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1.
Mem Inst Oswaldo Cruz ; 116: e200572, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33886871

RESUMO

BACKGROUND: The genetic heterogeneity of Leishmania parasites is a major factor responsible for the wide variety of Leishmania-associated manifestations. Consequently, understanding the genetic make-up of Leishmania species using suitable molecular markers is an important component of realising local and regional scale disease risk. The cytochrome b (cytb) is frequently used to type New World Leishmania species. However, its potential to discriminate Leishmania species and variants requires further evaluation. OBJECTIVES: To explore the capacity of cytb gene to identify New World Leishmania species and variants and to develop an approach able to type local Leishmania species and variants. METHODS: We retrieved 360 partial and complete Leishmania cytb gene sequences publicly available in GenBank database to study all single nucleotide polymorphisms (SNPs) across the cytb gene that differentiate New World Leishmania species. This information was used to develop an approach based upon the polymorphisms found in a DNA segment of 948bp. We also compared the typing results found with this technique with the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) profiling obtained using HSP70 gene as target. One hundred Panamanian isolates were used to both typed Leishmania species and assess local genetic variability. FINDINGS: We found complete agreement between our cytb approach and the PCR-RFLP profiling method based on HSP70 for Leishmania species identification. Ninety-two isolates were identified as L. panamensis, although other Viannia species were found circulating at a lower frequency. Three L. panamensis haplotypes were identified in Panamanian provinces. We also provide an initial report of L. guyanensis haplotypes circulating in Panama. MAIN CONCLUSIONS: Cytb gene sequence encompasses key main SNPs that aid to identify Leishmania species. The cytb approach developed with this information was able to identify and assess genetic variability of local Leishmania species found in this study.


Assuntos
Leishmania , Leishmaniose Cutânea , Citocromos b/genética , DNA de Protozoário/genética , Humanos , Leishmania/genética , Panamá , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição
2.
Int J Mol Sci ; 22(4)2021 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-33670016

RESUMO

Atovaquone (ATQ) is a drug used to prevent and treat malaria that functions by targeting the Plasmodium falciparum cytochrome b (PfCytb) protein. PfCytb catalyzes the transmembrane electron transfer (ET) pathway which maintains the mitochondrial membrane potential. The ubiquinol substrate binding site of the protein has heme bL, heme bH and iron-sulphur [2FE-2S] cluster cofactors that act as redox centers to aid in ET. Recent studies investigating ATQ resistance mechanisms have shown that point mutations of PfCytb confer resistance. Thus, understanding the resistance mechanisms at the molecular level via computational approaches incorporating phospholipid bilayer would help in the design of new efficacious drugs that are also capable of bypassing parasite resistance. With this knowledge gap, this article seeks to explore the effect of three drug resistant mutations Y268C, Y268N and Y268S on the PfCytb structure and function in the presence and absence of ATQ. To draw reliable conclusions, 350 ns all-atom membrane (POPC:POPE phospholipid bilayer) molecular dynamics (MD) simulations with derived metal parameters for the holo and ATQ-bound -proteins were performed. Thereafter, simulation outputs were analyzed using dynamic residue network (DRN) analysis. Across the triplicate MD runs, hydrophobic interactions, reported to be crucial in protein function were assessed. In both, the presence and absence of ATQ and a loss of key active site residue interactions were observed as a result of mutations. These active site residues included: Met 133, Trp136, Val140, Thr142, Ile258, Val259, Pro260 and Phe264. These changes to residue interactions are likely to destabilize the overall intra-protein residue communication network where the proteins' function could be implicated. Protein dynamics of the ATQ-bound mutant complexes showed that they assumed a different pose to the wild-type, resulting in diminished residue interactions in the mutant proteins. In summary, this study presents insights on the possible effect of the mutations on ATQ drug activity causing resistance and describes accurate MD simulations in the presence of the lipid bilayer prior to conducting inhibitory drug discovery for the PfCytb-iron sulphur protein (Cytb-ISP) complex.


