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1.
Adv Exp Med Biol ; 1232: 285-290, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31893422

RESUMO

In neonatal intensive care units (NICUs), 87.5% of alarms by the monitoring system are false alarms, often caused by the movements of the neonates. Such false alarms are not only stressful for the neonates as well as for their parents and caregivers, but may also lead to longer response times in real critical situations. The aim of this project was to reduce the rates of false alarms by employing machine learning algorithms (MLA), which intelligently analyze data stemming from standard physiological monitoring in combination with cerebral oximetry data (in-house built, OxyPrem). MATERIALS & METHODS: Four popular MLAs were selected to categorize the alarms as false or real: (i) decision tree (DT), (ii) 5-nearest neighbors (5-NN), (iii) naïve Bayes (NB) and (iv) support vector machine (SVM). We acquired and processed monitoring data (median duration (SD): 54.6 (± 6.9) min) of 14 preterm infants (gestational age: 26 6/7 (± 2 5/7) weeks). A hybrid method of filter and wrapper feature selection generated the candidate subset for training these four MLAs. RESULTS: A high specificity of >99% was achieved by all four approaches. DT showed the highest sensitivity (87%). The cerebral oximetry data improved the classification accuracy. DISCUSSION & CONCLUSION: Despite a (as yet) low amount of data for training, the four MLAs achieved an excellent specificity and a promising sensitivity. Presently, the current sensitivity is insufficient since, in the NICU, it is crucial that no real alarms are missed. This will most likely be improved by including more subjects and data in the training of the MLAs, which makes pursuing this approach worthwhile.


Assuntos
Unidades de Terapia Intensiva Neonatal , Terapia Intensiva Neonatal , Aprendizado de Máquina , Monitorização Fisiológica , Oximetria , Teorema de Bayes , Circulação Cerebrovascular , Humanos , Recém-Nascido , Recém-Nascido Prematuro , Terapia Intensiva Neonatal/métodos , Monitorização Fisiológica/métodos , Oximetria/métodos , Oximetria/normas
2.
Syst Biol ; 69(1): 155-183, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31173141

RESUMO

We describe an "embarrassingly parallel" method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo (SMC), based on recent advances in the SMC literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed SMC by reviewing and comparing with other computational Bayesian phylogenetic methods, in particular, different marginal likelihood estimation methods. Unlike previous SMC methods in phylogenetics, our annealed method can utilize standard Markov chain Monte Carlo (MCMC) tree moves and hence benefit from the large inventory of such moves available in the literature. Consequently, the annealed SMC method should be relatively easy to incorporate into existing phylogenetic software packages based on MCMC algorithms. We illustrate our method using simulation studies and real data analysis.


Assuntos
Algoritmos , Classificação/métodos , Filogenia , Teorema de Bayes , Método de Monte Carlo , Software
3.
Food Microbiol ; 85: 103285, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31500704

RESUMO

The objective of this study was to determine the kinetic parameters and apply Markov Chain Monte Carlo (MCMC) simulation to predict the growth of Clostridium perfringens from spores in cooked ground chicken meat during dynamic cooling. Inoculated samples were exposed to various cooling conditions to observe dynamic growth. A combination of 4 cooling profiles was used in one-step inverse analysis with the Baranyi model as the primary model and the cardinal parameters model as the secondary model. Six kinetic parameters of the Baranyi model and the cardinal parameters model, including Q0, Ymax, µopt, Tmin, Topt, and Tmax, were estimated. The estimated Tmin, Topt, and Tmax were 14.8, 42.9, and 50.5 °C, respectively, with a µopt of 5.25 h-1 and maximum cell density of 8.4 log CFU/g. Correlation analysis showed that both Q0 and Ymax are weakly correlated to other parameters, while the remaining parameters are mostly mildly to strongly correlated with each other. Although it may be difficult to estimate highly correlated parameters using a single temperature profile, one-step analysis with multiple different temperature profiles helped estimate them successfully. The estimated parameters were used as the prior information to construct the posterior distribution for Bayesian analysis. MCMC simulation was used to predict the bacterial growth using different dynamic temperature profiles for validation of the accuracy of the predictive models. The MCMC simulation results showed that the Bayesian analysis produced more accurate predictions of bacterial growth during cooling than the deterministic method. With Bayesian analysis, the root-mean-square-error (RMSE) of prediction was only 0.1 log CFU/g with all residual errors within ±0.25 log CFU/g. Therefore, Bayesian analysis is recommended for predicting the growth of C. perfringens in cooked meat during cooling.


