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1.
Med Sci (Paris) ; 36(10): 945-948, 2020 Oct.
Artigo em Francês | MEDLINE | ID: mdl-33026341

RESUMO

More than 10 million enslaved Africans were transported to the Americas between 1500 and 1900. Recent genetic studies investigate regional African ancestry components in present-day Africa-Americans, and allow comparison with the extensive records documenting these deportations. The genetic evidence generally agrees with the historical records but brings additional insights in this dark episode of human history.


Assuntos
Afro-Americanos/genética , Pessoas Escravizadas , Escravização/história , Genética Populacional , África , Oceano Atlântico , Comércio/história , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Pessoas Escravizadas/história , Fluxo Gênico/fisiologia , Variação Genética , História do Século XVI , História do Século XVII , História do Século XVIII , História do Século XIX , Humanos , Padrões de Herança/genética , Estados Unidos
2.
PLoS One ; 15(9): e0238306, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32911497

RESUMO

Abra de Zamora is an important biodiversity hotspot in southern Ecuador. Between 1938 and 2010, eleven species of frogs were described from here: Lynchius flavomaculatus, Gastrotheca psychrophila, Pristimantis balionotus, P. colodactylus, P. cryptomelas, P. percultus, P. versicolor, P. vidua, Telmatobius cirrhacelis, P. andinognomus, and Atelopus podocarpus. Unfortunately, many of these species were not re-encountered after their original description, and for the majority DNA samples were not available, making their phylogenetic position unknown. In this study, we assess the current state of the amphibians from Abra de Zamora, by: i. redescribing the species which were first reported from the area, by contributing genetic delimitation (for L. flavomaculatus, P. balionotus, P. colodactylus, P. percultus, and P. vidua), release call (L. flavomaculatus) and advertisement call descriptions (for P. balionotus, P. vidua and P. versicolor); ii. presenting an updated amphibian species list of Abra de Zamora, with the description of two additional Pristimantis species; iii. updating the distribution of these species, including data collected in similar montane habitats from surrounding areas; and iv. amending recommendations regarding their conservation status.


Assuntos
Distribuição Animal , Anuros/anatomia & histologia , Anuros/classificação , Biodiversidade , DNA Mitocondrial/genética , Ecossistema , Filogenia , Animais , Anuros/genética , DNA Mitocondrial/análise , Equador , Feminino , Masculino
3.
PLoS One ; 15(6): e0234745, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32544213

RESUMO

PCR inhibitors are a formidable problem to the study of aged, degraded, and/or low copy number DNA. As a result, there is a need to find alternate methods that ameliorate the efficacy of PCR. In this study, we attempted to use genetic methods to identify the species of salmonid (Oncorhynchus spp.) remains recovered from archaeological sites along the Feather River located in northern California, United States. In the process of doing so, we compared the efficacy of a PCR enhancer cocktail called "PEC-P" and a reagent rich PCR recipe called "rescue PCR" over standard PCR. Across all treatments (full concentration and 1:10 dilute eluates subjected to standard PCR, PEC-P, and rescue PCR) species identification was possible for 74 of 93 archaeological fish specimens (79.6%). Overall, six of the 93 samples (6.5%) consistently yielded species identification across all treatments. The species of ten specimens (10.8%) were uniquely identified from amplicons produced with either PEC-P or rescue PCR or both. Notably, the species of seven samples (7.5%) were uniquely identified with standard PCR over the alternative treatments. Considering both full concentration and 1:10 dilute eluates (N = 186), standard PCR performed as well as PEC-P (p = 0.1451) and rescue (p = 0.6753). Yet, considering results from full concentration eluates alone (N = 93), PEC-P (60.2%) outperformed both standard PCR (44.1%; p = 0.0277) and rescue PCR (40.9%; p = 0.0046). Stochasticity observed in our study cautions us against choosing a "best" performing method of those explored here and suggests their respective potentials to improve success may be sample dependent. When working with samples compromised by PCR inhibitors, it is useful to have alternative methodologies for subduing the problem. Both PEC-P and rescue PCR represent useful alternative methods for the study of aged, degraded, and/or low copy number DNA samples compromised by PCR inhibitors.


