Analysis of Genetic Diversity of cytb gene from Babesia gibsoni Isolates from Naturally Infected Dogs in Karnataka, India

PURPOSE

The study aimed to investigate genetic diversity in Babesia gibsoni, the causative agent of canine babesiosis, and to assess the presence of atovaquone-resistant isolates in naturally infected dogs.

METHODS

A total of 24 blood samples confirmed for B. gibsoni infection was subjected to PCR amplification and sequencing based on cytb gene. Genetic characterization of B. gibsoni as well as attempts to detect the point mutation rendering atovaquone resistance was carried out based on the analysis of nucleotide sequence of cytb gene using bioinformatics software.

RESULTS

The findings indicated that the B. gibsoni isolates in the investigation exhibited a high nucleotide identity with the Asian genotype, ranging from 98.41 to 98.69%. Notably, none of the isolates carried cytb gene variants associated with atovaquone resistance. Phylogenetic analysis revealed clustering of most isolates with those from Japan and China, except for one isolate forming a distinct subclade. Haplotype network analysis indicated a high diversity with 22 distinct haplotypes among the B. gibsoni isolates, emphasizing the genetic variability within the studied population.

CONCLUSION

In conclusion, the cytb gene exhibited remarkable conservation among the twenty-four B. gibsoni isolates studied and the study represents the first genetic diversity assessment of B. gibsoni using the cytb gene in dogs from India. These findings shed light on the genetic characteristics of B. gibsoni in the region and provide valuable insight for addressing the challenges posed by this life-threatening disease in dogs.

Avian Malaria in wild birds from a wildlife rehabilitation center in Central Portugal

Avian haemosporidian (Haemoproteus, Leucocytozoon, Plasmodium) are vector-transmitted protozoan parasites highly prevalent in various bird species. Still, their importance for bird health, species decline, or impact on rehabilitation success is underestimated. This study aimed to determine the occurrence and diversity of haemosporidian parasites after necropsies of seventy wild birds from thirty-four species of twelve taxonomic orders. Detection of avian haemosporidian DNA was evaluated using PCR amplification of the cytochrome b gene. 48.6% of all sampled birds were positive, with 24.3% positive for Plasmodium spp./Haemoproteus spp. and 44.3% for Leucocytozoon spp. Mixed infections corresponded to 20% of all tested birds. Sequencing of several selected samples revealed the infection of Plasmodium matutinum, Plasmodium relictum and different lineages of Leucocytozoon spp. This study provides a baseline description of haemosporidian infections in wild birds from a rehabilitation center in central Portugal. The results show the necessity to test and monitor possible infections that undermine recovery processes for different birds. Further research into the occurrence of these haemosporidian species in birds kept in conservation centers is needed to understand the impact on bird health.

Baseline study of the morphological and genetic characteristics of Haemoproteus parasites in wild pigeons (Columba livia) from paddy fields in Thailand

Haemoproteus columbae is a common haemosporidian parasite of wild pigeons (Columba livia) reported worldwide. In Thailand, the wild pigeon population is increasing due to paddy field monoculture. However, there are limited reports on the presence of H. columbae in these pigeon populations. The aim of the study was to characterize H. columbae in wild pigeons. A total of 87 wild pigeons were examined using microscopic and molecular methods. Haemoproteus columbae was detected in approximately 27.6% of pigeons and their morphological characteristics were described. The partial cytochrome b (cyt b) gene sequence of H. columbae was then characterized into three common lineages (HAECOL1, COLIV03, and COQUI05). By highlighting the morphologic and genetic characteristics of H. columbae commonly found in this population of pigeons, this study provides essential regional knowledge about haemosporidian parasites that could benefit future taxonomic and phylogeographic studies.

