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The distribution of species and the way that lineages are structured are the result of intrinsic historical processes of the species and their relationships with landscape features. Paleosuchus palpebrosus is one of the smallest crocodilians in the world and has a wide geographic distribution in South America, occurring in different habitats. Here, we analyzed mitochondrial cytochrome b sequences of 227 individuals, investigated how elements of landscape heterogeneity impact genetic differentiation, and evaluated the evolutionary and phylogeographic history of the species. Thus, we hypothesized that landscape structures, such as aridity and slope, should act as resistance surfaces to population connectivity, while rivers could mediate the dispersion of the species as a conductor of the gene flow. The analyses recovered three main lineages of P. palpebrosus. While most of the observed genetic variation was explained by geographic resistance distance, river connectivity had a smaller contribution for the observed variation. We also found a recent history with limited genetic divergence throughout the wide distribution of the species. Our findings highlight the main drivers for the evolutionary history of the species and how landscape features can shape the diversification, especially if we consider rivers as a facilitator of gene flow. [ABSTRACT FROM AUTHOR]

Simple Summary: African tropical regions have a remarkably high bird diversity, yet few studies have tried to unravel the presence of blood parasites in birds found in conservation areas. Knowing which blood parasites are present will help us to prepare for potential disease outbreaks. We test the hypothesis that conservation regions have a high diversity of parasites. Molecular methods were used to screen 1035 blood samples from 55 bird species for blood infections on sites inside and adjacent to the Kruger National Park in South Africa. Overall, 28.41% of birds were found infected with at least one type of blood parasites. Bird malaria of the type Haemoproteus and Plasmodium was found in 17.39% and 4.64% of the birds respectively. Leucocytozoon blood parasite was found in 9.24% of birds. One hundred distinct blood parasite types were detected, of which 56 were new types. Similar bird malaria (Haemoproteus and Plasmodium) infections were found in closely related birds, while Leucocytozoon was found in almost every bird type. Sites with a high bird diversity also had a high parasite diversity. These findings provide insight of how birds can gradually survive their blood parasite infections. Afrotropical regions have high bird diversity, yet few studies have attempted to unravel the prevalence of avian haemosporidia in conservation areas. The diversity and host specificity of parasites in biodiversity hotspots is crucial to understanding parasite distribution and potential disease emergence. We test the hypothesis that biodiverse regions are associated with highly diverse parasites. By targeting the cytochrome b (Cytb) gene, we molecularly screened 1035 blood samples from 55 bird species for avian haemosporidia infections to determine its prevalence and diversity on sites inside and adjacent to the Kruger National Park. Overall infection prevalence was 28.41%. Haemoproteus, Leucocytozoon, and Plasmodium presented prevalences of 17.39%, 9.24%, and 4.64%, respectively. One hundred distinct parasite lineages were detected, of which 56 were new lineages. Haemoproteus also presented the highest diversity compared to Leucocytozoon and Plasmodium with varying levels of specificity. Haemoproteus lineages were found to be specialists while Plasmodium and Leucocytozoon lineages were generalists. We also found a positive relationship between avian host diversity and parasite diversity, supporting an amplification effect. These findings provide insight data for host–parasite and co-evolutionary relationship models. [ABSTRACT FROM AUTHOR]

Simple Summary: The present study aimed to assemble and annotate the mitochondrial genome of Keenocardium buelowi and conducted an in-depth analysis to investigate the molecular features of this mitochondrial genome. Our findings established phylogenetic relationships within the Cardiidae family. Additionally, evidence of selection pressure on the cytochrome b gene was detected, suggesting its important role in the evolution of K. buelowi. The mitochondrial genome provides valuable data for phylogenetic analysis and evolutionary research. In this study, we sequenced, assembled, and annotated the mitochondrial genome of Keenocardium buelowi using the Illumina platform. The genome spanned 16,967 bp and included 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs. All PCGs utilized standard ATN start codons and TAN stop codons. The phylogenetic tree based on maximum likelihood and Bayesian inference analyses revealed Clinocardiinae as the sister group to Trachycardiinae, with the estimated divergence time being 44.5 million years ago (MYA) between K. buelowi and Vasticardium flavum. Notably, the cytochrome b gene (cob) exhibited a positive selection signal. Our findings provide valuable insights into the evolutionary history and molecular phylogeny of K. buelowi. [ABSTRACT FROM AUTHOR]

The common opossum (Didelphis marsupialis) is a marsupial widely distributed in the Neotropics, where it lives in urbanized environments. The apparent scarcity and fragmentation of available habitat, and high rates of vehicle collisions, may represent barriers to dispersal. To assess the functional connectivity of this species and its potential use as a model in urban ecology, we evaluated the structure and genetic diversity of opossums in the metropolitan area of the Aburrá Valley (AMVA), Colombia, using sequences of the mitochondrial Cytochrome B (Cytb) gene and nine autosomal microsatellite loci. Although Cytb presented low levels of variation, microsatellite markers revealed high genetic diversity (He = 0.852 and Ho = 0.698). The geographic distribution of mitochondrial lineages and a spatial principal component analysis (sPCA) of microsatellites showed the absence of genetic structure and effective barriers to dispersal of opossums in the study area. This scenario suggests that hostile landscapes such as those in urban environments may be suitable enough to allow the effective connectivity of some species such as the common opossum and others with high dispersal ability in urbanized areas. Nonetheless, it is necessary to evaluate the impact of releases of rescued fauna made by the environmental authority on the population structure of urban opossums. [ABSTRACT FROM AUTHOR]

Barramundi, or Asian seabass Lates calcarifer, is a commercially important food fish with a wide geographic distribution in the Indo-West Pacific region. Despite its economic significance, particularly in Taiwan, information on the sources of fertilized eggs, fry and stock management practices remains largely unavailable. To ensure sustainable exploitation and effective selective breeding programs, assessing the genetic diversity and population genetic structure of barramundi is crucial. This study investigated the genetic diversity and population genetic structure of three cultured populations (Chiayi A, Chiayi B, and Tainan) and one wild-caught population in Taiwan using mitochondrial DNA cytochrome b and eight microsatellite loci as genetic markers. The analysis of haplotype network revealed that all populations shared an ancestral haplotype, yet each population had its own unique haplotype. Notably, the wild and cultured populations showed the largest genetic distance. However, overall, the genetic distances among all populations were small and similar. This finding suggests potential gene exchange, possibly through broodstock exchange practices between farms. The valuable genetic information obtained from this study holds the potential to improve aquaculture programs through targeted breeding initiatives and inform the development of sustainable management policies for barramundi. [ABSTRACT FROM AUTHOR]

BACKGROUND: Wheat crown rot (WCR), primarily caused by Fusarium pseudograminearum has become more and more prevalent in winter wheat areas in China. However, limited fungicides have been registered for the control of WCR in China so far. Pyraclostrobin is a representative quinone outside inhibitor (QoI) with excellent activity against Fusarium spp. There is currently limited research on the resistance risk and resistance mechanism of F. pseudograminearum to pyraclostrobin. RESULTS: Here, we determined the activity of pyraclostrobin against F. pseudograminearum. The EC50 values ranged from 0.022 to 0.172 μg mL−1 with an average EC50 value of 0.071 ± 0.030 μg mL−1. Four highly pyraclostrobin‐resistant mutants were obtained from two sensitive strains by ultraviolet (UV) mutagenesis in the laboratory. The mutants showed decreased mycelial growth rate and virulence as compared with the corresponding wild‐type strains, indicating that pyraclostrobin resistance suffered a fitness penalty in F. pseudograminearum. It was found that the high resistance of four mutants was caused by the G143S mutation in Cytb. Molecular docking analysis also further confirms that the G143S mutation in Cytb decreased the binding affinity between pyraclostrobin and Cytb. CONCLUSION: The resistance risk of F. pseudograminearum to pyraclostrobin could be low to medium. Although a mutation at the G143S position of Cytb could potentially occur, this mutation decreases the fitness of the mutant, which may reduce its survival in the environment. Therefore, the negative consequences of a possible mutation are lower. This makes pyraclostrobin a good candidate for controlling crown rot in wheat. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Populations of plants and animals at the edge of a species' range may exhibit lower genetic diversity due to a combination of historical (e.g., postglacial dispersal) and contemporary (e.g., low effective population size, strong genetic drift or bottlenecks) processes. In this study, we analysed the genetic structure of populations of the European pond turtle (Emys orbicularis) in the northern part of the Pannonian Basin (Slovakia, Hungary, Austria), which represents the edge of the species' range. Using mitochondrial DNA (mtDNA) and microsatellite markers, we aimed to assign individuals and populations into phylogeographic lineages and to determine genetic variation and population structure. Our study revealed that most individuals from natural populations belong to mtDNA lineage II (widely distributed haplotype IIa, and likely endemic haplotypes IIl and IIo), which is typical for the whole Pannonian region. However, non-native haplotypes were detected in one Slovak population (haplotype Ib) and in the Austrian Donau Auen National Park (haplotype IVa). Microsatellite markers revealed high variability comparable to that in other parts of the range, suggesting that marginal populations may not necessarily have reduced genetic diversity. A genetically mixed population was found in the Donau Auen National Park, consisting of turtles belonging to mtDNA lineage II (taxonomically assessed as subspecies E. orbicularis orbicularis) and lineage IV (taxonomically assessed as E. orbicularis hellenica), which is native to the circum-Adriatic region. The admixture suggests intense hybridization and introgression between the two lineages (subspecies). [ABSTRACT FROM AUTHOR]

