Concatenated Data Research Articles

The phylogenetic authentication of Ophiocordyceps sphecocephala from Lang Biang Biosphere Reserve, Lam Dong, Vietnam

During our expedition at Lang Biang Biosphere Reserve, samples of DL0023, parasitizing on wasps, were collected, then sent to the biology laboratory, Dalat University, Lam Dong Province, Vietnam, to preliminarily morphologically identify the name of this species as Ophiocordyceps sphecocephala. The method of Phenol (pH = 8)/Chloroform method was applied to isolated DNA. The PCR assays and sequencing were performed to amplify and sequencing ITS, nrLSU, and nrSSU, respectively. The phylogenetic methods of neighbor-joining, maximum likelihood, and maximum parsimony were constructed to identify the relationship between DL0023 and referent sequences. We successfully amplified and sequenced the target genes, and constructed concatenated data containing 29, 33, and 30 sequences of ITS, nrLSU and nrSSU, respectively, belonging to Clavicipitaceae clade A, clade B and clade C, and 02 sequences belonged to Glomerellaceae. The results of phylogenetic analysis shown that DL0023 was accepted at Ophiocordyceps and strongly formed the monophyletic group Ophiocordyceps sphecocephala with a high supported value. In conclusion, the concatenated dataset’s phylogenetic analyses effectively supported the identification of DL0023 as Ophiocordyceps sphecocephala.

Multilocus-phylogeny of the lichen-forming genus Bacidia s. str. (Ramalinaceae, Lecanorales) with special emphasis on the Russian Far East

AbstractTo clarify deep relationships among species lineages within Bacidia s. str., and to investigate the robustness of the deeper branches, we combined data from three traditionally used RNA-coding genes (nrITS, nrLSU and mtSSU) with two protein-coding genes (RPB1 and RPB2). The multigene phylogeny contained 48 newly generated sequences from the Russian Far East and all Bacidia s. str. sequences from GenBank (131 sequences). We subjected the alignments for the single and concatenated data sets to Bayesian inference (BI) and two maximum likelihood (ML) analyses (RAxML and IQ-TREE). The topologies of phylogenetic trees recovered from BI and ML analyses were highly concordant. The multilocus phylogeny of Bacidia s. str. was congruent with previous results based on nrITS sequences from the Russian Far East but with considerably higher support values for most of the deeper branches. A correlation between the recovered clades and apothecial pigments in the upper part of the hymenium and lateral exciple was observed. Based on morphological and molecular evidence, Bacidia obtecta is described as new to science. It was recovered as the sister lineage of B. elongata. The two species are alike in having up to four enlarged lumina cells along the exciple edge, but B. obtecta differs in the abundant crystals found in the upper hymenium and lateral exciple, and by having spores with fewer septa.

Asymmetric Ensemble of Asymmetric U-Net Models for Brain Tumor Segmentation With Uncertainty Estimation.

Accurate brain tumor segmentation is crucial for clinical assessment, follow-up, and subsequent treatment of gliomas. While convolutional neural networks (CNN) have become state of the art in this task, most proposed models either use 2D architectures ignoring 3D contextual information or 3D models requiring large memory capacity and extensive learning databases. In this study, an ensemble of two kinds of U-Net-like models based on both 3D and 2.5D convolutions is proposed to segment multimodal magnetic resonance images (MRI). The 3D model uses concatenated data in a modified U-Net architecture. In contrast, the 2.5D model is based on a multi-input strategy to extract low-level features from each modality independently and on a new 2.5D Multi-View Inception block that aims to merge features from different views of a 3D image aggregating multi-scale features. The Asymmetric Ensemble of Asymmetric U-Net (AE AU-Net) based on both is designed to find a balance between increasing multi-scale and 3D contextual information extraction and keeping memory consumption low. Experiments on 2019 dataset show that our model improves enhancing tumor sub-region segmentation. Overall, performance is comparable with state-of-the-art results, although with less learning data or memory requirements. In addition, we provide voxel-wise and structure-wise uncertainties of the segmentation results, and we have established qualitative and quantitative relationships between uncertainty and prediction errors. Dice similarity coefficient for the whole tumor, tumor core, and tumor enhancing regions on BraTS 2019 validation dataset were 0.902, 0.815, and 0.773. We also applied our method in BraTS 2018 with corresponding Dice score values of 0.908, 0.838, and 0.800.