Genetic characterization of Dibothriocephalus latus and Dibothriocephalus dendriticus (Cestoda: Diphyllobothriidae) from Chile based on haplotype analysis using mitochondrial DNA markers

Dibothriocephalus latus and Dibothriocephalus dendriticus are found throughout the temperate and sub-arctic zones of the northern hemisphere, but they are also found in the southern core countries of South America, Chile and Argentina. Genetic characteristics of D. latus and D. dendriticus from South America have yet to be fully defined. The present study aimed to understand the genetic characteristics of D. latus and D. dendriticus from Chile by haplotype network analysis of mitochondrial cytochrome c oxidase subunit I gene (cox1) and cytochrome b gene (cob), as well as their origins. Dibothriocephalus latus and D. dendriticus plerocercoid larvae were obtained from feral and/or wild salmonids captured in Lake Llanquihue in Región de Los Lagos, and Lake Panguipulli in Región de Los Ríos, located south of central Chile. Haplotype analysis of D. latus revealed that H1 in cox1 and H2 in cob are the key haplotypes common to D. latus across the world, including Chile, and both genes exhibited limited genetic diversity in D. latus. It was assumed that D. latus was brought into South America by European and Russian immigrants in the 19th century as previously reported. In contrast, both the cox1 and cob of D. dendriticus display considerable genetic diversity, with no common haplotypes between D. dendriticus populations from Chile and the northern hemisphere. More intriguingly, two cob haplotypes (H24, H25) detected in Chilean D. dendriticus were closely linked to haplotypes (H30,H31) detected in North American D. dendriticus, strongly implying that D. dendriticus in Chile was brought by piscivorous migrating birds from North America. It has also been estimated that the D. dendriticus from Chile genetically diverged from the D. dendriticus from the northern hemisphere approximately 1.11 million years ago, long before humans migrated to the southern parts of South America.

First report of Babesia bigemina in Lama glama in a zoological garden of Veracruz, Mexico

Zoological gardens represent specialised centres for the preservation of biological inventories and genetic diversity, allowing the recognition of multiple species in critical conservation categories. However, the close coexistence of multiple species of vertebrates that may be associated with various species of ectoparasites may be the cause of the transmission of multiple infectious agents, among which tick-borne pathogens stand out. In these areas, several animal species usually live in a small space and proximity to other wildlife, visitors and keepers. In Mexico, little is known about the disease agents transmitted by arthropods in zoological gardens. For this reason, the aim of this study was to identify the presence of Babesia/Theileria in animals maintained in captivity. As a part of a project identifying vector-borne pathogens in wildlife, 24 animals were sampled in the Miguel Angel de Quevedo zoo. Molecular identification of Babesia/Theileria was realised through amplification of a fragment of the mitochondrial cytB gene and the ribosomal 18S-rDNA. Two neotropical camelids (Lama glama) tested positive (2/3 = 66.6%) to Babesia bigemina. Our results represent the first record of B. bigemina in animals in captivity in a zoological garden in Mexico and the first finding of this haemoparasite in neotropical camelids in Mexico.

Co-infections of Plasmodium relictum lineages pSGS1 and pGRW04 are readily distinguishable by broadly used PCR-based protocols, with remarks on global distribution of these malaria parasites

