scholarly journals Natural hybridization between two species of green Anoles: morphological and genetic evidence

2020 ◽  
pp. 73-95
Author(s):  
Eveling Gabot-Rodríguez ◽  
Sixto J. Incháustegui ◽  
Markus Pfenninger ◽  
Barbara Feldmeyer ◽  
Gunther Kӧhler
Keyword(s):  
Introduced Species ◽  
Endemic Species ◽  
Sequence Data ◽  
Natural Hybridization ◽  
Data Sets ◽  
Negative Consequences ◽  
Santo Domingo ◽  
Pure Species ◽  
Wide Range ◽  
16S Sequence

Anoles are a group of lizards that offer a wide range of opportunities to study different biological topics. In this work, we examined some aspects of the morphology from 139 individuals of green anoles collected in urban parks of Santo Domingo and the Distrito Nacional. We investigated evidence of hybridization between the two Hispaniola endemic species Anolis chlorocyanus and A. cyanostictus and the introduced species A. porcatus. We categorized the individuals in pure species and intermediates based on their phenotype. Additionally, mitochondrial 16S sequence data was generated from the collected specimens, to compare molecular and phenotypic species assignments. We consider the general congruence between both data sets in most but inconsistency in a few specimens as evidence for hybridization between the two endemic species. However, we did not find evidence of hybridization between any of these species and the introduced species A. porcatus. Nevertheless, the continuous expansion of the distribution of this invasive species possibly will have drastic negative consequences for the populations of the endemic species.

scholarly journals mtDNAcombine: tools to combine sequences from multiple studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Eleanor F. Miller ◽  
Andrea Manica
Keyword(s):  
Sequence Data ◽  
Data Extraction ◽  
Bayesian Skyline Plot ◽  
Model Organisms ◽  
Data Sets ◽  
Data Handling ◽  
Online Database ◽  
Genetic Studies ◽  
Wide Range ◽  
Existing Data

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

scholarly journals Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

2020 ◽  
Vol 37 (11) ◽  
pp. 3363-3379 ◽  
Author(s):  
Sebastian Duchene ◽  
Philippe Lemey ◽  
Tanja Stadler ◽  
Simon Y W Ho ◽  
David A Duchene ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Ancient Dna ◽  
Time Window ◽  
Sequence Data ◽  
H1n1 Influenza ◽  
Rate Variation ◽  
Data Sets ◽  
Molecular Sequence Data ◽  
Wide Range ◽  
Sampling Times

Abstract Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.

scholarly journals Seabird Supertrees: Combining Partial Estimates of Procellariiform Phylogeny

The Auk ◽  
2002 ◽  
Vol 119 (1) ◽  
pp. 88-108 ◽  
Author(s):  
Martyn Kennedy ◽  
Roderic D. M. Page
Keyword(s):  
Dna Hybridization ◽  
Sequence Data ◽  
Matrix Representation ◽  
Data Sets ◽  
Conservative Estimate ◽  
Phylogenetic Studies ◽  
Combining Data ◽  
Wide Range ◽  
Source Studies ◽  
Phylogenetic Hypotheses

Abstract The growing use of comparative methods to address evolutionary questions has generated an increased need for robust hypotheses of evolutionary relationships for a wide range of organisms. Where a phylogeny exists for a group, often more than one phylogeny will exist for that group, and it is uncommon that the same taxa are in each of the existing trees. The types of data used to generate evolutionary trees can also vary greatly, and thus combining data sets is often difficult or impossible. To address comparative questions for groups where multiple phylogenetic hypotheses already exist, we need to combine different hypotheses in a way that provides the best estimate of the phylogeny for that group. Here, we combine seven seabird phylogenies (based on behavioral, DNA–DNA hybridization, isozyme, life history, morphological, and sequence data) to generate a comprehensive supertree for the Procellariiformes using matrix representation with parsimony. This phylogeny contains 122 taxa and represents a conservative estimate of combined relationships presented in the original seven source trees. We compared the supertree with results of a combined sequence data supermatrix for 103 seabird taxa. Results of the two approaches are broadly concordant, but matrix representation with parsimony provides a more comprehensive and more conservative estimate of the phylogeny of the group because it is less influenced by the largest of the source studies (which uses a single, relatively quickly evolving gene). Genetic data sets that can be combined in a supermatrix approach are currently less likely to be available than phylogenies that can be combined using some form of supertree approach. Although there are limitations to both of those approaches, both would be simpler if all phylogenetic studies made both their data sets and trees they generate available through databases such as TREEBASE.

scholarly journals Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

2019 ◽  
Author(s):  
Sebastian Duchene ◽  
Philippe Lemey ◽  
Tanja Stadler ◽  
Simon YW Ho ◽  
David A Duchene ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Ancient Dna ◽  
Time Window ◽  
Sequence Data ◽  
H1n1 Influenza ◽  
Rate Variation ◽  
Data Sets ◽  
Molecular Sequence Data ◽  
Wide Range ◽  
Sampling Times

AbstractPhylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behaviour of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.