Assuntos
Atovaquona/farmacologia , Citocromos b/genética , Resistência a Medicamentos/genética , Proteínas com Ferro-Enxofre/genética , Bicamadas Lipídicas/metabolismo , Mutação/genética , Fosfolipídeos/metabolismo , Plasmodium falciparum/genética , Animais , Atovaquona/química , Domínio Catalítico , Bovinos , Resistência a Medicamentos/efeitos dos fármacos , Entropia , Proteínas com Ferro-Enxofre/metabolismo , Ligantes , Modelos Moleculares , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Plasmodium falciparum/efeitos dos fármacos , Conformação Proteica , Mapas de Interação de Proteínas , Estabilidade Proteica
3.
Zhongguo Zhong Yao Za Zhi ; 46(5): 1102-1116, 2021 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-33787103

RESUMO

The identification of species primordium has been one of the hot issues in the identification of traditional Chinese medicine. Sea snake is one of the most valuable Chinese medicinal materials in China. In order to understand the origin and varieties of sea snake in the market, we studied the molecular identification of 46 sea snakes by cytochrome B(Cytb). After comparison and manual correction, the sequence length was 582 bp, and the content of A+T(58.9%) was higher than that of G+C(41.1%). There exist 197 variable sites and 179 parsimony-informative sites of the sequence. There are 44 kinds of sequence alignment with consistency equal to 100%, and 2 kinds equal to 96%. A total of 408 Cytb effective sequences were downloaded from GenBank database, with a total of 68 species. Phylogenetic tree of a total of 454 sea snake sequences with the samples in this study were constructed by neighbor-joining trees and Bayesian inference method, respectively, which can identify 42 samples of medicinal materials, while 4 samples can not be identified because of their low node support. The results showed that the species of the sea snake medicine were at least from 2 genera and 5 species, namely, Aipysurus eydouxii, Hydrophis curtus, H. caerulescen, H. curtus, H. ornatus and H. spiralis. This study suggested that the original species of commercial sea snake are very complex and can provide insight into the identification of sea snakes.


Assuntos
Hydrophiidae , Animais , Teorema de Bayes , China , Citocromos b/genética , Medicina Tradicional Chinesa , Filogenia
4.
Parasitol Res ; 120(2): 693-703, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33452590

RESUMO

Avian blood parasites have been shown to have significant health effects on avifauna worldwide. Sri Lanka, a tropical island rich with resident and migratory birds, has not been properly evaluated for avian blood parasites or their vectors. We investigated the presence of avian haemoparasites in Sri Lankan birds and the potential mosquito vectors of those pathogens. Blood samples were collected from local/migratory birds captured by standard mist nets from Anawilundawa bird sanctuary, Hanthana mountain range, and the University of Peradeniya park. Mosquitoes were collected from Halgolla forest reserve and the forest patches in Kurunegala and Gampola areas in addition to the above mist-netting localities. Part of the mitochondrial cytochrome b (cytb) gene was amplified and sequenced to detect the presence of haemoparasites from avian blood samples (86) and mosquito samples (480). Blood parasites of the two genera, i.e., Haemoproteus (4 species; Haemoproteus sp. 1-4) and Plasmodium (5 species; Plasmodium sp. 1-5) were identified from seven bird species (four resident and three migratory). Among these, three bird species (Red-vented bulbul (3/16), Asian Brown flycatcher (1/1), and India pitta (1/1)) were positive for Plasmodium spp., while four (Yellow-browed bulbul (1/4), oriental white-eye (1/4), brown-headed Barbet (1/4), and Indian blue robin (1/1)) were positive for Haemoproteus spp. Two mosquito species were also positive for Plasmodium (3) and Haemoproteus (1) species. Phylogenetic analysis and haplotype networks created using positive sequences of haemoparasites showed that a Plasmodium clade was shared by Cx nigropunctatus mosquitoes and the migratory bird, Indian pitta. The majority (85%) of the Plasmodium and Haemoproteus sequences of this study were not linked to the well-characterized species suggesting the distinct nature of the lineages. Associations between mosquito species and blood parasites of birds suggest the possible vector status of these mosquitoes.