Plasmodium relictum is the most common generalist avian malaria parasite, which was reported in over 300 bird species of different orders, particularly often in passerines. This malaria infection is often severe in non-accustomed avian hosts. Currently, five distinct cytochrome b gene lineages have been assigned to P. relictum, with the lineages pSGS1 and pGRW04 being the most common. Based on molecular screenings, the transmission of these two parasite lineages might occur in sympatry, particularly often in sub-Saharan Africa, but they also have been reported to have different areas of transmission globally, with the lineages pSGS1 and pGRW04 being of low (if at all) transmission in huge regions of Americas and Europe, respectively. It remains unclear why these lineages are more often reported in some geographical areas, even though their susceptible vertebrate hosts and vectors are present globally. Co-infections of malaria parasites and other haemosporidians belonging to different species and subgenera are prevalent and even predominate in many bird populations, however, PCR-based protocols using commonly used primers often do not read such co-infections. Because information about the sensitivity of these protocols to read co-infections of the lineages pSGS1 and pGRW04 is absent, this study aimed to unravel this issue experimentally. Blood samples of birds experimentally infected with the single parasite lineages pSGS1 and pGRW04 were used to prepare various combinations of mixes, which were tested by two PCR-based protocols, which have been often used in current avian malaria research. Single infections of the same lineages were used as controls. Careful examination of the sequence electropherograms showed the presence of clear double peaks on polymorphic sites, indicating co-infections. This experiment shows that the broadly used PCR-based protocols can readily distinguish co-infections of these parasite lineages. In other words, the available information about patterns of the geographical distribution of the P. relictum lineages pSGS1 and pGRW04 likely mirrors the existing epidemiological situation but is not a result of the bias due to preferable DNA amplification of one of these lineages during their possible co-infections. This calls for further ecological research aiming determination of factors associated with the transmission of the lineages pSGS1 and pGRW04 in different regions of the globe.

Molecular epidemiology of Theileria annulata infection of cattle in Layyah District, Pakistan

Theileria annulata is the cause of tropical theileriosis in cattle in Pakistan, where it has a significant impact on the cattle industry. Here we report the molecular detection and seasonal prevalence and blood parameters of T. annulata infection in crossbred, Holstein Frisian and Sahiwal breed in Layyah District in the Punjab. In total, 844 blood samples (cross = 244, Holstein Frisian = 300, Sahiwal breed = 300) collected in 2017 and 2018 were tested. Blood smear screening revealed 125/844 (15%) of cattle positive for Theileria species. PCR amplification of cytochrome b gene indicated an overall T. annulata prevalence of 21% (174/844). The highest prevalence was observed in autumn season (53%), followed by winter (20%), summer (14%) and spring (3%). Crossbred cattle were the most susceptible to T. annulata (28%) followed by Sahiwal (19%) and Holstein Frisian. Representative partial cytochrome b gene sequences of T. annulata revealed phylogenetic similarities with sequences submitted from India, Iran, China, Turkey and Spain. Small numbers of ticks, including Hyalomma anatolicum, Hyalomma excavatum, Rhipicephalus microplus, and Haemaphysalis punctata, were identified from cattle but none of them was found PCR positive for the presence of T. annulata. Analysis of the hematology data indicated that red blood cell, hemoglobin, mean cell hemoglobin, mean corpuscular hemoglobin, lymphocyte (%), monocyte (%) and platelet count were significantly altered in T. annulata-positive cattle of all three breeds. Screening of cattle by PCR for the detection of T. annulata is recommended for diagnosis and treatment.

Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation

Quaternary environmental changes fundamentally influenced the genetic diversity of temperate-zone terrestrial animals, including those in the Japanese Archipelago. The genetic diversity of present-day populations is taxon- and region-specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1140 bp) of mitochondrial DNA (mtDNA) to elucidate the factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura, which occur in central and southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta, which occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (τ values) were grouped into five classes in terms of the level, implying the occurrence of five stages for rapid expansion. It is conceivable that severe cold periods and subsequent warm periods during the late Quaternary were responsible for the population expansion events. The first and third oldest events included island-derived haplotypes, indicative of the involvement of land bridge formation between remote islands, hence suggesting an association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third event was followed by the fourth, it is plausible that the termination of the Younger Dryas and subsequent abrupt warming ca. 11,500 years ago facilitated the fourth expansion event. The second event most likely corresponded to early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period were predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500 years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing a time-dependent manner whose pattern was similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5800 years ago with a rate of 0.10 substitutions/site/million years ago during the mid-Holocene, suggestive of the influence of humans or other unspecified reasons, such as the Jomon marine transgression.

