Population Structure Diversity Research Articles

Genetic diversity and population structure of Philippine strawberry germplasm based on genome-wide simple sequence repeat markers

Abstract. Elec VH, Cadorna CAE, Tad-Awan BA, Basquial DA, Dumaslan MR, Rey JD. 2024. Genetic diversity and population structure of Philippine strawberry germplasm based on genome-wide simple sequence repeat markers. Biodiversitas 25: 2969-2979. Strawberry is a globally recognized fruit due to its health benefits and economic significance. Determining the level of genetic diversity and the relationship between germplasm resources involved in the breeding program is critical for effective crop improvement strategies. This study used 197 Simple Sequence Repeat (SSR) markers to assess the genetic diversity and population structure of 24 strawberry germplasm from the Benguet State University (BSU) collection. In this study, 70% of the markers used were polymorphic with reproducible fragments. A total of 792 alleles were detected, with an average of six per marker. The diversity indices indicated an intermediate level of diversity among the germplasm based on the Jaccard coefficient. Results from cluster analysis generated three groups, separating the Red Milky Way and Summer Princess cultivars from the rest of the germplasm evaluated, while a third cluster was further divided into six subgroups. Furthermore, identified clustering patterns of the evaluated genotypes showed independence from the region of origin, coinciding with Principal Component Analysis (PCA) and population structure analysis results. This study reveals the genetic diversity level and population structure of the strawberry cultivars in the Philippines using SSR markers, facilitating accurate identification and informed parental selection for breeding objectives.

Integrating multilocus genome-wide association studies in chickpea landraces to discern the genetics of drought tolerance

In chickpea breeding, drought is a major concern and a complex trait controlled by several genes. To develop drought-tolerant varieties, it is essential to use the available germplasm and genomic resources. Over the years, the landraces have proven to be a good source for the dissection of genes for different yield and yield-related traits. The present investigation for marker–trait associations (MTAs) and candidate gene identification was conducted by studying 125 chickpea landraces collected from the West Asia and North Africa (WANA) region, along with 4 varieties suitable for irrigated and rainfed environments. This study analyzed 13 physio-morphological traits in 2 consecutive years at two isolated locations (IARI, New Delhi, and Dharwad). A strong correlation coefficient was observed between the trait seed yield (SY) and biological yield (BY) under both conditions. The Drought Susceptibility Index (DSI) ranged from 0.02 to 1.84 and 0.10 to 2.04 at the IARI, New Delhi and Dharwad locations, respectively. The genotypic data of 6,367 single nucleotide polymorphisms (SNPs) distributed across the genome were used for genetic diversity study, population structure, and genome-wide association study (GWAS). The average polymorphic information content (PIC) value observed was 0.25, and the average linkage disequilibrium (LD) decay distance was 152,269 bp across the genome. A total of four subgroups were observed within the population for genotypic data. Fixed and random model Circulating Probability Unification (FarmCPU) was used for the GWAS analysis, which considered both fixed- and random-effect models. A total of 52 significant SNPs were reported in both irrigated and rainfed conditions at low locations; 7 SNPs were associated with more than one trait, which may have pleiotropic effects. Significant SNPs were annotated in the pulse database. The identified genomic region found in or near MTA under rainfed conditions encodes for guard cell hydrogen peroxide-resistant1 (GHR1), late embryogenesis-abundant, E3 ubiquitin-protein ligase, walls are thin1 (WAT1), and beta-galactosidase that are known to be associated with drought tolerance.

Phenotypic and genotypic analysis of antimicrobial resistance and population structure of gastroenteritis-related Aeromonas isolates