Assuntos
Clostridium perfringens/crescimento & desenvolvimento , Culinária , Manipulação de Alimentos , Produtos da Carne/microbiologia , Temperatura Ambiente , Animais , Teorema de Bayes , Galinhas , Contagem de Colônia Microbiana , Simulação por Computador , Cinética , Cadeias de Markov , Modelos Biológicos , Método de Monte Carlo , Esporos Bacterianos/crescimento & desenvolvimento
4.
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi ; 36(6): 916-923, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31875364

RESUMO

The clinical manifestations of patients with schizophrenia and patients with depression not only have a certain similarity, but also change with the patient's mood, and thus lead to misdiagnosis in clinical diagnosis. Electroencephalogram (EEG) analysis provides an important reference and objective basis for accurate differentiation and diagnosis between patients with schizophrenia and patients with depression. In order to solve the problem of misdiagnosis between patients with schizophrenia and patients with depression, and to improve the accuracy of the classification and diagnosis of these two diseases, in this study we extracted the resting-state EEG features from 100 patients with depression and 100 patients with schizophrenia, including information entropy, sample entropy and approximate entropy, statistical properties feature and relative power spectral density (rPSD) of each EEG rhythm (δ, θ, α, ß). Then feature vectors were formed to classify these two types of patients using the support vector machine (SVM) and the naive Bayes (NB) classifier. Experimental results indicate that: ① The rPSD feature vector P performs the best in classification, achieving an average accuracy of 84.2% and a highest accuracy of 86.3%; ② The accuracy of SVM is obviously better than that of NB; ③ For the rPSD of each rhythm, the ß rhythm performs the best with the highest accuracy of 76%; ④ Electrodes with large feature weight are mainly concentrated in the frontal lobe and parietal lobe. The results of this study indicate that the rPSD feature vector P in conjunction with SVM can effectively distinguish depression and schizophrenia, and can also play an auxiliary role in the relevant clinical diagnosis.


Assuntos
Depressão , Esquizofrenia , Teorema de Bayes , Eletroencefalografia , Humanos , Processamento de Sinais Assistido por Computador , Máquina de Vetores de Suporte
5.
BMC Ecol ; 19(1): 53, 2019 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-31861996

RESUMO

BACKGROUND: Pleistocene glaciations have had an important impact on the species distribution and community composition of the North American biota. Species survived these glacial cycles south of the ice sheets and/or in other refugia, such as Beringia. In this study, we assessed, using mitochondrial DNA from three Diptera species, whether flies currently found in Beringian grasslands (1) survived glaciation as disjunct populations in Beringia and in the southern refugium; (2) dispersed northward postglacially from the southern refugium; or (3) arose by a combination of the two. Samples were collected in grasslands in western Canada: Prairies in Alberta and Manitoba; the Peace River region (Alberta); and the southern Yukon Territory. We sequenced two gene regions (658 bp of cytochrome c oxidase subunit I, 510 bp of cytochrome b) from three species of higher Diptera: one with a continuous distribution across grassland regions, and two with disjunct populations between the regions. We used a Bayesian approach to determine population groupings without a priori assumptions and performed analysis of molecular variance (AMOVA) and exact tests of population differentiation (ETPD) to examine their validity. Molecular dating was used to establish divergence times. RESULTS: Two geographically structured populations were found for all species: a southern Prairie and Peace River population, and a Yukon population. Although AMOVA did not show significant differentiation between populations, ETPD did. Divergence time between Yukon and southern populations predated the Holocene for two species; the species with an ambiguous divergence time had high haplotype diversity, which could suggest survival in a Beringian refugium. CONCLUSIONS: Populations of Diptera in Yukon grasslands could have persisted in steppe habitats in Beringia through Pleistocene glaciations. Current populations in the region appear to be a mix of Beringian relict populations and, to a lesser extent, postglacial dispersal northward from southern prairie grasslands.


