Testing depth-related multivariate patterns of macrofauna on the Indian continental shelf using reduced taxonomic resolution and data transformation

2011 ◽  
Vol 93 (1) ◽  
pp. 37-45 ◽  
Author(s):  
T.V. Joydas ◽  
R. Damodaran
Keyword(s):  
Continental Shelf ◽  
Multivariate Analyses ◽  
Geographical Area ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Depth Gradient ◽  
Data Set ◽  
Level Data ◽  
Two Samples ◽  
Family Level

Although taxonomic sufficiency (TS) was developed for rapid environmental assessments, it has recently been adopted to study the spatial patterns of macrobenthos in relation to natural environmental gradients. To accept TS as a routine approach in wider benthic studies, it needs to be valid for various taxa and geographically different water masses. This study examined the effects of taxonomic resolution on depth-related multivariate patterns of macrobenthic polychaetes on the western Indian continental shelf. An extensive data set based on samples collected from a wide geographical area (7°–22°N latitudes) covering a large depth gradient (30–200 m) has been analysed. Species level polychaete community data had shown a significant variation between shallow and deeper waters. Our results indicated that generic and family level data also can detect community shifts along a depth gradient in a similar way to species level data. The entire western continental margin (200 m depth) is lying in the oxygen minimum zone (dissolved oxygen <0.5 ml l−1). This study indicated that family level results were sufficient to document the correlations of low oxygen on macrobenthic polychaetes. This study also tested the effects of transformations on depth-related patterns of polychaetes. In multivariate analyses, transformations play a role in defining the balance between contributions from common and rare species in the measure of similarity of two samples. Our results showed that the type of transformations did not make any prominent differences in the multivariate analyses.

Taxonomic and numerical sufficiency in depth- and salinity-controlled marine paleocommunities

Paleobiology ◽  
2017 ◽  
Vol 43 (3) ◽  
pp. 463-478 ◽  
Author(s):  
Martin Zuschin ◽  
Rafał Nawrot ◽  
Mathias Harzhauser ◽  
Oleg Mandic ◽  
Adam Tomašových
Keyword(s):  
Compositional Data ◽  
Environmental Gradients ◽  
Community Response ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Physical Parameters ◽  
Level Data ◽  
Numerical Transformation ◽  
Variation Explained ◽  
Intertidal Habitats

AbstractNumerical and taxonomic resolution of compositional data sets affects investigators’ abilities to detect and measure relationships between communities and environmental factors. We test whether varying numerical (untransformed, square-root- and fourth-root-transformed relative abundance and presence–absence data) and taxonomic (species, genera, families) resolutions reveals different insights into early to middle Miocene molluscan communities along bathymetric and salinity gradients. The marine subtidal has a more even species-abundance distribution, a higher number of rare species, and higher species:family and species:genus ratios than the three habitats—marine and estuarine intertidal, estuarine subtidal—with higher fluctuations in salinity and other physical parameters. Taxonomic aggregation and numerical transformation of data result in very different ordinations, although all habitats differ significantly from one another at all taxonomic and numerical levels. Rank correlations between species-level and higher-taxon, among-sample dissimilarities are very high for proportional abundance and decrease strongly with increasing numerical transformation, most notably in the two intertidal habitats. The proportion of variation explained by depth is highest for family-level data, decreases gradually with numerical transformation, and is higher in marine than in estuarine habitats. The proportion of variation explained by salinity is highest for species-level data, increases gradually with numerical transformation, and is higher in subtidal than in intertidal habitats. Therefore, there is no single best numerical and taxonomic resolution for the discrimination of communities along environmental gradients: the “best” resolution depends on the environmental factor considered and the nature of community response to it. Different numerical and taxonomic transformations capture unique aspects of metacommunity assembly along environmental gradients that are not detectable at a single level of resolution. We suggest that simultaneous analyses of community gradients at multiple taxonomic and numerical resolutions provide novel insights into processes responsible for spatial and temporal community stability.

scholarly journals Reliability of Taxonomic Sufficiency for Simplifying Benthic Index M-AMBI Methodology in A Heavily Polluted Estuary