BackgroundThe population structure and the correlation between antimicrobial resistance (AMR) phenotypes and genotypes in Aeromonas species isolated from patients with gastroenteritis are not well understood. The aims of the study were to: (1) investigate the antimicrobial susceptibility profiles of Aeromonas species isolated from patients with gastroenteritis; (2) explore the relationship between AMR genes and resistance phenotypes; and (3) describe the population structure of these isolates and provide evidence of transmission events among them.MethodsThis microbiological survey was performed at the Microbiology Laboratory of the Emek Medical Center in Afula, Israel. Cultivation of Aeromonas was attempted from stool samples that tested positive by PCR. Antimicrobial susceptibility testing (AST) was performed using the Sensititre GN3F microdilution panel. Whole genome sequencing (WGS) was done using the Illumina NextSeq500/550 system. Phylogenetic studies involved multi-locus sequence typing (MLST) and core genome (cg) MLST. Resistance mechanisms were identified using the Comprehensive Antibiotic Resistance Database and compared with the AST results.ResultsThe study included 67 patient-unique isolates. The species that were identified included A. caviae (n = 58), A. dhakensis (n = 3), A. media (n = 2), A. veronii (n = 2) and A. hydrophila (n = 2). Isolates were almost uniformly susceptible to amikacin, gentamicin, aztreonam, cefepime, ceftazidime, ciprofloxacin and meropenem. All isolates with the exception of 1–2 isolates were resistant to ampicillin, cefazolin and ampicillin-sulbactam which was compatible with the presence of the blaOXA genes. Variable resistance rates were observed to cefuroxime, cefoxitin, ceftriaxone, piperacillin-tazobactam that were not correlated with the presence of other β-lactamase genes. Resistance to tetracycline and trimethoprim-sulfamethoxazole correlated with the presence of tetA and sul1, respectively. The population structure of A. caviae was highly diverse with the minority of the isolates (16/57) clustering into six defined sequence types. A cgMLST-based distance of four genes was found in one pair of isolates, suggesting common source transmission.ConclusionsA. caviae is the dominant species related to gastroenteritis and is characterized by a diverse population structure, with almost no evidence for common-source transmission. Resistance rates to most antimicrobial agents were low and partially matched with the presence of resistance genes.

The International Union for Conservation of Nature Red List does not account for intraspecific diversity

Abstract The International Union for Conservation of Nature (IUCN) Red List identifies threatened and endangered species and is a key instrument in global biodiversity conservation efforts. Our understanding of the structure and value of genetic biodiversity below the species level is rapidly increasing. Nonetheless, the IUCN assessment criteria overlook genetic variation within species. Here, we address this blind spot and discuss the principles of species conservation status classification relative to intraspecific biodiversity. We focus on coastal species, which thrive in heterogeneous environments known to drive genetic differentiation. The focal example species, Atlantic cod and sugar kelp, have contrasting life histories, are ecologically and economically important constituents of the coastal ecosystem, and are currently not classified as threatened in Norway and Canada. We expose important variation in population structure, the presence of ecotypes and genetic-environment covariation, as well as loss of ecotypes that threatens the conservation of these species. Because the genetic makeup of species directly influences their resilience, omitting this information from conservation status assessments can result in loss of adaptive capacity to future stressors, such as climate change. Consequently, recognizing and preserving intraspecific variation emerges as vital for species’ abilities to adapt to and survive in future ocean conditions.

Stock Assessment of the Commercial Small Pelagic Fishes in the Beibu Gulf, the South China Sea, 2006-2020.

Long-term variations in population structure, growth, mortality, exploitation rate, and recruitment pattern of two major commercial small pelagic fishes (CSPFs) (Decapterus maruadsi and Trachurus japonicus) are reported based on bottom trawl survey data collected during 2006-2020 in the Beibu Gulf, South China Sea. All individuals collected during each sampling quarter over a period of 15 years were subjected to laboratory-based analysis. In this study, the stock of D. maruadsi and T. japonicus inhabiting the Beibu Gulf was assessed using length-based methods (bootstrapped electronic length frequency analysis (ELEFAN)) to complete stock assessment in different fishery management periods (the division of fisheries management periods was based on China's input and output in the South China Sea offshore fisheries over 15 years, specifically divided into period I (2006-2010), period II (2011-2015), and period III (2016-2020)). The results showed that the mean body length, dominant body size, and estimated asymptotic length of two CSPFs decreased, whereas their growth coefficient decreased, indicating miniaturization and slower growth, respectively. Estimated exploitation rates and catching body length for two CSPFs indicated that both stocks in the Beibu Gulf were overexploited in period I and moderately exploited after 2011. These stocks were taking a good turn in status in period III, with the exploitation rate much lower than the initial period and reversing the downward trend in catching body length. Furthermore, the variations in the spawning season of the two CSPF stocks and their barely satisfactory expected yield indicated the complexity of the current fishery management in the Beibu Gulf. These results suggest that management measures to reduce fishing pressure may have a positive influence on the biological characteristics of those CSPFs in the Beibu Gulf; however, the stock structure already affected by overfishing will be a huge challenge for the conservation and restoration of fisheries resources in the future. Given that the current stocks of D. maruadsi and T. japonicus in the Beibu Gulf still have low first-capture body length (Lc) and high fishing mortality (F) (compared to F0.1), we identify a need to refine population structure by controlling fishing efforts and increasing catchable size, and more consideration should be given to the local fishery resource status in fisheries management.