Assuntos
Dípteros , Alberta , Animais , Teorema de Bayes , DNA Mitocondrial , Variação Genética , Haplótipos , Manitoba , América do Norte , Filogenia , Filogeografia
6.
Oecologia ; 191(4): 995-1002, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31691000

RESUMO

The responses of organisms to organic farming depend on the taxonomic group and landscape complexity. Following the intermediate landscape complexity hypothesis, organic farming can compensate for the lack of complexity in simple landscapes. Argentinian farmlands are simple with large fields and scarce linear habitat array, and conventional agriculture is almost the only agriculture practice. We hypothesize that there is an interaction effect of landscape complexity and farming practices on occupancy and species richness of small mammals in farmland of central Argentina. We selected circular landscapes under organic farming and low- and high-intensity conventional farming and quantified heterogeneity in each landscape considering different cover types (crops, resting plots, fallow land, border habitats, grasslands and man-made structures). We used multi-species occupancy models accounting for multiple seasons with a Bayesian approach to make the estimates. Landscapes under organic farms had the highest level of landscape heterogeneity. In simple Argentinian farmlands, organic farming benefited species richness and occupancy of all small mammal species. Some management strategies used in organic farming (wide and vegetated border habitats, diversity in types of production, winter cover crops, natural or semi-natural patches) should be taken into account to increase landscape complexity in conventional farming.


Assuntos
Agricultura , Biodiversidade , Animais , Argentina , Teorema de Bayes , Ecossistema , Fazendas , Mamíferos
7.
Zootaxa ; 4695(2): zootaxa.4695.2.3, 2019 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-31719354

RESUMO

The marine Chironomidae Ainuyusurika Sasa et Shirasaka, 1988, previously known from the adults only, is associated with its immature stages for the first time based on reared specimens from Oriental China. The larva resembles those of Sergentia Kieffer and Endochironomus Kieffer in the ventromental plate with an anteromedial projection and the 5-segmented antenna with opposite Lauterborn organs. The pupal thoracic horn has 12 branches at maximum and netted tergite spinulation which appears to be similar to those of Polypedilum Kieffer, Endotribelos Grodhaus, Phaenopsectra Kieffer and Sergentia. The phylogenetic relationship was furtherly explored through molecular analysis based on concatenation of five gene makers (18S, 28S, CAD1, CAD4 and COI-3P) using both mixed-model Bayesian and maximum likelihood inference methods. The result shows Ainuyusurika is nested with an assemblage of Endochironomus, Phaenopsectra and Endotribelos. We concluded that Ainuyusurika is a good independent genus showing affinity with Endochironomus-Phaenopsectra related genera.


Assuntos
Chironomidae , Animais , Teorema de Bayes , China , Larva , Filogenia , Pupa
8.
Zootaxa ; 4686(1): zootaxa.4686.1.6, 2019 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-31719502

RESUMO

An illustrated morphological description of the adult males of Tanytarsus heliomesonyctios Langton, 1999, is provided for the first time. The males were found in mountain lakes Bolshoi Darpir (Momsky District of the Republic of Sakha (Yakutia)) and Momontai (Susumansky District of the Magadan Region), located in the Kolyma River basin. Females, pupae and larvae of T. heliomesonyctios was previously described from Spitsbergen, Jan Mayen (Norway) and Ellesmere Island (Arctic Canada), and considered parthenogenetic. Tanytarsus heliomesonyctios is here for the first time noted for the fauna of Russia. Comparison of DNA barcodes shows high K2P nucleotide distances (1.7%) between the sexual populations (Norway and Russia) and the parthenogenetic populations (Svalbard and Canada). In the Bayesian tree, the COI- sequences from adult males group as sister to a strongly supported clade of sequences from parthenogenetic populations. This apparently indicates a single origin of parthenogeneticity, perhaps due to extreme environmental conditions.