2020 ◽  
Author(s):  
Hongjun Li ◽  
Yi Sun ◽  
Yanbin Gu ◽  
Pengfei Xie ◽  
Yuan Liu ◽  
...  
Keyword(s):  
Species Level ◽  
Biotic Index ◽  
Ecological Quality ◽  
Taxonomic Sufficiency ◽  
As Species ◽  
Level Data ◽  
Ecological Quality Status ◽  
Family Level ◽  
Benthic Index ◽  
The Relationship

Abstract In order to assess the ecological quality status of coastal environments in Europe, the AZTI’s Marine Biotic Index (AMBI) and multivariate-AMBI (M-AMBI) have been developed. However, the applicability and validity of these methods worldwide remains in question, particularly for complex ecosystems such as estuaries. The present study, therefore, is an investigation of the relationship between the M-AMBI and different contamination variables in a eutrophic estuary in three seasons (i.e., spring, summer and autumn). In addition, the reliability of taxonomic sufficiency for simplifying M-AMBI operation was tested. The results showed that genus- and family-level data accurately reproduced the spatial-temporal patterns of species-level community assemblages. The M-AMBI values showed a consistent spatial distribution pattern in all sampling seasons, with a decreasing trend along the increasing distance from the estuary inlet. Furthermore, both genus- and family-level results performed nearly as well as species-level data in detecting the seasonal variations of different contaminants (i.e., nutrients and organic enrichment). The taxonomic sufficiency succeeded in this temperate ecoregion is owing to the high aggregation ratios at different taxonomic levels in all sampling events. In general, these findings suggested that application of taxonomic sufficiency based on the M-AMBI provides a simple and efficient method for evaluating variations of ecological quality in the Liaohe Estuary.

Evolution in a pelagic planktic system: A paleobiologic test of models of multispecies evolution

Paleobiology ◽  
1984 ◽  
Vol 10 (1) ◽  
pp. 9-33 ◽  
Author(s):  
Antoni Hoffman ◽  
Jennifer A. Kitchell
Keyword(s):  
Species Level ◽  
Extinction Probability ◽  
Red Queen ◽  
Stationary Model ◽  
Data Set ◽  
Geologic Time ◽  
Extinction Rates ◽  
Level Data ◽  
The Red Queen ◽  
Age Independent

Two rival models of evolution in multispecies systems are tested against empirical species-level data. The two models are the Red Queen model of Van Valen as reformulated by Stenseth and Maynard Smith, which assumes that evolution is driven principally by biotic interactions, and the Stationary model of Stenseth and Maynard Smith, which assumes that evolution is propelled primarily by abiotic factors and will cease in the absence of changes in abiotic parameters. Testing refers to the models' predictions regarding the behavior of extinction and origination rates, and assumptions regarding equilibrium diversity and a constant effective environment. The data set includes the dates of origination and extinction for all coccolith, planktic foraminifer, and radiolarian species recorded in the Oligocene through Holocene, and all planktic diatom and silicoflagellate and ebridian species recorded in the Middle Miocene through Holocene in 111 DSDP sites of the low- to mid-latitude Pacific Ocean.The condition of stable specific age distribution over geologic time is met, which allows one to perform survivorship analysis on extinction rates. The best fit survivorship curve is a decreasing function of age for both coccolith and foraminifer species, and an increasing function of age for radiolarian species. Neither model predicts age dependence of the probability of extinction. The small disparity between these curves and age-independent curves for each group indicates, however, that an age-independent interpretation of extinction probability is a reasonable first approximation. Rates of origination are analyzed in terms of species accretion, introduced to represent the cumulative origination of species within a higher taxon as a function of the age or duration of the community. Accretion analysis indicates that the probability of accretion is both diversity-dependent and absolute time-dependent.The assumption of a constant effective environment is tested by polycohort analysis and nonparametric logistic regression analysis of true species cohorts. Both techniques indicate considerable variation in extinction probability over geologic time. When the predictions of the two evolutionary models are adjusted to take this variation into account, the results of both survivorship and accretion analysis seem to conform more closely to the predictions of the Red Queen than to the Stationary model. However, as the speed with which the effective environment changes is increased relative to speciation-extinction rates, it becomes increasingly difficult to differentiate patterns predicted by the two models. The assumption of equilibrium diversity can be neither corroborated nor rejected, since the species-level data are compatible with both an equilibrium and a nonequilibrium view of diversity behavior. Reservations concerning the basic assumptions of both models indicate an ultimate test requires that both models be reformulated to make precise and distinctive predictions under a varying effective environment.