Population Structure and Genomic Characterisation of the Ashanti Dwarf Pig of Ghana.

There is still limited information on the genomic structure and genetic diversity of African pigs. Genetic diversity studies can contribute significantly to the genetic improvement and conservation of African pigs. This study presents a genetic diversity analysis and population structure of pig breeds in Ghana, with a focus on the Ashanti Dwarf pig (ADP), an indigenous pig breed of Ghana. A total of 167 pigs sampled in Ghana and populations consisting of Ashanti Dwarf pigs (n = 106), exotics (mostly European pigs) (n = 11), crosses (between indigenous and exotic breeds) (n = 44), and unknown breeds (nondescript) (n = 6) were genotyped using Porcine SNP60K BeadChip. Moderate heterozygosity levels, ranging from 0.28 for Ashanti Dwarf pigs to 0.31 for exotic pigs (mostly European pigs), were observed. Principal component analysis of the pig populations within Ghana resulted in two distinct clusters of pigs: (i) Northern and (ii) Southern regional clusters. The PCA based on breed also resulted in four clusters: (i) ADPs; (ii) exotics (iii) crossbreeds between ADP and exotics; (iv) unknown breed types. The PCA demonstrated that the clustering was influenced by genetics, geographical location, production systems, and practices. ADMIXTURE-based analysis also showed that the populations within Ghana are admixed. FST analysis revealed SNPs associated with QTLs for traits such as disease resilience and growth among ADP populations within the different regional and ecological zones of Ghana.

High genetic diversity and weak population structure of Leptobotia elongata from different markers

To study genetic diversity and population structure of Leptobotia elongata in China, nine populations in the upper reaches of the Yangtze River (Lizhuang (LZ), Jiangnan (JN), Yalong (YL), Xuifeng (XF), Chengjiang (CJ), Xiqu (XQ), Chuxiong (CX), Shizhu (SZ), and Pingshan (PS)) were analogized base on D-Loop gene and nuclear gene. The results showed that 81 mutation sites and 64 haplotypes were detected in 246 D-Loop sequences, and the average haplotype diversity (Hd) and average nucleotide diversity (Pi) were 0.878 and 0.0029, respectively. For L. elongata population, the average number of Alleles per locus was 6.68, the average PIC of each locus was 0.818, the average Shannon index was 1.28, the average Ho was 0.798, and the average He was 0.844. Molecular analysis of variance (AMOVA) showed that Fst > 0.5, There were no individuals independently assigned to one group, and individuals at each sampling site showed similar patterns, with no significantly differentiated geographical groups in Structure analysis. These results can provide an important scientific basis for the protection of L. elongata and wild species with similar life histories.

Genetic structure of the commercially important Asian monsoon scallop, Amusium pleuronectes (Linnaeus 1758), across the Indonesian Archipelago

AbstractThe Asian monsoon scallop, Amusium pleuronectes, is a key member of the most commercially harvested shellfish community in Asia. Patterns of genetic diversity and natural population structure in the target species were investigated to gain a better understanding of its evolutionary history. Samples were collected from five sites across the Indonesian Archipelago. We characterized sequence variation in an mtDNA control region fragment in 249 individuals. The genetic diversity (h = ranging from 0.83 to 0.92) and nucleotide diversity (π = ranging from 0.24 to 0.32) were low compared to the estimates reported for many other similar shellfish taxa. Nonetheless, analysis of molecular variance revealed significant genetic differentiation, FST = 0.0203 (p < .005 after Bonferroni corrections). Furthermore, both Pairwise fixation index values showed significance among majority population sites, indicating that dispersal potential and gene flow were low in the past. This pattern likely reflects a low dispersal potential, potentially allowing local adaptation to sites that augment any oceanographic and geographic contribution to genetic structure. The results described herein provide a foundation for developing better conservation strategies for the target species in the future.