Background: Southeast Asia is well known as a hotspot of biodiversity. However, very little is known about cave-dwelling hematophagous insects that are medically important. Taxonomic knowledge and ecology of phlebotomine sand flies are very poorly studied in Laos, as well as in other countries in the region. Herein, we report species diversity data and some notes on the ecology of the detected species from these karstic limestone areas of Laos. Methods: Phlebotomine sand flies were collected using Centers for Disease Control and Prevention (CDC) light traps from limestone cave locations in three districts of Vientiane Province, Laos. Both morphological and molecular techniques were used for sand fly identification. Species diversity and abundance were analyzed according to sites, locations, collection seasons, and trapping positions. Results: A total of 6564 sand flies, of which 5038 were females and 1526 were males, were morphologically identified into 20 species belonging to five genera (Chinius, Idiophlebotomus, Phlebotomus, Sergentomyia, and Grassomyia). The most abundant species were Chinius eunicegalatiae, Phlebotomus stantoni, Sergentomyia hivernus, Se. siamensis, and Idiophlebotomus longiforceps. Cytochrome b analysis results supported the morphological identification and revealed that Se. siamensis was separated from other members of the Se. barraudi group. Two new species, Se. dvoraki n. sp. and Se. marolii n. sp., were described. Sand fly density was generally high except in a cave in Vangvieng, with species richness ranging from 14 to 18 across different caves. Outside caves had higher species richness (R = 20) and diversity (H = 2.50) than cave entrances (R = 18, H = 2.41) and interiors (R = 16, H = 2.13). Seasonal variations showed high sand fly density in Feung and Hinheup during both dry and rainy seasons, while Vangvieng had a notable decrease in density during the dry season (D = 6.29). Conclusions: This study revealed that the diversity of phlebotomine sand fly fauna in Laos, particularly in karstic limestone areas, is greater than previously known. However, the taxonomic status of many species in Laos, as well as Southeast Asia, still needs more in-depth study using both morphological characters and molecular methods. Many species could be found from inside, at the entrance, and outside of caves, indicating a wide range of host-seeking behavior or possible natural breeding in the karstic cave areas. [ABSTRACT FROM AUTHOR]

In this work, we describe a new species of the genus Oreonectes, Oreonectes yuedongensis sp. nov., collected from the Lianhua Mountains in eastern Guangdong, China. Phylogenetic trees constructed based on the mitochondrial cytochrome b (Cyt b) gene showed that this new species represents an independent evolutionary lineage, with uncorrected genetic distances (Kimura 2‐parameter model) from congeners ranging from 5.1% to 8.3%. In addition, nuclear DNA analysis indicated O. yuedongensis as an independent lineage separate from its closely related species. Morphologically, the new species can be distinguished from other six species in the genus Oreonectes by a combination of serial characters. The description of this new species suggests that it is necessary to reassess the biodiversity of Oreonectes platycephalus as a complex, especially in the middle reaches of the Pearl River near the border between Guangdong and Guangxi. Morphological and genetic evidence supports O. yenlingi as a synonym of O. platycephalus. [ABSTRACT FROM AUTHOR]

Tenualosa ilisha is an anadromous fish from the Clupidae family that is distributed in several Asian countries. The relationship between T. ilisha from Indonesian waters and other waters in Asia is unknown, therefore this study was conducted to provide an overview of the relationship between T. ilisha from Indonesia and other waters in Asia based on the Cytochrome b gene (Cyt b) of mitochondrial DNA (mtDNA). The base sequence of T. ilisha from Labuhanbatu with a length of 568-572 base pairs (bp) was analyzed, then compared with Genbank data. All sequences compared showed that the composition of A+T (52.5%) was greater than G+C (47.5%). Genetic distance was calculated using Kimura two parameter (K2P); the lowest genetic distance of 0.000 was obtained between T. ilisha Labuhanbatu and Iraq with accession numbers LC619671.1; LC619673.1; LC619674.1. Meanwhile, the highest genetic distance is known to be 0.021 between T. ilisha Labuhanbatu and Bangladesh with the accession numbers MN748964.1, and MN748966.1. Neighbor-joining and maximum likelihood with 1000x repetition were the phylogenetic methods used to analyze the evolutionary relationships of T. ilisha. In general, both methods showed the same result that T. ilisha from Indonesia and other Asian waters are the same population. [ABSTRACT FROM AUTHOR]

Neotoma magister (Allegheny Woodrat) has a conservation status of vulnerable or at even greater risk across 13 eastern US states. A lack of recent museum vouchers at the southern limit of its distribution, where its sister species Neotoma floridana (Eastern Woodrat) occurs, creates uncertainty as to the current range of the Allegheny Woodrat in Alabama. We opportunistically collected woodrat scat samples for species identification using mitochondrial cytochrome b comparisons that provided genetic evidence of Allegheny Woodrats in Alabama north of the Tennessee River, consistent with its recognized distribution. These new samples of Allegheny Woodrats are most closely related to Allegheny Woodrats from Pennsylvania, Virginia, and West Virginia, and with greater intraspecific cyt b variation (5%) than previously reported. Comparisons between our woodrat samples from Alabama (2 north and 2 south of the Tennessee River), and published Allegheny and Eastern Woodrat sequences revealed a clear distinction between species even at small geographic distances, with mean interspecific divergence values of over 8%. We add to the known genetic variation of Allegheny Woodrats, and further characterize their genetic differentiation from Eastern Woodrats. Additional data are needed to delimit the distributional boundaries of the 2 species in Alabama and beyond. [ABSTRACT FROM AUTHOR]

Significance: Hyperspectral imaging sensors have rapidly advanced, aiding in tumor diagnostics for in vivo brain tumors. Linescan cameras effectively distinguish between pathological and healthy tissue, whereas snapshot cameras offer a potential alternative to reduce acquisition time. Aim: Our research compares linescan and snapshot hyperspectral cameras for in vivo brain tissues and chromophore identification. Approach: We compared a linescan pushbroom camera and a snapshot camera using images from 10 patients with various pathologies. Objective comparisons were made using unnormalized and normalized data for healthy and pathological tissues. We utilized the interquartile range (IQR) for the spectral angle mapping (SAM), the goodness-of-fit coefficient (GFC), and the root mean square error (RMSE) within the 659.95 to 951.42 nm range. In addition, we assessed the ability of both cameras to capture tissue chromophores by analyzing absorbance from reflectance information. Results: The SAM metric indicates reduced dispersion and high similarity between cameras for pathological samples, with a 9.68% IQR for normalized data compared with 2.38% for unnormalized data. This pattern is consistent across GFC and RMSE metrics, regardless of tissue type. Moreover, both cameras could identify absorption peaks of certain chromophores. For instance, using the absorbance measurements of the linescan camera, we obtained SAM values below 0.235 for four peaks, regardless of the tissue and type of data under inspection. These peaks are one for cytochrome b in its oxidized form at λ = 422 nm, two for HbO2 at λ = 542 nm and λ = 576 nm, and one for water at λ = 976 nm. Conclusion: The spectral signatures of the cameras show more similarity with unnormalized data, likely due to snapshot sensor noise, resulting in noisier signatures post-normalization. Comparisons in this study suggest that snapshot cameras might be viable alternatives to linescan cameras for real-time brain tissue identification. [ABSTRACT FROM AUTHOR]