Assuntos
Aves/parasitologia , Mosquitos Vetores/parasitologia , Infecções Protozoárias em Animais/parasitologia , Infecções Protozoárias em Animais/transmissão , Animais , Aves/sangue , Aves/classificação , Sangue/parasitologia , Citocromos b/genética , Haemosporida/classificação , Haemosporida/genética , Haemosporida/isolamento & purificação , Mosquitos Vetores/classificação , Filogenia , Plasmodium/classificação , Plasmodium/genética , Plasmodium/isolamento & purificação , Infecções Protozoárias em Animais/epidemiologia , Sri Lanka/epidemiologia
5.
Mol Phylogenet Evol ; 157: 107046, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33421613

RESUMO

Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.


Assuntos
Lagartos/classificação , Análise de Variância , Animais , Citocromos b/genética , DNA Mitocondrial , Loci Gênicos , Geografia , Hibridização Genética , Lagartos/anatomia & histologia , Lagartos/genética , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal , Especificidade da Espécie
6.
Mol Phylogenet Evol ; 154: 106994, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33250446

RESUMO

Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.


Assuntos
Passeriformes/classificação , Filogenia , Animais , Teorema de Bayes , Comportamento de Escolha , Clima , Citocromos b/genética , Análise Discriminante , Ecossistema , Plumas/anatomia & histologia , Voo Animal/fisiologia , Geografia , Umidade , Passeriformes/anatomia & histologia , Passeriformes/fisiologia , Chuva , Especificidade da Espécie , Temperatura , Vocalização Animal/fisiologia
7.
Gene ; 772: 145375, 2021 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-33359125

RESUMO

The genetic diversity and phylogenetic relationships of sika deer of different subspecies are uncertain. In order to explore the phylogenetic relationship of different sika deer subspecies, this study used a wider sample collection to analyze mitochondrial sequences and nuclear microsatellites of sika deer. The full lengths of cytochrome-b gene of 134 sika deer were sequenced, and 16 haplotypes were obtained. Based on phylogenetic and haplotype networks analysis, the sika deer was not clustered according to subspecies but was divided into four lineages. Lineage I includes individuals from C.n.kopschi, C.n.sichuanicus, and C.n.hortulorum subspecies; Lineage II includes individuals from C.n.hortulorum subspecies; Lineage III includes individuals from C.n.centralis, C.n.yakushime, C.n.mageshimae, and C.n.keramae subspecies, namely southern Japanese population; Lineage IV includes individuals from C.n.centralis and C.n.yesoensis subspecies, namely northern Japanese population. The microsatellite analysis showed that the sika deer in China and Japan originated independently. The three subspecies of China have significant genetic differentiation, while the three subspecies of Japan have no significant differentiation. This study provides reference for the research of genetic diversity and phylogenetic relationship of sika deer, and also provides scientific data for the evaluation, protection, and utilization of sika deer resources.


Assuntos
Citocromos b/genética , Cervos/classificação , Variação Genética , Repetições de Microssatélites , Animais , Núcleo Celular/genética , China , Cervos/genética , Genética Populacional , Haplótipos , Japão , Mitocôndrias/genética , Filogenia , Filogeografia
8.
PLoS One ; 15(12): e0244750, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33382800

RESUMO

Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.


Assuntos
Quirópteros/genética , Citocromos b/genética , DNA Mitocondrial/genética , Variação Genética , Animais , Argentina , Filogenia
9.
PLoS One ; 15(12): e0243927, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33320915

RESUMO

Phylogenetic analyses can provide a wealth of information about the past demography of a population and the level of genetic diversity within and between species. By using special computer programs developed in recent years, large amounts of data have been produced in the molecular genetics area. To analyze these data, powerful new methods based on large computations have been applied in various software packages and programs. But these programs have their own specific input and output formats, and users need to create different input formats for almost every program. R is an open source software environment, and it supports open contribution and modification to its libraries. Furthermore, it is also possible to perform several analyses using a single input file format. In this article, by using the multiple sequences FASTA format file (.fas extension) we demonstrate and share a workflow of how to extract haplotypes and perform phylogenetic analyses and visualizations in R. As an example dataset, we used 120 Bombus terrestris dalmatinus mitochondrial cytochrome b gene (cyt b) sequences (373 bp) collected from eight different beehives in Antalya. This article presents a short guide on how to perform phylogenetic analyses using R and RStudio.