Assuntos
Chironomidae , Animais , Teorema de Bayes , Canadá , Código de Barras de DNA Taxonômico , Feminino , Masculino , Noruega , Federação Russa , Svalbard
9.
Prog Orthod ; 20(1): 41, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31728776

RESUMO

BACKGROUND: Growth and development can be determined by cervical vertebrae stages that were defined on the cephalometric radiograph. Artificial intelligence has the ability to perform a variety of activities, such as prediction-classification in many areas of life, by using different algorithms, In this study, we aimed to determine cervical vertebrae stages (CVS) for growth and development periods by the frequently used seven artificial intelligence classifiers, and to compare the performance of these algorithms with each other. METHODS: Cephalometric radiographs, that were obtained from 300 individuals aged between 8 and 17 years were included in our study. Nineteen reference points were defined on second, third, and 4th cervical vertebrae, and 20 different linear measurements were taken. Seven algorithms of artificial intelligence that are frequently used in the field of classification were selected and compared. These algorithms are k-nearest neighbors (k-NN), Naive Bayes (NB), decision tree (Tree), artificial neural networks (ANN), support vector machine (SVM), random forest (RF), and logistic regression (Log.Regr.) algorithms. RESULTS: According to confusion matrices decision tree, CSV1 (97.1%)-CSV2 (90.5%), SVM: CVS3 (73.2%)-CVS4 (58.5%), and kNN: CVS 5 (60.9%)-CVS 6 (78.7%) were the algorithms with the highest accuracy in determining cervical vertebrae stages. The ANN algorithm was observed to have the second-highest accuracy values (93%, 89.7%, 68.8%, 55.6%, and 78%, respectively) in determining all stages except CVS5 (47.4% third highest accuracy value). According to the average rank of the algorithms in predicting the CSV classes, ANN was the most stable algorithm with its 2.17 average rank. CONCLUSION: In our experimental study, kNN and Log.Regr. algorithms had the lowest accuracy values. SVM-RF-Tree and NB algorithms had varying accuracy values. ANN could be the preferred method for determining CVS.


Assuntos
Ortodontia , Adolescente , Algoritmos , Inteligência Artificial , Teorema de Bayes , Vértebras Cervicais , Criança , Crescimento e Desenvolvimento , Humanos
10.
Zootaxa ; 4638(4): zootaxa.4638.4.1, 2019 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-31712456

RESUMO

The montane agamid lizard genus Oriocalotes is currently considered monotypic, represented by the species, O. paulus. The systematic status of this taxon has remained questionable since its initial descriptions in the mid-1800s. A detailed molecular and morphological study was carried out to assess the validity of this genus, and its systematic position within the Asian agamid subfamily, Draconinae. Freshly collected and historical museum specimens from the type locality of O. paulus were examined morphologically, along with additional samples collected from localities in Mizoram state, Northeast India. Utilising newly generated molecular sequences (two mitochondrial and three nuclear genes), combined with those previously published for representative genera from the subfamilies Draconinae and Agaminae, Maximum Likelihood and Bayesian phylogenetic trees were constructed. Phylogenetic results suggest that Oriocalotes is part of the widespread South and Southeast Asian radiation of Calotes. Comparative morphological studies (including external morphology, hemipenis and osteology) between Oriocalotes and related genera further support this systematic placement. Oriocalotes is herein regarded as a junior subjective synonym of Calotes. Calotes paulus comb. nov. is also assigned a lectotype and given a detailed redescription based on the lectotype, paralectotypes and additional topotypic material. Furthermore, the specimens collected from Mizoram populations are found to be morphologically and genetically distinct from Calotes paulus comb. nov., and are described herein as a new species, Calotes zolaiking sp. nov.