Deep in the systematics of Camallanidae (Nematoda): using integrative taxonomy to better understand the phylogeny and consistency of diagnostic traits.

Due to conflicts between classic and molecular systematics of Camallanidae, different data types were used for the first time, to better understand the evolutionary history and taxa consistency within this family. Genetic [18S and 28S rDNA; cytochrome c oxidase subunit I (COI) mtDNA], morphological and life history traits were used to infer phylogenies using Bayesian inference, reconstructed from separated and concatenated datasets. The consistency of tree and morphological traits was evaluated using the consistency index. Characters were mapped on the trees and the phylogenetic informativeness of genetic markers was estimated. Phylogenetic informativeness of 18S provided better resolution for outer nodes, COI for inners and 28S had an intermediate profile. New sequences for two camallanid species were obtained. Phylogenies of genetic and concatenated data largely agreed, showing more divergence in the COI dataset, due to its higher mutation rate vs stable morphology for diagnosing higher taxa. No genus sustained monophyly. The lack of autapomorphy and phylogenetic proximity supported the partition of Batrachocamallanus as synonym of Procamallanus and Spirocamallanus, which should not be considered as subgenera. Although traits of buccal capsule, male tail, habitat, host and biogeographic were highly consistent, intrinsic patterns varied according to different taxa assemblages. Morphological systematics of Camallanidae, based on buccal capsule, is artificial for certain taxa.

First report of Stemphylium leaf spot caused by Stemphylium vesicarium on alfalfa (Medicago sativa) in Peru.

Alfalfa (Medicago sativa) is the most cultivated fodder crop in Peru with 172,000 ha cultivated (MINAM 2019), and Arequipa is the top producing region with 40% of the national production in 2015 (Santamaría et al. 2016). In January-April 2019 (av. 20°C and 70% RH), most alfalfa fields in Majes-Pedregal, Arequipa were affected by an unidentified foliar disease. One of the fields was located at the farm of the Universidad Nacional de San Agustín de Arequipa (16°19'29.6" S, 72°12'59.9" W). Symptoms appeared as elliptical light brown spots witdark brown borders (Fig. S1a and b). The field (~60 × 60 m) was divided into ~30 × 12 m sections and two plants in each section were collected (20 plants total). Plants were digitized and the leaflet diseased area was calculated with ImageJ 1.53a, from which an incidence of 100% and a severity of 38.7 ± 4.4 % were estimated. Microscopical observations at the leaflet spots revealed consistently the presence of oblong multiseptated conidia (23.6-42.8 × 16.5-25.2 µm; av. 33.3 × 20.9 µm; n = 40) of the genus Stemphylium (Simmons 1969; Woudenberg et al. 2017) (Fig. S1c). We obtained 10 pure cultures by placing conidia from the spots directly onto potato dextrose agar medium with the aid of stereoscope and sterile forceps. Two isolates (UNSA-StemV01 and UNSA-StemV02) were incubated further until ascospore production at room temperature with no special light stimulus. After 45 days of growth, globose pseudothecia and ellipsoidal ascospores (25.4-38.7 × 11.2-16.6 µm; av. 31.9 × 13.7 µm; n = 30) formation occurred (Fig. S1d and e). We extracted the DNA from these two isolates using Wizard® Purification Kit (Promega Corp., Madison, WI) and sequenced the internal transcribed spacer 1 and 2 intervening 5.8S rDNA subunit (GenBank accessions: MT371236-37), and the glyceraldehyde-3-phosphate dehydrogenase (MT375513-14) and the calmodulin (MT375515-16) genes, highly resolutive markers to identify Stemphylium species, following Woudenberg et al. (2017). We retrieved sequence data available from 43 isolates of nine Stemphylium species (Han et al. 2019; Woudenberg et al. 2017), and built a mid-point rooted phylogeny with the three-loci concatenated data set (Fig. S2). We identified our isolates as S. vesicarium (Fig. S2). Koch's postulates were fulfilled by spray-inoculation with conidia from isolate UNSA-StemV01 suspended in sterile water (1×104 / mL) to two healthy 50-day old alfalfa plants growing on pots in the university greenhouse (av. 25°C and 70% RH). Two plants sprayed with sterile water without conidia served as control. Symptoms appeared after 21 days of inoculation, and when conidia were re-isolated, they were the same as originally obtained. No symptoms developed in the control plants. This confirmed that S. vesicarium is the causal agent of the alfalfa disease in Majes-Pedregal, identified as Stemphylium leaf spot. revious studies documented S. vesicarium on asparagus and onion in Peru (Castillo Valiente 2018; Vásquez Salas 2018; Vásquez Sangay 2013), but molecular characterization has only been applied to S. lycopersici from potatoes (Woudenberg et al. 2017). Stemphylium vesicarium has been documented in various crops, including alfalfa, and countries in Europe, North America, Africa, Asia and in Australia and New Zealand (Han et al. 2019; Woudenberg et al. 2017). This occurrence is the first report of S. vesicarium on alfalfa in Peru. The disease compromises the quality of this fodder crop, so actions need to be taken in Arequipa.