Assuntos
DNA/análise , Oncorhynchus/genética , Reação em Cadeia da Polimerase/métodos , Animais , Arqueologia , Osso e Ossos/metabolismo , DNA/metabolismo , DNA Mitocondrial/análise , DNA Mitocondrial/metabolismo , Fatores de Tempo
4.
Sci Rep ; 10(1): 8108, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32415152

RESUMO

Phylogeographic studies can resolve relationships between genetic population structure of organisms and geographical distributions. Raccoons have become feral in Japan, and in Hokkaido island, they have been rapidly increasing in number and spreading since the 1970s. We analyzed mitochondrial (mtDNA) and microsatellite DNA to understand the current phylogenetic distribution and invasive founder events. Overall, Hokkaido raccoons maintained high genetic diversity (i.e., the level of heterozygosity was comparable to the original habitat, North America). Based on mtDNA distribution and microsatellite diversity, Hokkaido raccoons were divided into six management units. However, mtDNA haplotype distributions and genetic structures based on microsatellites did not always correspond to each other (e.g., two geographically and genetically separated populations showed similar mtDNA distributions). In addition, a high degree of genetic admixture was observed in every unit, and the degree of genetic differentiation was low even between regions separated by long distances. Compared with other countries in Europe where genetic distribution of introduced raccoons is more clearly structured, the current results represent a unique and complex phenomenon of pet escape/abandonment in Hokkaido: i.e., genetically related colonies were introduced into multiple regions as founder events, resulting in the current state in which raccoons are not clearly genetically differentiated even 40 years after introduction.


Assuntos
DNA Mitocondrial/análise , Ecossistema , Genética Populacional , Espécies Introduzidas/estatística & dados numéricos , Repetições de Microssatélites , Guaxinins/crescimento & desenvolvimento , Guaxinins/genética , Estações do Ano , Animais , Feminino , Japão , Masculino , Filogenia
5.
Ann Endocrinol (Paris) ; 81(2-3): 68-77, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32409007

RESUMO

OBJECTIVE: While the most frequent mutation responsible for mitochondrial diabetes is the point mutation m.3243 A>G of mitochondrial DNA (mtDNA), few data are available about the role of rare mtDNA mutations in the pathophysiology of diabetes. The main objective of our study was to describe the phenotypic characteristics of patients suffering from diabetes linked to rare mtDNA mutations. RESEARCH DESIGN AND METHODS: We performed a post-hoc analysis of a prospective multicenter cohort of 743 patients with mitochondrial disorder (previously published by the French Network of Mitochondrial Diseases), associated to a literature review of the PubMed database from 1992 to May 2016. We extracted all reported patients with diabetes and identified rare mtDNA mutations and described their clinical and metabolic phenotypes. RESULTS: The 50 identified patients (10 from the princeps study; 40 from the review of the literature) showed a heterogeneous metabolic phenotype in terms of age, symptoms prior to diagnosis, treatments, and associated clinical and biological signs. However, neurological symptoms were more frequent in case of rare mtDNA mutations compared to the classical m.3243 A>G mutation (P=0.024). In contrast, deafness (65% vs. 95%, P=3.7E-5), macular pattern dystrophy (20% vs. 86%, P=1.6E-10) and nephropathy (8% vs. 28%, P=0.018) were significantly less frequent than in case of the classical m.3243 A>G mutation. CONCLUSION: Although no specific metabolic phenotype could be identified suggesting or eliminating implication of rare mtDNA mutations in diabetes, clinical phenotypes featured more frequent neurological signs.


Assuntos
DNA Mitocondrial/genética , Diabetes Mellitus/genética , Doenças Mitocondriais/genética , Mutação , Adolescente , Adulto , Idoso , Criança , Pré-Escolar , Estudos de Coortes , Análise Mutacional de DNA , DNA Mitocondrial/análise , Surdez/epidemiologia , Surdez/genética , Diabetes Mellitus/epidemiologia , Diabetes Mellitus/etiologia , Diabetes Mellitus Tipo 2/epidemiologia , Diabetes Mellitus Tipo 2/genética , Feminino , França/epidemiologia , Frequência do Gene , Estudos de Associação Genética , Humanos , Lactente , Recém-Nascido , Síndrome MERRF/epidemiologia , Síndrome MERRF/genética , Masculino , Pessoa de Meia-Idade , Doenças Mitocondriais/complicações , Doenças Mitocondriais/epidemiologia , Fenótipo , Estudos Prospectivos
6.
Am J Pathol ; 190(7): 1565-1579, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32304697