Background: Porcine cysticercosis, caused by Cysticercus cellulosae a larval stage of adult Taenia solium, is a zoonotic parasitic disease where pigs harbour intermediate stage and human being acts as a definite host. The people of north eastern region of India are mostly non-vegetarian and consumption of pork is very much preferred by the people of this region. Hence, it is essential to detect C. cellulosae infections in pork. But traditional method of detection of C. cellulosae by post mortem examination of pork has disadvantages like need of expert and may be over lookedin case of light infections. Molecular diagnosis have been reported to be highly specific and sensitive for its diagnosis. Keeping in view of the above, the present study on molecular detection of larval cestode C. cellulosae of pigs was undertaken. A study on phylogenetic relation of C. cellulosae of pigs or human Taenae solium of this region was done to know its relation with other parts of the world, as not yet done so far. Methods: A total of 654 pig carcasses in 17 market places of three prime districts of state Arunachal Pradesh, India were examined to detect Cysticercus cellulosae of pigs. The cysticerci samples were obtained manually from the infected muscles and organs of the infected pigs that were preserved in phosphate buffer saline until DNA extraction. Stool samples of human patients who attended out-patient department (OPD) of Community Health Centers, Nursing homes and District etc. of study area of Aunachal Pradesh, India were collected randomly and examined by salt flotation technique for the presence of T. solium eggs. The segments of tapeworm voided by patientswere then identified for species identification and T. solium segments were collected in normal saline solutions (NSS) after clearing the debris and faecal materials. Genomic DNA extraction from 3-4 numbers of cysticerci and T. solium segments collected from affected human being were extractedusing a spin column kit (D Neasy tissue kit: QUIGEN). The technique polymerase chain reaction (PCR) with published primers were used for molecular detection of C. cellulosae and to get molecular (PCR) products of T. solium for further study. The mitochondrial gene cytochrome b oxidase subunit was amplified by PCR. The PCR products were purified, sequenced and phylogenetic tree was constructed using the neighbor-joining method. Result: The present study recorded a PCR amplification of cytochrome b oxidase genes with a definite product size of 1068 bp from DNA extracted from C. cellulosae and T. solium. The product size obtained from C. cellulosae will be helpful for meat inspection by molecular detection of C. cellulosae infections in pork. The present finding signifies that the same genomic isolate of both the larval cestode and adult parasite of T. solium is prevailing in the study areas. The neighbors-joining phylogenic tree shows close similarity of the present isolates with that prevailing in other South East Asian countries and thus it can be assumed from the present finding that the same genotypic isolate of T. solium parasite is prevalent in the whole of South East Asian region. [ABSTRACT FROM AUTHOR]

The variability of the cytochrome b gene in 11 individuals of Korean field mouse from the Ussuri Nature Reserve located on the southern spurs of the Sikhote-Alin in the Przewalski Mountains has been analyzed. In the population, a high level of genetic diversity was identified owing to the discovery of individuals with haplotypes of three phylogenetic lineages, i.e., Amur, Korea, and Manchuria. The majority of individuals (72.73%) in the population had Amur haplotypes. A significantly lower frequency of occurrence of individuals with Korea haplotypes in the Ussuri Nature Reserve (9.09%) compared to the previously analyzed population of the Khasansky district (38.46%) located in the very south of the Primorsky krai was noted. In the Ussuri Nature Reserve, for the first time in the Russian Far East, two individuals with Manchuria haplotypes were discovered. Previously, only one finding of an individual with a similar haplotype was noted in the literature in the Heilongjiang province of Northeast China. It was suggested that individuals with haplotypes of the Korea phylogroup penetrate into the south of Sikhote-Alin from South Korea and with haplotypes of the Manchuria phylogroup from Northeast China. [ABSTRACT FROM AUTHOR]

The Caucasian pine vole Microtus daghestanicus was characterized by high karyotypic and molecular genetic variability. However, in the eastern part of the Greater Caucasus, the populations of this species were poorly studied. To reveal the genetic characteristics of these populations and their phylogenetic relationships with other conspecific populations, a sample of Caucasian pine voles from the south of the Chechen Republic (Daikhokh Mount) was analyzed. Immunocytochemical analysis of the synaptonemal complexes at meiotic prophase I showed the belonging of the studied population to the most widespread 54-chromosomal form of M. daghestanicus. Analysis of the complete sequence of the mitochondrial cytochrome b gene showed that on the phylogenetic tree, specimens from the Chechen Republic and the previously studied Caucasian pine vole from North Georgia grouped into one compact cluster. It indicates that they belong to a distinct genetic form. Within the studied sample from the Chechen Republic, variation of the BRCA1 and XIST nuclear genes was revealed that probably reflects complex history of this population associated with alternating events of its isolation from neighboring populations and restoration of contacts between them. [ABSTRACT FROM AUTHOR]

Alternaria brown spot (ABS), caused by Alternaria alternata, is one of the main citrus diseases that causes heavy production losses and reductions in fruit quality worldwide. The application of chemical fungicides has a key role in the management of ABS. In this study, 48 isolates of A. alternata collected from citrus orchards since 2014 were tested in vitro for their sensitivity to pyraclostrobin and fludioxonil, the latter being temporarily registered in Italy since 2020. Pyraclostrobin sensitivity was determined using spore germination and mycelial growth assays. The effective concentration inhibiting 50% of fungal growth (EC50) was determined for each isolate. The sensitivity assays showed that the majority of A. alternata isolates tested were sensitive to pyraclostrobin. EC50 values of fludioxonil in a mycelial growth assay indicated that 100% of isolates were sensitive to this fungicide. The analysis of the cytochrome b gene showed that none of the 40 isolates with a different sensitivity profile had the G143A mutation, and the subgroup of 8 isolates analyzed by real-time PCR did not carry the G137R and F129L mutations. A subset of four more sensitive and two reduced-sensitive isolates was chosen to assess sensitivity on detached citrus leaves treated with pyraclostrobin at the maximum recommended label rate. Disease incidence and symptom severity were significantly reduced, with a small reduction reported in leaves inoculated with the reduced-sensitive isolates. Furthermore, there was no correlation between sensitivity and fitness parameters evaluated in vitro (mycelium growth and sporulation rate). These findings help the development of monitoring resistance programs and, consequently, set up effective anti-resistance strategies for managing ABS on citrus orchards. [ABSTRACT FROM AUTHOR]

The house mouse is the best-studied mammal species after humans, yet our understanding of its evolutionary history remains incomplete. Here, we focused on the colonisation of Europe by two subspecies and formation of a hybrid zone between them. We carried out a large-scale study of ~7000 mice sampled across an area embracing an ~900 km long portion of the zone, supplemented with cytochrome b and D-loop sequencing of ~1200 individuals collected worldwide. We demonstrate that the course of the mtDNA contact front is intricate and highly discordant with the consensus front for autosomal and X-linked markers, suggesting that local snapshots of mtDNA introgression may be misleading when treated in isolation. While multiple unrelated M. m. domesticus haplotypes occur in the zone area, the diversity of M. m. musculus haplotypes is limited. Moreover, we uncovered a vast region of domesticus introgression into musculus territory in northern areas and showed this introgression is unlikely to be driven by positive selection. We consider two previously published hypotheses explaining this phenomenon and put forth an alternative scenario assuming associations between mice and humans in northern Europe during the Nordic Bronze Age and subsequent zone movement associated with the expansion of Balto-Slavic peoples. [ABSTRACT FROM AUTHOR]

Simple Summary: Correct taxonomic identification is essential for conducting successful biological research, especially with regard to economically important insects, such as jumping plant lice or psyllids. In the present study, we identify and diagnose the morphologically characterised aphalarid species from Bulgaria using two molecular markers, cytochrome c oxidase I and cytochrome b. A total of 80 sequences of 25 Aphalaridae species were obtained and included in the BOLD and GenBank databases. This should enable even non-experts to identify these species quickly and accurately. The results of the current study show that two barcode genes are sufficient to distinguish most aphalarid species. Psyllids (Hemiptera: Psylloidea) are plant sap-sucking insects whose identification is often difficult for non-experts. Despite the rapid development of DNA barcoding techniques and their widespread use, only a limited number of sequences of psyllids are available in the public databases, and those that are available are often misidentified. Here, we provide 80 sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and cytochrome b (Cytb), for 25 species of Aphalaridae, mainly from Bulgaria. The DNA barcodes for 15 of these species are published for the first time. In cases where standard primers failed to amplify the target gene fragment, we designed new primers that can be used in future studies. The distance-based thresholds for the analysed species were between 0.0015 and 0.3415 for COI and 0.0771 and 0.4721 for Cytb, indicating that the Cytb gene has a higher interspecific divergence, compared to COI, and therefore allows for more accurate species identification. The species delimitation based on DNA barcodes is largely consistent with the differences resulting from morphological and host plant data, demonstrating that the use of DNA barcodes is suitable for successful identification of most aphalarid species studied. The phylogenetic reconstruction based on maximum likelihood and Bayesian inference analyses, while showing similar results at high taxonomic levels to previously published phylogenies, provides additional information on the placement of aphalarids at the species level. The following five species represent new records for Bulgaria: Agonoscena targionii, Aphalara affinis, Colposcenia aliena, Co. bidentata, and Craspedolepta malachitica. Craspedolepta conspersa is reported for the first time from the Czech Republic, while Agonoscena cisti is reported for the first time from Albania. [ABSTRACT FROM AUTHOR]