Further insights into the phylogeny of peniculid ciliates (Ciliophora, Oligohymenophorea) based on multigene data

Peniculids comprise a large order of ciliated protists in Class Oligohymenophorea having many unresolved evolutionary relationships. Herein, we report 27 new sequences, including 18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA and the mitochondrial cox1 genes of eight peniculids. We conducted phylogenetic analyses based on each these markers and on a four-gene concatenated data set (18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA, and cox1 gene). The main findings are: 1) subclass Peniculia and family Parameciidae are monophyletic, with genus Frontonia remaining non-monophyletic; 2) Urocentrids have traditionally been regarded as a family, multi-gene analyses support the rank of Urocentrida and consistently recovers this order as sister to Peniculida, and Urocentrida and Peniculida comprise subclass Peniculia in agreement with Lynn’s (2008) classification; 3) discrepancies between multiple-gene phylogenies, and conflicts with morphologic data regarding genus Frontonia necessitate expansion and revision of species diagnoses and we propose consideration of Group III of Frontonia (including F. didieri, F. ocularis, F. anatolica, F. pusilla and F. elegans) as incertae sedis in Peniculida; 4) multi-gene analyses of Parameciidae support five previously established subgenera. Paramecium buetschlii is placed in subgenus Chloroparamecium, and P. chlorelligerum into subgenus Viridoparamecium.

Genetic data support speciation between Panstrongylus howardi and Panstrongylus chinai, vectors of Chagas disease in Ecuador

Limited genetic data are currently available for three vectors of Chagas disease in Ecuador, Panstrongylus howardi, P. chinai, and P. rufotuberculatus. Previously regarded as mainly sylvatic, these species have been poorly studied. Recently, they have been more frequently reported in domiciles and peridomiciles and are now considered true secondary vectors of Chagas disease in a country where an estimated 200,000 people are infected by Trypanosoma cruzi, a causative agent of this disease.In order to fill this gap, we obtained DNA for sequencing from 53 insects belonging to these three species and mainly sampled from the two Ecuadorian provinces of Loja and Manabí. We used six mitochondrial loci (COI, COII, ND4, CytB, 16S, and 12S) and two nuclear ones (ITS2 and 18S). We interpreted the phylogenetic trees built with single and concatenated data through maximum likelihood, Bayesian Markov chain Monte Carlo, and maximum parsimony methods.We provide evidence that P. chinai and P. howardi are indeed two supported species closely related and derived from a common ancestor. Additionally, the phylogenetic position of P. rufotuberculatus was confirmed as being distant from P. chinai and P. howardi and clustered with Triatoma dimidiata, a species belonging to the Northern American Triatoma clade.