Detection and molecular identification of Leucocytozoon and Plasmodium species from village chickens in different areas of Myanmar

Village chicken production, a traditional, small-scale, and extensive backyard poultry industry, has been profitable for local farmers in Myanmar. However, there is scanty information available concerning the infection of these chickens with avian pathogens, including haemoprotozoan parasites. In the present study, we provide the first report of microscopic detection and molecular identification of Leucocytozoon and Plasmodium parasites from seven different areas of Myanmar. Leucocytozoon gametocytes were detected in 17.6% (81/461) of the blood smears from village chickens. The nested polymerase chain reaction (PCR) for targeting Leucocytozoon mitochondrial cytochrome b (cyt b) genes had a 17.6% positive rate. Although the positive rate of nested PCR targeting Plasmodium/Haemoproteus cyt b was 34.3%, the PCR protocol was observed to possibly amplify DNA of a certain species of Leucocytozoon. There were no obvious clinical signs in the infected birds. Statistical analysis of the microscopic detection and PCR detection rates using the age and sex of birds as internal factors revealed that the statistical significances differed according to the study area. The sequencing of 32 PCR products obtained from each study area revealed infection by Leucocytozoon caulleryi in three birds, Leucocytozoon sabrazesi in two birds, Leucocytozoon schoutedeni in two birds, Leucocytozoon sp. in eighteen birds, and Plasmodium juxtanucleare in seven birds; however, Haemoproteus infection was not detected. While L. sabrazesi was detected in chickens from the central region of Myanmar, the other haemosporidians were detected in those from different areas. In the haplotype analysis, we detected 17 haemosporidian cyt b haplotypes, including two for L. caulleryi, one for L. sabrazesi, two for L. schoutedeni, nine for Leucocytozoon sp., and three for P. juxtanucleare. Phylogenetic analysis of the cyt b haplotypes revealed a considerably close genetic relationship among chicken haemosporidians detected in Myanmar, Thailand, and Malaysia. These results indicate that well-recognized widespread species of chicken Leucocytozoon and Plasmodium are distributed nationwide in Myanmar, providing new insights into the ecosystem and control strategies of haemosporidian parasites in domesticated chickens in Myanmar.

Sporogony of four Haemoproteus species (Haemosporida: Haemoproteidae), with report of in vitro ookinetes of Haemoproteus hirundinis: phylogenetic inference indicates patterns of haemosporidian parasite ookinete development

BACKGROUND

Haemoproteus (Parahaemoproteus) species (Haemoproteidae) are widespread blood parasites that can cause disease in birds, but information about their vector species, sporogonic development and transmission remain fragmentary. This study aimed to investigate the complete sporogonic development of four Haemoproteus species in Culicoides nubeculosus and to test if phylogenies based on the cytochrome b gene (cytb) reflect patterns of ookinete development in haemosporidian parasites. Additionally, one cytb lineage of Haemoproteus was identified to the species level and the in vitro gametogenesis and ookinete development of Haemoproteus hirundinis was characterised.

METHODS

Laboratory-reared C. nubeculosus were exposed by allowing them to take blood meals on naturally infected birds harbouring single infections of Haemoproteus belopolskyi (cytb lineage hHIICT1), Haemoproteus hirundinis (hDELURB2), Haemoproteus nucleocondensus (hGRW01) and Haemoproteus lanii (hRB1). Infected insects were dissected at intervals in order to detect sporogonic stages. In vitro exflagellation, gametogenesis and ookinete development of H. hirundinis were also investigated. Microscopic examination and PCR-based methods were used to confirm species identity. Bayesian phylogenetic inference was applied to study the relationships among Haemoproteus lineages.

RESULTS

All studied parasites completed sporogony in C. nubeculosus. Ookinetes and sporozoites were found and described. Development of H. hirundinis ookinetes was similar both in vivo and in vitro. Developing ookinetes of this parasite possess long outgrowths, which extend longitudinally and produce the apical end of the ookinetes. A large group of closely related Haemoproteus species with a similar mode of ookinete development was determined. Bayesian analysis indicates that this character has phylogenetic value. The species identity of cytb lineage hDELURB2 was determined: it belongs to H. hirundinis.

