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  1 / 9243 MEDLINE  
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[PMID]:29179671
[Au] Autor:Hudaiberdiev S; Shmakov S; Wolf YI; Terns MP; Makarova KS; Koonin EV
[Ad] Endereço:National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
[Ti] Título:Phylogenomics of Cas4 family nucleases.
[So] Source:BMC Evol Biol;17(1):232, 2017 Nov 28.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci (solo-Cas4) and is also found in mobile genetic elements (MGE-Cas4). RESULTS: As part of our ongoing investigation of CRISPR-Cas evolution, we explored the phylogenomics of the Cas4 family. About 90% of the archaeal genomes encode Cas4 compared to only about 20% of the bacterial genomes. Many archaea encode both the CRISPR-associated form (CAS-Cas4) and solo-Cas4, whereas in bacteria, this combination is extremely rare. The solo-cas4 genes are over-represented in environmental bacteria and archaea with small genomes that typically lack CRISPR-Cas, suggesting that Cas4 could perform uncharacterized defense or repair functions in these microbes. Phylogenomic analysis indicates that both the CRISPR-associated cas4 genes are often transferred horizontally but almost exclusively, as part of the adaptation module. The evolutionary integrity of the adaptation module sharply contrasts the rampant shuffling of CRISPR-cas modules whereby a given variant of the adaptation module can combine with virtually any effector module. The solo-cas4 genes evolve primarily via vertical inheritance and are subject only to occasional horizontal transfer. The selection pressure on cas4 genes does not substantially differ between CAS-Cas4 and solo-cas4, and is close to the genomic median. Thus, cas4 genes, similarly to cas1 and cas2, evolve similarly to 'regular' microbial genes involved in various cellular functions, showing no evidence of direct involvement in virus-host arms races. A notable feature of the Cas4 family evolution is the frequent recruitment of cas4 genes by various mobile genetic elements (MGE), particularly, archaeal viruses. The functions of Cas4 in these elements are unknown and potentially might involve anti-defense roles. CONCLUSIONS: Unlike most of the other Cas proteins, Cas4 family members are as often encoded by stand-alone genes as they are incorporated in CRISPR-Cas systems. In addition, cas4 genes were repeatedly recruited by MGE, perhaps, for anti-defense functions. Experimental characterization of the solo and MGE-encoded Cas4 nucleases is expected to reveal currently uncharacterized defense and anti-defense systems and their interactions with CRISPR-Cas systems.
[Mh] Termos MeSH primário: Sistemas CRISPR-Cas/genética
Endonucleases/genética
Genômica
Família Multigênica
[Mh] Termos MeSH secundário: Archaea/enzimologia
Archaea/genética
Bactérias/enzimologia
Bactérias/genética
Sequência de Bases
Elementos de DNA Transponíveis/genética
Transferência Genética Horizontal/genética
Loci Gênicos
Genoma Arqueal
Genoma Bacteriano
Filogenia
Seleção Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Transposable Elements); EC 3.1.- (Endonucleases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1081-1


  2 / 9243 MEDLINE  
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[PMID]:28461121
[Au] Autor:Hall JPJ; Brockhurst MA; Dytham C; Harrison E
[Ad] Endereço:Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
[Ti] Título:The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories?
[So] Source:Plasmid;91:90-95, 2017 May.
[Is] ISSN:1095-9890
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Conjugative plasmids are widespread and play an important role in bacterial evolution by accelerating adaptation through horizontal gene transfer. However, explaining the long-term stability of plasmids remains challenging because segregational loss and the costs of plasmid carriage should drive the loss of plasmids though purifying selection. Theoretical and experimental studies suggest two key evolutionary routes to plasmid stability: First, the evolution of high conjugation rates would allow plasmids to survive through horizontal transmission as infectious agents, and second, compensatory evolution to ameliorate the cost of plasmid carriage can weaken purifying selection against plasmids. How these two evolutionary strategies for plasmid stability interact is unclear. Here, we summarise the literature on the evolution of plasmid stability and then use individual based modelling to investigate the evolutionary interplay between the evolution of plasmid conjugation rate and cost amelioration. We find that, individually, both strategies promote plasmid stability, and that they act together to increase the likelihood of plasmid survival. However, due to the inherent costs of increasing conjugation rate, particularly where conjugation is unlikely to be successful, our model predicts that amelioration is the more likely long-term solution to evolving stable bacteria-plasmid associations. Our model therefore suggests that bacteria-plasmid relationships should evolve towards lower plasmid costs that may forestall the evolution of highly conjugative, 'infectious' plasmids.