Intra- and inter-drainage variation in population structure, body condition, shape morphology and sexual dimorphism in Mauremys leprosa saharica from southern Morocco

The Mediterranean pond turtle Mauremys leprosa is widely distributed in Morocco. Significant variations could be observed in this species due to the fact that it occupies a vast and environmentally diverse area. Thus, the analysis of population parameters is crucial in elucidating the differences between populations. Differences between individuals may be linked to environmental factors, including many habitat characteristics. In the present study, variation in population structure, body condition, morphology and sexual dimorphism, were examined for the Sahara Desert blue-eyed turtle M. l. saharica in southern Morocco from seven distinct localities distributed in four different drainages in southern Morocco. A total of 224 turtles were captured, sexed, weighed and then measured for their carapace and tail dimensions before being released. Among the studied populations, four were dominated by adult individuals (Taakilt: 96%, Oued Guir: 87%, Oued Ziz: 75%, Sidi ElMehdaoui: 70%), two comprised 100% of adults (Oued Noun and Tarmigt) and one population consisted of 50% adults (Lower Draa). The sex ratio was significantly different between populations, being balanced in two populations (Tarmigt and Sidi El Mehdaoui), male-biased in three populations (Oued Zizi, Oued Noun, Lower Draa) and female-biased in the two remaining populations (Oued Guir and Taakilt). Body Condition Index (BCI, g/cm3) was significantly different among populations but not between sexes, or for the Sex × Locality interaction. The Sexual Size Dimorphism (SSD), females being larger than males, varies among population with the greatest degree observed in Oued Guir population (SSD = 0.41) and the lowest in Sidi El Mehdaoui population (SSD = -0.14). Length-Weight Relation (LWR) shows that M. l. saharica has isometric growth for both male and female of Oued Guir and Tarmigt, for female of Oued Ziz, Taakilt, Oued Noun and lower Draa and hypo-allometric for male of Oued Ziz, Taakilt, Oued Noun, Lower Draa and for both male and female of Sidi El Mehdaoui. Morphological variation of carapace is shown in this species associated with population variation among basins. Increased understanding of population characteristics and their fitness status must be considered in conservation and management action plans for the species and its habitat.

Amplicon deep sequencing of five highlypolymorphic markers of Plasmodium falciparum reveals high parasite genetic diversity and moderate populationstructure in Ethiopia

BackgroundPlasmodium falciparum genetic diversity can add information on transmission intensity and can be used to track control and elimination interventions.MethodsDried blood spots (DBS) were collected from patients who were recruited for a P. falciparum malaria therapeutic efficacy trial in three malaria endemic sites in Ethiopia from October to December 2015, and November to December 2019. qPCR-confirmed infections were subject to amplicon sequencing of polymorphic markers ama1-D3, csp, cpp, cpmp, msp7. Genetic diversity, the proportion of multiclonal infections, multiplicity of infection, and population structure were analysed.ResultsAmong 198 samples selected for sequencing, data was obtained for 181 samples. Mean MOI was 1.38 (95% CI 1.24–1.53) and 17% (31/181) of infections were polyclonal. Mean He across all markers was 0.730. Population structure was moderate; populations from Metema and Metehara 2015 were very similar to each other, but distinct from Wondogent 2015 and Metehara 2019.ConclusionThe high level of parasite genetic diversity and moderate population structure in this study suggests frequent gene flow of parasites among sites. The results obtained can be used as a baseline for additional parasite genetic diversity and structure studies, aiding in the formulation of appropriate control strategies in Ethiopia.

Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province.