RESUMO

Mitochondria regulate ATP production, metabolism, and cell death. Alterations in mitochondrial DNA (mtDNA) sequence and copy number are implicated in aging and organ dysfunction in diverse inherited and sporadic diseases. Because most measurements of mtDNA use homogenates of complex tissues, little is known about cell-type-specific mtDNA copy number heterogeneity in normal physiology, aging, and disease. Thus, the precise cell types whose loss of mitochondrial activity and altered mtDNA copy number that result in organ dysfunction in aging and disease have often not been clarified. Here, an in situ hybridization approach to generate a single-cell-resolution atlas of mtDNA content in mammalian tissues was validated. In hierarchically organized self-renewing tissues, higher levels of mtDNA were observed in stem/proliferative compartments compared with differentiated compartments. Striking zonal patterns of mtDNA levels in the liver reflected the known oxygen tension gradient. In the kidney, proximal and distal tubules had markedly higher mtDNA levels compared with cells within glomeruli and collecting duct epithelial cells. In mice, decreased mtDNA levels were visualized in renal tubules as a function of aging, which was prevented by calorie restriction. This study provides a novel approach for quantifying species- and cell-type-specific mtDNA copy number and dynamics in any normal or diseased tissue that can be used for monitoring the effects of interventions in animal and human studies.


Assuntos
Proliferação de Células , DNA Mitocondrial/análise , Células-Tronco , Envelhecimento/fisiologia , Animais , Atlas como Assunto , Variações do Número de Cópias de DNA , Feminino , Humanos , Hibridização In Situ/métodos , Masculino , Camundongos , Camundongos Endogâmicos C57BL
7.
Lett Appl Microbiol ; 71(2): 171-178, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32270506

RESUMO

The filamentous fungus Neurospora crassa is a popular model organism used in a wide range of biochemical and genetic studies and vastly used in mitochondrial research. Despite the relevance of mitochondria in N. crassa biology, no method for quantification of mitochondrial DNA (mtDNA) is currently available. Quantitative real-time PCR (qPCR) is a powerful tool, with a wide range of applications, and has been used for the quantification of nucleic acids in humans and a few other species. Here we present a new qPCR assay for relative quantification of N. crassa mtDNA. Three sets of qPCR primers targeting different regions of the mitochondrial genome were tested for mtDNA quantification. The qPCR was successfully validated in N. crassa strains from different geographical locations, representing the vast genetic diversity of this species, and knockout mutant strains. Moreover the assay proved to be efficient in templates with varied amounts of mitochondria, obtained through different DNA extraction methods. The qPCR performed well in all tested samples revealing a higher amount of mtDNA than nuclear DNA in all cases. This technique will facilitate the characterization of mtDNA of N. crassa in future studies and can be used as a tool to validate methods of mitochondria isolation. SIGNIFICANCE AND IMPACT OF THE STUDY: The standardization of quantitative real-time PCR (qPCR) techniques is essential to enable and facilitate future comparisons. Neurospora crassa is a model organism with a lot of potential in different fields of study. Here we use N. crassa to develop and establish an assay to quantify mitochondrial DNA using qPCR. We tested strains with different geographical background and our data demonstrated the usefulness of this assay to quantify mitochondrial DNA in N. crassa. This technique can be useful in a wide variety of applications and in different types of studies.


Assuntos
DNA Fúngico/análise , DNA Mitocondrial/análise , Neurospora crassa/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , Primers do DNA/genética , DNA Fúngico/genética , DNA Mitocondrial/genética , Humanos , Mitocôndrias/genética
8.
PLoS One ; 15(3): e0230496, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32187203

RESUMO

Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigations and environmental surveys, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and describe procedures to perform DNA extraction and analysis from a variety of archeological samples within 4 hours. The process is carried out on 50 mg samples that are identified at the species level using custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated the potential of this approach in museums lacking facilities for DNA studies by analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3 deposits), and also performed experiments during an excavation campaign at the Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples only yielded DNA for the extinct steppe bison (Bison priscus), whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta crocuta spelaea) DNA together, for some of them, with DNA for the European bison sister species/subspecies (Bison schoetensacki/Bb1-X), thus highlighting the cave hyena diet. Roc-en-Pail Bovinae bone and tooth samples also contained DNA for the Bison schoetensacki/Bb1-X clade, and Cervidae bone samples only yielded reindeer (Rangifer tarandus) DNA. Subsequent DNA sequencing analyses confirmed that correct species identification had been achieved using our TaqMan assays, hence validating these assays for future studies. We conclude that our approach enables the rapid genetic characterization of tens of millennia-old archeological samples and is expected to be useful for the on-site screening of museums and freshly excavated samples for DNA content. Because our mobile laboratory is made up of commercially available instruments, this approach is easily accessible to other investigators.