Assuntos
Lagartos , Animais , Teorema de Bayes , Índia , Osteologia , Filogenia
11.
Zootaxa ; 4638(2): zootaxa.4638.2.1, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31712473

RESUMO

An integrative taxonomic analysis of the Ptychozoon lionotum group across its range in Indochina and Sundaland recovers P. lionotum sensu lato Annandale, 1905 as paraphyletic with respect to P. popaense Grismer, Wood, Thura, Grismer, Brown, Stuart, 2018a and composed of four allopatric, genetically divergent, ND2 mitochondrial lineages. Multivariate and univariate analyses of continuous and discrete morphological and color pattern characters statistically and discretely diagnose each lineage from one another and together, with maximum likelihood and Bayesian inference analyses, provide the foundation for the recognition of each lineage as a new species-hypotheses corroborated with a Generalized Mixed Yule Coalescent species delimitation analysis. Ptychozoon cicakterbang sp. nov. ranges throughout Peninsular Malaysia to Pulau Natuna Besar, Indonesia; P. kabkaebin sp. nov. is endemic to northern and central Laos; and P. tokehos sp. nov. ranges from southern Thailand south of the Isthmus of Kra northward to Chiang Mai, fringing the Chao Phraya Basin and ranging southward through Cambodia to southern Vietnam. Ptychozoon lionotum sensu stricto ranges from northwestern Laos through southern Myanmar to eastern India. The phylogeographic structure within each species varies considerably with P. lionotum s.s. showing no genetic divergence across its 1,100 km range compared to P. cicakterbang sp. nov. showing upwards of 8.2% sequence divergence between syntopic individuals. Significant phylogeographic structure exists within P. tokehos sp. nov. and increased sampling throughout Thailand may require additional taxonomic changes within this species.


Assuntos
Lagartos , Filogenia , Animais , Ásia , Teorema de Bayes , Variação Genética , Indochina
12.
Zootaxa ; 4625(1): zootaxa.4625.1.1, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-31712545

RESUMO

The bumblebees of the subgenus Alpinobombus of the genus Bombus are unusual among bees for specialising in many of the most northerly vegetated arctic habitats on Earth. Most named taxa in this group (37 available names from a total of 67 names) were described originally from differences in the colour patterns of the hair. Previous revisions have shown unusually little agreement, recognising a range of 6‒9 species, in part because of pronounced intraspecific variation in both skeletal morphology and in the colour patterns of the hair. Here we examine variation among 4622 specimens from throughout the group's global range. Bayesian inference of the gene tree for the fast evolving mitochondrial COI gene combined with Poisson-tree-process analysis of this tree shows support for 10 gene lineages as candidates for being putative species lineages. Integrative assessment shows that the interpretation of these results is not straightforward. Evidence from the fast evolving mitochondrial 16S ribosomal RNA gene supports two of the COI gene alleles (from the samples B. kluanensis s. str. and 'unnamed2') as being associated with just one 16S allele. Double COI bands on the PCR gels for these individuals and double peaks on sequence traces (in one case with both COI alleles sequenced from one individual) identifies this as a likely case of COI paralogy that has resulted in mitochondrial heteroplasmy. Evidence from morphology also supports only the remaining nine lineages as separate. Evidence from extracts of cephalic labial gland secretions (CLGS, with components believed to function as sex pheromones) reported by others shows small diagnostic differences between all of the candidate species examined (although B. kluanensis s. l. was not examined) and shows larger differences between all of the species pairs that we find are likely to have co-occurred at least in the past, revealing a likely limitation to the CLGS approach in cases of recent and continuously allopatric species. Consequently we infer nine species in the subgenus Alpinobombus (so that B. kluanensis s. str. and 'unnamed2' are interpreted as conspecific, as B. kluanensis s. l.). We provide distribution maps and identification keys for the nine species. The morphology of the male of B. kluanensis is described for the first time, including a unique, unusually dense pad of short hair on the mandible that may have a function involving CLGS in mate-searching behaviour. In seeking to identify the valid names for these species, seven new lectotypes are designated and support is provided for synonymizing 10 names as proposed in a recent summary table of names. The prevailing usage of Bombus balteatus Dahlbom is maintained as valid by proposing Bombus nivalis Dahlbom and Bombus tricolor Dahlbom as nomina oblita and by proposing Bombus balteatus Dahlbom as a nomen protectum. The prevailing usage of Bombus hyperboreus Schönherr is maintained as valid by supporting Apis arctica Quensel as a nomen oblitum and by supporting Bombus hyperboreus Schönherr as a nomen protectum. We then use sequence data from COI and 16S together with nuclear PEPCK and opsin genes to estimate dated phylogenetic relationships among the nine species, allowing for incongruent gene trees with *BEAST. If crown-group divergence within the subgenus Alpinobombus coincided with the global climate cooling and with the growth of the northern ice sheets at the end of the Miocene at ca 7.2 Ma, then divergences between each of the three pairs of sister species are likely to have coincided with fluctuations in vegetated land connections across the Bering Strait after ca 2.5 Ma.


