Non-model Groups Research Articles

Phylogenomics of Lasiodoriforms: reclassification of the South American genus Vitalius Lucas, Silva and Bertani and allied genera (Araneae: Theraphosidae)

Theraphosinae is the most diverse subfamily of Theraphosidae spiders, but their evolutionary history remains unresolved to date. This problem is common in taxonomic groups with phylogenetic hypotheses that have often been based only on qualitative morphological characters and, rarely, on molecular analyses. Phylogenomics has significantly contributed to the understanding of the evolution of many non-model groups, such as spiders. Herein, we employed ultraconserved elements (UCEs) phylogenomics to propose a new hypothesis for a group of Theraphosinae genera, namely Lasiodoriforms: Vitalius, Lasiodora, Eupalaestrus, Pterinopelma, Proshapalopus, and Nhandu. We propose three genera and their respective morphological diagnoses are provided. Our phylogeny supports the transfer of species from the genus Vitalius to Pterinopelma and Proshapalopus and from Proshapalopus to Eupalaestrus. Finally, we describe a new species of Vitalius from Southern Brazil. Based on these three new generic descriptions and transferred species, the Lasiodoriform tarantulas comprise nine genera from Argentina, Brazil, Paraguay, and Uruguay, and the genus Vitalius now includes seven species.

Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals

Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a "deep diversity" of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.

Clinical application of vancomycin population pharmacokinetics model in patients with hematological diseases and neutropenia.

To explore the clinical application of a population pharmacokinetics (PPK) model of vancomycin in patients with hematological diseases and neutropenia. Patients with hematological diseases and neutropenia were included in the PPK model study. Nonlinear mixed effect modeling approach (NONMEM) was used for model establishment. Monte Carlo simulation was carried out. A total of 74 patients were divided into model group and non‐model group for clinical application research. The model group was given the initial dose of 1g q8h, and the non‐model group was given 1g q12h as an empiric initial dosage. The follow‐up dose adjustments were made according to the concentration results. This two‐compartment model showed good stability and accuracy. The first trough concentration (C 0) and the compliance rate of the first C 0 were much higher in the model group than that in the non‐model group (14.30 ± 4.73 μg/ml and 59.38% vs. 8.02 ± 2.61 μg/ml, 35.71%). Less patients needed dose adjustments and fewer adjustment times in the model group than those in the non‐model group (12.50% and 0.13 ± 0.34 times vs. 50.00% and 0.61 ± 0.66 times). This suggested that for those patients who had a Creatinine clearance rate (CLCR) ≥ 90 ml/min/1.73 m2, the initial dose of 1g q8h may help to reach the target C 0 (10∼20 μg/ml) quickly. It also helped to reduce the times and number of patients who need dose adjustments. Our PPK model of vancomycin in patients with hematologic diseases and neutropenia can be used to shorten the time to reach the target concentration and reduce the number of dose adjustments.Clinical trial registration: Not applicable (Retrospective study).

A guide for optimal iodine staining and high-throughput diceCT scanning in snakes.

Diffusible iodine‐based contrast‐enhanced computed tomography (diceCT) visualizes soft tissue from micro‐CT (µCT) scans of specimens to uncover internal features and natural history information without incurring physical damage via dissection. Unlike hard‐tissue imaging, taxonomic sampling within diceCT datasets is currently limited. To initiate best practices for diceCT in a nonmodel group, we outline a guide for staining and high‐throughput µCT scanning in snakes. We scanned the entire body and one region of interest (i.e., head) for 23 specimens representing 23 species from the clades Aniliidae, Dipsadinae, Colubrinae, Elapidae, Lamprophiidae, and Viperidae. We generated 82 scans that include 1.25% Lugol's iodine stained (soft tissue) and unstained (skeletal) data for each specimen. We found that duration of optimal staining time increased linearly with body size; head radius was the best indicator. Postreconstruction of scans, optimal staining was evident by evenly distributed grayscale values and clear differentiation among soft‐tissue anatomy. Under and over stained specimens produced poor contrast among soft tissues, which was often exacerbated by user bias during “digital dissections” (i.e., segmentation). Regardless, all scans produced usable data from which we assessed a range of downstream analytical applications within ecology and evolution (e.g., predator‐prey interactions, life history, and morphological evolution). Ethanol destaining reversed the known effects of iodine on the exterior appearance of physical specimens, but required substantially more time than reported for other destaining methods. We discuss the feasibility of implementing diceCT techniques for a new user, including approximate financial and temporal commitments, required facilities, and potential effects of staining on specimens. We present the first high‐throughput workflow for full‐body skeletal and diceCT scanning in snakes, which can be generalized to any elongate vertebrates, and increases publicly available diceCT scans for reptiles by an order of magnitude.

RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles

Study of repetitive DNA elements in model organisms highlights the role of repetitive elements (REs) in many processes that drive genome evolution and phenotypic change. Because REs are much more dynamic than single-copy DNA, repetitive sequences can reveal signals of evolutionary history over short time scales that may not be evident in sequences from slower-evolving genomic regions. Many tools for studying REs are directed toward organisms with existing genomic resources, including genome assemblies and repeat libraries. However, signals in repeat variation may prove especially valuable in disentangling evolutionary histories in diverse non-model groups, for which genomic resources are limited. Here, we introduce RepeatProfiler, a tool for generating, visualizing, and comparing repetitive element DNA profiles from low-coverage, short-read sequence data. RepeatProfiler automates the generation and visualization of RE coverage depth profiles (RE profiles) and allows for statistical comparison of profile shape across samples. In addition, RepeatProfiler facilitates comparison of profiles by extracting signal from sequence variants across profiles which can then be analysed as molecular morphological characters using phylogenetic analysis. We validate RepeatProfiler with data sets from ground beetles (Bembidion), flies (Drosophila), and tomatoes (Solanum). We highlight the potential of RE profiles as a high-resolution data source for studies in species delimitation, comparative genomics, and repeat biology.

Is it possible to use behavior characters for evolutionary reconstruction in marine invertebrates? A methodological approach using Ethokit Logger.

The use of behavioral data is quite common in studies of chordate animals and some groups of arthropods; however, these data are usually used in ecological and conservation studies. Their use remains uncommon in phylogenetic reconstructions, especially for non-model groups in behavioral studies. This study aims to evaluate the methodological use of behavioral (feeding process) data with EthoKit Logger in the phylogenetic reconstruction of the Cnidaria, a group in the so-called 'lower' Metazoa. The results indicate considerable cohesion with reconstructions based on molecular data available in previous studies. We therefore suggest that the use of behavioral characters can possible be a useful secondary tool or a proof test for molecular evolutionary reconstructions.

Streamlining universal single-copy orthologue and ultraconserved element design: A case study in Collembola.

Genomic data sets are increasingly central to ecological and evolutionary biology, but far fewer resources are available for invertebrates. Powerful new computational tools and the rapidly decreasing cost of Illumina sequencing are beginning to change this, enabling rapid genome assembly and reference marker extraction. We have developed and tested a practical workflow for developing genomic resources in nonmodel groups with real-world data on Collembola (springtails), one of the most dominant soil animals on Earth. We designed universal molecular marker sets, single-copy orthologues (BUSCOs) and ultraconserved elements (UCEs), using three existing and 11 newly generated genomes. Both marker types were tested in silico via marker capture success and phylogenetic performance. The new genomes were assembled with Illumina short reads and 9,585-14,743 protein-coding genes were predicted with ab initio and protein homology evidence. We identified 1,997 benchmarking universal single-copy orthologues (BUSCOs) across 14 genomes and created and assessed a custom BUSCO data set for extracting single-copy genes. We also developed a new UCE probe set containing 46,087 baits targeting 1,885 loci. We successfully captured 1,437-1,865 BUSCOs and 975-1,186 UCEs across 14 genomes. Phylogenomic reconstructions using these markers proved robust, giving new insight on deep-time collembolan relationships. Our study demonstrates the feasibility of generating thousands of universal markers from highly efficient whole-genome sequencing, providing a valuable resource for genome-scale investigations in evolutionary biology and ecology.

Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes.

Plants in the Burseraceae are globally recognized for producing resins and essential oils with medicinal properties and have economic value. In addition, most of the aromatic and non-aromatic components of Burseraceae resins are derived from a variety of terpene and terpenoid chemicals. Although terpene genes have been identified in model plant crops (e.g., Citrus, Arabidopsis), very few genomic resources are available for non-model groups, including the highly diverse Burseraceae family. Here we report the assembly of a leaf transcriptome of Protium copal, an aromatic tree that has a large distribution in Central America, describe the functional annotation of putative terpene biosynthetic genes and compare terpene biosynthetic genes found in P. copal with those identified in other Burseraceae taxa. The genomic resources of Protium copal can be used to generate novel sequencing markers for population genetics and comparative phylogenetic studies, and to investigate the diversity and evolution of terpene genes in the Burseraceae.

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism.

The relative ease of high throughput sequencing is facilitating comprehensive phylogenomic and gene expression studies, even for nonmodel groups. To date, however, these two approaches have not been merged; while phylogenomic methods might use transcriptome sequences to resolve relationships, assessment of gene expression patterns in a phylogenetic context is less common. Here we analyzed both carbon assimilation and gene expression patterns of closely related species within the Agavoideae (Asparagaceae) to elucidate changes in gene expression across weak and strong phenotypes for Crassulacean acid metabolism (CAM). Gene expression patterns were compared across four genera: Agave (CAM), which is paraphyletic with Polianthes (weak CAM) and Manfreda (CAM), and Beschorneria (weak CAM). RNA-sequencing was paired with measures of gas exchange and titratable acidity. Climate niche space was compared across the four lineages to examine abiotic factors and their correlation to CAM. Expression of homologous genes showed both shared and variable patterns in weak and strong CAM species. Network analysis highlights that despite shared expression patterns, highly connected genes differ between weak and strong CAM, implicating shifts in regulatory gene function as key for the evolution of CAM. Variation in carbohydrate metabolism between weak and strong CAM supports the importance of sugar turnovers for CAM physiology. Integration of phylogenetics and RNA-sequencing provides a powerful tool to study the evolution of CAM photosynthesis across closely related but photosynthetically variable species. Our findings regarding shared or shifted gene expression and regulation of CAM via carbohydrate metabolism have important implications for efforts to engineer the CAM pathway into C3 food and biofuel crops.