The European eel (Anguilla anguilla (L.)) is a unique catadromous euryhaline fish and the only anguillid eel species classified as 'critically endangered'. The Baltic Lakeland area contains naturally recruited and introduced eels. There is great uncertainty regarding a baseline for the location and number of naturally dispersed eels in the region. Little is known about the genetic structure of the European eel populations in Baltic countries. The estimation of population genetic structure is important for the efficient management of naturally recruited and introduced eels. Two mitochondrial regions were used to investigate the genetic structure within and between eel samples from 11 waterbodies. In this study, new, unique, and widely distributed haplotypes were revealed. The studied eel population in the Baltic Lakeland shows high genetic diversity, which is possibly a result of intensive restocking programs. Sequences characterized for Anguilla rostrata were revealed in both mitochondrial regions. Understanding the genetic structure of eel populations worldwide is crucial for conservation efforts. Eel restocking in waterbodies where natural migration is restricted contributes to diversity loss for the world gene pool of eels. [ABSTRACT FROM AUTHOR]

The hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae. The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy. [ABSTRACT FROM AUTHOR]

Binturong (Arctictis binturong) is a threatened carnivore that inhabits the forests of South and Southeast Asia. Despite its wide range, binturong is relatively scarce across its habitat distribution and is currently under the threat of poaching and illegal trade. Captive breeding has unfortunately been conducted rather haphazardly with a lack of origin record maintained, implicating potential risks to the management such as inbreeding or genetic swamping. This study thus aims to characterise the phylogenetic relationship of Indonesian binturong within the context of Southeast Asian binturong and further probe the distinctness of lineages originating from Java, Sumatra, Indonesian Borneo, and Bangka using Cytochrome B (CytB) and Cytochrome C Oxidase Subunit 1 (CO1). Genetic distance, phylogram topology, and haplotype analysis of both encoding genes further corroborate the distinctness of Java, Borneo, and Bangka binturong from other binturong from Indochinese regions such as India, Laos, and Myanmar. Search for prospective single nucleotide polymorphism markers to discriminate island lineages consistently found that each Java, Bangka, and Bornean binturong be distinct from each other and other lineages, especially when assessed using haplotype-based clustering. Assigning binturong originated from Sumatra is nonetheless more complicated, suggesting the possibility. Our findings substantiated the much-needed systematic research of Southeast Asian binturong as ex-situ insurance population management grows in Indonesia and other parts of the world to protect the diversity of binturong lineages and their corresponding unique evolutionary history. [ABSTRACT FROM AUTHOR]

The taxonomy of the freshwater featherback fish genus Chitala (Osteoglossomorpha: Notopteridae) remains unsettled because delimiting and naming Chitala species based solely on morphology led to different hypotheses. In this study, we aim to determine the number and identity of Chitala species present in Peninsular Malaysia by employing an integrative taxonomic approach that combines morphology and two mitochondrial markers: the cytochrome c oxidase subunit I (COI) and cytochrome b genes. A total of 60 specimens of Chitala were collected throughout Peninsular Malaysia. Initially, all specimens were sorted into three distinct categories based on their body marking patterns. A molecular phylogenetic analysis revealed that each of these groups was monophyletic, and an automated species partition method further recognized them as distinct species. These results support the presence of three Chitala species in Peninsular Malaysia, even though a multivariate morphometric analysis failed to fully differentiate each of these three species. Comparison with original species descriptions and genetic data from an additional 70 Chitala specimens from neighbouring regions allowed us to name these species as Chitala lopis, Chitala borneensis, and Chitala ornata. We also showed the presence of two undescribed species in Indonesia. [ABSTRACT FROM AUTHOR]

The current study aimed to detect the genetic variability of mitochondrial DNA (mtDNA) cytochrome B (CYTB) gene in 80 native Egyptian rabbits (NER) belonging to three populations in three different agriculture regions (Delta, Middle, and Upper Egypt) and also investigate the origin of these breeds by phylogenetic relationship analysis. A total of 62 haplotypes were recorded among the three NER populations. The native Upper Egypt rabbits (NUER) expressed the highest number of haplotypes, mutations, polymorphic sites, and haplotype diversity (23, 55, 51, and 1.00, respectively). While it gave the lowest values of nucleotide diversity (0.0262) and Tajima’s D (− 0.01435), the percentage of mutual haplotypes was 4.8 % between the Middle and Delta Egypt populations. The phylogenetic analysis showed that there were more separated haplotypes of NUER compared to other populations. The same finding was also observed when supported by 31 sequences of different rabbit breeds retrieved from the GeneBank database. A mutual haplotype was observed between native Delta Egyptian rabbits (NDER) and New Zealand (NWZ) rabbits. The results of this study shed light on the importance of indigenous breeds in rural areas through mtDNA, which contributes to finding sustainable strategies to conserve and improve genetic resources in Egyptian rural areas. [ABSTRACT FROM AUTHOR]

The evolutionary dynamics of the ecoregions of southern South America and the species that inhabit them have been poorly studied, and few biogeographic hypotheses have been proposed and tested. Quaternary climatic oscillations are among the most important processes that have led to the current distribution of genetic variation in different regions of the world. In this work, we studied the evolutionary history and distribution of the Córdoba vesper mouse (Calomys venustus), a characteristic rodent of the region of which little is known about its natural history. Since the population dynamics of this species are influenced by climatic factors, this rodent is a suitable model to study the effects of Quaternary climatic oscillations in central Argentina. The mitochondrial cytochrome b gene was sequenced to analyze the phylogeography of C. venustus, and ecological niche modeling tools were used to map its potential distributions. The results of these approaches were combined to provide additional spatially explicit information about this species' past. Our results suggest that the Espinal was the area of origin of this species, which expanded demographically and spatially during the last glacial period. A close relationship was found between the Espinal and the Mountain Chaco. These results are consistent with previous studies and emphasize the role of the Espinal in the biogeographic history of southern South America as an area of origin of several species. [ABSTRACT FROM AUTHOR]

The Eichwald Toad, Bufo eichwaldi is one of the endemic amphibians distributed throughout Hyrcanian forests, marshes, wetlands, and streams in the north of Iran and the south of Azerbaijan. Populations of B. eichwaldi have previously been studied based on a few molecular and morphological data. Here, we undertake taxonomic and phylogenetic analyses based on morphological and morphometric features for 56 specimens of B. eichwaldi from Iran, and mitochondrial cyt b marker for 20 specimens from the whole species range in the west and east Caspian Sea lowland. Molecular analyses based on 794 bp of cyt b gene demonstrated two clusters: the east Caspian Sea lowland (A1) and the west Caspian Sea lowland (A2) clusters. Univariate analyses indicated six out of 25 morphometric variables in male B. eichwaldi specimens from the east (A1) are significantly different from male specimens of B. eichwaldi from the west Caspian Sea (A2; P≤0.05). Females have been also significantly different between two clusters in one character (distance between lids; P≤0.05). Sexual size dimorphism was also significantly different within and between populations in some variables. However, the PCA analyses show no differentiation among B. eichwaldi populations in the east and west Caspian Sea lowland. Based on p-distance parameter, the east and west groups showed a low level of genetic differentiation (0.2%). [ABSTRACT FROM AUTHOR]

The clinical implications of Theileria sp. Yokoyama, a recently identified Theileria species in cattle, remain uncertain. The objective of the present study was to evaluate the anemia status in cattle infected with Theileria sp. Yokoyama. Blood samples were collected from 206 cattle across seven Veterinary Ranges in Sri Lanka and analyzed for red blood cell (RBC) indices, including hemoglobin concentration, hematocrit, and RBC counts. Additionally, DNA was extracted from the samples and screened with a newly developed Theileria sp. Yokoyama-specific PCR assay targeting the cytochrome b gene. The PCR results revealed that 60 (29.1%) of the surveyed cattle tested positive for Theileria sp. Yokoyama, with 47 (78.3%) of them being co-infected with other hemopathogen species. Our findings revealed that the cattle breeds, management systems, and tick infestations are potential risk factors for the Theileria sp. Yokoyama infection. Next, we evaluated the anemia status among the surveyed cattle based on the RBC indices. We found that all non-infected cattle were non-anemic. By contrast, anemia was observed in 15 Theileria sp. Yokoyama-infected cattle, including 3 singly infected (anemia rate 3/13, 23.1%) and 12 co-infected cattle (12/47, 25.5%). Our findings suggest that Theileria sp. Yokoyama causes anemia in infected cattle. [ABSTRACT FROM AUTHOR]

