Genetic Distance Analysis Research Articles

Hidden diversity revealed by DNA barcoding of paralichthyidae fish along the caribbean and brazilian coast.

DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.

A dual typing system establishment and global diversity analysis for sapoviruses

BackgroundThe genus Sapovirus in the family Caliciviridae comprises of a genetically diverse group of viruses that are responsible for causing acute gastroenteritis in both human and animals globally. As the number of sequences continues to grow and more recombinant sequences are identified, the classification criteria of genogroups and genotypes of sapovirus need to be further refined. In this study, we aimed to optimize the classification of sapoviruses.ResultsThrough evolutionary clustering and genetic distance analysis, we have updated the classification criteria for VP1 genogroup and genotypes. We adjusted the original mean values ± 3 standard deviations (SD) of genetic distances to mean values ± 2.5SD, resulting the corresponding cutoff values for the same genotype and genogroup set at <0.161 and <0.503, respectively. Additionally, we established classification criteria for RdRp types and groups, referred to as P-types and P-groups,, with mean values ± 2SD and cutoff values of <0.266 and <0.531 for the same type and group, respectively. This refinement has expanded the VP1 genogroups to thirty-four and identified twenty-four P-groups. For human sapoviruses, the new criteria have resulted in the addition of one genotype, GV.PNA1. Moreover, the new criteria defined three P-groups and 21 P-types for human sapoviruses. Spatial-temporal analysis revealed no specific distribution pattern for human sapoviruses.ConclusionsWe established a dual typing system on classification based on VP1 and RdRp nucleotide sequences for sapoviruses.

An integrative species delimitation approach uncovers eriophyoid mite Diptilomiopus ligustri species complex (Acariformes: Eriophyoidea)

AbstractEriophyoid mites (Acari: Eriophyoidea) are among the smallest terrestrial arthropods possessing simplified morphological characters, which challenges the traditional morphology‐based species delimitation. The Diptilomiopus spp. exhibit further morphological degeneration (e.g., lack of genus on both legs and some opisthosoma setae). Especially, they possess high similarity in the reticulate prodorsal shield patterns, leading to cryptic species complex and hampering our understanding of species diversity. In this study, we implemented an integrated approach, including genetic distance analysis, phylogenetic analysis, population genetic structure construction, introgression test, and morphometric analysis, to delimitate the Diptilomiopus ligustri complex. We obtained 52 mitochondrial COI gene sequences and 19 whole‐genome sequences across 18 sample sites of this complex. All samples were collected from Ligustrum plants in China, which may cover their main distribution ranges. Our results demonstrate that the D. ligustri complex consists of at least four distinct species (i.e., D. ligustri, D. cf. ligustri sp1., D. cf. ligustri sp2., and D. cf. ligustri sp3.), which are genetically divergent but do not differ morphologically, assessed by principal component analysis of 27 morphological characteristics. No significant gene flow was observed among this complex. Divergence time estimates further showed that most Diptilomiopus species diverged in a short time interval at the Paleogene–Neogene boundary, indicating a rapid radiation. Our results highlight the integrated approaches in eriophyoid mite species complex delimitation.

Pre-breeding highlights of intraspecific polymorphism and genetic estimates of seed traits of African yam bean (Sphenostylis stenocarpa Hochst Ex. A. Rich.) Harms breeding lines

Abstract Discriminatory morpho-metric features are obvious on legume seeds. This study utilized seven quantitative and 11 qualitative seed traits to characterize 139 African yam bean (AYB) breeding lines which were developed through single seed descent procedure. The seven quantitative data were subjected to analysis of variance, their means were combined with qualitative scores for genetic distance, principal component (PC) and clustering analyses. Significant (P ≤ 0.001) variation existed among the breeding lines for the seven traits. Mean ranges of seed length (SL), width (SW), thickness (ST) and a single seed weight (SSW) among the 139 breeding lines were respectively: 6.77–10.22 mm, 5.70–7.86 mm, 4.96–7.45 mm and 0.15–0.42 g. Positive and significant (P ≤ 0.05) genotypic correlation existed among SSW, SL, SW and ST. Seed colours, pattern, shapes, sizes, surface texture, brilliance varied among the breeding lines. Ranges of phenotypic and genotypic coefficient of variation and broadsense heritability were: 5.49–23.84%, 2.95–19.88% and 28.91–69.54% respectively. Fourteen (quantitative and qualitative) traits contributed higher (≥ 0.30) eigenvector loadings to the first three PC axes which explained 57.9% of the total variation among the breeding lines. Similarity among the lines was 0.75. Four clusters ensued in the dendrograph and each group had genetic similarities of: 0.85 (I), 0.82 (II), 0.78 (III) and 0.80 (IV). This research unveiled significant variation among AYB breeding lines with promising reliability for breeding opportunities of the qualitative and quantitative seed traits, which could contribute to higher grain yield and acceptability.