CONCLUSIONS

Culicoides nubeculosus is susceptible to and is a likely natural vector of numerous species of Haemoproteus parasites, thus worth attention in haemoproteosis epidemiology research. Data about in vitro development of haemoproteids provide valuable information about the rate of ookinete maturation and are recommended to use as helpful step during vector studies of haemosporidian parasites, particularly because they guide proper dissection interval of infected insects for ookinete detection during in vivo experiments. Additionally, in vitro studies readily identified patterns of morphological ookinete transformations, the characters of which are of phylogenetic value in haemosporidian parasites.

Partial mtDNA sequencing data of vulnerable Cephalopachus bancanus from the Malaysian Borneo

Tarsier is an endangered nocturnal primate in the family Tarsiidae and is an endemic to Sundaic islands of Philippine (Carlito syrichta), Sulawesi (Tarsius tarsier-complex) and Borneo (Cephalopachus bancanus). Recent records indicated that most molecular studies were done on the Eastern Tarsier and little information for the other group of tarsiers. Here, we present a partial cytochrome b data set of C. bancanus in Sarawak, Malaysian Borneo. Standard mist nets were deployed at strategic locations in various habitat types. A total of 18 individuals were caught, measured and weighed. Approximately, 2 × 2 mm of tissue samples were taken and preserved in molecular grade alcohol. Out of 18, only 11 samples were screened with partial mtDNA (cytochrome b) and the DNA sequences were registered in the GenBank (accession numbers: KY794797-KY794807). Phylogenetic trees were constructed with 20 additional mtDNA sequences downloaded from GenBank. The data are valuable for the management authorities to regulate the type of management units for the metapopulation to sustain population genetics integrity of tarsiers in the range countries across the Sunda Shelf.

What is the taxonomic status of East Asian otter species based on molecular evidence?: focus on the position of the Japanese otter holotype specimen from museum

The Japanese otter (Lutra nippon), once inhabited in most islands of Japan, is now considered as an extinct species. Although the Japanese otter is regarded as a distinct species from the Eurasian otter (L. lutra), its phylogeny and taxonomic status are based on limited information on morphological and genetic data, and thus further clarification is required. Here, we assessed the phylogenetic relationship among the genus Lutra and taxonomic status of L. nippon by using the complete sequences of cytochrome b gene of its holotype. The present phylogenic trees supported that the genus Lutra specimens largely formed monophyletic group, with L. sumatrana as a basal to other Lutra species. Within Lutra species, L. nippon was distantly related with L. lutra. The European otter population of L. l. lutra were clustered together with its subspecies, L. l. chinensis rather than the same subspecies, Korean otter population. The discrepancy between the genetic data and traditional taxonomy justifies the necessity of reexamination of the current subspecific classification system of Eurasian otters. Level of genetic divergence between the holotype of L. nippon and L. lutra was two to three-fold lower than those among the other sister species of the Lutrinae. Based on the level of divergence between the L. nippon and L. lutra, and insufficient evidence of morphological difference between them, it is suggested that designation of Japanese otter as a separate species from L. lutra will be reconsidered.

Further characterisation of Leucocytozoon podargii in wild tawny frogmouths (Podargus strigoides) in Western Australia