[Mh] Termos MeSH primário: Bactérias/genética
Conjugação Genética
Regulação Bacteriana da Expressão Gênica
Transferência Genética Horizontal
Modelos Estatísticos
Plasmídeos/química
[Mh] Termos MeSH secundário: Bactérias/metabolismo
Evolução Biológica
Cromossomos Bacterianos/química
Cromossomos Bacterianos/metabolismo
Aptidão Genética
Loci Gênicos
Mutagênese Insercional
Plasmídeos/metabolismo
Seleção Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE


  3 / 9243 MEDLINE  
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[PMID]:28453699
[Au] Autor:Zhang L; Ye Y; Tu H; Hildebrandt MA; Zhao L; Heymach JV; Roth JA; Wu X
[Ad] Endereço:Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA.
[Ti] Título:MicroRNA-related genetic variants in iron regulatory genes, dietary iron intake, microRNAs and lung cancer risk.
[So] Source:Ann Oncol;28(5):1124-1129, 2017 05 01.
[Is] ISSN:1569-8041
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Background: Genetic variations in MicroRNA (miRNA) binding sites may alter structural accessibility of miRNA binding sites to modulate risk of cancer. This large-scale integrative multistage study was aimed to evaluate the interplay of genetic variations in miRNA binding sites of iron regulatory pathway, dietary iron intake and lung cancer (LC) risk. Patients and methods: The interplay of genetic variant, dietary iron intake and LC risk was assessed in large-scale case-control study. Functional characterization of the validated SNP and analysis of target miRNAs were performed. Results: We found that the miRNA binding site SNP rs1062980 in 3' UTR of Iron-Responsive Element Binding protein 2 gene (IREB2) was associated with a 14% reduced LC risk (P value = 4.9×10 - 9). Comparing to AA genotype, GG genotype was associated with a 27% reduced LC risk. This association was evident in males and ever-smokers but not in females and never-smokers. Higher level of dietary iron intake was significantly associated with 39% reduced LC risk (P value = 2.0×10 - 8). This association was only present in individuals with AG + AA genotypes with a 46% reduced risk (P value = 1.0×10 - 10), but not in GG genotype. The eQTL-analysis showed that rs1062980 significantly alters IREB2 expression level. Rs1062980 is predicted to alter a miR-29 binding site on IREB2 and indeed the expression of miR-29 is inversely correlated with IREB2 expression. Further, we found that higher circulating miR-29a level was significantly associated with 78% increased LC risk. Conclusion: The miRNA binding site SNP rs1062980 in iron regulatory pathway, which may alter the expression of IREB2 potentially through modulating the binding of miR-29a, together with dietary iron intake may modify risk of LC both individually and jointly. These discoveries reveal novel pathway for understanding lung cancer tumorigenesis and risk stratification.
[Mh] Termos MeSH primário: Ferro na Dieta/metabolismo
Neoplasias Pulmonares/genética
MicroRNAs/genética
Polimorfismo de Nucleotídeo Único
[Mh] Termos MeSH secundário: Estudos de Associação Genética
Loci Gênicos
Predisposição Genética para Doença
Seres Humanos
Neoplasias Pulmonares/metabolismo
Redes e Vias Metabólicas/genética
Fatores de Risco
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Iron, Dietary); 0 (MicroRNAs)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/annonc/mdx046


  4 / 9243 MEDLINE  
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[PMID]:28453670
[Au] Autor:Adams RH; Schield DR; Card DC; Blackmon H; Castoe TA
[Ad] Endereço:Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA.