Assuntos
Citocromos b/genética , DNA Mitocondrial/genética , Filogenia , Software , Animais , Biologia Computacional , Citocromos b/classificação , DNA Mitocondrial/classificação , Haplótipos/genética , Humanos , Alinhamento de Sequência/métodos , Análise de Sequência de DNA/métodos , Fluxo de Trabalho
10.
PLoS One ; 15(9): e0237590, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32925949

RESUMO

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation.


Assuntos
Animais Selvagens , Carne/provisão & distribução , Zoonoses/etiologia , Animais , Animais Selvagens/genética , Búfalos/genética , Comércio , Citocromos b/genética , Ecossistema , Equidae/genética , Girafas/genética , Humanos , Parques Recreativos , Tanzânia/epidemiologia
11.
PLoS Negl Trop Dis ; 14(8): e0008380, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32797078

RESUMO

In French Guiana, five species are associated with Cutaneous Leishmaniasis (CL). Though infections with Leishmania guyanensis, L. (V.) braziliensis and L. (L.) amazonensis have been extensively described, there are few available clinical and genetic data on L. (V.) lainsoni and L. (V.) naiffi. We determined the clinical and epidemiological features of all cases of CL due to L. (V.) naiffi and L. (V.) lainsoni diagnosed in French Guiana between 2003 and 2019. Phylogenetic analysis was performed by sequencing a portion of HSP70 and cyt b genes. Five cases of L. naiffi and 25 cases of L. lainsoni were reported. Patients infected by L. (V.) lainsoni were usually infected on gold camps, mostly along the Maroni river (60%), while L. naiffi was observed in French patients infected on the coast (100%). A high number of pediatric cases (n = 5; 20%) was observed for L. (V.) lainsoni. A mild clinical course was observed for all cases of L. (V.) naiffi. HSP70 and cyt b partial nucleotide sequence analysis revealed different geographical clusters within L. (V.) naiffi and L. (V.) lainsoni but no association were found between phylogenetic and clinical features. Our data suggest distinct socio-epidemiological features for these two Leishmania species. Patients seem to get infected with L. (V.) naiffi during leisure activities in anthropized coastal areas, while L. (V.) lainsoni shares common features with L. (V.) guyanensis and braziliensis and seems to be acquired during professional activities in primary forest regions. Phylogenetic analysis has provided information on the intraspecific genetic variability of L. (V.) naiffi and L. (V.) lainsoni and how these genotypes are distributed at the geographic level.


Assuntos
Leishmania/classificação , Leishmaniose Cutânea/tratamento farmacológico , Leishmaniose Cutânea/epidemiologia , Adolescente , Adulto , Criança , Pré-Escolar , Citocromos b/genética , Feminino , Guiana Francesa/epidemiologia , Proteínas de Choque Térmico HSP70/genética , Humanos , Lactente , Leishmania/genética , Leishmania/patogenicidade , Leishmaniose Cutânea/patologia , Atividades de Lazer , Masculino , Pessoa de Meia-Idade , Mineração , Doenças Negligenciadas , Filogenia , Estudos Retrospectivos , Análise de Sequência de DNA
12.
Sci Data ; 7(1): 268, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792559