GENETIC CHARACTERIZATION OF KISSING GOURAMI (Helostoma temminckii Cuvier, 1829) IN OGAN RIVER, SOUTH SUMATRA INFERRED FROM 16S rRNA AND COI MITOCHONDRIAL GENES

Genetic characterization data of kissing gourami are important to understand historical lineage thus enhancing sustainability of the species and to establish regulation for sustainable management of the fish stock in their habitat. However, investigation of genetic characterization of kissing gourami, one of native Indonesian freshwater fishes has poorly understood. Therefore, the aim of this study was to examine genetic characterization of the fish species collected from Ogan River, South Sumatra using partial sequences of two mitochondrial genes, 16S rRNA and COI. The results revealed that for the 621 bp determined in 16S rRNA gene of the samples, five sites were variable, of which one was parsimony informative. Concatenate data revealed three haplotypes with an overall haplotype diversity of 0.833±0.222 and nucleotide diversity of 0.003±0.001. The genetic divergence varied from 0-0.49%. Next, sequence analysis of COI gene exhibited 609 bp which can be translated into 203 amino acids. For the 609 bp sequence determined in the fish samples, three haplotypes were revealed with nine variable sites and two parsimony informatives. Haplotype diversity and nucleotide diversity of the fish samples were 0.833±0.22 and 0.00794±0.0025, respectively. The haplotype divergence between the fish samples was also supported by three nonsynonymous codons. In addition, the genetic divergence varied from 0 % to 1.16 %. The results suggest that genetic variation of the kissing gourami has to be monitored and further studies are needed to compare the same species from different location to know the historical lineage and demography.

Single stage DOA-frequency representation of the array data with source reconstruction capability

In this paper, a new signal processing framework is proposed, in which the array time samples are represented in DOA-frequency domain through a single stage problem. It is shown that concatenated array data is well represented in a G dictionary atoms space, where columns of G correspond to pixels in the DOA-frequency image. We present two approaches for the G formation and compare the benefits and disadvantages of them. A mutual coherence guaranteed G construction technique is also proposed. Furthermore, unlike most of the existing methods, the proposed problem is reversible into the time domain, therefore, source recovery from the resulted DOA-frequency image is possible. The proposed representation in DOA-frequency domain can be simply transformed into a group sparse problem, in the case of non-multitone sources in a given bandwidth. Therefore, it can also be utilized as an effective wideband DOA estimator. In the simulation part, two scenarios of multitone sources with unknown frequency and DOA locations and non-multitone wideband sources with assumed frequency region are examined. In multitone scenario, sparse solvers yield more accurate DOA-frequency representation compared to some noncoherent approaches. For non-multitone wideband source scenario, the proposed method with group sparse solver outperforms some existing wideband DOA estimators in low SNR regime. In addition, simultaneous sources’ recovery and DOA estimation shows significant improvement compared to the conventional delay and sum beamformer and without prerequisites required in sophisticated wideband beamformers.

Morphological and molecular characterization of Cystoisospora sp. from Asian small-clawed otters Aonyx cinereus.

In this study, we provide the first description of Cystoisospora infection in Asian small-clawed otters (Aonyx cinereus). In July 2017, three juvenile otters recently imported from the Republic of Indonesia showed severe diarrhea and were diagnosed with coccidial infection; two of them eventually died. Fecal examination revealed the presence of numerous oocysts. Sporulated oocysts showed typical Cystoisospora features, measuring 24.6 ± 1.6 (22.0–27.0) × 21.8 ± 1.4 (19.0–25.0) μm, with an oocyst length/width ratio of 1.1 ± 0.1 (1.0–1.3). Each sporocyst contained four sporozoites in a head-to-tail arrangement. The Stieda body was absent, and the sporocyst residuum was present. These morphological characteristics differentiated this species from the other valid Cystoisospora species described from mustelids. Molecular analysis was conducted at two loci: the nuclear 18S ribosomal RNA and mitochondrial cytochrome c oxidase subunit I genes. The 18S sequence showed high similarity with canine Cystoisispora ohioensis (1-bp difference, 1422/1423 [99.9%]). At the cytochrome c oxidase subunit I gene locus, the sequence from otters was identical to that of feline Cystoisospora rivolta (847/847 [100%]). Phylogenetic analyses using concatenated data demonstrated that Cystoisospora sp. from otters and C. rivolta grouped together in the same Cystoisospora clade. Based on these data, we concluded that Cystoisospora sp. detected from otters appeared to be highly similar to C. rivolta.