Assuntos
DNA Antigo/análise , Análise de Sequência de DNA/métodos , Animais , Arqueologia , Bison , DNA Mitocondrial/análise , Fósseis , Reação em Cadeia da Polimerase em Tempo Real
9.
BMC Evol Biol ; 20(1): 36, 2020 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-32171237

RESUMO

BACKGROUND: The family Aegisthidae is known as typical component of deep-sea hyperbenthic waters that gradually colonized other marine environments. The phylogenetic relationships within this family have been examined here including hyperbenthic, planktonic, benthic forms and two associated Aegisthidae species. RESULTS: Ninety four specimens belong to 14 genera were studied using 18S and 28S rRNA and COI mtDNA. Bayesian analysis supports the monophyly of 10 genera whereas Andromastax, Jamstecia, Nudivorax and Aegisthus revealed to be paraphyletic. The first offshoot of the phylogenetic tree is a clade consists of the undescribed genus Aegisthidae gen.1 sister to the two monophyletic genera Cerviniella and Hase, whereas the other Cerviniinae members (represented by Cervinia and Expansicervinia) assemble a monophylum, sister to the hyperbenthic and planktonic aegisthid genera, resulting in the paraphyly of the subfamily Cerviniinae. Hence, we defined the new subfamily Cerviniellinae subfam. nov. encompassing the three benthic genera Cerviniella, Hase and Eucanuella. The subfamily Cerviniinae has been re-defined to include Cervinia, Expansicervinia and Paracerviniella. Members of the subfamily Pontostratiotinae were clustered into two clades, one consists of the genus Stratiopontotes sister to an undescribed genus + Cerviniopsis and Siphonis. The second contains Pontostratiotes sister to the members of the planktonic subfamily Aegisthinae, resulting in the paraphyly of the Pontostratiotinae. Therefore, the Pontostratiotinae has been re-defined to include only members of the genus Pontostratiotes; whereas the subfamily Cerviniopseinae has been re-erected and re-defined containing Stratiopontotes, Cerviniopsis, Siphonis, Aegisthidae gen. 2, Herdmaniopsis, Hemicervinia and Tonpostratiotes. Within this subfamily, the associated Siphonis clusters as sister to the Cerviniopsis represents an example of convergent evolution in which the possession of a stylet-like mandible and an oral cone reminiscent of the Siphonostomatoida. The planktonic Aegisthus, Andromastax, Jamstecia, Nudivorax and Scabrantenna confirm the monophylom Aegisthinae, sister to the Pontostratiotinae. CONCLUSIONS: Our DNA based phylogeny reveals the deep-sea origin of Aegisthidae by placing benthic Aegisthidae gen.1 and Cerviniellinae subfam. nov. as the most basal lineages. Secondary adaptations to hyperbenthic and planktonic realms, as well as associated lifestyle were discovered here by the derived positions of Pontostratiotinae, Aegisthinae and Siphonis respectively.


Assuntos
Aclimatação/fisiologia , Copépodes/anatomia & histologia , Copépodes/classificação , Ecossistema , Água do Mar , Animais , Copépodes/genética , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Ecótipo , Filogenia , Filogeografia , RNA Ribossômico 28S/análise , RNA Ribossômico 28S/genética , Análise de Sequência de DNA
10.
PLoS One ; 15(3): e0229119, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32130230

RESUMO

The cephalochordates amphioxus or lancelets are benthic marine animals representing the earliest divergent evolutionary lineage within chordates. Although amphioxus are present in most of the world's tropical and temperate oceans, only about thirty different species grouped into three different genera, Branchiostoma, Epigonichthys and Asymmetron have been described. In the genus Asymmetron, only two species have been characterized, although for one of them, A. lucayanum, several cryptic lineages exist. In this work we have sequenced and analyzed the mitogenome of an A. lucayanum population previously described in the Red Sea. The phylogenetic study using this complete mitogenome as well as the analysis of COI gene sequences of several individuals of this Red Sea population show that the Red Sea population is a new cryptic species. We propose to call this new species Asymmetron rubrum.


