Phylogeography and demographic dynamics of Rhipicephalus microplus from North India

Mitochondrial genetic markers based phylogenetic analyses of Hyalomma dromedarii Koch, 1844 (Acari: Ixodidae)

The hard tick Hyalomma dromedarii, a vector for numerous animal and human pathogens, was investigated for genetic diversity using the mitochondrial cytochrome C oxidase subunit I (cox I) and 16S ribosomal RNA (16S rRNA) genes. Hyalomma dromedarii sequences (n = 11 cox I; n = 7 16S rRNA) were deposited in GenBank (LC761179-89, LC761173-78, LC654692), showing 99.52-100 % (cox I) and 98.15-100 % (16S rRNA) similarity to existing GenBank sequences. Phylogenetic analysis revealed monophyletic clades for H. dromedarii sequences from this study and GenBank. Haplotype network analysis identified 34 and 11 haplotypes for the cox I and 16S rRNA genes, respectively, displaying stellate configurations. The overall cox I dataset showed very low nucleotide diversity (0.0019 ± 0.0002) and high haplotype diversity (0.535 ± 0.052). In contrast, the 16S rRNA gene dataset displayed low nucleotide (0.00211 ± 0.00071) and haplotype (0.351 ± 0.079) diversities. Neutrality tests showed significant negative values (Tajima's D, Fu and Li's D, and Fu and Li's F), indicating recent population expansion or selective sweep. Pairwise FST values (-0.00942 to 0.02007 for cox I; -0.04878 to 0 for 16S rRNA) suggested non-significant genetic differentiation between populations, supported by high gene flow (Nm) values. This study provided novel insights into H. dromedarii population genetics, revealing recent expansion, weak population differentiation, and high gene flow. These findings have implications for understanding the tick's evolutionary history and epidemiological significance.

Cladistics and population structure analysis of Anaplasma marginale (Rickettsiales: Anaplasmataceae) in Haryana, India based on genes encoding the major surface proteins

Anaplasma marginale, a tick-borne obligate intracellular rickettsia is incriminated to cause heavy economic losses throughout the tropical and subtropical regions, including India. However, studies highlighting the phylogeography and demographic dynamics of A. marginale are very scant from India. Thus, the present study assessed the cladistics and population structure of Anaplasma marginale based on the genes encoding the major surface proteins (MSP) 4 and 5. The cladistics based on phylogenetic tree including the sequences generated herein with the GenBank archived sequences of A. marginale was performed. The relationship between A. marginale haplotypes based on both the genetic markers was estimated by performing median joining (MJ) haplotype network analysis. Demographic dynamics involving population diversity indices and neutrality indices was also performed. The cladistics and MJ haplotype network analysis corresponding to both the markers demonstrated the presence of three distinct clades (1-3) of A. marginale. Population structure analysis revealed low nucleotide (0.00236 ± 0.00064 and 0.00955 ± 0.00101) and haplotype (0.321 ± 0.073 and 0.493 ± 0.083) diversities for the MSP4 and MSP5 genes, respectively. High genetic structuring and low gene flow [Nm values ranging between 0.044481 and 0.208337 for the MSP4 gene and 0.032735 (clades 1 and 2) for the MSP5 gene] was also recorded among the different clades of A. marginale, based on both genetic markers. The present study highlighted the presence of different clades of A. marginale distributed worldwide. The isolates circulating in north India belonged to the dominant clade prevalent throughout the globe.

Genetic diversity and molecular evolution of the internal transcribed spacer regions (ITS1-5.8S-ITS2) of Babesia vogeli

Canine babesiosis, a severe haemoparasitic disease caused by Babesia species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of B. vogeli on the basis of the internal transcribed spacer regions (ITS1-5.8S-ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (n = 62) exhibited 92.5-100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5-93.8 % between them. Notably, the newly generated Indian sequences (n = 21) demonstrated a high degree of homology, with 98.3-100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different B. vogeli populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2-25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The B. vogeli populations between Thailand and Tunisia exhibited the highest genetic differentiation (FST = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of B. vogeli indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-term molecular surveillance program. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of B. vogeli were observed on the basis of internal transcribed spacer regions (ITS1-5.8S-ITS2).