The present study assessed the prevalence and morphology of Leucocytozoon podargii from wild tawny frogmouths (Podargus strigoides) in Western Australia (WA) and genetically characterised the cytochrome b gene (cyt b) of L. podargii in wild tawny frogmouths from WA and Queensland (QLD). The prevalence of L. podargii in wild tawny frogmouths from WA was 93.3% (14/15; 95% CI, 68.1-99.8%). The morphological characters of L. podargii from WA were similar to L. podargii from QLD: the gametocytes were round-oval shape, approximately 8-12 μm in diameter; the macrogametocytes were 12.4 μm in diameter; microgametocytes were 10.4 μm in diameter; and the ratio of macrogametocytes and microgametocytes was 3:2. Sequence analysis of partial cyt b gene fragments revealed that L. podargii sequences isolated from wild tawny frogmouths in WA shared the highest similarity (99.8% at nucleotide level and 100% at protein level) with L. podargii isolated from wild tawny frogmouths in QLD. The mitochondrial 18S rRNA gene of L. podargii gametocytes was quantified using droplet digital PCR (ddPCR), and the highest gametocyte load was detected in the lung. This finding corresponds to the results of the histological study. Based on the morphological and molecular studies, it was concluded that the Leucocytozoon parasite identified from wild tawny frogmouths in WA is consistent with L. podargii from wild tawny frogmouths in QLD, and the present study has genetically characterised two different L. podargii genotypes (QLD and WA) for the first time.

Notes on the distribution and phylogeography of two rare small Gerbillinae (Rodentia, Muridae) in Morocco: Gerbillus simoni and Gerbillus henleyi

Even though Gerbillinae rodents represent an important part of the mammalian fauna in North Africa, many gaps remain in our understanding of the distribution, ecology, evolution, and systematics of some lesser known species in this family. We present in this study the most recent findings on two of these species. The first species, Gerbillus simoni Lataste, 1881, is a short-tailed, small gerbil, endemic to North Africa. In Morocco, it is present only in a small area in the northeast, where it has not been caught since 1970. In 2014, we captured a small gerbil in this region that was identified as G. simoni based on morphology and molecular data (cytochrome b gene sequencing). This study represents the first genetic characterization of G. simoni in Morocco and the first one outside Tunisia. Populations from Morocco and Tunisia (mainland and Kerkennah Islands) show very little genetic differentiation. The second species, Gerbillus henleyi de Winton, 1903, is a long-tailed small gerbil that lives in the Sahel and North Africa with an extension to the Middle East. In Morocco, this species was only known in the southwest. Between 2014 and 2015, we have captured four gerbils in the northeast of the country, which were confirmed genetically and morphologically as belonging to this species. This represents an extension of its known distribution of about 370km to the northeast of the country. These new Moroccan specimens form a distinct lineage. High genetic diversity is observed throughout the geographic range of G. henleyi, suggesting the existence of several cryptic species.

Resolving the phylogenetic status and taxonomic relationships of the Hangul (Cervus elaphus hanglu) in the family Cervidae

The Hangul (Cervus elaphus hanglu) is a "Least Concern" deer species, and it is the only survivor of the Red Deer group in the Indian subcontinent. The phylogenetic status of the Hangul relative to the other members of the family Cervidae is not known because sequence data are not available in public databases. Therefore, this study was carried out to determine the phylogenetic status and delineate the genetic boundaries of the Hangul with respect to the other Red Deer subspecies on the basis of cytochrome b gene sequence data (ca 421 bp). There are three major monophyletic groups of the Red Deer in the phylogenetic tree, which are referred to as the western (Hap-01 to Hap-10), eastern (Hap-11 to Hap-20) and tarim (Hap-21 to Hap-25) groups. The overall haplotype diversity and per-site nucleotide diversity were 0.9771 (±0.0523) and 0.0388 (±0.00261), respectively. In the phylogenetic tree, the Hangul clustered with the tarim group (Yarkand and Bactrian Red Deer) with a strong bootstrap support (92%) and was found to be genetically closer to the Bactrian Red Deer than to the Yarkand Red Deer. Our molecular analysis supported the idea that the Hangul diverged from the Bactrian Red Deer and migrated to India from Tajikistan approximately 1.2 MYA.