Assuntos
Himenópteros , Animais , Regiões Árticas , Teorema de Bayes , Abelhas , Himenópteros/genética , Masculino , Filogenia , Especificidade da Espécie
13.
Zootaxa ; 4679(2): zootaxa.4679.2.7, 2019 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-31715962

RESUMO

A new species, Baetis pentaphyllus sp. nov., is described on the basis of larvae from the Far East of Russia (type locality Bolshoi Garmakan River). Larvae of Baetis pentaphyllus sp. nov. may be distinguished from other Baetis species by the presence of only five pairs of tergalii on segments III-VII. The mitochondrial COI sequence obtained from the described species was compared with the data present in GeneBank and BOLD. The DNA barcodes allowed discrimination of B. pentaphyllus sp. nov. from other species of Baetis with available sequence data. The average interspecific K2P distances were 10-15%, which are values well above those associated with intraspecific variation. COI sequences as well as 36 morphological larval characters were analysed using Bayesian inference to relate the described species to the recognized species-groups of the Baetis genus. B. pentaphyllus sp. nov formed a sister clade to B. vardarensis + B. lutheri which belong to the Baetis lutheri species-group.


Assuntos
Ephemeroptera , Animais , Teorema de Bayes , Extremo Oriente , Larva , Federação Russa
14.
Zootaxa ; 4674(2): zootaxa.4674.2.4, 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31716012

RESUMO

Illustrated redescription of adult male and description for the first time of pupa and fourth instar larva, as well as DNA barcoding, of Hydrobaenus laticaudus Sæther in comparison with close related known species of Hydrobaenus Fries, and an updated part of a key to species of Hydrobaenus from the Russian Far East are provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. For the estimation of interspecific distances and constructing detailed Bayesian tree within Hydrobaenus, we have obtained DNA barcoding for the two other species, H. distinctus and Hydrobaenus sp.1. The intraspecific sequence divergence of H. laticaudus based on the Kimura-2-parameter (K2P) distance ranged from 0.0-0.031, whereas the interspecific sequence divergence based on the K2P distance ranged from 0.106-0.197% between H. laticaudus and other species of genus Hydrobaenus. The well-supported monophyly as well as results of an ABGD analysis confirms the validity of H. laticaudus.


Assuntos
Chironomidae , Animais , Teorema de Bayes , Chironomidae/genética , Código de Barras de DNA Taxonômico , Extremo Oriente , Masculino , Filogenia , Rios , Federação Russa
15.
Zootaxa ; 4671(4): zootaxa.4671.4.8, 2019 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-31716036

RESUMO

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae).