The Biology of Mediterranean-Type Ecosystems

2018 ◽  
Author(s):  
Karen J. Esler ◽  
Anna L. Jacobsen ◽  
R. Brandon Pratt
Keyword(s):  
Climate Change ◽  
South Africa ◽  
Invasive Species ◽  
Habitat Loss ◽  
Endemic Species ◽  
Geographic Area ◽  
Cutting Edge ◽  
Wide Range ◽  
The Mediterranean ◽  
Mediterranean Type Ecosystems

The world’s mediterranean-type climate regions (including areas within the Mediterranean, South Africa, Australia, California, and Chile) have long been of interest to biologists by virtue of their extraordinary biodiversity and the appearance of evolutionary convergence between these disparate regions. Comparisons between mediterranean-type climate regions have provided important insights into questions at the cutting edge of ecological, ecophysiological and evolutionary research. These regions, dominated by evergreen shrubland communities, contain many rare and endemic species. Their mild climate makes them appealing places to live and visit and this has resulted in numerous threats to the species and communities that occupy them. Threats include a wide range of factors such as habitat loss due to development and agriculture, disturbance, invasive species, and climate change. As a result, they continue to attract far more attention than their limited geographic area might suggest. This book provides a concise but comprehensive introduction to mediterranean-type ecosystems. As with other books in the Biology of Habitats Series, the emphasis in this book is on the organisms that dominate these regions although their management, conservation, and restoration are also considered.

scholarly journals Healthcare Providers’ Perceptions of Challenges with Frequent Users of Emergency Department Care in Switzerland: A Qualitative Study

2021 ◽  
Vol 58 ◽  
pp. 004695802110281
Author(s):  
Patrick Bodenmann ◽  
Miriam Kasztura ◽  
Madison Graells ◽  
Elodie Schmutz ◽  
Oriane Chastonay ◽  
...  
Keyword(s):  
Online Survey ◽  
Emergency Services ◽  
Healthcare Providers ◽  
Negative Consequences ◽  
Emergency Department Care ◽  
Frequent Users ◽  
Complex Needs ◽  
Wide Range ◽  
Ed Overcrowding ◽  
Ed Visits

Frequent users of emergency departments (FUED; ≥ 5 ED visits/year) commonly cumulate medical, social, and substance use problems requiring complex and sustained care coordination often unavailable in ED. This study aimed to explore ED healthcare providers’ challenges related to FUED care to gain insight into the support and resources required to address FUED complex needs. An online survey was sent to all general adult emergency services within Switzerland (N = 106). Participants were asked to indicate the extent to which they perceived that FUED represented a problem and to describe the main challenges encountered. In total, 208 physicians and nurses from 75 EDs (70.7%) completed the survey. Among the 208 participants, 134 (64%) reported that FUED represented a challenge and 133 described 1 to 5 challenges encountered. A conventional content analysis yielded 4 main categories of perceived challenges. Negative consequences in the ED secondary to FUED’s presence (eg, ED overcrowding, staff helplessness, and fatigue) was the most frequently reported challenge, followed by challenges related to FUEDs’ characteristics (eg, mental health and social problems) leading to healthcare complexity. The third most frequently encountered challenge was related to the ED inappropriateness and inefficiency to address FUEDs’ needs. Finally, challenges related to the lack of FUED healthcare network were the least often mentioned. ED healthcare providers experience a wide range of challenges related to FUED care. These findings suggest that currently EDs nor their staff are equipped to address FUEDs’ complex needs.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

scholarly journals MUREN: a robust and multi-reference approach of RNA-seq transcript normalization

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yance Feng ◽  
Lei M. Li
Keyword(s):  
Biological Significance ◽  
Housekeeping Genes ◽  
R Package ◽  
Data Sets ◽  
Statistical Regression ◽  
Rna Seq ◽  
Least Trimmed Squares ◽  
Standard Data ◽  
Wide Range ◽  
Multiple References