Phylogenetic affinities of the Fregetta storm-petrels are not black and white

The Fregetta storm-petrels generally are regarded to comprise two species: black-bellied storm-petrels F. tropica (monotypic) breed at Antarctic and sub-Antarctic islands (46-63°S), and white-bellied storm-petrels F. grallaria breed at south temperate islands (28-37°S), with four recognized subspecies. Confusion surrounds the status of birds at Gough Island (40°S), central South Atlantic, which have been attributed usually to a white-bellied form of black-bellied storm-petrel F. t. melanoleuca. We use cytochrome b and nuclear β-fibrinogen gene sequences to show that F. t. melanoleuca are present during the breeding season at Gough and islands in the nearby Tristan da Cunha archipelago (37°S), exhibiting limited divergence from F. t. tropica. We also show that there is greater diversity among F. grallaria populations, with eastern South Pacific F. g. segethi and F. g. titan differing by c. 0.011, and both differing from western South Pacific nominate F. g. grallaria by c. 0.059. The Tristan archipelago supports a population of F. grallaria closely allied to the nominate form, as well as a distinct form identified as F. g. leucogaster. Further research is needed to assess how F. grallaria and F. tropica segregate in sympatry at Tristan and Gough, and why this is the only location where both species have white-bellies.

Origins of Wohlfahrtia magnifica in Italy based on the identification of mitochondrial cytochrome b gene haplotypes

To identify the geographical origins of larvae of Wohlfahrtia magnifica (Diptera: Sarcophagidae) causing myiasis of sheep in Italy, comparative DNA sequence analysis of the mitochondrial cytochrome b gene was performed, based on gene fragments amplified by PCR from genomic DNA isolated from individual specimens. DNA extractions of 19 larvae from Lazio, Molise, Puglia, and Sicilia generated 17 readable sequences homologous to 2 haplotypes, either CB_magn01 or CB_magn02; DNA extracts from 4 adult flies from Calabria (reared from larvae) produced 4 readable sequences belonging to the haplotype CB_magn01. The two haplotypes found represent both the East and West phylogenetic lineages of W. magnifica, which is consistent with the species' arrival from central/southeast Europe (East lineage) and/or from southwest Europe/northwest Africa (West lineage). This is the first report of the sympatric occurrence of the two lineages, which could have resulted from natural or human-assisted dispersal. Polymorphic nuclear loci will have to be characterized in order to explain the origins and lack of mitochondrial haplotype diversity of this pest in Italy, where it poses increasing veterinary problems.

Molecular phylogeny of some avian species using Cytochrome b gene sequence analysis

Veritable identification and differentiation of avian species is a vital step in conservative, taxonomic, forensic, legal and other ornithological interventions. Therefore, this study involved the application of molecular approach to identify some avian species i.e. Chicken (Gallus gallus), Muskovy duck (Cairina moschata), Japanese quail (Coturnix japonica), Laughing dove (Streptopelia senegalensis), and Rock pigeon (Columba livia). Genomic DNA was extracted from blood samples and partial sequence of the mitochondrial cytochrome b gene (358 bp) was amplified and sequenced using universal primers. Sequences alignment and phylogenetic analyses were performed by CLC main workbench program. The obtained five sequences were deposited in GenBank and compared with those previously registered in GenBank. The similarity percentage was 88.60% between Gallus gallus and Coturnix japonica and 80.46% between Gallus gallus and Columba livia. The percentage of identity between the studied species and GenBank species ranged from 77.20% (Columba oenas and Anas platyrhynchos) to 100% (Gallus gallus and Gallus sonneratii, Coturnix coturnix and Coturnix japonica, Meleagris gallopavo and Columba livia). Amplification of the partial sequence of mitochondrial cytochrome b gene proved to be practical for identification of an avian species unambiguously.

Development of a multiplex PCR-ELISA method for the genetic authentication of Thunnus species and Katsuwonus pelamis in food products

In the present work a PCR-ELISA technique for the authentication of Thunnus species was developed. This method is composed by four systems that can be used in a hierarchical way allowing the identification of several scombroids species; or each individual system independently. The hierarchical strategy, proposes a first step, to assign one sample to the Thunnus genus. Next, if the result is positive, several tests can be applied to assign the sample to some particular species of the Thunnus genus. In the case that the result is negative (absence of Thunnus species), it is possible to verify if Katsuwonus pelamis is included in the sample. The method even allows the detection of mixtures of these species in relatively low amounts (up to 1%). Finally, this method was applied to 11 commercial samples to verify the labelling status of tuna products in the market, detecting that 18% were mislabelling.