Rhipicephalus simus ticks: new hosts for phleboviruses.

Ticks are widespread arthropods that transmit microorganisms of veterinary and medical significance to vertebrates, including humans. Rhipicephalus simus, an ixodid tick frequently infesting and feeding on humans, may play a crucial role in transmitting infectious agents across species. Despite the known association of many Rhipicephalus ticks with phleboviruses, information on R. simus is lacking. During a study in a riverine area in Lusaka Zambia, ten R. simus ticks were incidentally collected from the grass and bushes and subjected to metagenomic next generation sequencing (mNGS) in 2 pools of 5. Analysis detected a diverse microbial profile, including bacteria 82% (32/39), fungi 15.4% (6/39), and viruses 2.6% (1/39). Notably, viral sequence LSK-ZM-102022 exhibited similarity to tick phleboviruses, sharing 74.92% nucleotide identity in the RdRp gene and 72% in the NP gene with tick-borne phlebovirus (TBPV) from Greece and Romania, respectively. Its RNA-dependent RNA polymerase (RdRp) encoding region carried conserved RdRp and endonuclease domains characteristic of phenuiviridae viruses. Phylogenetic analysis positioned LSK-ZM-102022 in a distinct but lone lineage within tick phleboviruses basal to known species like brown dog tick phlebovirus and phlebovirus Antigone. Pair-wise genetic distance analysis revealed similar findings. This study emphasizes the urgency of further research on the ecology, transmission dynamics, and pathogenic potential of LSK-ZM-102022 and related TBPVs, crucial for local and global preparedness against emerging tick-borne diseases.

Assessing population structure and morpho-molecular characterization of sunflower (Helianthus annuus L.) for elite germplasm identification.

Sunflower (Helianthus annuus L.), known for its adaptability and high yield potential, is vital in global edible oil production. Estimating genetic diversity is a key pre-breeding activity in crop breeding. The current study comprised of 48 genotypes which were assessed for their biometrical traits at department of Oilseeds, Tamil Nadu Agricultural University, during the rainy season of 2022. The lines were subsequently characterised using 103 simple sequence repeat (SSR) markers for molecular diversity analysis. The results indicated that the net nucleotide distances indicated varying genetic divergence, with subpopulations II and V showing the highest (0.056) and I and IV the lowest (0.014). Subpopulation IV exhibited the highest heterozygosity (0.352), while subpopulation III had the lowest heterozygosity and a low Fst (0.173). Principal components analysis (PCA) and hierarchical cluster analysis were employed for assessing the morphological diversity, facilitating genotype grouping and parent selection for breeding programs. The first four components cumulatively accounted for 86.72% of the total variation. Cluster Analysis grouped 48 sunflower genotypes into three clusters based on genetic diversity. COSF 13B stands out for its high head diameter, oil content, seed yield, and oil yield based on mean performance of morphological data. Principal coordinate analysis (PCoA) mirrored the groupings from the Neighbor Joining method, with the first three components explaining 27.24% of the total variation. Molecular data analysis identified five distinct clusters among the germplasm. By integrating morphological and molecular marker data with genetic distance analysis, substantial diversity was revealed with the genotypes RHA 273 and GMU 325 consistently demonstrated high oil yield per plant. The genotypes GMU 477, GMU 450, COSF 13B, RHA 102, CMS 1103B, and RHA GPR 58 have been identified as suitable parents for enhancing oil content in sunflower breeding programs. These findings also aid in selecting SSR markers for genotype characterization and in choosing diverse parents for breeding programs.

Utilizing SSR-based core collection development to improve conservation and utilization of Corylus L. genetic resources.