scholarly journals Is it possible to simplify environmental monitoring? Approaches with zooplankton in a hydroelectric reservoir

2017 ◽  
Vol 29 (0) ◽  
Author(s):  
Ana Caroline de Alcântara Missias ◽  
Leonardo Fernandes Gomes ◽  
Hasley Rodrigo Pereira ◽  
Leo Caetano Fernandes da Silva ◽  
Ronaldo Angelini ◽  
...  
Keyword(s):  
Zooplankton Community ◽  
Mantel Test ◽  
Species Level ◽  
Hydropower Plant ◽  
Taxonomic Resolution ◽  
Density Data ◽  
Biological Surveys ◽  
Numerical Resolution ◽  
Community Monitoring ◽  
Family Level

Abstract Aim: In order to contribute to the knowledge about the simplification of biological surveys, this study evaluated the use of substitute groups, numeric and taxonomic resolution for the three main groups of zooplankton (cladocerans, copepods and rotifers) in a Hydropower Plant (UHE). The following issues were addressed: (i) the patterns of spatial and/or temporal ordering generated between each zooplankton group are in concordance? (ii) The concordance is maintained using presence/absence data instead of density data? (iii) The identification of organisms to the species level can be replaced by genus or family level? Methods Samples were taken in seven sample units over five campaigns between 2009 and 2010 in the UHE Serra da Mesa (Goiás, Brazil). To evaluate the correlation between each pair of matrices was used the Mantel test. Results The results demonstrate that the replacements should not be made among the zooplanktonic groups, requiring the monitoring of three groups (copepods, cladocerans and rotifers). Furthermore, the results suggest the use of density data of individuals rather than just presence/absence of species. Finally, the results of this study indicate the possibility to use data at species level instead of data at genus or family level. Conclusion For zooplankton community monitoring purposes only the use of taxonomic resolution showed to be efficient for this area of study, not being recommended the use of surrogate groups or numerical resolution.

Integrative Data Analysis from a Unifying Research Synthesis Perspective

2018 ◽  
Author(s):  
Eun-Young Mun ◽  
Anne E. Ray
Keyword(s):  
Data Analysis ◽  
Large Scale ◽  
Research Synthesis ◽  
Alcohol Intervention ◽  
Data Set ◽  
Integrative Data Analysis ◽  
Level Data ◽  
Model Complex ◽  
Wide Range ◽  
Individual Participant

Integrative data analysis (IDA) is a promising new approach in psychological research and has been well received in the field of alcohol research. This chapter provides a larger unifying research synthesis framework for IDA. Major advantages of IDA of individual participant-level data include better and more flexible ways to examine subgroups, model complex relationships, deal with methodological and clinical heterogeneity, and examine infrequently occurring behaviors. However, between-study heterogeneity in measures, designs, and samples and systematic study-level missing data are significant barriers to IDA and, more broadly, to large-scale research synthesis. Based on the authors’ experience working on the Project INTEGRATE data set, which combined individual participant-level data from 24 independent college brief alcohol intervention studies, it is also recognized that IDA investigations require a wide range of expertise and considerable resources and that some minimum standards for reporting IDA studies may be needed to improve transparency and quality of evidence.