[Ti] Título:GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data.
[So] Source:Bioinformatics;33(9):1414-1415, 2017 May 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Summary: We introduce GppFst, an open source R package that generates posterior predictive distributions of FST and dx under a neutral coalescent model to identify putative targets of selection from genomic data. Availability and Implementation: GppFst is available at ( https://github.com/radamsRHA/GppFst ). Contact: todd.castoe@uta.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Loci Gênicos
Genética Populacional/métodos
Modelos Genéticos
Polimorfismo de Nucleotídeo Único
Software
[Mh] Termos MeSH secundário: Algoritmos
Animais
Crotalus/genética
Genoma
Genômica/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw795


  5 / 9243 MEDLINE  
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[PMID]:27770636
[Au] Autor:Mez J; Chung J; Jun G; Kriegel J; Bourlas AP; Sherva R; Logue MW; Barnes LL; Bennett DA; Buxbaum JD; Byrd GS; Crane PK; Ertekin-Taner N; Evans D; Fallin MD; Foroud T; Goate A; Graff-Radford NR; Hall KS; Kamboh MI; Kukull WA; Larson EB; Manly JJ; Haines JL; Mayeux R; Pericak-Vance MA; Schellenberg GD; Lunetta KL; Farrer LA; Alzheimer's Disease Genetics Consortium
[Ad] Endereço:Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Alzheimer's Disease and CTE Center, Boston University School of Medicine, Boston, MA, USA. Electronic address: jessemez@bu.edu.
[Ti] Título:Two novel loci, COBL and SLC10A2, for Alzheimer's disease in African Americans.
[So] Source:Alzheimers Dement;13(2):119-129, 2017 Feb.
[Is] ISSN:1552-5279
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:INTRODUCTION: African Americans' (AAs) late-onset Alzheimer's disease (LOAD) genetic risk profile is incompletely understood. Including clinical covariates in genetic analyses using informed conditioning might improve study power. METHODS: We conducted a genome-wide association study (GWAS) in AAs employing informed conditioning in 1825 LOAD cases and 3784 cognitively normal controls. We derived a posterior liability conditioned on age, sex, diabetes status, current smoking status, educational attainment, and affection status, with parameters informed by external prevalence information. We assessed association between the posterior liability and a genome-wide set of single-nucleotide polymorphisms (SNPs), controlling for APOE and ABCA7, identified previously in a LOAD GWAS of AAs. RESULTS: Two SNPs at novel loci, rs112404845 (P = 3.8 × 10 ), upstream of COBL, and rs16961023 (P = 4.6 × 10 ), downstream of SLC10A2, obtained genome-wide significant evidence of association with the posterior liability. DISCUSSION: An informed conditioning approach can detect LOAD genetic associations in AAs not identified by traditional GWAS.
[Mh] Termos MeSH primário: Afroamericanos/genética
Doença de Alzheimer/etnologia
Doença de Alzheimer/genética
Loci Gênicos
Proteínas dos Microfilamentos/genética
Transportadores de Ânions Orgânicos Dependentes de Sódio/genética
Polimorfismo de Nucleotídeo Único
Simportadores/genética
[Mh] Termos MeSH secundário: Transportadores de Cassetes de Ligação de ATP/genética
Idoso
Idoso de 80 Anos ou mais
Apolipoproteínas E/genética
Complicações do Diabetes/etnologia
Complicações do Diabetes/genética
Escolaridade
Feminino
Predisposição Genética para Doença
Estudo de Associação Genômica Ampla
Seres Humanos
Masculino
Prevalência
Fumar/etnologia
Fumar/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (ABCA7 protein, human); 0 (ATP-Binding Cassette Transporters); 0 (Apolipoproteins E); 0 (Cobl protein, human); 0 (Microfilament Proteins); 0 (Organic Anion Transporters, Sodium-Dependent); 0 (Symporters); 145420-23-1 (sodium-bile acid cotransporter)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


  6 / 9243 MEDLINE  
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[PMID]:28460474
[Au] Autor:Chen BD; Chen XC; Pan S; Yang YN; He CH; Liu F; Ma X; Gai MT; Ma YT
[Ad] Endereço:Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.