Assuntos
Genoma Mitocondrial , Lepidópteros , Filogenia , Animais , Teorema de Bayes , Genoma de Inseto , Insetos , Lepidópteros/genética , RNA Ribossômico , RNA de Transferência
16.
Zootaxa ; 4671(2): zootaxa.4671.2.7, 2019 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-31716058

RESUMO

Labrys khuzestanensis n. sp. was recovered from the rhizosphere of a palm tree in southwestern Iran and described using morphological and molecular data. The new species was characterized by combination of the following features: its 590-675 µm long body, finely annulated cuticle in light microscopy (LM), lateral field with two smooth incisures, cephalic region dorso-ventrally flattened with protuberant, elongate and laterally extended labial plate, appearing a V-shaped piece in lateral view, amphidial openings as longitudinal slits confined to labial plate in scanning electron microscopic (SEM) images, stylet 7.5-9.0 µm long, elongated fusiform median bulb with faint valvular apparatus, excretory pore wide with moderately sclerotized duct and elongate filiform tail with finely rounded tip. Compared to four currently known species under the genus, the new species has a remarkably larger and more prominent labial plate as revealed by SEM and trapezoid cephalic region under LM. The molecular phylogenetic analyses of the new species using partial SSU rDNA revealed it has close affinity with three species of Labrys (L. chinensis, L. fuzhouensis and L. filiformis) in Bayesian inference (BI) and maximum likelihood (ML) methods and occupied a placement inside their clade. L. fujianensis, the other species of the genus, occupied a distant placement to the aforementioned clade. This is the second species of Labrys being originally described from Iran, representing the third species of Labrys occurring in the country.


Assuntos
Nematoides , Tylenchoidea , Animais , Teorema de Bayes , DNA Ribossômico , Irã (Geográfico) , Filogenia
17.
Zootaxa ; 4590(4): zootaxa.4590.4.3, 2019 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-31716081

RESUMO

Deep-sea shrimps of the species Plesionika acanthonotus (Smith, 1882) and P. holthuisi Crosnier Forest, 1968 are morphologically similar and exhibit overlapping amphi-Atlantic distributions. In the literature, through morphological studies, there are reports of doubts about the validity of P. holthuisi and some authors believe that the eastern and western Atlantic populations of P. acanthonothus could represent two distinct species. The objective of the present study was to use molecular data to elucidate the taxonomic status of the two populations of P. acanthonothus. DNA sequences of two mitochondrial genes (16S rDNA and Cytochrome Oxidase subunit I) and a nuclear gene (Histone 3) were obtained for both species and for both populations of P. acanthonotus. The sequences were also obtained from Genbank for comparison. The trees (separate and multi-locus/partitioned genes) were generated by Bayesian Inference analyzes, and genetic divergence (Kimura-2-parameters) was also calculated. All specimens that had their DNA sequenced were examined morphologically to confirm their identification; morphological variations were noted. The genetic data showed that Plesionika holthuisi is closely related to P. acanthonotus, but clearly separated, indicating that P. holthuisi is a valid species. In the multi-locus analysis, the P. acanthonothus specimens were divided into two clades, one with the eastern Atlantic specimens and another with the western Atlantic specimens. However, this genetic separation was considered to be a population structuring for three reasons: (1) the genetic divergences of the two mitochondrial genes between these two groups (eastern Atlantic X western Atlantic) were smaller than the interspecific divergence for Plesionika; (2) the P. acanthonothus sequences of the Histone 3 gene showed no genetic variation; (3) in the analyzed individuals, no valid morphological character was found to support this separation. Thus, the conclusion of this study is that P. holthuisi probably is a valid species and P. acanthonothus presents two populations with mitochondrial divergences that could be in the process of speciation, but which currently represent only one species.