Discriminative Representation Learning with Supervised Auto-encoder

Auto-encoders have been proved to be powerful unsupervised learning methods that able to extract useful features from input data or construct deep artificial neural networks by recent studies. In such settings, the extracted features or the initialized networks only learn the data structure while contain no class information which is a disadvantage in classification tasks. In this paper, we aim to leverage the class information of input to learn a reconstructive and discriminative auto-encoder. More specifically, we introduce a supervised auto-encoder that combines the reconstruction error and the classification error to form a unified objective function while taking the noisy concatenate data and label as input. The noisy concatenate input is constructed in such a method that one third has only original data and zero labels, one third has only label and zero data, the last one third has both original data and label. We show that the representations learned by the proposed supervised auto-encoder are more discriminative and more suitable for classification tasks. Experimental results demonstrate that our model outperforms many existing learning algorithms.

Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales)

ABSTRACT A large polyporoid mushroom from the West Usambara Mountains in North-eastern Tanzania produces dark brown, up to 60-cm large fruiting bodies that at maturity may weigh more than 10 kg. It has a high rate of mycelial growth and regeneration and was found growing on both dry and green leaves of shrubs; attached to the base of living trees, and it was also observed to degrade dead snakes and insects accidentally coming into contact with it. Phylogenetic analyses based on individual and concatenated data sets of nrLSU, nrSSU and the RPB2 and TEF1 genes showed it, together with Laetiporus, Phaeolus, Pycnoporellus and Wolfiporia, to form a monophyletic group in Polyporales. Based on morphological features and molecular data, it is described as Kusaghiporia usambarensis.

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation.

Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with $k$ classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately $k$/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.

Molecular systematics of the New World clingfish genus Gobiesox (Teleostei: Gobiesocidae) and the origin of a freshwater clade

The phylogenetic relationships between marine and freshwater members of the New World clingfish genus Gobiesox are investigated using both mitochondrial and nuclear sequence data. Phylogenetic hypotheses are derived from Bayesian and maximum parsimony analyses of a six-gene concatenated data set (2 mitochondrial and 4 nuclear markers; 4098bp). Gobiesox is paraphyletic, due to the inclusion of Pherallodiscus, in phylogenetic hypotheses resulting from all analyses and its two included species are reassigned to Gobiesox. Within the expanded genus Gobiesox, the freshwater species (G. cephalus, G. juradoensis, G. mexicanus and G. potamius) represent a monophyletic group that is nested inside of a paraphyletic marine group. Based on the monophyly of the freshwater clingfishes, a habitat transition from marine to freshwater is inferred to have occurred only once in the evolutionary history of the group (potentially in the mid-Miocene). Gobiesox is obtained as part of a larger clade of New World clingfishes, including also members of Acyrtops, Acyrtus, Arcos, Rimicola, Sicyases and Tomicodon equivalent to the subfamily Gobiesocinae. The phylogenetic hypotheses obtained are discussed briefly in relation to the two alternative classifications currently in use simultaneously for the Gobiesocidae. A rediagnosis and list of included species is provided for Gobiesox.

A Methodology for Using Workforce Data to Decide Which Specialties and States to Target for Graduate Medical Education Expansion.

