Testing the accuracy of genus-level data to predict species diversity in Cenozoic marine diatoms

Geology ◽  
2016 ◽  
Vol 44 (12) ◽  
pp. 1051-1054 ◽  
Author(s):  
Robert Wiese ◽  
Johan Renaudie ◽  
David B. Lazarus
Keyword(s):  
Species Diversity ◽  
Marine Diatoms ◽  
Genus Level ◽  
Level Data

Diatoms in the Early Valdai (Weichselian) sediments in Lake Ladoga basin

2019 ◽  
pp. 225-228
Author(s):  
Anna V. Ludikova
Keyword(s):  
Species Diversity ◽  
High Energy ◽  
Lake Ladoga ◽  
Diatom Assemblages ◽  
Marine Diatoms ◽  
Selective Preservation

The pioneer diatom study of the Early Weichselian (Valdai) sediments in Lake Ladoga basin was performed. The specifics of the diatom assemblages (co-occurrence of ecologically incompatible taxa, poor species diversity, low diatom concentration and selective preservation) suggest that during the Early Weichselian time intense erosion of previously deposited marine Eemian (Mikulino) sediments prevailed, which resulted in re-deposition of marine diatoms. The sedimentation took place in high-energy environments unfavorable for diatom accumulation and preservation.

scholarly journals Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11437
Author(s):  
Sungju Lim ◽  
Shilpa Rajagopal ◽  
Ye Ryn Jeong ◽  
Dumebi Nzegwu ◽  
Michelle L. Wright
Keyword(s):  
Systematic Review ◽  
Group B Streptococcus ◽  
Taxonomic Composition ◽  
Vaginal Microbiome ◽  
Large Variability ◽  
Microbiome Analysis ◽  
Genus Level ◽  
Level Data ◽  
Subsequent Birth ◽  
Group B

Background Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. Methodology A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms “vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”. Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. Results Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. Conclusion Considerable differences in study design and data formatting methods may contribute to underrepresentation of GBS, and other known pathogens, in existing vaginal microbiome literature. Previous studies have identified considerable variation in methodology across vaginal microbiome studies. This study adds to this body of work because in addition to laboratory or statistical methods, how results and data are shared (e.g., only analyzing genus level data or 20 most abundant microbes), may hinder reproducibility and limit our understanding of the influence of less abundant microbes. Sharing detailed methods, analysis code, and raw data may improve reproducibility and ability to more accurately compare microbial communities across studies.

scholarly journals Ecological studies of mayflies (Insecta, Ephemeroptera): Can sampling effort be reduced without losing essential taxonomic and ecological information?

2018 ◽  
Vol 48 (2) ◽  
pp. 137-145 ◽  
Author(s):  
Yulie SHIMANO ◽  
Mylena CARDOSO ◽  
Leandro JUEN
Keyword(s):  
Species Composition ◽  
Species Abundance ◽  
Taxonomic Resolution ◽  
Sampling Effort ◽  
Ecological Information ◽  
Genus Level ◽  
Level Data ◽  
Group A ◽  
Species Richness And Abundance ◽  
Laboratory Time

ABSTRACT The present study evaluated the potential for the reduction of sampling effort in studies of ephemeropteran nymphs in Brazilian Amazon streams, Pará State, Brazil, without the loss of ecological information (species composition, abundance, and richness), and the congruence of different levels of taxonomic resolution (morphospecies, genus, family and functional group). Test groups of 15, 10 and five subsamples were selected from the 20 subsamples collected per stream (40 streams sampled), and were compared in terms of their species richness and abundance (ANOVA), and composition (Procrustes). Taxonomic resolution was also analyzed in Procrustes. Species abundance (F(3, 156) = 25.426; p < 0.001) and richness (F(3, 156) = 13.866, p < 0.001) varied significantly among sample groups, while the results of the 15-S group were statistically similar, in both cases, to those of the 20-S group. A similar pattern was found for species composition. The genus-level taxonomic resolution produced results 99% similar to those found for the species-level data. The results indicate that the reduction in sampling effort from 20 to 15 subsamples per site and a genus-level taxonomic resolution would not affect the reliability of analyses significantly. A reduction of five samples per site would result in a decrease of effort in the field and the amount of material to be processed, reducing laboratory time. In addition to a reduction in the time and resources needed to identify specimens, the adoption of a genus-level taxonomic resolution could help minimize errors of under- or over-estimation in the processing of the results.

Long-term patterns of net phytoplankton and hydrography in coastal SE Arabian Sea: What can be inferred from genus level data?