Hazelnuts are traditional woody oilseed plants. Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus L. germplasms using 16 simple sequence repeat (SSR) markers. Based on this, 11 pairs of core primers were selected, a fingerprint database of germplasm resources was constructed, and a primary core collection was screened. The results indicated that these tested Corylus L. germplasms exhibited a high level of genetic diversity, with an average number of alleles (Na) per locus of 14.5 and a polymorphic information content of 0.777. The phylogenetic relationships among various hazelnut cultivars were characterized by complexity, and they were delineated into four distinct groups facilitated by genetic distance analyses. An SSR fingerprint database for 331 Corylus L. germplasms was successfully constructed using the 11 obtained core SSR markers to increase the discrimination efficiency. Ultimately, 127 primary core accessions of Corylus L. were selected. The retention rate for the observed Na and MAF (the minor allele frequency) in the primary core germplasm constructed based on a sampling proportion of 38.36% was 100% and 94.7%, respectively. Shannon's information index (I) was highly consistent between the core and original germplasms, indicating that the core germplasm could fully represent the genetic diversity of the original germplasm. Additionally, the principal coordinate analysis of the selected primary core germplasm was essentially consistent with that of the entire original germplasm, further supporting the broad representativeness of the core germplasm. This study provided a basis for precisely identifying and efficiently utilizing Corylus L. accession.

Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand

The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8–9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.

Phylogenetic and Genetic Variation Analysis of ITS1 Gene of Trypanosoma lewisi in Wild Rats Using Polymerase Chain Reaction

Murine Trypanosomiasis is a disease caused by the blood protozoan Trypanosoma lewisi in rats, with the transmission process mediated by the flea species Xenopsylla cheopis and Nosopsyllus fasciatus. Cases of trypanosomiasis have been documented due to Trypanosoma lewisi infecting rats and humans in various countries. Diagnosis of T. lewisi is typically conducted using polymerase chain reaction (PCR), which amplifies target DNA using specific primers. One such target gene for detection is the Internal Transcribed Spacer-1 (ITS1). Subsequent sequencing of PCR products enables analysis of genetic variation employing parameters such as nucleotide composition, genetic distance, and phylogenetic analysis with MEGA software. Test results based on percent identity values indicated a 98.51% homology of blood samples with the Chinese strain of T. lewisi (FJ011094.1), demonstrating genetic variation. Phylogram reconstruction revealed that samples 18, 19, and 37 of T. lewisi exhibit very close intraspecies relationships with T. lewisi from NCBI genebank with genetic distance ranging from 0.007 to 0.01. While the closest interspecies relationship was found with T. cruzi (KT305857.1) with a genetic distance of (d = 0.61).

Genetic Structure and Phylogeographic Divergence of Thymallus brevicephalus in the Ob‐Irtysh River Headwaters

ABSTRACTClarifying the genetic structure and population history of a species can reveal the impacts of historical climate and geological changes, providing critical insights for developing effective conservation strategies for ecologically significant fish. The Markakol grayling (Thymallus brevicephalus), an endangered species found in the Altai‐Sayan Mountain region of Central Asia, serves as an ideal model for studying these factors. In this study, populations of a grayling (Thymallus) species discovered in the upper Irtysh River headwaters in Xinjiang, China, were analyzed to assess genetic diversity and population structure. Mitochondrial DNA sequences (cytochrome b and control region), along with 10 microsatellite markers, were used to examine genetic variation. Phylogenetic and genetic distance analyses confirmed the species, long misidentified as Arctic grayling (T. arcticus), as T. brevicephalus. This species can be divided into two distinct geographic groups: eastern and western, with the Crane River acting as the boundary. The divergence between these groups likely corresponds to refugia formed during the Pleistocene glaciation of the Altai Mountains, approximately 0.48 MA (million years ago) (range: 0.30 to 0.71 Ma). High haplotype diversity (Hd &gt; 0.5) and low nucleotide diversity (π &lt; 0.005) suggest that, despite the species' genetic richness, T. brevicephalus remains vulnerable to genetic drift, which could threaten its long‐term survival. This vulnerability may stem from inbreeding within small refugial populations during the glacial period, followed by gradual population expansion. Our study offers novel insights into grayling populations, with results that have direct implications for management by serving as a tool for the identification of conservation units.