[Ti] Título:TT genotype of rs2941484 in the human HNF4G gene is associated with hyperuricemia in Chinese Han men.
[So] Source:Oncotarget;8(16):26918-26926, 2017 Apr 18.
[Is] ISSN:1949-2553
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The aim of the study is to investigate the association between the human hepatocyte nuclear factor 4 gamma (HNF4G) gene and hyperuricemia in Chinese Han population. A total of 414 hyperuricemia patients and 406 gender and age-matched normouricemic controls were enrolled. Four single nucleotide polymorphisms were genotyped as genetic markers for the human HNF4G gene (rs2977939, rs1805098, rs2941484, rs4735692). Data were analyzed for two separate groups: men and women. For rs2941484, the genotype distribution frequency in hyperuricemic subjects and was significantly different from that in normouricemic controls in men (P = 0.038). Meanwhile, in recessive model of rs2941484, the distribution frequency of TT genotype and CC+CT genotypes also differed significantly between the hyperuricemia men and normouricemic men (P = 0.011). For the other 3 SNPs in both men and women, there was no difference in the genotype and allele and distribution frequency between the hyperuricemia patients and normouricemic controls. In men, after adjustments for BMI, SBP, DBP, fasting glucose, total cholesterol, triglycerides, low density lipoprotein cholesterol and creatinine, the men with the TT genotype of rs2941484 were found to have significantly higher probability of suffering from hyperuricemia than the ones with CT and CC genotypes (OR = 2.170, P < 0.001). Therefore, TT genotype of rs2941484 in the human HNF4G gene might be a gender-specific genetic marker for hyperuricemia in Chinese Han men.
[Mh] Termos MeSH primário: Alelos
Grupo com Ancestrais do Continente Asiático/genética
Predisposição Genética para Doença
Genótipo
Fator 4 Nuclear de Hepatócito/genética
Hiperuricemia/genética
Polimorfismo de Nucleotídeo Único
[Mh] Termos MeSH secundário: Adulto
Idoso
Biomarcadores
China
Fatores de Confusão (Epidemiologia)
Feminino
Estudos de Associação Genética
Loci Gênicos
Seres Humanos
Hiperuricemia/diagnóstico
Masculino
Meia-Idade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers); 0 (Hepatocyte Nuclear Factor 4)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE
[do] DOI:10.18632/oncotarget.15851


  7 / 9243 MEDLINE  
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[PMID]:28458444
[Au] Autor:Beaney KE; Smith AJP; Folkersen L; Palmen J; Wannamethee SG; Jefferis BJ; Whincup P; Gaunt TR; Casas JP; Ben-Shlomo Y; Price JF; Kumari M; Wong A; Ong K; Hardy R; Kuh D; Wareham N; Kivimaki M; Eriksson P; Humphries SE; Consortium U
[Ad] Endereço:Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, Institute of Cardiovascular Science, University College London, University Street, London, UK.
[Ti] Título:Functional Analysis of the Coronary Heart Disease Risk Locus on Chromosome 21q22.
[So] Source:Dis Markers;2017:1096916, 2017.
[Is] ISSN:1875-8630
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:. The coronary heart disease (CHD) risk locus on 21q22 (lead SNP rs9982601) lies within a "gene desert." The aim of this study was to assess if this locus is associated with CHD risk factors and to identify the functional variant(s) and gene(s) involved. . A phenome scan was performed with UCLEB Consortium data. Allele-specific protein binding was studied using electrophoretic mobility shift assays. Dual-reporter luciferase assays were used to assess the impact of genetic variation on expression. Expression quantitative trait analysis was performed with Advanced Study of Aortic Pathology (ASAP) and Genotype-Tissue Expression (GTEx) consortium data. . A suggestive association between QT interval and the locus was observed (rs9982601 = 0.04). One variant at the locus, rs28451064, showed allele-specific protein binding and its minor allele showed 12% higher luciferase expression ( = 4.82 × 10 ) compared to the common allele. The minor allele of rs9982601 was associated with higher expression of the closest upstream genes ( 1.30-fold increase = 3.98 × 10 ; 1.15-fold increase = 9.60 × 10 ) in aortic intima media in ASAP. Both rs9982601 and rs28451064 showed a suggestive association with expression in relevant tissues in the GTEx data. . A candidate functional variant, rs28451064, was identified. Future work should focus on identifying the pathway(s) involved.