To outline a methodology for allocating graduate medical education (GME) training positions based on data from a workforce projection model. Demand for visits is derived from the Medical Expenditure PanelSurvey and Census data. Physician supply, retirements, and geographic mobility are estimated using concatenated AMA Masterfiles and ABMS certification data. The number and specialization behaviors of residents are derived from the AAMC's GMETrack survey. We show how the methodology could be used to allocate 3,000 new GME slots over 5years-15,000 total positions-by state and specialty to address workforce shortages in 2026. We use the model to identify shortages for 19 types of health care services provided by 35 specialties in 50 states. The new GME slots are allocated to nearly all specialties, but nine states and the District of Columbia do not receive any new positions. This analysis illustrates an objective, evidence-based methodology for allocating GME positions that could be used as the starting point for discussions about GME expansion or redistribution.

Increased phylogenetic resolution within the ecologically important Rhizopogon subgenus Amylopogon using 10 anonymous nuclear loci

ABSTRACTRhizopogon species are ecologically significant ectomycorrhizal fungi in conifer ecosystems. The importance of this system merits the development and utilization of a more robust set of molecular markers specifically designed to evaluate their evolutionary ecology. Anonymous nuclear loci (ANL) were developed for R. subgenus Amylopogon. Members of this subgenus occur throughout the United States and are exclusive fungal symbionts associated with Pterospora andromedea, a threatened mycoheterotrophic plant endemic to disjunct eastern and western regions of North America. Candidate ANL were developed from 454 shotgun pyrosequencing and assessed for positive amplification across targeted species, sequencing success, and recovery of phylogenetically informative sites. Ten ANL were successfully developed and were subsequently used to sequence representative taxa, herbaria holotype and paratype specimens in R. subgenus Amylopogon. Phylogenetic reconstructions were performed on individual and concatenated data sets by Bayesian inference and maximum likelihood methods. Phylogenetic analyses of these 10 ANL were compared with a phylogeny traditionally constructed using the universal fungal barcode nuc rDNA ITS1-5.8S-ITS2 region (ITS). The resulting ANL phylogeny was consistent with most of the species designations delineated by ITS. However, the ANL phylogeny provided much greater phylogenetic resolution, yielding new evidence for cryptic species within previously defined species of R. subgenus Amylopogon. Additionally, the rooted ANL phylogeny provided an alternate topology to the ITS phylogeny, which inferred a novel set of evolutionary relationships not identified in prior phylogenetic studies.

Global diversity and phylogeny of Onnia (Hymenochaetaceae) species on gymnosperms

ABSTRACTOnnia includes white rotting polypores with annual basidiocarps, a duplex context, monomitic hyphal structure, hymenial setae, and hyaline, thin-walled, smooth basidiospores. Specimens of Onnia, originating mainly from East Asia, Europe, and North America, were studied using both morphology and phylogenetic analyses. Our concatenated data set was derived from 25 collections and included (i) 25 nuc rDNA internal transcribed spacer region sequences (ITS1-5.8S-ITS2 = ITS), 17 generated in this study; and (ii) 14 nuc rDNA 28S rDNA sequences, including the D1–D2 domains, 11 of them generated in this study. The resulting maximum likelihood and Bayesian phylogenies recovered all sampled collections of Onnia as a well-supported clade. In this clade, three previously accepted species, viz., Onnia leporina, O. tomentosa, and O. triquetra, received strong support, whereas three additional lineages with strong support represent the new species described in this paper, O. subtriquetra, O. microspora, and O. tibetica. Of the six Onnia species occurring on gymnosperms, O. tomentosa and O. leporina grow mainly on Picea and have circumboreal distribution in the Northern Hemisphere. In contrast, other species that mostly grow on Pinus are geographically restricted to limited regions, viz., O. triquetra in Europe, O. subtriquetra in North America, and O. microspora and O. tibetica in Asia.