RESUMO

Genetic data are a crucial and exponentially growing resource across all biological sciences, yet curated databases are scarce. The widespread occurrence of sequence and (meta)data errors in public repositories calls for comprehensive improvements of curation protocols leading to robust research and downstream analyses. We collated and curated all available GenBank cytochrome-b sequences for amphibians, a benchmark marker in this globally declining vertebrate clade. The Amphibia's Curated Database of Cytochrome-b (ACDC) consists of 36,514 sequences representing 2,309 species from 398 genera (median = 2 with 50% interquartile ranges of 1-7 species/genus). We updated the taxonomic identity of >4,800 sequences (ca. 13%) and found 2,359 (6%) conflicting sequences with 84% of the errors originating from taxonomic misidentifications. The database (accessible at https://doi.org/10.6084/m9.figshare.9944759 ) also includes an R script to replicate our study for other loci and taxonomic groups. We provide recommendations to improve genetic-data quality in public repositories and flag species for which there is a need for taxonomic refinement in the face of increased rate of amphibian extinctions in the Anthropocene.


Assuntos
Anfíbios/genética , Citocromos b/genética , Bases de Dados de Ácidos Nucleicos , Anfíbios/classificação , Animais
13.
PLoS Negl Trop Dis ; 14(7): e0008385, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32614914

RESUMO

Anopheles sundaicus s.l. is an important malaria vector primarily found in coastal landscapes of western and central Indonesia. The species complex has a wide geographical distribution in South and Southeast Asia and exhibits ecological and behavioural variability over its range. Studies on understanding the distribution of different members in the complex and their bionomics related to malaria transmission might be important guiding more effective vector intervention strategies. Female An. sundaicus s.l. were collected from seven provinces, 12 locations in Indonesia representing Sumatra: North Sumatra, Bangka-Belitung, South Lampung, and Bengkulu; in Java: West Java; and the Lesser Sunda Islands: West Nusa Tenggara and East Nusa Tenggara provinces. Sequencing of ribosomal DNA ITS2 gene fragments and two mitochondrial DNA gene markers, COI and cytb, enabled molecular identification of morphologically indistinguishable members of the complex. Findings allowed inference on the distribution of the An. sundaicus s.l. present in Indonesia and further illustrate the phylogenetic relationships of An. epiroticus within the complex. A total of 370 An. sundaicus s.l specimens were analysed for the ITS2 fragment. The ITS2 sequence alignment revealed two consistent species-specific point mutations, a T>C transition at base 479 and a G>T transversion at base 538 that differentiated five haplotypes: TG, CG, TT, CT, and TY. The TG haplotype matched published An. epiroticus-indicative sequences from Thailand, Vietnam and peninsular Malaysia. The previously described insertion event (base 603) was observed in all identified specimens. Analysis of the COI and cytb genes revealed no consistent nucleotide variations that could definitively distinguish An. epiroticus from other members in the Sundaicus Complex. The findings indicate and support the existence of An. epiroticus in North Sumatra and Bangka-Belitung archipelago. Further studies are recommended to determine the full distributional extent of the Sundaicus complex in Indonesia and investigate the role of these species in malaria transmission.


Assuntos
Anopheles , Malária/transmissão , Mosquitos Vetores , Animais , Anopheles/genética , Citocromos b/genética , Demografia , Complexo IV da Cadeia de Transporte de Elétrons/genética , Feminino , Humanos , Indonésia , Filogenia
14.
Parasitol Res ; 119(9): 2975-2981, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32683557

RESUMO

Haemosporidia infections may cause major damage to avian populations and represent a concern for veterinarians working in zoological parks or wildlife rescue centres. Following the fatal infection of 9 Great grey owls (Strix nebulosa) at Mulhouse zoological park, between summer 2013 and 2015, a prospective epidemiological investigation was performed in captive strigiform birds in France in 2016. The purpose was to evaluate the prevalence of haemosporidian parasites in captive Strigiformes and to estimate the infection dynamics around the nesting period. Blood samples were taken from 122 strigiform birds representing 14 species from 15 French zoological parks. Parasites were detected by direct examination of blood smears and by PCR targeting the mitochondrial cytochrome b gene. Haemosporidian parasites were detected in 59 birds from 11 zoos. Three distinct Haemoproteus mitochondrial cytochrome b sequences (haplotypes A and C for H. syrnii and haplotype B for Haemoproteus sp.) as well as two species of Plasmodium were detected. The overall prevalence of Haemoproteus infection was 12.8%. The percentage of birds infected by Haemoproteus varied according to the period of sampling. Nesting season seemed to be at greater risk with an average prevalence of 53.9% compared with winter season with an average prevalence of 14.8%, related to the abundance of the vectors. The prevalence of Plasmodium infection in Strigiformes did not exceed 8% throughout the year. This study confirmed how significant Haemosporidia infection could be in Strigiformes from zoological parks in France. The nesting season was identified as a period of higher risk of infection and consequently the appropriate period to apply prophylactic measures.