Background: Amblyomma spp. ticks, known for their long mouthparts, bright ornate appearance and aggressive hunting behaviour, are vectors of a number of important pathogens. In southern Africa, 17 Amblyomma spp. are currently documented. Of these species, Amblyomma hebraeum and Amblyomma variegatum have been well studied due to their wide geographical range and their status as competent vectors of pathogens that are of veterinary and medical importance. Studies on other Amblyomma spp. in southern Africa have been neglected, fostering ongoing debates on the validity of certain species such as Amblyomma pomposum. This study investigated the inter- and intra-species variation of Amblyomma ticks collected in southern Africa, focusing on resolving the dispute about A. pomposum and A. variegatum being distinct species. Methods: Four Amblyomma tick species were collected from Angola, Mozambique, South Africa, Zambia and Zimbabwe, and were identified morphologically as Amblyomma eburneum (208), A. hebraeum (4758), A. pomposum (191) and A. variegatum (2577) using identification keys. Gene amplification targeting the 12S and 16S rRNA, cytochrome oxidase I, cytochrome B and internal transcribed spacer-2 genes was conducted for 204 ticks, for which varying success was achieved during amplification for each of the markers. Maximum likelihood analyses were performed in IQ-TREE. Results: The phylogenetic topologies and ABGD analyses of each individual gene clustered A. pomposum within the A. variegatum clade, while clearly separating A. eburneum and A. hebraeum from all other species. None of the genetic markers indicated intraspecific structuring on the basis of geographical origin, despite great distances between sampling sites. Conclusion: Our study concludes that there is insufficient molecular evidence to differentiate A. pomposum and A. variegatum from each other. We highlight the need for whole mitochondrial genome sequencing of these two species to resolve the ongoing controversies. Furthermore, we propose mating and hybrid viability studies between the two species to confirm their reproductive isolation. [ABSTRACT FROM AUTHOR]

Introduction: Leucocytozoon is an intracellular blood parasite that affects various bird species globally and is transmitted by blackfly vectors. This parasite is responsible for leucocytozoonosis, a disease that results in significant economic losses due to reduced meat and egg production. There is limited knowledge about the epidemiological pattern of leucocytozoonosis and its causative species in Egypt, particularly in pigeons. Methods: The current study involved the collection of 203 blood samples from domestic pigeons from various household breeders and local markets across Qena Province, Upper Egypt. Samples were initially examined for potential Leucocytozoon infection using blood smears, followed by an evaluation of associated risk factors. Molecular identification of the parasite in selected samples (n = 11), which had initially tested positive via blood smears, was further refined through nested PCR and sequence analysis of the mitochondrial cytochrome b gene to ascertain the Leucocytozoon species present. Additionally, histopathological examination of the liver, spleen, and pancreas was conducted on animals that tested positive by blood smears. Results: Interestingly, 26 out of 203 samples (12.08%) had confirmed Leucocytozoon infections based on microscopic analysis. Additionally, all 11 samples that initially tested positive via blood smears were confirmed positive through nested PCR analysis, and their sequencing revealed the presence of Leucocytozoon sabrazesi, marking the first report of this parasite in Egypt. The study into potential risk factors unveiled the prevalence of Leucocytozoon spp. seems host gender-dependent, with males exhibiting a significantly higher infection rate (33.33%). Additionally, adult birds demonstrated a significantly higher infection prevalence than squabs, suggesting an age-dependent trend in prevalence. Seasonality played a significant role, with the highest occurrence observed during summer (37.25%). Histopathological examination revealed the presence of numerous megaloschizonts accompanied by lymphocytic infiltration and multiple focal areas of ischemic necrosis. Conclusion: To our knowledge, this is the first study to shed light on the epidemiological characteristics and molecular characterization of leucocytozoonosis in pigeons in Egypt. Further research endeavors are warranted to curb the resurgence of Leucocytozoon parasites in other avian species across Egypt, thereby refining the epidemiological understanding of the disease for more effective control and prevention measures. [ABSTRACT FROM AUTHOR]

Investigations of host feeding behaviour in haematophagous insects are critical to assess transmission routes of vector‐borne diseases. Understanding if a certain species has ornithophilic or mammalophilic feeding behaviour can facilitate future studies focused on pathogens transmission to and from certain host species. Culicoides Latreille (Diptera: Ceratopogonidae) are vectors of several pathogens, which include arboviruses, bacteria and parasites to a considerable diversity of vertebrate hosts. However, most of the studies focused on feeding habits target Culicoides species that could transmit the Bluetongue virus, consequently with a mammalophilic feeding behaviour, leaving aside the Culicoides species that are involved in the transmission of vector‐borne parasites to birds, such as Haemoproteus Kruse (Haemosporida: Haemoproteidae). This study aimed to investigate the source of blood meals of wild‐caught Culicoides using molecular‐based methods and to correlate our findings with the reports of Haemoproteus parasites in Culicoides species. Engorged Culicoides females were collected using ultraviolet (UV)‐light traps at seven different localities in Lithuania in 2021–2023. Biting midges were dissected, and the abdomens of engorged females were used for molecular investigation of the blood meal source. A polymerase chain reaction (PCR) protocol that amplifies a fragment of the Cytochrome B gene of vertebrates was used. Obtained sequences were compared to available information in GenBank database to confirm the source of the blood meal. In total, 258 engorged Culicoides females, representing nine different species, were analysed. The source of blood meal was identified in 29.1% of them with most of the insects having fed on birds (74.7%) and the remaining on mammals (25.3%). Culicoides segnis Campbell, Pelham‐Clinton was the only species to feed exclusively on birds; Culicoides from the Obsoletus group, C. pallidicornis Kieffer and C. punctatus Latreille were found to feed exclusively on mammals; C. festivipennis Kieffer, C. kibunensis Tokunaga and C. pictipennis Staeger had an opportunistic feeding behaviour, with the first two preferably feeding on birds. Due to their feeding behaviour and the presence of Haemoproteus parasites reported in the literature, C. festivipennis, C. kibunensis, C. pictipennis, and C. segnis play an important role in the transmission of those avian vector‐borne parasite in the wild. These Culicoides species were already confirmed as being able to support the development of several Haemoproteus species and lineages. Future studies focused on understanding the epidemiology of avian pathogens transmitted by Culicoides should target these species. [ABSTRACT FROM AUTHOR]

Background: Rift Valley fever virus (RVFV) is a zoonotic mosquito-borne virus with serious implications for livestock health, human health, and the economy in Africa, and is suspected to be endemic in north-eastern KwaZulu-Natal (KZN), South Africa. The vectors of RVFV in this area are poorly known, although several species, such as Aedes (Neomelaniconion) mcintoshi, Aedes (Neomelaniconion) circumluteolus, Aedes (Aedimorphus) durbanensis, and Culex (Lasioconops) poicilipes may be involved. The aim of the study was to determine the vertebrate blood meal sources of potential RVFV mosquito vectors in north-eastern KZN and to characterize the host-biting network. Methods: Blood-fed mosquitoes were collected monthly from November 2019 to February 2023 using a backpack aspirator, CO2-baited Centers for Disease Control and Prevention (CDC) miniature light traps and tent traps, in the vicinity of water bodies and livestock farming households. The mosquitoes were morphologically identified. DNA was extracted from individual mosquitoes and used as templates to amplify the vertebrate cytochrome c oxidase I (COI) and cytochrome b (cytb) genes using conventional polymerase chain reaction (PCR). Amplicons were sequenced and queried in GenBank and the Barcode of Life Data systems to identify the vertebrate blood meal sources and confirm mosquito identifications. All mosquitoes were screened for RVFV using real time reverse transcription (RT)-PCR. Results: We identified the mammalian (88.8%) and avian (11.3%) blood meal sources from 409 blood-fed mosquitoes. Aedes circumluteolus (n = 128) made up the largest proportion of collected mosquitoes. Cattle (n = 195) and nyala (n = 61) were the most frequent domestic and wild hosts, respectively. Bipartite network analysis showed that the rural network consisted of more host-biting interactions than the reserve network. All mosquitoes tested negative for RVFV. Conclusions: Several mosquito species, including Ae. circumluteolus, and vertebrate host species, including cattle and nyala, could play a central role in RVFV transmission. Future research in this region should focus on these species to better understand RVFV amplification. [ABSTRACT FROM AUTHOR]