Engagement Through the Diaspora Channel

2017 ◽  
Author(s):  
Michael S. Danielson
Keyword(s):  
Civil Society ◽  
Statistical Models ◽  
State Level ◽  
The State ◽  
Multivariate Statistical ◽  
Political Factors ◽  
Data Set ◽  
Level Data ◽  
Municipal Level

The first empirical task is to identify the characteristics of municipalities which US-based migrants have come together to support financially. Using a nationwide, municipal-level data set compiled by the author, the chapter estimates several multivariate statistical models to compare municipalities that did not benefit from the 3x1 Program for Migrants with those that did, and seeks to explain variation in the number and value of 3x1 projects. The analysis shows that migrants are more likely to contribute where migrant civil society has become more deeply institutionalized at the state level and in places with longer histories as migrant-sending places. Furthermore, the results suggest that political factors are at play, as projects have disproportionately benefited states and municipalities where the PAN had a stronger presence, with fewer occurring elsewhere.

scholarly journals Evaluating Metagenomic Analysis for Pathogen Transmission in Healthcare Settings

2020 ◽  
Vol 41 (S1) ◽  
pp. s224-s224
Author(s):  
Curt Hewitt ◽  
Katharina Weber ◽  
Danielle LeSassier ◽  
Anthony Kappell ◽  
Kathleen Schulte ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Dna Analysis ◽  
Pathogen Transmission ◽  
Species Level ◽  
Metagenomic Analysis ◽  
Skin Microbiome ◽  
Limited Information ◽  
Culture Methods ◽  
Data Set ◽  
Skin Contact

Background: The prevalence of healthcare-acquired infections (HAIs) and rising levels of antimicrobial resistance place a significant burden on modern healthcare systems. Cultures are typically used to track HAIs; however, culture methods provide limited information and are not applicable to all pathogens. Next-generation sequencing (NGS) can detect and characterize pathogens present within a sample, but few research studies have explored how NGS could be used to detect pathogen transmission events under HAI-relevant scenarios. The objective of this CDC-funded project was to evaluate and correlate sequencing approaches for pathogen transmission with standard culture-based analysis. Methods: We modeled pathogen transfer via hand contact using synthetic skin. These skin coupons were seeded with a community of commensal organisms to mimic the human skin microbiome. Pathogens were added at physiologically relevant high or low levels prior to skin-to-skin contact. The ESKAPE pathogens: E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp plus C. difficile were employed because they are the most common antibiotic resistant HAIs. Pathogen transfer between skin coupons was measured following direct skin contact and fomite surface transmission. The effects of handwashing or fomite decontamination were also evaluated. Transferred pathogens were enumerated via culture to establish a robust data set against which DNA and RNA sequence analyses of the same samples could be compared. These data also provide a quantitative assessment of individual ESKAPE+C pathogen transfer rates in skin contact scenarios. Results: Metagenomic and metatranscriptomic analysis using custom analysis pipelines and reference databases successfully identified the commensal and pathogenic organisms present in each sample at the species level. This analysis also identified antibiotic resistance genes and plasmids. Metatranscriptomic analysis permitted not only gene identification but also confirmation of gene expression, a critical factor in the evaluation of antibiotic resistance. DNA analysis does not require cell viability, a key differentiator between sequencing and culturing reflected in simulated handwashing data. Sensitivity remains a key limitation of metagenomic analysis, as shown by the poor species identification and gene content characterization of pathogens present at low abundance within the simulated microbial community. Species level identification typically failed as ratios fell below 1:1,000 pathogen CFU:total community CFU. Conclusions: These findings demonstrate the strengths and weaknesses of NGS for molecular epidemiology. The data sets produced for this study are publicly available so they can be employed for future metagenomic benchmarking studies.Funding: NoneDisclosures: None

The Optimal Diversification Strategy in Pharmaceutical Industry: Balance-centred or Hetero-centred?