Assuntos
Doenças das Aves/parasitologia , Haemosporida/isolamento & purificação , Infecções Protozoárias em Animais/parasitologia , Estrigiformes/parasitologia , Animais , Doenças das Aves/sangue , Doenças das Aves/epidemiologia , Citocromos b/genética , França/epidemiologia , Haemosporida/classificação , Haemosporida/genética , Haplótipos , Filogenia , Estudos Prospectivos , Infecções Protozoárias em Animais/sangue , Infecções Protozoárias em Animais/epidemiologia , Proteínas de Protozoários/genética
15.
Am J Trop Med Hyg ; 103(2): 752-755, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32524951

RESUMO

An 88-year-old man with mutilating mucosal leishmaniasis (ML) involving septal perforation, with granulomas in the pharynx and larynx, was treated with oral miltefosine, 50 mg three times/day for 28 days. Miltefosine, an antineoplastic agent, is considered an alternative option for the treatment of ML, showing efficacies of 75-92% in Bolivia, Brazil, and Argentina. The patient denied having previous cutaneous (CL) leishmaniasis, and no CL lesions were recognized by physical examination. Parasites obtained from mucosal lesions were identified by cytochrome b gene sequencing as Leishmania guyanensis. Clinical cure was observed 2 months posttreatment, and no evidence of reactivation was observed in the 3-year follow-up. Adverse effects such as nausea, loss of appetite, and epigastric pain were experienced during treatment with miltefosine. There is a need for improved access to miltefosine in leishmaniasis-endemic areas of Latin America and a greater awareness of ML and its treatment among physicians working in endemic countries.


Assuntos
Antiprotozoários/uso terapêutico , Leishmaniose Mucocutânea/tratamento farmacológico , Doenças Nasais/tratamento farmacológico , Doenças Faríngeas/tratamento farmacológico , Fosforilcolina/análogos & derivados , Idoso de 80 Anos ou mais , Citocromos b/genética , Disfonia/etiologia , Humanos , Leishmania guyanensis/genética , Leishmania guyanensis/isolamento & purificação , Masculino , Perfuração do Septo Nasal/etiologia , Doenças Nasais/complicações , Doenças Nasais/patologia , Doenças Faríngeas/complicações , Doenças Faríngeas/patologia , Fosforilcolina/uso terapêutico , Índice de Gravidade de Doença
16.
PLoS One ; 15(6): e0234377, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32542044