[Mh] Termos MeSH primário: Cromossomos Humanos Par 21/genética
Doença das Coronárias/genética
Loci Gênicos
Síndrome do QT Longo/genética
[Mh] Termos MeSH secundário: Células Hep G2
Seres Humanos
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1155/2017/1096916


  8 / 9243 MEDLINE  
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[PMID]:28951253
[Au] Autor:Musher LJ; Cracraft J
[Ad] Endereço:The Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA; Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA. Electronic address: lmusher@amnh.org.
[Ti] Título:Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus).
[So] Source:Mol Phylogenet Evol;118:204-221, 2018 Jan.
[Is] ISSN:1095-9513
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families. Additionally, the phylogenetic relationships within Pachyramphus are unresolved due to insufficient sampling of taxa and populations across species' ranges. We used target capture of ultraconserved elements for 62 individuals representing 42 taxa, and sequenced two mitochondrial genes and two nuclear introns covering 265 individuals of 51 taxa, including all recognized species, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. We delimited species using a traditional taxonomic approach and then tested them under a Bayesian multi-species coalescent framework. In doing so, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches and a high number of intraspecific lineages across the tree suggest that at least 50% of species diversity may be unrecognized.
[Mh] Termos MeSH primário: Genômica
Passeriformes/classificação
Passeriformes/genética
Filogenia
Clima Tropical
[Mh] Termos MeSH secundário: Animais
Argentina
Sequência de Bases
Teorema de Bayes
DNA Mitocondrial/genética
Loci Gênicos
Funções Verossimilhança
México
Filogeografia
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180302
[Lr] Data última revisão:
180302
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170928
[St] Status:MEDLINE


  9 / 9243 MEDLINE  
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[PMID]:28919503
[Au] Autor:Caviedes-Solis IW; Nieto-Montes de Oca A
[Ad] Endereço:Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, México Distrito Federal 04510, Mexico. Electronic address: itzuecs@uw.edu.
[Ti] Título:A multilocus phylogeny of the genus Sarcohyla (Anura: Hylidae), and an investigation of species boundaries using statistical species delimitation.
[So] Source:Mol Phylogenet Evol;118:184-193, 2018 Jan.
[Is] ISSN:1095-9513
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The genus Sarcohyla is composed by 24 species endemic to México. Despite the large number of phylogenetic studies focusing on the family Hylidae, the relationships among the species of Sarcohyla are still poorly known, and the scarce numbers of specimens and tissue samples available for some of the species has hampered an appropriate phylogenetic analysis. We present the most comprehensive molecular phylogenetic study of Sarcohyla to date. We included 17 species of the genus Sarcohyla using data from two mitochondrial (ND1 and 12S) and three nuclear genes (Rag-1, Rhod, and POMc). We performed phylogenetic analyses using Bayesian inference, and the absence of conflicts with strong support between the separate gene trees indicates that incomplete lineage sorting and/or introgressive hybridization are negligible. A coalescent-based species-tree analysis of the four independent loci (three nuclear genes+mtDNA) mostly supports the same species-level relationships as the analysis of the concatenated data. By including new samples from additional species and localities, we find that: (1) the widely distributed species S. bistincta is a complex of at least three species, (2) another undescribed species exists in the group, (3) the species S. ephemera is not valid and it corresponds to a junior synonym of S. calthula. In addition, we conducted marginal likelihood estimation and used Bayes factors to test alternative species delimitation models for S. bistincta, the most widespread nominal species in the group. Our findings support three independent lineages of S. bistincta group, which are paraphyletic with respect to S. pentheter and S. calthula.