Cladistics of Rhipicephalus microplus and laboratory assessment of acaricidal efficacy of different Cassia fistula extracts against R. microplus larvae

The present study aimed to analyze the cladistics and population structure analysis of Rhipicephalus microplus ticks infesting buffaloes in Haryana, India, as well as the assessment of the anti-tick efficacy of the ethanolic extracts of Cassia fistula (bark, pod pulp, and flowers) against R. microplus larvae. The molecular characterization and population structure analysis were performed by targeting the amplification of the partial mitochondrial cytochrome C oxidase subunit 1 (cox1) gene, whereas anti-tick efficacy was evaluated using a larval packet test. The sequences generated herein revealed a homology of 98.26-100% to the GenBank-archived R. microplus sequences. In population structure analysis, high haplotype (0.500 ± 0.265) and low nucleotide (0.002 ± 0.001) diversities were recorded for the sequences generated in this study. Significantly negative neutrality indices were recorded for the overall dataset. The extracts were found to significantly affect mortality rates in a dose-dependent manner, and the ethanolic extracts of the bark, pod pulp, and flowers of C. fistula exhibited median lethal concentration (LC50) values of 27.989, 40.457, and 49.43 mg/mL, respectively. The LC50 value recorded for the combination of the ethanolic extracts of the bark, flower, and pod pulp of C. fistula was 19.724 mg/mL, whereas the synthetic acaricide ivermectin had an LC50 value of 351.56 mg/mL. In conclusion, R. microplus populations infesting cattle and buffalo hosts in India exhibited negligible genetic differentiation and high gene flow between them. Additionally, the combination of all C. fistula extracts could serve as a potential substitute for the synthetic acaricide.

Population genetics of Babesia vogeli based on the mitochondrial cytochrome b gene

The current study aimed at population genetic characterization of B. vogeli based on the cytochrome b (cyt b) gene sequences (≥ 685 bp) available in the GenBank. Phylogenetic trees placed all the sequences of B. vogeli in a single large monophyletic clade; however, it was further divided into two subclades (Bv1 and Bv2). Out of seven nucleotide variations observed between Bv1 and Bv2 subclades, four were synonymous (G92A, C170T, T488C and A659G), and three were non-synonymous (G324A, C438A and G465A) resulting in amino acid substitutions at three places (V108I, L146I and V155I). Within different B. vogeli populations, the nucleotide and haplotype diversities were low. The median-joining haplotype network revealed only two haplotypes (Hap_1 and Hap_2). A geographical sub-structuring was noticed in the B. vogeli populations, with moderate genetic differentiation (FST = 0.05000; P < 0.05) and a very high gene flow (Nm = 4.75) between Indian and Chinese populations. Neutrality tests and mismatch distributions for the Indian population and the overall dataset of B. vogeli indicated a constant population size. This study provides the first insight into the genetic characterization, population genetics and haplotype network of B. vogeli based on the cyt b gene.

First Insight into the Phylogenetic Diversity of Bovicola caprae Infesting Goats of Different Agro-climatic Locations in India