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches.

Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages.

Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): A next-generation sequencing transcriptomic approach

Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3′ untranslated regions (3′-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3′-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3′-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3′-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.

Qualidade de vida de adolescentes modelos profissionais

Muitas adolescentes deixam suas famílias para seguir a profissão de modelo, sonhando com um futuro glamoroso. O presente estudo caso-controle analisou a qualidade de vida de 74 adolescentes do sexo feminino, sendo 37 modelos, agenciadas em São Paulo, com delineamento transversal, utilizando o World Health Organization Quality of Life - versão breve (WHOQOL-BREF), que avalia qualidade de vida global e os domínios físico, psicológico, social e ambiental. Utilizou-se o Critério Brasil 2008, para avaliação do nível socioeconômico e para parear o grupo controle. Em geral, o grupo de modelos obteve médias superiores ao grupo de não modelos, sendo esta diferença significante apenas no domínio psicológico. Observou-se que as adolescentes modelos apresentaram uma qualidade de vida semelhante à das não modelos.

Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi

Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species.

Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008

Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008

Structure and Evolution of a New Avian MHC Class II B Gene in a Sub-Antarctic Seabird, the Thin-Billed Prion (Procellariiformes: Pachyptila belcheri)

The major histocompatibility complex encodes molecules that present foreign peptides to T cells of the immune system. The peptide binding region (PBR) of these molecules is among the most polymorphic regions found in vertebrate taxa. Genomic cloning approaches are improving our understanding of the evolution of this multigene family in nonmodel avian groups. By building a cosmid library, a new MHC class II B gene, Pabe-DAB1, was isolated and characterized at the genomic level in a sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri). Pabe-DAB1 exhibits the hallmark structural features of functional MHC class II loci. Direct sequencing of the PBR encoding exon in a panel of prions revealed significantly higher levels of genetic diversity compared to two noncoding neutral loci, with most alleles differing by at least one replacement substitution in the peptide binding codons. We estimated evolutionary dynamics for Pabe-DAB1 using a variety of Bayesian and other approaches. Evidence for balancing selection comes from a spatially variable ratio of nonsynonymous-to-synonymous substitutions (mean d (N)/d (S) = 2.87) in the PBR, with sites predicted to be functionally relevant exhibiting the highest omega values. We estimate the population recombination rate to be approximately 0.3 per site per generation, indicating an important role for recombination in generating polymorphism at this locus. Pabe-DAB1 is among the few avian class II loci characterized at the genomic level and with a known intron-exon structure, a feature that greatly facilitated the amplification and sequencing of a single MHC locus in this species.

The Effects of Social Learning Context and Modeling on Persistence and Dynamism in Academic Activities

Abstract The authors investigated 138 third-and fourth-grade students' responses to failures and successes in a mathematics computation task in four experimental conditions varied by the two independent variables of social learning context and modeling. Interaction effects indicated that a collaborative learning context increased students' persistence following failures and dynamism after successes in a nonmodeling group, and modeling enhanced persistence and dynamism in an individual learning context. The enhancing effects of the collaborative learning context can be best explained by the familiarity with the problem solving, and the enhancing effects of modeling may be best explained by the identification between students and the model. Findings from this study demonstrate the motivational advantages of both collaborative learning and modeling.

The Effect of User-Developed DSS Applications on Forecasting Decision-Making Performance in an Experimental Setting

Abstract:A primary assumption of decision support systems (dss) is that their use will result in more effective decision making. Using a repeated measures design, we conducted an experimental gaming study to investigate the effect of user-developed dss applications on the decision maker’s ability to forecast his or her actual gaming results.The findings of this study support the proposition that user-developed dss models lead to more effective decision making. Subjects in the dss modeling group made significantly better forecasts of their firm’s performance than did those in the non-modeling group.

Training speech pathologists through microtherapy

Two microtraining models were evaluated for training speech pathologists in the acquisition of skills utilized in treating misarticulations. Fifteen subjects in an introductory class in speech pathology were randomly placed in two groups (modeling, video replay, and counseling versus video replay and counseling). The training included reading a manual about the skills and a sequence of three teach sessions. The control group did not view the video model. According to the results, the model group made a greater gain score ( M = 8.38) than the nonmodel group ( M = 3.88). Significant gains were made for both experimental groups between teach sessions one and two, but no significant gains were made between the second and third teach sessions.

Effects of minimal models on inkblot percepts

Three experiments using brief, audio tape recordings as models, demonstrated observational learning of inkblot percept categories. The tapes created significant increases over baseline scores for all three classes of determinants, and two of three location classes studied; with the exception noted, Ss generalized to a new set of inkblot stimuli the percept categories they had heard. Further, except for one class of determinants, the modeling tapes induced increases in all other categories significantly greater than the spontaneous changes of a non-modeling control group. The implications of the results for observational learning of cognitive behavior and for clinical use of projective techniques were discussed.