Assuntos
Cefalocordados/classificação , Filogenia , Animais , Evolução Biológica , Cefalocordados/genética , Cefalocordados/crescimento & desenvolvimento , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Especiação Genética , Genoma Mitocondrial , Larva , Especificidade da Espécie
11.
Nat Commun ; 11(1): 671, 2020 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-32015346

RESUMO

Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.


Assuntos
Canidae/classificação , Canidae/genética , Genômica , Filogenia , Migração Animal , Animais , Ásia Sudeste , Austrália , DNA Mitocondrial/análise , Cães/classificação , Cães/genética , Variação Genética , Genética Populacional , Genoma Mitocondrial , Nova Guiné , Polimorfismo de Nucleotídeo Único , Fatores de Troca de Nucleotídeo Guanina Rho/genética , Lobos/classificação , Lobos/genética
12.
BMC Evol Biol ; 20(1): 22, 2020 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-32024460

RESUMO

BACKGROUND: Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, particularly those addressing the relationships among the major chiton lineages. RESULTS: Here, we present a mitogenomic phylogeny of chitons based on 13 newly sequenced mitochondrial genomes along with eight available ones and RNAseq-derived mitochondrial sequences from four additional species. Reconstructed phylogenies largely agreed with the latest advances in chiton systematics and integrative taxonomy but we identified some conflicts that call for taxonomic revisions. Despite an overall conserved gene order in chiton mitogenomes, we described three new rearrangements that might have taxonomic utility and reconstructed the most likely scenario of gene order change in this group. Our phylogeny was time-calibrated using various fossils and relaxed molecular clocks, and the robustness of these analyses was assessed with several sensitivity analyses. The inferred ages largely agreed with previous molecular clock estimates and the fossil record, but we also noted that the ambiguities inherent to the chiton fossil record might confound molecular clock analyses. CONCLUSIONS: In light of the reconstructed time-calibrated framework, we discuss the evolution of key morphological features and call for a continued effort towards clarifying the phylogeny and evolution of chitons.


Assuntos
Genoma Mitocondrial , Poliplacóforos/classificação , Poliplacóforos/genética , Animais , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Evolução Molecular , Fósseis , Ordem dos Genes , Genoma Mitocondrial/genética , Moluscos/classificação , Moluscos/genética , Filogenia , Análise de Sequência de DNA/métodos
13.
Chem Commun (Camb) ; 56(12): 1859-1862, 2020 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-31950954

RESUMO

We present the design and synthesis of water-soluble quinoline-indole-based derivatives (IM-1, IM-2, and IM-3) with three-photon absorption activity. IM-3 can specifically target DNA and RNA accompanied by an obvious three-photon fluorescence enhancement in the second near-infrared window (1000-1700 nm). The in vitro experiments demonstrate that IM-3 can simultaneously stain mitochondria and the nucleolus both in living and fixed cells. The organelle-specific targeting behaviour is successfully visualized under stimulated emission depletion (STED) nanoscopy.


Assuntos
DNA Mitocondrial/análise , Corantes Fluorescentes/química , Indóis/química , Fótons , Quinolinas/química , RNA Neoplásico/análise , Nucléolo Celular/química , Células Hep G2 , Humanos , Estrutura Molecular , Imagem Óptica , Solubilidade , Água/química
14.
Gene ; 731: 144362, 2020 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-31935512

RESUMO

Acrididae family is characterized by diverse phylogenetic uncertainties, with different paraphyletic subfamilies. This study characterized the mitogenome of the grasshopper Rhammatocerus brasiliensis and determined its phylogenetic position in the family Acrididae. Sequencing was performed on an Illumina platform. The Short Oligonucleotide Analysis Package (SOAP) was used for genome assembly and the MITOS Web Server for annotation. Phylogenetic analysis was performed using mtDNA nucleic acid and protein sequences of R. brasiliensis and more 63 species belonging to 12 subfamilies of Acrididae. Phylogenetic trees were reconstructed using Bayesian inference with a relaxed molecular clock to estimate the speciation divergence time between taxa. The mitochondrial genome of R. brasiliensis has 15,571 bp of length, is rich in AT (72%), and contains 37 genes, including 13 protein-encoding genes, 22 genes encoding transfer RNA and two genes encoding ribosomal RNA. In addition, we also have annotated intergenic spacers and gene overlaps. The phylogenetic trees based on nucleic acid and amino acid sequences showed similar topologies. Phylogenetic analysis revealed that R. brasiliensis is grouped as an early offset of the Acrididae family. Phylogenetic analyses also corroborated the presence of several paraphyletic subfamilies in the family Acrididae including Gomphocerinae. The positioning of R. brasiliensis in the mtDNA phylogenetic tree further supports paraphyly of this subfamily. Moreover, the basal position of R. brasiliensis suggests that Gomphocerinae probably originated in South America.