[Mh] Termos MeSH primário: Anuros/classificação
Loci Gênicos
Filogenia
Estatística como Assunto
[Mh] Termos MeSH secundário: Animais
Anuros/genética
Teorema de Bayes
DNA Mitocondrial/genética
Geografia
Funções Verossimilhança
México
Modelos Biológicos
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180302
[Lr] Data última revisão:
180302
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170919
[St] Status:MEDLINE


  10 / 9243 MEDLINE  
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[PMID]:28834700
[Au] Autor:Bowie RCK; Pasquet E; McEntee JP; Njilima F; Fjeldså J
[Ad] Endereço:Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Science Building, University of California, Berkeley, CA 94720-3160, USA. Electronic address: bowie@berkeley.edu.
[Ti] Título:The systematics and biogeography of African tailorbirds (Cisticolidae: Artisornis) with comment on the choice of Bayesian branch-length prior when analyzing heterogeneous data.
[So] Source:Mol Phylogenet Evol;118:172-183, 2018 Jan.
[Is] ISSN:1095-9513
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The Long-billed Tailorbird (Artisornis moreaui), one of Africa's rarest birds, has a strikingly disjunct distribution, the origin of which has long puzzled biogeographers. One small population (subspecies moreaui) occurs in sub-montane forest in the East Usambara Mountains, a sky island near the coast of northern Tanzania, and another (subspecies sousae) on Serra Jeci in northwestern Mozambique, 950km away. The African Tailorbird, the putative sister-species of Long-billed Tailorbird, also occurs in the East Usambara Mountains and on Serra Jeci, but in addition occupies all the Eastern Arc Mountain forests between these disjunct sites. Stuart (1981) hypothesized that the two tailorbird distributions could be explained by strong ecological competition, with African Tailorbird populations having eliminated Long-billed Tailorbird populations via competitive exclusion in montane forests between the East Usambara and Serra Jeci. If such competitive exclusion explains these geographic distributions, the co-occurrence of the two species in the East Usambara and at Serra Jeci may be ephemeral, with the status of Long-billed Tailorbird especially in doubt. We sought to (1) determine whether the two species of African tailorbirds are indeed sister-species, and (2) test predictions from Stuart's (1981) competitive exclusion hypothesis using genetic data. Phylogenetic analyses of our seven gene dataset (3 mtDNA, 4 introns; 4784bp) indeed place these two species together in the genus Artisornis. Instead of finding shallow divergence among African Tailorbird populations and deep divergence between Long-billed Tailorbird populations as expected from Stuart's hypothesis, we recover deep genetic divergence and geographic structure among populations of both tailorbird species. This result is consistent with long-term co-existence of the two species at East Usambara and Serra Jeci. Observational data from both the East Usambara and Serra Jeci suggest that the two species have diverged in use of forest canopy strata. From a conservation standpoint, our results suggest that extinction of the Long-billed Tailorbird as a function of competition with African Tailorbird is highly unlikely, and should not be viewed as imminent. Threats to its survival are instead anthropogenic, and conservation measures should take this into account. Finally, our empirical results suggest that mis-specification of the branch-length prior in Bayesian analyses of mitochondrial DNA data can have a profound effect on the overall tree-length (sum of branch-lengths), whereas the topology and support values tend to remain more stable. In contrast, mis-specification of the branch-length prior had a lesser impact on all aspects of the nuclear-only DNA analyses. This problem may be exacerbated when mitochondrial and nuclear DNA analyses are combined in a total evidence approach.
[Mh] Termos MeSH primário: Passeriformes/classificação
Filogeografia
Estatística como Assunto
[Mh] Termos MeSH secundário: Animais
Teorema de Bayes
DNA Mitocondrial/genética
Loci Gênicos
Moçambique
Passeriformes/genética
Filogenia
Tanzânia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180302
[Lr] Data última revisão:
180302
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170824
[St] Status:MEDLINE



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