Aim: The central and western Amazonia underwent several landscape changes during the Quaternary. Whereas the Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of Amazonia biota. Here, we tested how river rearrangements influenced the evolutionary history of uakari monkeys, genus Cacajao, a primate genus primarily associated with seasonally flooded forests in central and western Amazonia. Location: Central and Western Amazonia. Taxon: The genus Cacajao, including the black uakaris (C. melanocephalus, C. ayresi, C. hosomi); and the bald‐headed uakaris (C. calvus, C. amuna, C. rubicundus, C. ucayalii, C. novaesi). Methods: We performed a continuous phylogeographic analysis using 77 cytochrome b sequences to identify the origin and dispersal of Cacajao lineages. We used genome‐wide SNP variation (ddRADseq) to investigate population structure, gene flow and demographic history in Cacajao populations and used digital elevation models to identify landscape and riverscape characteristics that may have influenced the geographic distribution of Cacajao. Results: Our continuous phylogeographic reconstruction pointed out that the ancestral Cacajao lineage occupied the flooded forests of the Solimões River, in central Amazonia, at ~1.7 Mya and descendant lineages dispersed throughout central and western Amazonia more recently. We identified gene flow in both black and bald‐headed uakari populations, even across rivers considered barriers (e.g. the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. Historical demographic analyses suggest varied scenarios of population size changes among Cacajao monkeys consistent with periods of intense dynamism in flooded habitats and the formation of non‐flooded upland forests. Main Conclusion: Our results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent changes in demographic histories in species with a restricted geographic distribution. [ABSTRACT FROM AUTHOR]

The complex III of the mitochondrial respiration chain is an effective fungicidal target in plant pathogenic fungi. Especially the QoIs (FRAC Group 11 and 11A) fungicides cover a broad pathogen spectrum, that includes ascomycetes, basidiomycetes and oomycetes, by inhibiting the complex III at the outer binding site. Many of the target pathogens have developed resistance mediated by the target site mutation G143A. All fungicides that belong to Group 11 are affected by this mutation. Metyltetraprole has been recently developed, and it also binds at the Qo-site but is not affected by the G143A mutation and has therefore been classified differently (FRAC Group 11A). In experiments on solid medium with sequential exposure to complex III inhibitors, laboratory mutants of Zymoseptoria tritici with a resistance to metyltetraprole could be selected. Resistance to metyltetraprole was mediated by the target site mutation in the cytochrome B gene leading to the aa change Y132C. Metyltetraprole resistant isolates could only be generated from wildtype parents, but not from G143A parents. Further experiments used serial batch cultivations in liquid media with increasing fungicide concentrations. These were aimed to select double mutants that harboured both G143A and Y132C. Several different parental strains were treated with increasing concentrations of metyltetraprole, but no Y132C mutants were found when G143A parents were used. When Y132C mutants were used as the initial inoculum, and these were exposed to increasing concentrations of pyraclostrobin, the parental mutation was replaced by G143A within a few cycles; this could suggest that both mutations are incompatible. [ABSTRACT FROM AUTHOR]

Chemical control of grape black rot, caused by Phyllosticta ampelicida, relies mainly on the use of demethylation inhibitors (DMIs) and quinone outside inhibitors (QoIs). The effectiveness of QoI fungicides is influenced by alternative respiration activity, and the exon/intron structure and point mutations in the target protein's gene, the cytochrome b (cytb) gene. Our study aims to investigate the QoI fungicide sensitivity of 48 P. ampelicida isolates in vitro by measuring EC50 and the molecular characteristics of the cytb gene and its mRNA in P. ampelicida and other Phyllosticta species. Mycelial growth tests revealed that the P. ampelicida isolates were sensitive to both azoxystrobin and trifloxystrobin; baseline EC50 values were 0.029 and 0.022 μg/mL, respectively. Addition of salicylhydroxamic acid (SHAM) resulted in lower EC50 values (0.024 and 0.017 μg/mL, respectively). None of the typical point mutations conferring resistance to QoIs in some fungi were detected. A group I intron was present right after the 143rd codon in the cytb gene in four of the six Phyllosticta species examined. The sequence and exon/intron structure of the cytb gene of P. ampelicida isolated from Vitis vinifera is studied in detail and published here. Our results indicate a low risk of QoI resistance development via the G143A mutation in P. ampelicida. [ABSTRACT FROM AUTHOR]

Species of the Rhodnius genus have a complex taxonomy because the events of phenotypic plasticity and cryptic speciation make it difficult to correctly classify these vectors. During the taxonomic history of the genus, five synonymization events occurred. Additionally, some authors suggest that R. milesi possibly represent only phenotypic polymorphisms of R. neglectus. Thus, we analyzed the specific status of R. milesi in relation to R. neglectus using phylogenetic studies with the mitochondrial gene cytochrome B and the study of reproductive barriers. The phylogenetic reconstruction grouped R. milesi together with R. neglectus from different localities, demonstrating that these taxa represent the same species based on the phylogenetic species concept. Experimental crosses demonstrate the absence of pre- and postzygotic barriers under laboratory conditions. Additionally, when the hatch rates of crosses are compared to intraspecific crosses, it can be noted that they are high and very similar. Finally, the mortality rate of the hybrids does not indicate hybrid inviability, the absence of chromosome pairing errors does not indicate hybrid sterility, and the proportion between male and female hybrids demonstrates that Haldane's rule was not acting. Therefore, we perform the formal synonymization of R. milesi with R. neglectus. [ABSTRACT FROM AUTHOR]

Small and isolated populations are at risk of local extinction, either due to the reduction of genetic diversity or due to stochastic events. We assessed genetic diversity in populations of the red-spotted (Luscinia svecica svecica) and white-spotted bluethroat (L. s. cyanecula) subspecies from six European sites, focusing on a peripheral and declining, red-spotted population from Central Europe (Krkonoše Mountains, Czech Republic). Analysis of population structure using mitochondrial sequences (cytochrome b) and ddRAD genomic data revealed that the two subspecies form clearly defined clusters, but traces of possible admixture were found in three populations of the white-spotted bluethroat. Demographic history reconstruction indicates past population range expansion in both subspecies, while the occurrence of short (0.4 Mbp) runs of homozygosity (ROH) segments suggests possible inbreeding 50 to 200 generations ago. Interestingly, although established by a small number of individuals, the Krkonoše population show reduced genetic diversity in only one measure of summary statistics, possibly due to sustained gene flow. Correspondingly, nine highly homozygous genes were recovered within a 2.6-Mbp long ROH region on the Chr 5. Thus, we found only a small reduction of genetic diversity in a population facing extinction, contrary to the expectations for a geographically distant and small population. [ABSTRACT FROM AUTHOR]

Characterizing genetically distinct populations of primates is important for protecting biodiversity and effectively allocating conservation resources. Skywalker gibbons (Hoolock tianxing) were first described in 2017, with the only confirmed population consisting of 150 individuals in Mt. Gaoligong, Yunnan Province, China. Based on river geography, the distribution of the skywalker gibbon has been hypothesized to extend into Myanmar between the N'Mai Kha and Ayeyarwaddy Rivers to the west, and the Salween River (named the Thanlwin River in Myanmar and Nujiang River in China) to the east. We conducted acoustic point-count sampling surveys, collected noninvasive samples for molecular mitochondrial cytochrome b gene identification, and took photographs for morphological identification at six sites in Kachin State and three sites in Shan State to determine the presence of skywalker gibbons in predicted suitable forest areas in Myanmar. We also conducted 50 semistructured interviews with members of communities surrounding gibbon range forests to understand potential threats. In Kachin State, we audio-recorded 23 gibbon groups with group densities ranging between 0.57 and 3.6 group/km2. In Shan State, we audio-recorded 21 gibbon groups with group densities ranging between 0.134 and 1.0 group/km2. Based on genetic data obtained from skin and saliva samples, the gibbons were identified as skywalker gibbons (99.54–100% identity). Although these findings increase the species' known population size and confirmed distribution, skywalker gibbons in Myanmar are threatened by local habitat loss, degradation, and fragmentation. Most of the skywalker gibbon population in Myanmar exists outside protected areas. Therefore, the IUCN Red List status of the skywalker gibbon should remain as Endangered. [ABSTRACT FROM AUTHOR]

Background: West Nile virus (WNV), Everglades virus (EVEV), and five species of Orthobunyavirus were isolated from mosquitoes collected in the Everglades in 2016–2017. Prior studies of blood meals of mosquitoes in southern Florida have related findings to acquisition and transmission of EVEV, St. Louis encephalitis virus, and WNV, but not the Orthobunyavirus viruses associated with the subgenus Melanoconion of the genus Culex. Materials and Methods: In the present study, blood-fed mosquitoes were collected in the Everglades in 2016, 2017, 2021, and 2022, and from an industrial site in Naples, FL in 2017. Blood meals were identified to host species by PCR assays using mitochondrial cytochrome b gene. Results: Blood meals were identified from Anopheles crucians complex and 11 mosquito species captured in the Florida Everglades and from 3 species collected from an industrial site. The largest numbers of blood-fed specimens were from Culex nigripalpus, Culex erraticus, Culex cedecei, and Aedes taeniorhynchus. Cx. erraticus fed on mammals, birds, and reptiles, particularly American alligator. This mosquito species could transmit WNV to American alligator in the wild. Cx. nigripalpus acquired blood meals primarily from birds and mammals and frequently fed on medium-sized mammals and white-tailed deer. Water and wading birds were the primary avian hosts for Cx. nigripalpus and Cx. erraticus in the Everglades. Wading birds are susceptible to WNV and could serve as reservoir hosts. Cx. cedecei fed on five species of rodents, particularly black and hispid cotton rats. EVEV and three different species of Orthobunyavirus have been isolated from the hispid cotton rat and Cx. cedecei in the Everglades. Cx. cedecei is likely acquiring and transmitting these viruses among hispid cotton rats and other rodents. The marsh rabbit was a frequent host for An. crucians complex. An. crucians complex, and other species could acquire Tensaw virus from rabbits. Conclusions: Our study contributes to a better understanding of the host and viral associations of mosquito species in southwestern Florida. [ABSTRACT FROM AUTHOR]

