of the industrial fleet, along with the increase of artisanal fishing in estuarine areas and the low effectiveness of fishery legislation, led to a collapse of the pink shrimp fishery in the late 1990s. The present work aimed to assess the population genetics of the pink shrimp F. paulensis throughout its main distribution in the Southwestern Atlantic (SWA), to verify whether different fishing stocks also represent different genetic stocks. Based on the evaluation of the mtDNA control region (D-loop), we detected high connectivity and absence of genetic structure among F. paulensis groups in the SWA. Fixation indexes, Analysis of Molecular Variance and a haplotype network also showed no significant genetic differences, with individuals sharing haplotypes among more than one region. Mismatch analysis showed unimodal distributions for all the sampled populations with high haplotype diversity and low nucleotide diversity, showing a pattern of recent demographic expansion, which was corroborated by the Tajima's D and Fu's Fs neutrality tests. Estimates of migration rates indicated high gene flow, with a large number of migrants exchanged between regions. All obtained results are consistent with a panmitic population of F. paulensis. This scenario is a result of a complex interaction of several factors, from the influence of currents on larval dispersal to the effect of overfishing. The knowledge on the diversity and genetic structure of F. paulensis is a fundamental part of the scientific basis necessary for decision makers to elaborate adequate management strategies for pink shrimp stocks.

Genetic diversity of Haemaphysalis longicornis from China and molecular detection of Rickettsia

The tick Haemaphysalis longicornis (Neumann) (Acari, Ixodidae) is distributed throughout China and is the most notorious blood feeding ectoparasite of livestock. Haemaphysalis longicornis can transmit a large number of pathogens that cause human infectious diseases, such as Rickettsia spp. Here, we characterized the genetic structure of H. longicornis and tested for the presence of Rickettsia spp. from five regions in China. Analysis of the two mitochondrial marker sequences (16S rRNA and COI) and the nuclear sequence (ITS2) showed that the overall level of nucleotide diversity was low and the variability did not differ among the five regions. From the five locations, the infection rates of Rickettsia species ranged from 0 to 65%. The nucleotide diversities of the high-infected group were lower than those of the low- and uninfected group. And in neutrality tests for the high-infected group based on COI sequences, the Tajima's D and Fu's FS were coincidentally < 0 and significant, whereas they were closer to zero and non-significant in low- and uninfected groups.

Mitochondrial DNA diversity and origin of indigenous pigs in South China and their contribution to western modern pig breeds

Indigenous pigs in South China are valuable genetic resources with many specific and unique characters, which have played an important role in the establishment of some western modern pig breeds. However, the origin and genetic diversity of indigenous pigs in South China have not been fully understood. In the present study, we sequenced 534 novel mitochondrial DNA (mtDNA) D-loop and assembled 54 complete mitogenome sequences for all 17 indigenous pig breeds from Fujian, Guangdong, Guangxi and Hainan in South China. These data were analyzed together with previously published homologous sequences relevant to this study. We found that all 13 coding genes of the mitogenomes were under purifying selection, but ND1 had the most variable sites and CYTB contained the most non-synonymous SNPs. Phylogenetic analysis showed that all indigenous pigs in South China were clustered into the D haplogroup with D1a1, D1b, D1c and D1e sub-haplogroups found to be dominant. Haplotype and nucleotide diversities of D-loop sequences ranged from 0.427 to 0.899 and from 0.00342 to 0.00695, respectively, among which all pigs in Guangdong had the lowest diversity. The estimates of pairwise FST, gene flow (Nm) and genetic distance (Da) indicated that most of these indigenous pig breeds differentiated from each other significantly (P<0.05). Among the western modern breeds, Berkshire and Yorkshire had significant Asian matrilineal footprints from indigenous pigs in South China, especially the Spotted pigs distributed in Guangdong and Guangxi. The neutrality test (Fu's FS) indicated that indigenous pigs from Fujian and Guangxi had gone through recent population expansion events (P<0.05). It is concluded that indigenous pigs in South China were most likely derived from the Mekong region and the middle and downstream regions of Yangtze River through Guangxi and Fujian. Our findings provide a complete and in-depth insight on the origin and distribution pattern of maternal genetic diversity of indigenous pigs in South China.

Genetic variation and population structure of different geographical populations of Meretrix petechialis based on mitochondrial gene COI

The hard clam (Meretrix petechialis) is a commercially important shellfish in China. To provide valuable insights into management and conservation of M. petechialis, we investigated the genetic variation and population structure of M. petechialis by analysing samples from nine geographical populations. In this study, the genetic diversity and differentiation of nine populations of M. petechialis were assessed using the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. A total of 90 COI sequences were obtained and each COI sequence was 699 bp in length. Fifty-one haplotypes were identified with 10 haplotypes shared among populations. The haplotype diversity was highest in Fujian, Panjin and Jiangsu (0.9778 ± 0.0540) and lowest in Dalian (0.7778 ± 0.1374). The nucleotide diversity was highest in Panjin (0.453401 ± 0.240463) and lowest in Jiangsu (0.006213 ± 0.004141). Neutral test (Fu's Fs) and mismatch distribution analysis revealed that the hard clam experienced a population expansion event. Analysis of molecular variance (AMOVA) indicated that 91.7% of the genetic variance was within populations and 0.52% of the variance was among populations, demonstrating significant genetic differentiation among populations (P < 0.05). The neighbour-joining tree showed that the haplotypes were not clustered according to the geographical location, but some haplotypes from the same or neighbouring locations grouped together. The results obtained in this study provide useful information on the genetic diversity and population structure of M. petechialis and shed light on the management and protection of resources of M. petechialis in the northwestern Pacific.

Genetic diversity and population structure of goliath frogs (Conraua goliath) from Cameroon

The goliath frog (Conraua goliath) is an Endangered species exclusively found in Cameroon and Equatorial Guinea. Climate change, deforestation and overhunting are principal causes driving this species to extinction. Therefore, a better understanding of the genetic diversity and population structure of this species is necessary to improve conservation efforts. Here we used two mitochondrial genes (Cytochrome Oxidase subunit 1 (COI) and 16S) extracted from 54 C. goliath individuals from six localities in Cameroon to examine their genetic diversity. The result shows a low DNA substitution between the sequences. There were four 16S and two COI haplotypes in total. Overall, genetic diversity was very low for all the genes with nucleotide diversity of 0.00106 and 0.00007 for 16S and COI respectively. The Tajima D and Fu Fs statistics were negative. The TCS haplotype network revealed a predominant and ancestral haplotype (H1) for these genes which is distributed in the 6 populations. Pairwise genetic differentiation (FST) generated between these populations using 16S revealed very high differentiation between populations from Nkam and Mungo Administrative Divisions in Cameroon. In contrast, we observed low differentiation among the geographically clustered Mungo and Nkam populations. Overall, human activities and perhaps climate change can appear to have depleted genetic diversity in the scattered populations that remain of this amphibian. To sustain the Goliath frog, we suggest to the Cameroonian government to implement more effective strategies to conserve and manage remnant populations of this iconic species through more effort against poaching which contribute to reduce the genetic diversity.

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.