Assessment of nine markers for phylogeny, species and haplotype identification of Kappaphycus species and Eucheuma denticulatum (Solieriaceae, Rhodophyta)

ABSTRACT Molecular studies have contributed to the taxonomy of carrageenan-producing Kappaphycus spp. and Eucheuma denticulatum. However, unresolved species complexes and the lack of standardization in the use of genetic markers impede the identification of specimens and the delineation of a robust taxonomic framework. Here, nine molecular markers (cox1, cox2–3 spacer, cox2, cox3, COB, ITS, psbA, UPA and rbcL) were used to generate a multilocus phylogeny for 113 fresh eucheumatoid samples and four herbarium specimens. Analyses of species delineation and genetic distances confirmed the monophyly of currently accepted taxa. These analyses suggest that clades previously reported as K. striatus KS1 and KS2 are conspecific, and that E. denticulatum EDA ‘spinosum’ and EDB ‘endong/cacing’ are also conspecific. The results also unveiled possible new taxa from Hawaii and Indonesia. Each molecular marker and combinations thereof were assessed with regard to species identification, ease of amplification and sequencing, and haplotype characterization. All genetic markers recorded at least 94% success in the amplification and sequencing of fresh specimens, with cox1 being the most phylogenetically informative. Automatic partitioning, phylogenetic and tree-based assessments showed cox1, cox2–3 spacer, cox2 and rbcL were able to correctly identify species while cox1+ rbcL, COB+rbcL, cox2+ rbcL or cox1+ COB+rbcL trees best represented the phylogeny with consistently high nodal support. Among individual markers, cox1 identified the greatest number of haplotypes, while UPA, partial rbcL (750 bp), ITS, cox3 and cox2–3 spacer were able to retrieve information from herbarium specimens of 12–16 years of age. These molecular results provide a basis for a database essential for the taxonomic framework, cultivar development and germplasm conservation of eucheumatoids.

An explanation for the sister repulsion phenomenon in Patterson's f-statistics.

Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.

Mating Strategy in the Arab Horse Population Over 30 Years in Algeria

Abstract The objective of this research was to describe the variation in breeding practices in the population of Arabian horses in Algeria in relation to the population size drop observed in the 2000s, due to an increase in the cost of food and a change in interest in racing, related to the black decade. As a result, the breeders had to face two opposite constraints: enhancing reproduction to counter the population decline and preventing the loss of genetic diversity. The aim of the study was to evaluate the genetic consequences of the decisions taken over a period of 30 years, starting from 1988 to 2018. The study was based on the analyses of the stud-book and on 11 microsatellite markers in a group of 943 horses, distributed into 13 age classes. Between 2004 and 2008, the breeders purchased foreign sires and dams, allowing a relative stability in unbiased heterozygosity of about 71%, due to the high genetic distances between foreign and local horses. As these importations stopped from 2009 on, there was a decrease in allele numbers of about 20%. Moreover, from 2010 on, we observe an excess of inbreeding and an increase in genetic drift relative to the starting population, due to population size decline. From the analysis of genetic distances between local individuals, it seems that the only constraint for sires and dams allowed to mate was a null coefficient of inbreeding.

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994-2018) and four hyperendemic Lake Victoria fishing communities (2011-2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

GENETIC DISI'ANCE MEASURES AMONG FIVE INDIGENOUS CATTLE BREEDS IN NIGERIA

Genetic variation is the basis of effective improvement in farm animals. Population differentiation is used for objective choice of parental genotypes that constitutes new hybrids in crossbreeding. In Nigeria, population characteristics of selected indigenous cattle breeds have not been fully documented. Therefore, blood protein electrophoretic patterns of selected indigenous cattle breeds in Nigeria were assessed. Blood samples (5mL) were taken underneath the tail by venipuncture from 200 cattle (40/breed) randomly selected from the five indigenous cattle breeds. The samples were subjected to cellulose acetate electrophoresis to determine the genetic variants of haemoglobin (Hb), carbonic anhydrase (CA) and transferrin (TO. Data were analysed using Euclidean genetic distance and cluster analysis. Two main clusters from the dendrogram were observed for each of Hb, CA and TE Euclidean genetic distance at the Hb locus between WF and SG, WF and RB, WF and BK, WF and Muturu were 15.3, 15.7, 23.9 and 35.1 respectively, while the corresponding values at CA locus were 3.9, 3.3, 29.1 and 36.2, similarly, the corresponding values at Tf locus were 22.8, 25.8, 94.3 and 102.7. Genetic distance estimates were found to be higher between non-related breeds than between breeds which had common ancestors.