2021 ◽  
pp. 097172182110056
Author(s):  
Keungoui Kim ◽  
Junseok Hwang ◽  
Sungdo Jung ◽  
Eungdo Kim
Keyword(s):  
Business Performance ◽  
Business Environment ◽  
Product Diversification ◽  
Diversification Strategy ◽  
Firm Level ◽  
Data Set ◽  
Pharmaceutical Firms ◽  
Level Data ◽  
Market Product ◽  
High Uncertainty

Due to high uncertainty of product development and business environment, firm-level diversification has been regarded as one of the most effective methods in pharmaceutical firms. In previous study, firm-level diversification was discussed by different value chains of market, product, and technology. However, in most cases, the diversification itself was adopted in a simple manner although its property contains different aspects and the results varies depending on the diversity property of selected index. In addition, the existing approach for measuring firm’s product/market diversification using sales information distinguished by standard industry classification cannot provide direct implication as different strategies are made for market and product diversification. Therefore, this study examines the effects of firm-level diversification on business and innovation performances in pharmaceutical firms by considering (1) three diversification types: market, product, and technology, (2) clear separation between market and product diversification, and (3) two diversification perspectives: balance-centred and hetero-centred. For empirical analysis, an integrated firm-level data set combining from Medtrack, Orange Book, Compustat and Total Patent database is used. From the result, in case of market diversification, less market heterogeneity causes significant influence on business performance. For product and technology, a concentrated and greater heterogeneity of product diversification are turned out to promote business performance, while the more intensive and heterogeneous technology diversification has been shown to improve innovation performance.

HERITABILITY OF SINGLE PLANT YIELD AND INCIDENCE OF BLACK POD DISEASE IN COCOA

2007 ◽  
Vol 43 (4) ◽  
pp. 455-462 ◽  
Author(s):  
G. LOCKWOOD ◽  
F. OWUSU-ANSAH ◽  
Y. ADU-AMPOMAH
Keyword(s):  
Large Scale ◽  
Mass Selection ◽  
Single Plant ◽  
Plant Yield ◽  
Clone Selection ◽  
Level Data ◽  
Family Level ◽  
Black Pod ◽  
Black Pod Disease

Broad sense heritabilities were estimated in three long-term cocoa clone trials in Ghana, with 20, 18 and 15 entries. They were 0.15, 0.05 and 0.15 for yield in pods per plant, and 0.26, 0.19 and 0.40 for incidence of ‘bad’ pods, mostly due to black pod disease, caused by infection with Phytophthora spp. The low heritability of single plant yield, which has been known for 80 years, has been widely overlooked in cocoa research and extension, compromising the success of clone selection programmes. The heritability of the incidence of black pod disease is high enough to justify mass selection where family level data are not available. The findings will be applied in a new large-scale programme in Ghana to select clones that are high yielding in the presence of P. megakarya.

Calcareous nannoplankton ecology and community change across the Paleocene-Eocene Thermal Maximum

Paleobiology ◽  
10.1666/12050 ◽  
2013 ◽  
Vol 39 (4) ◽  
pp. 628-647 ◽  
Author(s):  
Leah J. Schneider ◽  
Timothy J. Bralower ◽  
Lee R. Kump ◽  
Mark E. Patzkowsky
Keyword(s):  
Nutrient Availability ◽  
Multivariate Analyses ◽  
Geochemical Modeling ◽  
Community Change ◽  
Open Ocean ◽  
Data Set ◽  
Long Term Effect ◽  
Term Change ◽  
Thermal Maximum

The Paleocene-Eocene Thermal Maximum (PETM; ca. 55.8 Ma) is thought to coincide with a profound but entirely transient change among nannoplankton communities throughout the ocean. Here we explore the ecology of nannoplankton during the PETM by using multivariate analyses of a global data set that is based upon the distribution of taxa in time and space. We use these results, coupled with stable isotope data and geochemical modeling, to reinterpret the ecology of key genera. The results of the multivariate analyses suggest that the community was perturbed significantly in coastal and high-latitudes sites compared to the open ocean, and the relative influence of temperature and nutrient availability on the assemblage varies regionally. The open ocean became more stratified and less productive during the PETM and the oligotrophic assemblage responded primarily to changes in nutrient availability. Alternatively, assemblages at the equator and in the Southern Ocean responded to temperature more than to nutrient reduction. In addition, the assemblage change at the PETM was not merely transient—there is evidence of adaptation and a long-term change in the nannoplankton community that persists after the PETM and results in the disappearance of a high-latitude assemblage. The long-term effect on communities caused by transient warming during the PETM has implications for modern-day climate change, suggesting similar permanent changes to nannoplankton community structure as the oceans warm.

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