Aim: Hyperglycemia damages mitochondria and downregulates transcription of mtDNA-encoded genes and the long noncoding RNA LncCytB, causing mitochondrial genomic instability. The genes encoded by mtDNA are transcribed as large polycistronic transcripts, and the 5′ ends of precursor tRNAs are processed by mitochondrial-targeted ribonuclease P (MRPPs). Our aim was to investigate the role of MRPP1 in the downregulation of LncCytB in diabetic retinopathy. Methods: Using human retinal endothelial cells incubated in 20 mM D-glucose for 96 h, the gene expression and mitochondrial localization (immunofluorescence) of MRPP1 and the interaction between MRPP1 and LncCytB (determined by RNA-FISH and RNA immunoprecipitation) were quantified. The results were confirmed in retinal microvessels from streptozotocin-induced diabetic mice and from human donors with documented diabetic retinopathy. Results: Compared to normal glucose, high glucose decreased mRNA and mitochondrial localization of MRPP1 and its interaction with LncCytB. While MRPP1 overexpression prevented glucose-induced decrease in MRPP1–LncCytB interaction, LncCytB expression and mitochondrial damage (reduction in protective nucleoids in mtDNA), MRPP1-siRNA further worsened them. Similar results were obtained from retinal microvessels from diabetic mice and from human donors with diabetic retinopathy. Conclusions: Downregulation of MRPP1 in diabetes suppresses LncCytB transcription, resulting in mitochondrial functional and genomic instability, ultimately leading to the development of diabetic retinopathy. Thus, preventing MRPP1 downregulation has the potential to inhibit retinopathy and prevent the fear of vision loss in diabetic patients. [ABSTRACT FROM AUTHOR]

Most Pamphagidae species are at risk of being endangered due to their flightlessness, low mobility, and small habitat range. For the same reason, Haplotropis brunneriana (Orthoptera: Pamphagidae) has been designated an endangered species in South Korea. Endangered species with small populations are difficult to observe and investigate because any damage or disturbance to them are prohibited. To address these problems, we first performed non-invasive genomic DNA (gDNA) extraction using exuviae to identify H. brunneriana. Second, we tested the limit of detection of gDNA in the exuviae and how long it could persist when exposed to artificial environmental conditions. Using exuviae, we identified cytochrome b as a species-specific marker of H. brunneriana that could distinguish them from other grasshoppers with sufficient specificity. In the limit of detection test, gDNA could persist and be amplified from exuviae for up to 40 days. Our results demonstrated that fewer than 10 days is recommended for amplifying gDNA from exuviae to obtain reproducible results. In conclusion, this non-invasive identification method using exuviae can be used as an alternative to species identification when it is difficult to find H. brunneriana in the habitat and has the advantage of allowing genetic research to be conducted without harming the endangered species. Implications for insect conservation: Our study used a non-invasive genomic DNA extraction method to conserve endangered grasshoppers. Using exuviae, endangered grasshopper species could be identified, thus confirming their presence or absence in the habitat. This identification method can be an alternative method that can be used when conducting genetic analyses accompanied by physical harm is difficult due to small populations, such as endangered and rare species. [ABSTRACT FROM AUTHOR]

Beluga sturgeon (Huso huso Linnaeus, 1758, acipenseridae) and Adriatic sturgeon (Acipenser naccarii, Bonaparte, 1836, acipenseridae) within the Po River basin have been recently assessed for the IUCN Red List of Threatened Species and were found to be Extinct in the Wild and Critically Endangered, respectively. Significant declines in both species' abundance have spurred major research efforts and management actions in recent decades. Recently, specific actions have been conducted to recover habitat connectivity through projects of river defragmentation and reintroduction plans have been implemented for both sturgeon species. To manage effective conservation efforts, knowledge of a species' distribution and abundance is critical, especially for adult sturgeon that are able to move hundreds of kilometers away from release sites. Here, two new quantitative PCR (qPCR) assays to detect beluga sturgeon and Adriatic sturgeon environmental DNA (eDNA) in water samples have been developed with the goal of providing an alternative method to monitor their presence. Two Taqman-based assays targeting the mitochondrial cytochrome b region were developed and showed no amplification of other related and co-occurring fishes. A mesocosm within the Ticino Park on the Ticino River (a main tributary of the Po River), where both species are bred, was used to develop and validate the assays. The LOQ for H. huso assay corresponded to Ct = 41 (7.33 × 107 DNA counts/µL of reaction) and for A. naccarrii it was Ct = 37 (2.23 × 1016 DNA counts/µL of reaction). Additionally, water samples were taken from the discard drainage, which flows directly into the Ticino River, testing positive detection of eDNA within a distance of up to 2 km. Overall, the results suggested that the two assays developed in this study could represent a promising new tool for monitoring both beluga and Adriatic sturgeon. [ABSTRACT FROM AUTHOR]

In addition to the issue of pork contamination, processed meats frequently contain traces of rat meat. Therefore, detection and quantification of the pork and rat DNA in cases of meat and processed meat adulteration are necessary. In the current study, two gene targets of the cytochrome b for pigs and the Mt‐atp6 of Rattus norvegicus for rats were used in the absolute multiplex quantitative real‐time PCR (m‐qPCR). The sample DNA was amplified with a standard as positive control in the various concentration of 1000 pg, 100 pg, 10 pg, 0.1 pg, 0.01 pg, and 0.001 pg. There were 25 processed meat samples and 5 fresh meat samples identified in this study. Among the total of 30 samples assessed, 6 samples were successfully detected and quantified their pork and rat DNA contamination. One sample was contaminated with pork DNA with a concentration of 2.451×10‐4 pg (“Meatball 3). Five samples were contaminated with rat DNA with a concentration of 3.603×10‐11 pg (“Sempol 3”), 2.196×10‐10pg (“Meatball 6”), 4.908×10‐11 pg (“Siomay 3”), 1.489×10‐10 pg (“Grinding 2”), and 3.564×10‐10 pg (“Grinding 4”). In this study, we have discovered that the contamination of pork and rat were detected in the samples. It suggested that this method is applicable for detecting the contaminant in processed meat samples

The current study aimed to detect the genetic variability of mitochondrial DNA (mtDNA) cytochrome B (CYTB) gene in 80 native Egyptian rabbits (NER) belonging to three populations in three different agriculture regions (Delta, Middle, and Upper Egypt) and also investigate the origin of these breeds by phylogenetic relationship analysis. A total of 62 haplotypes were recorded among the three NER populations. The native Upper Egypt rabbits (NUER) expressed the highest number of haplotypes, mutations, polymorphic sites, and haplotype diversity (23, 55, 51, and 1.00, respectively). While it gave the lowest values of nucleotide diversity (0.0262) and Tajima's D (−0.01435), the percentage of mutual haplotypes was 4.8 % between the Middle and Delta Egypt populations. The phylogenetic analysis showed that there were more separated haplotypes of NUER compared to other populations. The same finding was also observed when supported by 31 sequences of different rabbit breeds retrieved from the GeneBank database. A mutual haplotype was observed between native Delta Egyptian rabbits (NDER) and New Zealand (NWZ) rabbits. The results of this study shed light on the importance of indigenous breeds in rural areas through mtDNA, which contributes to finding sustainable strategies to conserve and improve genetic resources in Egyptian rural areas.

Research voyages onboard RV ‘Investigator’ in 2021 (IN2021_V08) and 2022 (IN2022_V04) sampled benthic communities of seamounts off Christmas Island and Cocos (Keeling) Islands, also known as Indian Ocean Australian Territories (IOT). Over 150 specimens of the family Serpulidae collected during the voyages were deposited in the Australian Museum. The animals belonged to the filogranin genera Apomatus, Bathyvermilia, Bathyvermiloides gen. nov., Filogranula, and Protis, as well as to serpulin genera Hyalopomatus, Placostegus and Vitreotubus. In total, 12 species were identified, including three named, but very poorly known serpulids Bathyvermilia challengeri, Filogranula stellata, and Vitreotubus digeromimoi. Nine species Apomatus nishii n. sp., Bathyvermilia rolandobastidai n. sp., Bathyvermiloides juliebrockae n. sp., Protis melmackenzieae n. sp., Protis perneti n. sp., Hyalopomatus nogueirai n. sp., Hyalopomatus rossanae n. sp., Hyalopomatus suelindsayae n. sp., and Placostegus leslieharrisae n. sp. were described. All species descriptions are accompanied by DNA sequence data and their phylogenetic positions in the family Serpulidae have been assessed.