RESUMO

In many aquatic species, alteration of habitats and human-induced barriers shape the population's genetic structure in rivers with longitudinal connectivity. The golden mahseer, Tor putitora (GM) is an endangered and sensitive cyprinid species. It is considered an indicator of a healthy freshwater ecosystem and is found in cold-water habitats. Therefore, it is crucial to understand how longitudinal connectivity and anthropogenic factors affect the diversity and population genetic structure of GM. The population genetic structure, gene flow and demography of the GM in four Himalayan rivers were investigated by mitochondrial cytochrome b gene (cyt b) as well as microsatellite genotyping. The results showed overall high mtDNA diversity (hd: 0.795) couple with low nucleotide diversity (π: 0.0012) in all GM populations. We also found significant levels of observed heterozygosity (ranging from 0.618 to 0.676), with three genetic clusters. The mtDNA and microsatellite analysis suggested that there are close genetic relationships between the Bhagirathi and Ganga populations; whereas, significant level of genetic differentiation was observed with that of Alaknanda and Yamuna populations. Haplotype distribution, unimodal distribution graph and results of the neutrality test indicated a sign of recent population growth in the GM population. Analysis of molecular variance (AMOVA) and spatial molecular variance (SAMOVA) revealed existence of genetic structures in GM populations. In addition, spatial genetic analysis detected a significant correlation between the pairwise genetic and geographical distances for the entire study area (Mantel test, rM = 0.126; P = 0.010). Considering the significant level of heterozygosity, high rate of unidirectional migration and the intra-population structuring in Alaknanda and Yamuna, it is crucial to propose an effective conservation plan for the GM populations. In general, dams obstruct continuous water flow and create isolated microhabitats. Therefore, we recommend the establishment of microscale protected areas near GM breeding sites and construction of fish pass to maintain the genetic connectivity of fish species that enhance viable populations.


Assuntos
Cyprinidae/genética , Distribuição Animal , Migração Animal , Animais , Conservação dos Recursos Naturais , Cyprinidae/classificação , Citocromos b/genética , DNA Mitocondrial/genética , Ecossistema , Espécies em Perigo de Extinção , Proteínas de Peixes/genética , Fluxo Gênico , Genes Mitocondriais , Variação Genética , Genética Populacional , Haplótipos , Heterozigoto , Índia , Repetições de Microssatélites , Filogeografia , Polimorfismo Genético , Rios
17.
Mol Phylogenet Evol ; 150: 106887, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32534184

RESUMO

The recently described genus Paragalago is a complex of several nocturnal and morphologically cryptic species distributed in the forests of eastern Africa. Species diversity within this genus has been mainly described using species-specific differences in their loud calls. However, molecular data are still lacking for this group and species boundaries remain unclear. In this study, we explore species diversity within the zanzibaricus-complex using a combination of mitochondrial and nuclear data and comparing multiple species delimitation methods. Our results consistently support the existence of three independent lineages, P. cocos, P. zanzibaricus, and P. granti, confirming previous hypotheses based on vocal data. We conclude that these three lineages represent valid cryptic species and we hypothesize that speciation within this complex was characterized by cycles of forest expansion and contraction in the Plio-Pleistocene.


Assuntos
Galagidae/classificação , Animais , Teorema de Bayes , Citocromos b/genética , Florestas , Galagidae/anatomia & histologia , Galagidae/genética , Mitocôndrias/genética , Filogenia , Especificidade da Espécie
18.
PLoS One ; 15(5): e0233333, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32437372

RESUMO

Goats were initially managed in the Near East approximately 10,000 years ago and spread across Eurasia as economically productive and environmentally resilient herd animals. While the geographic origins of domesticated goats (Capra hircus) in the Near East have been long-established in the zooarchaeological record and, more recently, further revealed in ancient genomes, the precise pathways by which goats spread across Asia during the early Bronze Age (ca. 3000 to 2500 cal BC) and later remain unclear. We analyzed sequences of hypervariable region 1 and cytochrome b gene in the mitochondrial genome (mtDNA) of goats from archaeological sites along two proposed transmission pathways as well as geographically intermediary sites. Unexpectedly high genetic diversity was present in the Inner Asian Mountain Corridor (IAMC), indicated by mtDNA haplotypes representing common A lineages and rarer C and D lineages. High mtDNA diversity was also present in central Kazakhstan, while only mtDNA haplotypes of lineage A were observed from sites in the Northern Eurasian Steppe (NES). These findings suggest that herding communities living in montane ecosystems were drawing from genetically diverse goat populations, likely sourced from communities in the Iranian Plateau, that were sustained by repeated interaction and exchange. Notably, the mitochondrial genetic diversity associated with goats of the IAMC also extended into the semi-arid region of central Kazakhstan, while NES communities had goats reflecting an isolated founder population, possibly sourced via eastern Europe or the Caucasus region.