Indigenous pig populations, including Bamei pigs (BM), Hezuo pigs (HZ), Huixian Qingni Black pigs (HX), and Minxian Black pigs (MX) in Gansu Province, live in a particular climate and a relatively closed geographical environment. These local pig breeds are characterized by excellent characteristics (e.g., cold tolerance, robust disease resistance, and superior meat quality). In the past few years, pig populations in Gansu Province have decreased significantly because of their poor lean meat percentage, high fat content, and slow growth rate. Maintaining the diversity of these four breeds can act as a source of new alleles to be incorporated into commercial breeds which are more susceptible to disease and less adaptable to changing conditions because of inbreeding. Genomic data analysis is adequate for determining the genetic diversity and livestock breeding population structure, even in local pig populations. However, the genetic diversity and population structure of the four native pig populations in Gansu Province are still unknown. Thus, we used "Zhongxin-I" porcine chip for the SNP detection of 102 individuals living on four pig conservation farms. A total of 57,466 SNPs were identified among the four pig breeds. The linkage disequilibrium (LD) plot showed that MX had the highest level of LD, followed by BM, HZ, and HX. The observed heterozygosity (Ho) in all four populations was higher than the expected heterozygosity (He). A principal component analysis (PCA) demonstrated that the four local pig populations were isolated. The identity displayed by the state matrix and G matrix heat map results indicated that small numbers of individuals among the four pig breeds had a high genetic distance and weak genetic relationships. The results of the population genetic structure of BM, HZ, HX, and MX pigs showed a slight genetic diversity loss. Our findings enabled us to better understand the genome characteristics of these four indigenous pig populations, which will provide novel insights for the future germplasm conservation and utilization of these indigenous pig populations.

Genetic Diversity and Fine-Scale Population Structure Analysis of the Placocheilus cryptonemus in the Nujiang River from mtDNA and Microsatellite Markers

Genetic Diversity and Fine-Scale Population Structure Analysis of the Placocheilus cryptonemus in the Nujiang River from mtDNA and Microsatellite Markers

Reassessing the genetic variability of Tectona grandis through high-throughput genotyping: Insights on its narrow genetic base.

Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its first sources of diversity and little is known about the genetic origin and genetic variability. Thus, this study aimed to investigate the genetic diversity and genetic population structure existing in a representative teak germplasm bank collection. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 3 giga bases per sample, the sequences are aligned using the genome, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four populations with considerable genetic variability between and within them. While the genetic variability in teak is generally known to be narrow, this study confirmed the presence of genetic variability scale in teak, which is contrary to what was initially expected.

Nosocomial dissemination of blaIMP-4 among Klebsiella pneumoniae by horizontal gene transfer and clonal spread: the epidemic IncN plasmids and the emerging high-risk IMP-4-producing ST101 clone.

To determine the genomic features of IMP-4-producing Klebsiella pneumoniae isolates recovered from paediatric patients and the transmission dynamics of blaIMP-4. IMP-producing K. pneumoniae isolates were collected from paediatric patients in Shanghai Children's Medical Center from 2013 to 2020. WGS was performed for all isolates, and the complete genomes of three IMP-4-producing isolates were generated. The distribution of blaIMP-4-harbouring plasmids was determined, and a conjugation assay was employed to investigate the horizontal transfer of blaIMP-4-harbouring plasmids. We collected 21 blaIMP-carrying K. pneumoniae isolates, with IMP-4 (16/21, 76.2%) as the predominant subtype, followed by IMP-8 (n = 3) and IMP-26 (n = 2). IMP-4-producing isolates displayed a diverse population structure and all blaIMP-4 genes were located on plasmids, including IncN (n = 9), IncHI5 (n = 5), IncFII(K) (n = 1) and IncFII(pKP91) (n = 1), although only IncN plasmids were conjugative. Clonal transmission of ST101 strains carrying IncHI5 blaIMP-4-harbouring plasmids was observed, and the acquisition of blaIMP-4 by the international high-risk ST101 clone constituted a novel combination of ST101 clone and carbapenemase genes. Plasmid analysis demonstrated that the conjugal transfer of the IncHI5 blaIMP-4-harbouring plasmid might be blocked by the ST101 bacterial host. The horizontal transfer of IncN plasmids and clonal spread of the international high-risk ST101 clone facilitated the nosocomial dissemination of blaIMP-4 among K. pneumoniae. The emerging IMP-4-producing ST101 clone displays diverse combinations of carbapenemase genes, and this clone could be a continually evolving threat and warrants prospective monitoring.

Same species, different population dynamics: Spatio-temporal differences of Undaria pinnatifida (Ochrophyta, Phaeophyceae) in the intertidal of North Patagonia, Argentina.