Thomasomys is the most diverse genus of the Sigmodontinae subfamily, comprising at least 51 species. Despite recent systematic advances, the monophyly of this genus, the proposed species groups and their content, and the species limits are not yet firmly established. Using a well‐sampled mitochondrial dataset, we aim to test the monophyly of the genus, infer phylogenetic relationships among species and species groups and test the limits between valid species and candidate species. For this, we used a large matrix of 272 partial non‐redundant sequences of the cytochrome b mitochondrial gene from 40 valid and 20 candidate species. Using probabilistic approaches on this dataset, we inferred Thomasomys phylogenetic relationships and explored species boundaries using four unilocus species delimitation methods (ABGD, ASAP, bPTP and GMYC). Thomasomys sensu stricto was recovered monophyletic and well‐supported, excluding a Peruvian lineage misidentified as part of the genus. Analyses consistently recovered 10 well‐supported major clades and several paraphyletic or polyphyletic species. Delimitation methods and genetic divergences estimated that Thomasomys comprises between 81 and 93 putative species, thus potentially doubling the species diversity of Thomasomys. Such a result clearly calls for an urgent taxonomic revision of this genus and the use of further molecular loci within an integrative taxonomic approach to describe its diversity and understand its evolutionary history. [ABSTRACT FROM AUTHOR]

The Javan tiger Panthera tigris sondaica and the Bali tiger P. tigris balica were categorized as Extinct on the IUCN Red List in both 2003 and 2008, leaving only the Sumatran subspecies P. tigris sumatrae extant in Indonesia. There have, however, been occasional, more recent reports of the Javan tiger but without conclusive evidence. Here, a potential observation in 2019 of a Javan tiger in a community plantation near the village of Cipendeuy in the forest of South Sukabumi, West Java, and a single hair found on a fence nearby, are assessed. The cytochrome b mitochondrial DNA (mtDNA) gene sequence of the putative Javan tiger hair were compared with that of a Javan tiger specimen in Museum Zoologicum Bogoriense, collected in 1930; hair samples of several tiger subspecies and the Javan leopard Panthera pardus melas were used as controls. The results showed that the genetic distances (d) of the putative Javan tiger hair with the Sumatran, Bengal P. tigris tigris and Amur P. tigris altaica tigers and the Javan leopard are 0.074 ± SE 0.009, 0.071 ± SE 0.009, 0.072 ± SE 0.009 and 0.088 ± SE 0.010, respectively, whereas the genetic distance of the putative Javan tiger hair with the Javan tiger museum specimen is 0.040 ± SE 0.006. In addition, phylogenetic trees showed that the putative Javan tiger hair sample belongs to the same group as the museum specimen of the Javan tiger, but is differentiated from other tiger subspecies and the Javan leopard. Whether the Javan tiger still occurs in the wild needs to be confirmed with further genetic and field studies.

Nile tilapia Oreochromis niloticus is one of the most important fishery resources and a valuable fish species for aquaculture programmes. It is found in almost all waters and is widely dispersed. Several natural populations of this species have been impacted by genetic pollution despite their significant economic relevance. Understanding population structure is a crucial first step in protecting this species in its native habitats as well as in choosing which wild stocks to use in hatchery initiatives. To demonstrate the genetic-population structure of this species, genetic differences among three geographically secluded populations of O. niloticus were investigated utilizing mitochondrial DNA cytochrome b gene sequences. The results were used to estimate the levels of genetic variability within and among the populations. The 56 cyt b (821 bp) sequences analysis revealed 21 haplotypes, with a nucleotide diversity of 0.0510 and a haplotype diversity of 0.881. In each of the populations, seven (7) singleton variable sites and 19 informative-parsimony sites, genetic diversity could be identified and few population haplotypes were found, indicating a minor genetic distinction between them. For the purpose of conservation and/or Nile tilapia breeding programmes, this information would assist in choosing the fish populations that maintain greater genetic variation in O. niloticus.

We report Bungarus suzhenae Chen, Shi, Vogel, Ding & Shi, 2021 and Ovophis zayuensis (Jiang, 1977) for the first time from India. Specimens of B. suzhenae and O. zayuensis were collected during our field surveys in north (Arunachal Pradesh) and south (Nagaland-Manipur border) of the river Brahmaputra. Species identity was supported by partial cytochrome b (cyt b), and 16s mitochondrial gene. We provide a detailed morphological description and a key to the two genera of this region. This report extends the westernmost distribution of B. suzhenae by ca. 300 km from Myanmar, and the southernmost range of O. zayuensis by 170 km from Tibet. Until now eight species of Bungarus and only one Ovophis species have been reported from India. Ovophis species are recently reported to be medically important venomous snakes whose venom properties have not been investigated in depth. [ABSTRACT FROM AUTHOR]

Background: Babesia spp. are protozoan parasites that infect the red blood cells of domesticated animals, wildlife and humans. A few cases of giant pandas (a flagship species in terms of wildlife conservation) infected with a putative novel Babesia sp. have been reported. However, comprehensive research on the morphological and molecular taxonomic classification of this novel Babesia sp. is still lacking. This study was designed to close this gap and formally describe this new Babesia sp. infecting giant pandas. Methods: Detailed morphological, molecular and phylogenetic analyses were conducted to characterise this Babesia sp. and to assess its systematic relationships with other Babesia spp. Blood samples from giant pandas infected with Babesia were subjected to microscopic examination. The 18S ribosomal RNA (18S rRNA), cytochrome b (cytb) and mitochondrial genome (mitogenome) of the new Babesia sp. were amplified, sequenced and assembled using DNA purified from blood samples taken from infected giant pandas. Based on the newly generated 18S rRNA, cytb and mitogenome sequences, phylogenetic trees were constructed. Results: Morphologically, the Babesia sp. from giant pandas exhibited various forms, including round to oval ring-shaped morphologies, resembling those found in other small canine Babesia spp. and displaying typical tetrads. Phylogenetic analyses with the 18S rRNA, cytb and mitogenome sequences revealed that the new Babesia sp. forms a monophyletic group, with a close phylogenetic relationship with the Babesia spp. that infect bears (Ursidae), raccoons (Procyonidae) and canids (Canidae). Notably, the mitogenome structure consisted of six ribosomal large subunit-coding genes (LSU1-6) and three protein-coding genes (cytb, cox3 and cox1) arranged linearly. Conclusions: Based on coupled morphological and genetic analyses, we describe a novel species of the genus Babesia, namely, Babesia ailuropodae n. sp., which infects giant pandas. [ABSTRACT FROM AUTHOR]

Introduction: Globally, rodents and shrew populations constitute crucial elements of diverse environments and animal communities. It is imperative to study their population dynamics to mitigate any potential negative impact on humans, as they can be involved in the transmission of critical zoonotic agents, such as Blastocystis. Therefore, this study aimed to identify the prevalence and genetic composition of Blastocystis in wild rodents and shrews residing in the Zhejiang provinces of China. Methods: A total of 652 wild rodents and and shrews were captured from three different regions in Zhejiang Province from April 1st to October 31, 2023. The DNA was isolated by collecting fresh feces from the intestines of each rodent or and shrew. Rodent and shrew species were examined by vertebrate cytochrome b (cytb) analysis and PCR amplification. Blastocystis was also found in all fecal samples using PCR analysis and sequencing of the partial small subunit of ribosomal RNA (SSU rRNA) gene. Results: Among all the samples, 6.6% (43/652) showed a positive result for Blastocystis. In the results, 6 species of rodent and shrew were identified with Blastocystis, including Apodemusagrarius (n = 36) (2.8%), Niviventer confucianus (n = 75) (17.3%), Rattus losea (n = 18) (5.6%), R. norvegicus (n = 155) (2.6%), R. tanezumi (n = 86) (3.5%), and Suncus murinus (n = 282) (7.4%). The existence of 6 Blastocystis subtypes, ST4 (n = 33), ST1 (4), ST7 (n = 3), ST2 (n = 1), ST3 (n = 1), and ST5 (n = 1), were confirmed by sequence analysis. Discussion: Based on the molecular data obtained, the wild rodents and shrews under investigation were found to be concurrently infected with zoonotic subtypes of Blastocystis, including ST1 to ST5 and ST7. This suggests that these animals could potentially pose a zoonotic threat to humans and other animals susceptible to Blastocystis infection. [ABSTRACT FROM AUTHOR]