2015 ◽  
Vol 162 ◽  
pp. 69-75 ◽  
Author(s):  
Anna Godhe ◽  
Chethan Narayanaswamy ◽  
Riina Klais ◽  
K.S. Venkatesha Moorthy ◽  
Rengaswamy Ramesh ◽  
...  
Keyword(s):  
Arabian Sea ◽  
Genus Level ◽  
Level Data ◽  
Net Phytoplankton

Revision of the status of some genus-level water mite taxa in the families Pionidae Thor, 1900, Aturidae Thor, 1900, and Nudomideopsidae Smith, 1990 (Acari: Hydrachnidiae)

Zootaxa ◽  
2015 ◽  
Vol 3919 (1) ◽  
pp. 111 ◽  
Author(s):  
IAN M. SMITH ◽  
DAVID R. COOK ◽  
REINHARD GERECKE
Keyword(s):  
Species Diversity ◽  
Current Knowledge ◽  
Family Group ◽  
Water Mites ◽  
Water Mite ◽  
Genus Level ◽  
The Family ◽  
The Status ◽  
Apparent Age

A number of changes to the status of genus group names in water mites are proposed to foster a more consistent and phylogenetically defensible approach to the ranking of taxa at this level of the classification. The water mite taxa Acercopsis Viets, 1926 (Pionidae: Tiphyinae), Madawaska Habeeb, 1954 (Pionidae: Foreliinae), Brachypodopsis Piersig, 1903, Cubanaxonopsis Orghidan & Gruia, 1981, Hexaxonopsis Viets, 1926, Paraxonopsis Motaş & Tanasachi, 1947, Vicinaxonopsis Cook, 1974, Parabrachypoda Viets, 1929, and Ocybrachypoda Cook, 1974 (Aturidae: Axonopsinae), Ameribrachypoda Smith, 1991 (Aturidae: Aturinae), and Allomideopsis Smith, 1990 (Nudomideopsidae) are elevated in rank from subgenera to full genera to reflect current knowledge of their species diversity, morphological distinctness, relationships and apparent age. In light of the above changes in the subfamily Axonopsinae, the subgenera Kalobrachypoda Viets, 1929 and Navinaxonopsis Cook, 1967 are transferred from the genus Axonopsis to the genus Brachypodopsis, the subgenus Plesiobrachypoda Viets, 1942 is transferred from the genus Axonopsis to the genus Hexaxonopsis, and the species formerly placed in the subgenus Hemibrachypoda Viets, 1937 are transferred from the genus Brachypoda to the genus Parabrachypoda Viets, 1929, and Hemibrachypoda is placed in synonymy with Parabrachypoda. The family group taxa to which all of these genera belong are reviewed to provide context for the proposed changes. 

New Evidence on the Construct Validity of the ASI-3 and the Dimensional Conceptualization of Trait Anxiety Sensitivity From IRT Modeling

2017 ◽  
Vol 33 (3) ◽  
pp. 181-189 ◽  
Author(s):  
Christoph J. Kemper ◽  
Michael Hock
Keyword(s):  
Construct Validity ◽  
Anxiety Sensitivity ◽  
Latent Class ◽  
Dimensional Structure ◽  
Sensitivity Index ◽  
Response Scale ◽  
Established Risk Factor ◽  
Irt Models ◽  
Level Data ◽  
Extreme Response

Abstract. Anxiety Sensitivity (AS) denotes the tendency to fear anxiety-related sensations. Trait AS is an established risk factor for anxiety pathology. The Anxiety Sensitivity Index-3 (ASI-3) is a widely used measure of AS and its three most robust dimensions with well-established construct validity. At present, the dimensional conceptualization of AS, and thus, the construct validity of the ASI-3 is challenged. A latent class structure with two distinct and qualitatively different forms, an adaptive form (normative AS) and a maladaptive form (AS taxon, predisposing for anxiety pathology) was postulated. Item Response Theory (IRT) models were applied to item-level data of the ASI-3 in an attempt to replicate previous findings in a large nonclinical sample (N = 2,603) and to examine possible interpretations for the latent discontinuity observed. Two latent classes with a pattern of distinct responses to ASI-3 items were found. However, classes were indicative of participant’s differential use of the response scale (midpoint and extreme response style) rather than differing in AS content (adaptive and maladaptive AS forms). A dimensional structure of AS and the construct validity of the ASI-3 was supported.

Modeling Intraindividual Variability in Three-Level Multilevel Models

Methodology ◽  
2018 ◽  
Vol 14 (3) ◽  
pp. 95-108 ◽  
Author(s):  
Steffen Nestler ◽  
Katharina Geukes ◽  
Mitja D. Back
Keyword(s):  
Multilevel Model ◽  
Multilevel Models ◽  
Mixed Effects ◽  
Repeated Measurements ◽  
Scale Model ◽  
Suggested Approach ◽  
Psychological Study ◽  
Level Data ◽  
Ecological Momentary ◽  
Momentary Assessment

Abstract. The mixed-effects location scale model is an extension of a multilevel model for longitudinal data. It allows covariates to affect both the within-subject variance and the between-subject variance (i.e., the intercept variance) beyond their influence on the means. Typically, the model is applied to two-level data (e.g., the repeated measurements of persons), although researchers are often faced with three-level data (e.g., the repeated measurements of persons within specific situations). Here, we describe an extension of the two-level mixed-effects location scale model to such three-level data. Furthermore, we show how the suggested model can be estimated with Bayesian software, and we present the results of a small simulation study that was conducted to investigate the statistical properties of the suggested approach. Finally, we illustrate the approach by presenting an example from a psychological study that employed ecological momentary assessment.

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