Abstract Background Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or implicitly, the justification of normalization requires a set of housekeeping genes. However, the existence of housekeeping genes common for a very large collection of samples, especially under a wide range of conditions, is questionable. Results We propose to carry out pairwise normalization with respect to multiple references, selected from representative samples. Then the pairwise intermediates are integrated based on a linear model that adjusts the reference effects. Motivated by the notion of housekeeping genes and their statistical counterparts, we adopt the robust least trimmed squares regression in pairwise normalization. The proposed method (MUREN) is compared with other existing tools on some standard data sets. The goodness of normalization emphasizes on preserving possible asymmetric differentiation, whose biological significance is exemplified by a single cell data of cell cycle. MUREN is implemented as an R package. The code under license GPL-3 is available on the github platform: github.com/hippo-yf/MUREN and on the conda platform: anaconda.org/hippo-yf/r-muren. Conclusions MUREN performs the RNA-seq normalization using a two-step statistical regression induced from a general principle. We propose that the densities of pairwise differentiations are used to evaluate the goodness of normalization. MUREN adjusts the mode of differentiation toward zero while preserving the skewness due to biological asymmetric differentiation. Moreover, by robustly integrating pre-normalized counts with respect to multiple references, MUREN is immune to individual outlier samples.

scholarly journals A Visual and VAE Based Hierarchical Indoor Localization Method

Sensors ◽  
2021 ◽  
Vol 21 (10) ◽  
pp. 3406
Author(s):  
Jie Jiang ◽  
Yin Zou ◽  
Lidong Chen ◽  
Yujie Fang
Keyword(s):  
Image Retrieval ◽  
Indoor Localization ◽  
Data Sets ◽  
Indoor Environments ◽  
Global Features ◽  
Data Set ◽  
Data Annotation ◽  
Wide Range ◽  
Annotation Costs ◽  
Global And Local

Precise localization and pose estimation in indoor environments are commonly employed in a wide range of applications, including robotics, augmented reality, and navigation and positioning services. Such applications can be solved via visual-based localization using a pre-built 3D model. The increase in searching space associated with large scenes can be overcome by retrieving images in advance and subsequently estimating the pose. The majority of current deep learning-based image retrieval methods require labeled data, which increase data annotation costs and complicate the acquisition of data. In this paper, we propose an unsupervised hierarchical indoor localization framework that integrates an unsupervised network variational autoencoder (VAE) with a visual-based Structure-from-Motion (SfM) approach in order to extract global and local features. During the localization process, global features are applied for the image retrieval at the level of the scene map in order to obtain candidate images, and are subsequently used to estimate the pose from 2D-3D matches between query and candidate images. RGB images only are used as the input of the proposed localization system, which is both convenient and challenging. Experimental results reveal that the proposed method can localize images within 0.16 m and 4° in the 7-Scenes data sets and 32.8% within 5 m and 20° in the Baidu data set. Furthermore, our proposed method achieves a higher precision compared to advanced methods.

scholarly journals An Interoperability Platform Enabling Reuse of Electronic Health Records for Signal Verification Studies

2016 ◽  
Vol 2016 ◽  
pp. 1-18 ◽  
Author(s):  
Mustafa Yuksel ◽  
Suat Gonul ◽  
Gokce Banu Laleci Erturkmen ◽  
Ali Anil Sinaci ◽  
Paolo Invernizzi ◽  
...  
Keyword(s):  
Real Life ◽  
Case Series ◽  
Background Information ◽  
Data Sets ◽  
Local Data ◽  
Lombardy Region ◽  
Common Information ◽  
Spontaneous Reports ◽  
Wide Range ◽  
Common Information Model

Depending mostly on voluntarily sent spontaneous reports, pharmacovigilance studies are hampered by low quantity and quality of patient data. Our objective is to improve postmarket safety studies by enabling safety analysts to seamlessly access a wide range of EHR sources for collecting deidentified medical data sets of selected patient populations and tracing the reported incidents back to original EHRs. We have developed an ontological framework where EHR sources and target clinical research systems can continue using their own local data models, interfaces, and terminology systems, while structural interoperability and Semantic Interoperability are handled through rule-based reasoning on formal representations of different models and terminology systems maintained in the SALUS Semantic Resource Set. SALUS Common Information Model at the core of this set acts as the common mediator. We demonstrate the capabilities of our framework through one of the SALUS safety analysis tools, namely, the Case Series Characterization Tool, which have been deployed on top of regional EHR Data Warehouse of the Lombardy Region containing about 1 billion records from 16 million patients and validated by several pharmacovigilance researchers with real-life cases. The results confirm significant improvements in signal detection and evaluation compared to traditional methods with the missing background information.

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