Bovicola caprae is an important obligate ectoparasite of goats worldwide including India. The present study aimed at the molecular confirmation, phylogenetics and population structure analyses of B. caprae infesting goats of three different agro-climatic locations in India, by targeting the mitochondrial cytochrome C oxidase subunit 1 (cox1) genetic marker. The phylogenetic tree exhibited the presence of two different lineages of B. caprae. The sequences generated herein clustered in lineage 2 along with the GenBank™ archived sequences from China and Iran. The sequences generated herein also showed the circulation of sub-lineages of B. caprae in India based on the analysis of pairwise genetic distances between sequences and median-joining haplotype network. The population structure analyses revealed low nucleotide (0.00353 ± 0.00291 and 0.02694 ± 0.00363) and high haplotype (0.667 ± 0.314 and 0.618 ± 0.104) diversities for the present study isolates as well as for the complete dataset, respectively, which evinced a recent demographic expansion. High genetic differentiation (FST value = 0.97826) and low gene flow (Nm = 0.00556) were also recorded in the different lineages/populations. In conclusion, the present study addressed the research gap and provided the first insight into the phylogenetics of the goat louse B. caprae and highlighted the circulation of sub-lineages of the ectoparasite in India.

Population structure and haplotype network analyses of Hyalomma anatolicum based on the large subunit ribosomal RNA (16S rRNA) gene

Hyalomma anatolicum, an Anatolian hard tick is a well-recognized vector involved in the transmission of various pathogens to animals and humans. The present study elucidated the population structure and haplotype network of H. anatolicum based on the mitochondrial large subunit ribosomal RNA (16S rRNA) gene sequence. The population structure and haplotype network analysis of 75 sequences archived in the GenBank, including the 15 sequences generated herein, yielded 24 haplotypes. Haplotype 1 (Hap_1) was the predominant haplotype consisting of 45 sequences from India, China, Pakistan, Turkey, Egypt, Iraq, and Tajikistan. The complete haplotype network exhibited a stellate conformation, highlighting a recent population expansion. The overall dataset, together with the sequences corresponding to India, China, and Pakistan, showed a high haplotype (0.638 ± 0.065, 0.671 ± 0.103, 0.753 ± 0.099, and 0.854 ± 0.061, respectively) and low nucleotide (0.00407 ± 0.00090, 0.00525 ± 0.00196, 0.00680 ± 0.00233, and 0.00453 ± 0.00056, respectively) diversity, further emphasized a recent population expansion. The neutrality indices including Tajima's D, Fu and Li's D, and Fu and Li's F for the complete dataset (- 2.661, - 6.008, and - 5.649, respectively) as well as for the sequences from India (- 2.223, - 3.414, and - 3.567, respectively) were negative, suggesting deviation from neutrality and a recent population expansion. The present study provided novel insights into the population structure and haplotype networks of H. anatolicum based on the mitochondrial 16S rRNA gene, and the different tests inferred a low genetic differentiation and suggested a recent population expansion of this economically important tick species.

Genetic Diversity of Rhipicephalus (Boophilus) microplus for a Global Scenario: A Comprehensive Review

Rhipicephalus microplus poses a substantial threat to livestock health and agricultural economies worldwide. Its remarkable adaptability to diverse environments and hosts is a testament to its extensive genetic diversity. This review delves into the genetic diversity of R. microplus, employing three pivotal genetic markers: the cytochrome c oxidase I (COX1) gene, ribosomal genes, and microsatellites. The COX1 gene, a crucial tool for genetic characterization and phylogenetic clustering, provides insights into the adaptability of ticks. Ribosomal genes, such as internal transcribed spacer regions (ITS-1 and2) as well as 18S and 28S, are routinely utilized for species differentiation. However, their use is limited due to indels (insertions and deletions). Microsatellites and minisatellites, known for their high polymorphism, have been successfully employed to study populations and genetic diversity across various tick species. Despite their effectiveness, challenges such as null alleles and marker variations warrant careful consideration. Bm86, a well-studied vaccine candidate, exhibits substantial genetic diversity. This diversity directly influences vaccine efficacy, posing challenges for developing a universally effective Bm86-based vaccine. Moreover, the review emphasizes the prevalence of genes associated with synthetic pyrethroid resistance. Identifying single nucleotide polymorphisms in the acaricide-resistant genes of R. microplus has facilitated the development of molecular markers for detecting and monitoring resistance against synthetic pyrethroids. However, mutations in sodium channels, the target site for synthetic pyrethroid, correlate well with the resistance status of R. microplus, which is not the case with other acaricide target genes. This study underscores the importance of understanding genetic diversity in developing effective tick management strategies. The choice of genetic marker should be tailored based on the level of taxonomic resolution and the group of ticks under investigation. A holistic approach combining multiple markers and integrating additional molecular and morphological data may offer a more comprehensive understanding of tick diversity and relationships. This research has far-reaching implications in formulating breeding programs and the development of vaccine against ticks and tick-borne diseases (TTBDs) as well as strategies for the management of resistant ticks.