Assuntos
Animais Domésticos/genética , DNA Mitocondrial/genética , Domesticação , Cabras/genética , Agricultura/história , Animais , Animais Selvagens/genética , Ásia , Citocromos b/genética , Ecossistema , Variação Genética , Genética Populacional/história , Haplótipos , História Antiga , Oriente Médio , Filogenia , Filogeografia
19.
Gene ; 751: 144762, 2020 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-32407767

RESUMO

We delineated the pattern of synonymous codon usage bias (CUB) and its determinants in mitochondrial CYB gene of respiratory chain across different amphibian groups namely orders anura, urodela and gymnophiona. We observed that CUB was low in CYB gene of amphibia. The gymnophionans had comparatively high bias followed by urodeles and anurans. The codons namely TCA, CCA, CAA, CGA, TGA, AAA and ACA were over-represented in all three orders. The codons such as GCC and TCC were over-represented in anura whereas in urodela, the over-represented codons were TTA, CTA, ATA, GTA, GAA, GGA and GCA. In gymnophiona, GCC, TTA, CTA, ATA, GTA, GAA and GGA codons were over-represented. The regression analysis between effective number of codons (ENC) and nucleobase at the 3rd position revealed that nucleobase A and C influenced CUB positively in order anura, while in urodela and gymnophiona, nucleobase A and T influenced the CUB positively. Mutation pressure and natural selection mutually illustrate the CUB of CYB gene (complex III gene) of amphibia as elucidated by correlation analysis between 3rd nucleotide in a codon and overall nucleotide content of the gene. However, neutrality plot showed that natural selection was the dominant evolutionary factor of CUB.


Assuntos
Anfíbios/genética , Uso do Códon , Citocromos b/genética , Animais , Anuros/genética , Composição de Bases , DNA Mitocondrial/química , Genes Mitocondriais , Nucleotídeos/análise , Seleção Genética , Urodelos/genética
20.
PLoS One ; 15(4): e0231621, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32298359

RESUMO

Of the sub-species of Holarctic wolf, the Woolly wolf (Canis lupus chanco) is uniquely adapted to atmospheric hypoxia and widely distributed across the Himalaya, Qinghai Tibetan Plateau (QTP) and Mongolia. Taxonomic ambiguity still exists for this sub-species because of complex evolutionary history anduse of limited wild samples across its range in Himalaya. We document for the first time population genetic structure and taxonomic affinity of the wolves across western and eastern Himalayan regions from samples collected from the wild (n = 19) using mitochondrial control region (225bp). We found two haplotypes in our data, one widely distributed in the Himalaya that was shared with QTP and the other confined to Himachal Pradesh and Uttarakhand in the western Himalaya, India. After combining our data withpublished sequences (n = 83), we observed 15 haplotypes. Some of these were shared among different locations from India to QTP and a few were private to geographic locations. A phylogenetic tree indicated that Woolly wolves from India, Nepal, QTP and Mongolia are basal to other wolves with shallow divergence (K2P; 0.000-0.044) and high bootstrap values. Demographic analyses based on mismatch distribution and Bayesian skyline plots (BSP) suggested a stable population over a long time (~million years) with signs of recent declines. Regional dominance of private haplotypes across its distribution range may indicate allopatric divergence. This may be due to differences in habitat characteristics, availability of different wild prey species and differential deglaciation within the range of the Woolly wolf during historic time. Presence of basal and shallow divergence within-clade along with unique ecological requirements and adaptation to hypoxia, the Woolly wolf of Himalaya, QTP, and Mongolian regions may be considered as a distinct an Evolutionary Significant Unit (ESU). Identifying management units (MUs) is needed within its distribution range using harmonized multiple genetic data for effective conservation planning.


Assuntos
Filogenia , Lobos/genética , Animais , Ásia , Teorema de Bayes , Citocromos b/genética , DNA Mitocondrial/genética , Ecossistema , Genética Populacional , Haplótipos , Lobos/classificação
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