The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea.

We collected 56 specimens ofLaelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507bp in size and contains 37 genes and a control region of 2380bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2bp and 16 spacer regions ranging from 1 to 48bp. We analyzed 13 protein-coding genes of L. chini mitogenome andfound that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species ofgamasid mites in the superfamily Dermanyssoidea from Genbank and theL. chini mitochondrial genometo analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species ofgamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.

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 theGenBank™ 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.

Genetic variability of Roma population in Serbia: The perspective from autosomal STR markers.

Genetic variability of Roma population was shaped by the strong influence of genetic drift and gene flow during the migrations from their ancestral homeland in Indian subcontinent towards Europe. In addition, social stigmatization in many European countries, as a consequence of different cultural heritage and social practices, induced further genetic differentiation and sub structuring within the population. Although many populations genetic studies on European Roma were carried out, the genetic structure of the Serbian Roma has not been described yet, since only the modest number of individuals from this territory was analyzed. The main aim of this study was the characterization of genetic variability of the Roma and the assessment of intrapopulation genetic differentiation based on the analysis of 21 autosomal STR loci of 259 self-identified unrelated individuals from Serbia. Intrapopulation analysis revealed divergence of Roma groups illustrating the effect of the historical events after their arrival on Balkan Peninsula and emphasizing significance of the religious affiliation on admixture with autochthonous population. Genetic distance analysis showed the greatest similarity of the studied population with the Middle Eastern populations, while South Asian and European population were more distant. Our results demonstrate that Roma groups in this region of Balkan Peninsula do not represent completely isolated, but rather admixed populations with different proportion of gene flow with other Roma and non-Roma groups.

Dendrodorididae (Heterobranchia, Nudibranchia) from Persian Gulf with a description of a new species of Doriopsilla and remarks on the family

The family Dendrodorididae has a global distribution, with prevalence in tropical and subtropical intertidal zones. Three species of Dendrodorididae were collected from the intertidal zone of the northern coast of the Persian Gulf in Iran. Based on anatomical, histological, and molecular investigations they can be assigned to Dendrodoris fumata, Dendrodoris nigra, and a new species of Doriopsilla, D. aroni sp. nov. Molecular analyses of CO1 and 16S, including all genera of Dendrodorididae, members of the sister taxon Phyllidiidae, and other dorid outgroups resulted in a polyphyletic genus Dendrodoris, which is in contrast to the nuclear gene studies. Our molecular results confirm the differentiation between Dendrodoris rubra and D. fumata. Dendrodoris nigra, D. fumata, and D. krusensternii each consist of several clades, indicating cryptic species complexes requiring further investigation. We describe the presence of bacteria for the first time in the vestibular gland of D. fumata. Validation of the specimens of Doriopsilla from the Persian Gulf as a new species is supported by haplotype networking, genetic distance, and ABGD analyses of mitochondrial genes. Our CO1 analysis confirms a previous hypothesis that Cariopsilla is a junior synonym of Doriopsilla.

Genetic diversity of astroviruses detected in wild aquatic birds in Hong Kong

Wild waterfowl serve as a reservoir of some astroviruses. Fecal samples from wild waterfowl collected at Hong Kong's Marshes were tested using pan-astrovirus reverse transcription-PCR. Positive samples underwent subsequent host identification using DNA barcoding. Based on deduced partial sequences, noteworthy samples from three astrovirus groups (mammalian, avian and unclassified astroviruses) were further analyzed by next-generation sequencing. One sample of Avastrovirus 4 clade, MP22-196, had a nearly complete genome identified. The results of ORF2 phylogenetic analysis and genetic distance analysis indicate that Avastrovirus 4 is classified as a distinct subclade within Avastrovirus. MP22-196 has typical astrovirus genome characteristics. The unique characteristics and potential differences of this genome, compared to other avian astrovirus sequences, involve the identification of a modified sgRNA sequence situated near the ORF2 start codon, which precedes the ORF1b stop codon. Additionally, the 3' UTR of MP22-196 is shorter than other avian astroviruses. This study expands our understanding of the Avastrovirus 4 clade.