Population genetic characterization of Theileria annulata based on the cytochrome b gene, with genetic insights into buparvaquone susceptibility in Haryana (India)

The present investigation was aimed at population genetic characterization of Theileria annulata on the basis of the cytochrome b (cyt b) gene along with the evaluation of status of buparvaquone resistance in Haryana (India). The sequences originating from China, Egypt, India, Iran, Iraq, Tunisia, Turkey and Sudan were included in the analysis. The maximum likelihood tree based on the Tamura-Nei (TN93+G) model placed all the sequences of T. annulata into a single clade. The median-joining haplotype network exemplified geographical clustering between T. annulata haplotypes originating from each country. Only five haplotypes (7.81 %) were shared between any two countries, while the remaining 59 haplotypes (92.19 %) were singleton and unique to one country. The values of pairwise genetic distance (FST) between all the populations indicated huge genetic differentiation (> 0.25) between different T. annulata populations, barring the FST value between Iraq and Turkey (0.14454) which suggested a moderate differentiation. Contrary to the FST index, the values of gene flow (Nm) between T. annulata populations were very low. The neutrality indices and mismatch distributions indicated a population expansion in the Indian T. annulata population. Furthermore, the secondary structure and homology modeling of the partial cyt b protein is also reported. The molecular analysis of newly generated sequences for buparvaquone resistance revealed that all the isolates were susceptible to buparvaquone treatment. However, two novel mutations at positions V203I and V219I in between the Q01 and Q02 drug-binding regions of the cyt b gene were observed for the first time.

Cladistics of Echinococcus granulosus Sensu Stricto Genotypes Infecting the Slaughtered Pigs

PURPOSE

Echinococcus granulosus sensu stricto (s. s.) consists of the most widespread genotypes (G1, G3) implicated in human cystic echinococcosis worldwide. The present study aimed to evaluate the role of pigs in the transmission dynamics of E. granulosus s. s. genotypes, including the phylogenetics, evolutionary divergence and haplotype network analyses of north Indian pig isolates along with GenBank™ archived sequences.

METHODS

In totality, 223 slaughtered pigs were thoroughly screened for the presence of hydatid cysts. The amplification of the partial mitochondrial cytochrome C oxidase subunit 1 gene was performed for the molecular confirmation and phylogenetics of the retrieved metacestodes.

RESULTS

The molecularly confirmed and sequenced present study isolates (n = 2) clustered with the E. granulosus genotype G3. The very low evolutionary divergence values (< 0.0027) of the present study isolates with E. ganulosus genotype G3 indicated the absence of diverged lineages. The significantly negative values of Tajima's D (- 2.598) and Fu and Li's D (- 4.054) of the overall dataset and for the Asian sequences signified an expansion of population size. The overall dataset exhibited low nucleotide (0.067 ± 0.055) and high haplotype (0.574 ± 0.015) diversities, also alluding to demographic expansion. The haplotype network showed that the pig isolates from South America and Europe constituted the predominant haplotype, Hap_2 along with Hap_3 and Hap_6, primarily associated to E. granulosus genotype G1; whereas, the Indian isolates formed different haplotypes (Hap_1 and Hap_5) belonging to genotype G3.

CONCLUSIONS

The present study highlighted the important role of pigs in the transmission of E. granulosus s. s., which is of paramount significance given the public health and economic impact of cystic echinococcosis.