Assuntos
Pandalidae , Animais , Teorema de Bayes , DNA Mitocondrial , DNA Ribossômico , Filogenia
18.
Zootaxa ; 4624(4): zootaxa.4624.4.1, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31716195

RESUMO

Several species of Glaucomastix lizards have been described over the past decade, most of these inhabit inland Brazil. Glaucomastix abaetensis is a threatened whiptail endemic to Brazilian coastal "restinga" (sandy habitats) from Bahia State to Sergipe, with a distribution limited by riverine barriers. In order to investigate the differentiation and relationships in G. abaetensis, we integrated phylogeographic analysis, Bayesian species delimitation and morphological data to detect geographical patterns and historical events responsible for its present distribution. We recovered two highly divergent clades along its range, one of them unnamed. Glaucomastix itabaianensis sp. nov. has a a yellowish green tail, 13-16 scales in the lateral flank, 22-33 scales around tail, 28-35 femoral pores and usually four supraocular scales with the smaller one disposed posteriorly. Our results retrieved the monophyly of Glaucomastix, with G. venetacauda and G. cyanurus being sister species to a clade formed by G. littoralis and G. abaetensis. Divergence between Glaucomastix abaetensis and the new species occurred roughly 2.39 Myr ago; posterior shallow genetic divergences occurred mainly in Pleistocene. Finally, we present data on the conservation of this clade of whiptail lizards.


Assuntos
Lagartos , Animais , Teorema de Bayes , Brasil , Ecossistema , Filogenia , Filogeografia
19.
Zootaxa ; 4624(1): zootaxa.4624.1.1, 2019 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-31716233

RESUMO

The snapping shrimp Alpheus macrocheles (Hailstone, 1835b) is widely distributed across the Atlantic Ocean and was originally described from Hastings, England, based on a very brief description with limited morphological details and diagnostic illustrations. The morphologically similar A. amblyonyx Chace, 1972, type locality Quintana Roo, Mexico, is a western Atlantic taxon. The superficial description of A. macrocheles by Hailstone and the high similarity with A. amblyonyx has led to taxonomic confusion regarding the precise identification of these species. Thus, our objective was to reexamine these two species, based on a combined analysis of morphological-including a redescription for A. macrocheles and new morphological characterization of A. amblyonyx-and molecular data. In total, 42 morphological characters were analyzed, in addition to a phylogenetic analysis of 16S ribosomal RNA (rRNA) gene sequences. A Bayesian Inference analysis recovered A. macrocheles and A. amblyonyx as distinct clades supporting the taxonomic distinction between them. The tree topology suggests that A. macrocheles is more closely related to A. crockeri (Armstrong, 1941) and A. puapeba (Christoffersen, 1979) than to A. amblyonyx, which forms the sister group to a well-supported clade containing these three species. This contribution conclusively distinguishes between A. macrocheles and A. amblyonyx and points out the need for a comprehensive review involving all species of the larger A. macrocheles group.


Assuntos
Animais , Oceano Atlântico , Teorema de Bayes , Inglaterra , México , Filogenia
20.
Zootaxa ; 4623(1): zootaxa.4623.1.1, 2019 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-31716271

RESUMO

A herpetological survey of the Indawgyi Wildlife Sanctuary in Kachin State, Myanmar resulted in the discovery of a new species of Cyrtodactylus Gray along the eastern watershed of the Mokso Mountains. An integrative taxonomic analysis based on the mitochondrial ND2 gene, morphology, and color pattern recovered this new species, Cyrtodactylus mombergi sp. nov., as the sister taxon to an undescribed species from Miao, Arunachal Pradesh, India. Bayesian and maximum likelihood analyses recovered notable genetically divergent (4.7%) phylogeographic structure between northern and southern populations of C. mombergi sp. nov. across only 14 km of continuous habitat. Conversely, genetic divergence did not exceed 9.2% between C. mombergi sp. nov. and the undescribed species from Miao from across 355 km of habitat. Cyrtodactylus mombergi sp. nov. belongs to a well-supported, mitochondrial clade of 18 other species which now compose an expanded and redefined C. gansi group. Cyrtodactylus mombergi sp. nov. is only the third species of Bent-toed Gecko reported from Kachin State and indicates that additional herpetological surveys are needed in unexplored forested areas.


Assuntos
Lagartos , Animais , Teorema de Bayes , Ecossistema , Florestas , Índia , Mianmar , Filogenia
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