A dual PCR-based sequencing approach for the identification and discrimination of Echinococcus and Taenia taxa

Reliable and rapid molecular tools for the genetic identification and differentiation of Echinococcus species and/or genotypes are crucial for studying spatial and temporal transmission dynamics. Here, we describe a novel dual PCR targeting regions in the small (rrnS) and large (rrnL) subunits of mitochondrial ribosomal RNA (rRNA) genes, which enables (i) the specific identification of species and genotypes of Echinococcus (rrnS + L-PCR) and/or (ii) the identification of a range of taeniid cestodes, including different species of Echinococcus, Taenia and some others (17 species of diphyllidean helminths). This dual PCR approach was highly sensitive, with an analytical detection limit of 1 pg for genomic DNA of Echinococcus. Using concatenated sequence data derived from the two gene markers (1225 bp), we identified five unique and geographically informative single nucleotide polymorphisms (SNPs) that allowed genotypes (G1 and G3) of Echinococcus granulosus sensu stricto to be distinguished, and 25 SNPs that allowed differentiation within Echinococcus canadensis (G6/7/8/10). In conclusion, we propose that this dual PCR-based sequencing approach can be used for molecular epidemiological studies of Echinococcus and other taeniid cestodes.

Differences in Perceived Need for Medical, Therapeutic, and Family Support Services Among Children With ASD.

Identifying racial and ethnic differences in perceived need for treatment among families of children with autism spectrum disorder (ASD) will improve understanding of disparities in care seeking. We described racial and ethnic differences in perceived need for services that children with ASD and their families frequently use. We conducted bivariate analyses of racial and ethnic categories and perceived need for 6 common services used by children with ASD as found in the 2005 to 2006 (n = 2123) and the 2009 to 2010 (n = 3055) National Survey of Children With Special Health Care Needs data sets. Multivariate logistic regressions within concatenated data sets were conducted to examine associations between racial and ethnic category and perceived service needs while controlling for predisposing, enabling, and child factors. Compared with caregivers of white non-Hispanic children with ASD, caregivers of Hispanic children reported less need for prescription medications in adjusted multivariate analyses. Caregivers of black non-Hispanic children with ASD reported less need for prescription medications and for child and family mental health services than caregivers of white non-Hispanic children. Both English-speaking Hispanic caregivers and black non-Hispanic caregivers reported greater need for occupational, speech, and physical therapy than white non-Hispanic caregivers. No racial or ethnic differences were found in perceived need for specialty medical care or respite care. Caregivers of children with ASD from different racial and ethnic backgrounds may differentially perceive need for different types of care. Their perceptions may in turn affect how they prioritize and seek care, independent of their child's specific needs.

Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genus Sorghum.

Sorghum is an essential grain crop whose evolutionary placement within the Andropogoneae has been the subject of scrutiny for decades. Early studies using cytogenetic and morphological data point to a poly- or paraphyletic origin of the genus; however, acceptance of poly- or paraphyly has been met with resistance. This study aimed to address the species relationships within Sorghum, in addition to the placement of Sorghum within the tribe, using a phylogenetic approach and employing broad taxon sampling. From 16 diverse Sorghum species, eight low-copy nuclear loci were sequenced that are known to play a role in morphological diversity and have been previously used to study evolutionary relationships in grasses. Further, the data for four of these loci were combined with those from 57 members of the Andropogoneae in order to determine the placement of Sorghum within the tribe. Both maximum likelihood and Bayesian analyses were performed on multilocus concatenated data matrices. The Sorghum-specific topology provides strong support for two major lineages, in alignment with earlier studies employing chloroplast and internal transcribed spacer (ITS) markers. Clade I is composed of the Eu-, Chaeto- and Heterosorghum, while clade II contains the Stipo- and Parasorghum. When combined with data from the Andropogoneae, Clade II resolves as sister to a clade containing Miscanthus and Saccharum with high posterior probability and bootstrap support, and to the exclusion of Clade I. The results provide compelling evidence for a two-lineage polyphyletic ancestry of Sorghum within the larger Andropogoneae, i.e. the derivation of the two major Sorghum clades from a unique common ancestor. Rejection of monophyly in previous molecular studies is probably due to limited taxon sampling outside of the genus. The clade consisting of Para- and Stiposorghum resolves as sister to Miscanthus and Saccharum with strong node support.