Genetic variation in Labeo fimbriatus (Cypriniformes: Cyprinidae) populations as revealed by partial cytochrome b sequences of mitochondrial DNA

Labeo fimbriatus, a medium sized carp is assessed as a commercially important aquaculture species in Indian subcontinent. In the present study, the genetic diversity and population structure of four Indian riverine populations of L. fimbriatus have been evaluated using partial cytochrome b sequences of mitochondrial DNA. Sequencing and analysis of this gene from 108 individuals defined 7 distinct haplotypes. Haplotype diversity (Hd) and nucleotide diversity (π) ranged from 0.067 to 0.405 and 0.00023 to 0.03231, respectively. The Mahanadi population had the highest π level. Analysis of molecular variance (AMOVA) indicated that 47.36% of genetic variation contained within population and 53.76% of genetic variation among groups. Pairwise FST analysis indicated that there was little or no genetic differentiation among populations (-0.0018 to 04572) from different geographical regions except Mahanadi population. The Mahanadi population can be considered as a separate stock from rest three riverine populations. Accordingly, the genetic information generated from this study can be implemented while taking decision in formulating base population for the sustainable selective breeding programs of this species.

Cytochrome b gene (cytb) sequence diversity in a Microtus oeconomus population from Bialowieza Primeval Forest

Based on published information about the glacial, postglacial, and recent distribution of the root vole, Microtus oeconomus, we hypothesized that a population inhabiting the pristine wetland in eastern Poland (Bialowieza Primeval Forest) might comprise a high diversity of haplotypes. The support for this hypothesis was provided by an analysis of partial cytb gene sequences from 149 voles sampled within a two-hectare plot during a nine-year study. In this population, we identified eight haplotypes (PLB1-PLB8), four of which were new to the root vole. These haplotypes were characterized by low nucleotide diversity (π = 0.0054, SE = 0.0019), the absence of transversional differences between sequences, and no changes in the encoded amino acid sequence: features suggesting a lack of immigration from the distant populations. The haplotype number and their frequency distribution in males and females did not differ significantly. An assessment of the persistence of matrilines in the local population throughout the study period revealed that the haplotype composition was relatively stable for only about 3 years. A more complete haplotype network for root voles in Europe was constructed by combining the newly identified haplotypes with the 45 previously described haplotypes. Two of the haplotypes detected in this study occupy key positions in this network: PLB5, as the closest link to the North European group, and PLB8, as an ancestor to many other Central European haplotypes.

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

Comparison of methods in the recovery and amplificability of DNA from fresh and processed sardine and anchovy muscle tissues

An important condition for a successful PCR amplification is an efficient DNA-extraction procedure out of a complex biological matrix such as canned fish. In this study we compared six extraction methods, including commercial kit, in terms of DNA yield, purity and time requirement. Such methods were applied to distinguish small pelagic fish species (Sardina pilchardus and Engraulisencrasicolus) among commercial canned products. The quantity and quality of DNA extracted were evaluated using the ratio A₂₆₀/A₂₈₀. Data were submitted to principal component analysis (PCA) in order to assess the differences between PCR results of fresh and processed anchovy and sardine muscles. Two main PC characterised the PCR of sardine and anchovy (70% and 69% of all variance): principal component 1 (PC1) (4% and 60%) and principal component 2 PC2 (66.0% and 9%) for sardine and anchovy, respectively. According to the PC1, the PCI/SDS and Chelex extractions (in decreasing order) were positively correlated with results of PCR for both species. Statistical results confirmed that the quality of DNA, with the highest amplicon length obtained from the fresh and the different canned fish, was best preserved using the SDS/PCI precipitation method.