Assuntos
Genoma Mitocondrial/genética , Gafanhotos/classificação , Gafanhotos/genética , Animais , Teorema de Bayes , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Filogenia , Análise de Sequência de DNA
15.
Parasitol Int ; 75: 102052, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31927138

RESUMO

Honeybee acarapiosis and vorrosis were designated as Notifiable Infectious Diseases in the Act on Domestic Animal Infectious Diseases Control by the Minister of Agriculture, Forestry and Fisheries of Japan in 1997. However, the prevalences of A. woodi and V. destructor in Japan, especially in the Tohoku region, have not been sufficiently elucidated. This study was designed to clarify the prevalence of A. woodi and V. destructor mites in Apis cerana japonica and Apis mellifera in the Tohoku region and the characteristics of their mitochondrial cytochrome c oxidase I (COI) DNA. Acarapis woodi mites were detected from 13.5% of A. c. japonica and 0% of A. mellifera. Aomori prefecture, Japan is a new distribution locality for A. woodi. None of the honeybees examined showed infection by V. destructor mites. The COI sequences (1638 bp) of A. woodi were identical and phylogenetically closely related to those of A. woodi from Japan and the UK, suggesting that the mite would have been introduced into Japan with A. mellifera during the last 150 years and spread throughout the country.


Assuntos
Abelhas/parasitologia , Ácaros/fisiologia , Animais , Proteínas de Artrópodes/análise , DNA Mitocondrial/análise , Complexo IV da Cadeia de Transporte de Elétrons/análise , Japão , Varroidae/fisiologia
16.
Sci Rep ; 10(1): 192, 2020 01 13.
Artigo em Inglês | MEDLINE | ID: mdl-31932637

RESUMO

Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these 'living fossils' using new molecular data, including the possibility of 'cryptic' species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.


Assuntos
Linhagem da Célula , Evolução Molecular , Peixes/genética , Variação Genética , Genoma Mitocondrial , Mitocôndrias/genética , Animais , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Peixes/classificação , Indonésia , Especificidade da Espécie
17.
Methods Mol Biol ; 2119: 25-42, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31989512

RESUMO

The study of mitochondrial DNA (mtDNA) integrity and how replication, transcription, repair, and degradation maintain mitochondrial function has been hampered due to the inability to identify mtDNA structural forms. Here we describe the use of 2D intact mtDNA agarose gel electrophoresis, or 2D-IMAGE, to identify up to 25 major mtDNA topoisomers such as double-stranded circular mtDNA (including supercoiled molecules, nicked circles, and multiple catenated species) and various forms containing single-stranded DNA (ssDNA) structures. Using this modification of a classical 1D gel electrophoresis procedure, many of the identified mtDNA species have been associated with mitochondrial replication, damage, deletions, and possibly transcription. The increased resolution of 2D-IMAGE allows for the identification and monitoring of novel mtDNA intermediates to reveal alterations in genome replication, transcription, repair, or degradation associated with perturbations during mitochondrial stress.


Assuntos
Replicação do DNA , DNA Mitocondrial , Eletroforese em Gel Bidimensional , Mitocôndrias/metabolismo , Animais , DNA Mitocondrial/análise , DNA Mitocondrial/metabolismo , Eletroforese em Gel de Ágar , Humanos
18.
Anal Chim Acta ; 1099: 68-74, 2020 Feb 22.
Artigo em Inglês | MEDLINE | ID: mdl-31986279

RESUMO

This work details the usage of EFIRM® (Electric Field Induced Release and Measurement) for PCR-free rapid electrochemical detection of mitochondrial DNA. EFIRM® was able to perform highly sensitive detection of animal species for meat contamination testing without multistep sample lysis, DNA extraction, or PCR amplification steps, demonstrating the capability to detect the presence of foreign meat species that only constituted 0.1% of the total mass of a food sample (achieving sensitivity equivalent to that of PCR). The EFIRM® strategy utilizes surface immobilized nucleic acid probes that complement to mitochondrial sequence of Ovis Aries, Sus Scrofa, and Bos Taurus and are immobilized in a polypyrrole matrix on a 96-electrode array. Quantification was performed through amperometric measurement of oxidation-reduction reactions on a streptavidin-peroxidase enzyme chain that completes the nucleic acid complex. All electrochemical procedures were performed using a high-throughput potentiostat system that allows parallelized electrochemical measurement and interfacing to the 96-electrode array.