Population dynamics can be influenced by physical and biological factors, particularly in stressful environments. Introduced species usually have great physiological plasticity, resulting in populations with different traits. Undaria pinnatifida, a macroalga originally described from northeast Asia, was introduced in Northern Patagonia, Argentina (San Matías Gulf) around 2010. To describe the spatio-temporal variability in population structure and morphometry of U. pinnatifida, we conducted monthly field samplings for 2 years at the intertidal area of two contrasting sites in the San Matías Gulf. Individuals of U. pinnatifida were classified by developmental stage, and their morpho-gravimetric variables were measured. In both intertidal sites juveniles were found in higher proportion during austral autumn and grew and matured during the autumn-winter months (from May onwards), and individuals senesced during early austral summer (December and January). Conversely, density and biomass were largely different between sites, and individuals showed slight morphological variability between sites. Environmental (e.g., nutrient concentration, available substrate) and biological factors (e.g., facilitation, competition) may explain the observed differences. Since there is not a macroalga with U. pinnatifida morphometrical characteristics in the intertidal environments of San Matías Gulf, studying this recent introduction gives us a better understanding of its potential ecological effects.

Geographic variation in population structure and grazing features of Calanus glacialis/marshallae in the Pacific Arctic Ocean

Calanus glacialis/marshallae is a dominant zooplankton species in the Pacific Arctic Ocean that is widely distributed in shelf areas, and it plays a vital role in connecting primary production to higher trophic levels. Its phenology is well adapted to hydrography, but there is little available information about regional and diel changes in population structure and grazing features. In this study, we investigated C. glacialis/marshallae during autumn 2019 in the Eastern and Northeastern Chukchi and Canadian basins to reveal geographic and diel variations in population structure, body size, grazing activity, and fatty acid composition. The abundance of C. glacialis/marshallae was found to be high on the slopes and low on the shelves. Body size (prosome length) was well described by the Bělehrádek equation combined with in-situ temperature throughout the sampling region. Cluster analyses based on hydrographic parameters were divided into four regions: southern shelf, northern shelf, slope, and basin. The southern shelf was dominated by copepodite stage five (C5) transported from the Bering Sea by Pacific waters. C4 and C5 were dominant on the northern shelf, suggesting that they grew slower than those on the southern shelf, and the populations also exhibited higher concentrations of fatty acids originating from dinoflagellates than those originating from the pan-Arctic Ocean, indicating low productivity in the region. The population on the slope had the highest abundance, C4 was dominant, and large amounts of diatom-derived eicosapentaenoic acid (EPA). These features are attributed to the upwelling of populations and nutrients that support diatom growth. In the basin, the early copepodite stages of composition were distinctly higher than those recorded in previous studies, because larger amounts of organisms flow into the region, resulting in more extended reproduction periods. In the basin, small and large forms of C5 were simultaneously found, and the small form exhibited a diel grazing activity pattern, but the large forms did not. These findings suggest their well adaptation in changing of the Pacific Arctic Ocean.

Genomic analysis of Plasmodium falciparum isolates across different altitudinal zones along the slope of Mount Cameroon

BackgroundMalaria elimination is threatened by the emergence and rapid spread of drug resistance. Understanding the demographic history of Plasmodium falciparum and the genetic basis of adaptation to antimalarial treatment and host immunity is critical to elimination efforts. This study sought to characterize the diversity of P. falciparum isolates across different altitudes along the slope of Mount Cameroon.MethodologyUsing the Illumina next-generation sequencing platform P. falciparum isolates from low, intermediate and high altitudes along the slope of Mount Cameroon were studied to determine their genetic diversity, population structures, and signatures of selection in known drug resistance alleles.ResultsA total of 77,253 single-nucleotide polymorphisms were identified from 220 quality P. falciparum clinical isolates from high (24,214), intermediate (24,426), and low (28,613) altitude. About 49%, 48.2% and 30% of the parasite isolates from high, intermediate, and low altitudes, respectively had FWS values > 0.95 indicative of dominant mixed genotype infections and low population sub-structure with high potential for out-crossing. No significant difference was observed in within-host diversity while population structure analysis did not separate the isolates in the three major altitudinal groups by PCA, FST and admixtures, suggesting bidirectional gene flow among the populations. A total of 94 antigenic genes under balancing selection were detected in the area including vaccine candidate gene ama1, eba175, msp1, trap, dblmsp, and clag2. Moreover, 17 of these genes were identified to be under both recent positive directional and positive balancing selection including the prominent host immune target genes surfin 8.2, trap, and ama1. Recent directional selection analysis using integrated standardized haplotype score (iHS) did not detect any selection signatures in the Pfdhfr, Pfdhps, Pfmdr1, and PfK13 genes. Furthermore, no PfKelch13 validated mutation associated with artemisinin resistance was identified in this study and no structural divergence was noticed among the P. falciparum parasite populations across different altitudes around the Mount Cameroon region.DiscussionFindings revealed high genetic diversity and low population structure suggesting that malaria transmission remain high in the study area and parasite populations circulating around the slope of Mount Cameroon are homogenous.

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing.

Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with Fst values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics.

Stock identification of Congaturi halfbeak (Hyporhamphus limbatus): insight into conventional and truss-based morphometrics

BackgroundWild fish stocks continuously decline in Bangladeshi rivers and oxbow lakes. Small indigenous fish species management solely depends on their population status and conservation. This study aimed to determine the population status of Hyporhamphus limbatus, in Southwestern Bangladesh using conventional and truss morphological characteristics.ResultsA total of 174 fish samples were procured from monsoon season i.e., May to August 2018 the Bhairab River, BR; Kopotakkho River, KR; and Baluhar Baor, BB in Bangladesh. Five meristics, six conventional and twelve truss-based morphometric characters, were considered for stock identification. The Kruskal–Wallis test helped to analyze the meristic characters, while ANOVA, principal component analysis (PCA), discriminant function analysis (DFA), correct classification analysis using DFA, and a UPGMA dendrogram formation were used to investigate the conventional and truss measurements. By the Kruskal–Wallis test, no meristic characters showed significant differences across different populations. Eleven of the 18 morphometric measurements showed significant differences among three populations through the univariate ANOVA. PCA specified the population structure variations and explained 67.438% of the total variance. The first and second discrimination functions accounted for 78.3% and 21.7%, representing 100% of the group variability. Similarly, 85.6% of the grouped cases and 77.6% of cross-validated grouped cases were initially effectively represented by their correct number of individuals. A dendrogram based on morphometric (conventional and truss) displayed three stocks grouped into two clusters, with BR forming a distinct cluster, while KR and BB creating a shared cluster.ConclusionIn conclusion, such morphological differences are most likely due to their distinctive ancestral origins. This study presents novel reports on the stock assessment of H. limbatus in their natural ecosystem. Furthermore, molecular research and an evaluation of the environmental impact on H. limbatus populations in Bangladesh are strongly recommended.

Genomic epidemiology of Vibrio parahaemolyticus from acute diarrheal patients in Shenzhen City from 2013 to 2021

Objective: To characterize the prevalence and genomic epidemiology of Vibrio parahaemolyticus from acute diarrheal patients in Shenzhen City from 2013 to 2021. Methods: Based on the Shenzhen Infectious Diarrhea Surveillance System, acute diarrheal patients were actively monitored in sentinel hospitals from 2013 to 2021. Whole-genome sequencing (WGS) of Vibrio parahaemolyticus isolates was performed, and the genomic population structure, serotypes, virulence genes and multilocus sequence typing were analyzed. Outbreak clusters from 2019 to 2021 were explored based on single-nucleotide polymorphism analysis. Results: A total of 48 623 acute diarrhea cases were monitored in 15 sentinel hospitals from 2013 to 2021, and 1 135 Vibrio parahaemolyticus strains were isolated, with a positive isolation rate of 2.3%. Qualified whole-genome sequencing data of 852 isolates were obtained. Eighty-nine serotypes, 21 known ST types and 5 new ST types were identified by sequence analysis, and 93.2% of strains were detected with toxin profile of tdh+trh-. 8 clonal groups (CGs) were captured, with CG3 as the absolute predominance, followed by CG189. The CG3 group was dominated by O3:K6 serotype and ST3 sequence type, while CG189 group was mainly O4:KUT, O4:K8 serotypes and ST189a and ST189 type. A total of 13 clusters were identified, containing 154 cases. About 30 outbreak clusters with 29 outbreak clusters caused by CG3 strains from 2019 to 2021. Conclusion: Vibrio parahaemolyticus is a major pathogen of acute infectious diarrhea in Shenzhen City, with diverse population structures. CG3 and CG189 have been prevalent and predominant in Shenzhen City for a long time. Scattered outbreaks and persistent sources of contamination ignored by traditional methods could be captured by WGS analysis. Tracing the source of epidemic clone groups and taking precise prevention and control measures are expected to significantly reduce the burden of diarrhea diseases caused by Vibrio parahaemolyticus infection in Shenzhen City.