Assuntos
Técnicas Biossensoriais , DNA Mitocondrial/análise , Técnicas Eletroquímicas , Carne/análise , Técnicas Biossensoriais/instrumentação , Técnicas Eletroquímicas/instrumentação , Eletrodos , Campos Eletromagnéticos
19.
Am J Phys Anthropol ; 171(3): 496-508, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31930493

RESUMO

OBJECTIVES: The Sahel belt is occupied by populations who use two types of subsistence strategy, nomadic pastoralism and sedentary farming, and who belong to three linguistic families, Niger-Congo, Nilo-Saharan, and Afro-Asiatic. Little is known, however, about the origins of these two populations and their mutual genetic relationships. MATERIALS AND METHODS: We have built a large dataset of mitochondrial DNA sequences and Y chromosomal STR haplotypes of pastoralists and farmers belonging to all three linguistic phyla in the western, central, and eastern parts of the Sahel. We calculated pairwise genetic, geographic, and linguistic distances between populations and analyzed the effects of geography, language, and subsistence on population genetic structure. RESULTS: We found that subsistence mode significantly contributed to the generally low population structure in the Sahel and that language affiliation plays a more important role for pastoralists than for farmers. We also demonstrated that geographic isolation significantly influenced the population structure of sedentary farmers but not of nomadic pastoralists. Finally, we found haplotypes shared between the Fulani and Arabic-speaking Baggara, supporting the theory of Baggarization, which explains the recent adaptation of Arabic-speaking nomads in the Sahel region through contact with autochthonous sub-Saharan populations. CONCLUSIONS: Based on various genetic and archaeological evidence pertaining to the Sahel, we suggest that the idea of a bidirectional Sahelian corridor is valid, but that pastoralists made a more important contribution to its population structure. It is also possible that agropastoralists diverged into farmers and pastoralists in the early stages of formation of the Sahelian gene pool.


Assuntos
Cromossomos Humanos Y , DNA Mitocondrial/análise , Variação Genética , Estilo de Vida , Repetições de Microssatélites , África Central , África Oriental , África Ocidental , Agricultura/classificação , Evolução Cultural , Migração Humana , Humanos , Estilo de Vida/etnologia , Masculino
20.
Integr Zool ; 15(3): 187-201, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31631516

RESUMO

In this study, we present an assessment of the evolutionary history and phylogenetic relationships of Asian mountain voles of the subgenus Aschizomys, genus Alticola, based on extensive sampling and phylogenetic analyses of data from mitochondrial and nuclear markers. Two species of this subgenus are widespread in the mountain areas of north-eastern Asia. However, both their distribution and taxonomic borders remained questionable for more than 100 years. Our study showed discordance in the phylogenetic patterns between nuclear and mtDNA markers. We found that mtDNA in A. lemminus is paraphyletic relative to A. macrotis, but nuclear markers demonstrated reciprocal monophyly. According to species distribution modeling, ranges of A. macrotis and A. lemminus experienced a secondary contact during the Last Glacial Maximum (approximately 22 kyr BP), and thus a hybridization event seems plausible during that period. Species tree analyses recovered a sister group relationship between the two species of the Aschizomys subgenus, with an estimated divergence date of around 0.8 Ma. Our results provided good support for currently recognized subspecies within both A. macrotis and A. lemminus based on mitochondrial and nuclear datasets. A new, yet undescribed form, supposedly of a subspecific status within A. lemminus, was found in the Bureinskiy Range in the Khabarovsk area. This finding expands the current species distribution range further to the southeast.


Assuntos
Arvicolinae/genética , Evolução Biológica , DNA/análise , Animais , Núcleo Celular/genética , DNA Mitocondrial/análise , Marcadores Genéticos , Federação Russa
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