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.

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.

scholarly journals Analysis of relative abundances on environmental gradients

2018 ◽  
Author(s):  
Fiona Chong ◽  
Matthew Spencer
Keyword(s):  
Compositional Data ◽  
Environmental Gradients ◽  
Compositional Data Analysis ◽  
Depth Gradient ◽  
Negative Numbers ◽  
Marine Communities ◽  
Rates Of Change ◽  
Compositional Approach ◽  
Vertical Slice ◽  
Relative Abundances

Ecologists often analyze relative abundances, which are compositions (sets of non-negative numbers with a fixed sum). However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data.

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.

Genetic diversity of three Aegla species (Decapoda, Anomura) revealed by AFLP and mtDNA markers

Crustaceana ◽  
2019 ◽  
Vol 92 (4) ◽  
pp. 445-462
Author(s):  
Bianca L. Zimmermann ◽  
Jober V. De Vargas Machado ◽  
Sandro Santos ◽  
Marlise L. Bartholomei-Santos
Keyword(s):  
Genetic Diversity ◽  
Distinct Species ◽  
Genetic Distances ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Similar Species ◽  
Southern Brazil ◽  
Low Levels ◽  
Management And Conservation ◽  
Mtdna Markers

Abstract Representatives of the genus Aegla present a conserved morphology; thus, the increased use of molecular markers has raised many taxonomic issues. We used AFLP and mtDNA to investigate the genetic differentiation and phylogenetic relationships of morphologically similar species with overlapping distribution areas in southern Brazil: A. georginae, A. ludwigi, and A. platensis. While A. platensis is widely distributed, the critically endangered A. georginae and A. ludwigi have limited distributions. Although both markers showed populations with low levels of genetic variability, they differed markedly in revealing relationships between populations; according to AFLP, the genetic distances between A. platensis populations were as high as those between distinct species, a result not observed when considering mtDNA data. We emphasize that the use of multiple lines of evidence is necessary for defining correct levels of genetic diversity and a good species-level taxonomic resolution. Such features are essential for the management and conservation of Aegla species.

scholarly journals Response of herbaceous vegetation functional diversity to land use change across five sites in Europe and Israel

2011 ◽  
Vol 57 (1-2) ◽  
pp. 53-72 ◽  
Author(s):  
Sandra Lavorel ◽  
Francesco de Bello ◽  
Karl Grigulis ◽  
Jan Lepš ◽  
Eric Garnier ◽  
...  
Keyword(s):  
Land Use ◽  
Land Use Change ◽  
Functional Diversity ◽  
Linear Models ◽  
Current Knowledge ◽  
Environmental Gradients ◽  
Functional Divergence ◽  
Grassland Management ◽  
Community Response ◽  
Mixed Linear Models

Only a few studies have examined responses of grassland functional diversity to management and major environmental gradients, in order to address the question of whether grassland use can promote functional divergence. For five grassland sites in Israel, Portugal, the Czech Republic, Mediterranean France, and the French Alps, where traditional grassland management is being abandoned, we quantified community-weighted means (CWM) and functional divergence (FDvg) for the three Leaf-Height-Seed (LHS) traits, individually and in combination. Responses of CWM and FDvg to land use were analyzed by mixed linear models with aridity, phosphorus, fertility, and the fractions of grasses and annuals as covariates.Responses of community-weighted traits to land use were consistent with current knowledge. More intense management favored plants with more rapid resource acquisition (high Specific Leaf Area, or SLA), whereas abandonment or less intense grassland management increased the dominance by tall plants with more conservative strategies (low SLA). Seed weight did not respond to land use. For the three traits and their combination, functional divergence decreased in response to land use change overall. Detailed responses, however, varied depending on sites and especially their climate. At the two French sites, traditional site management promoted functional divergence within communities by suppressing dominance by large perennial tussocks, whereas at the two Mediterranean sites it is likely that the drier climate promoted a functionally diverse pool of species tolerant to grazing.This study demonstrates how simultaneous analyses of variations in community-mean traits and functional divergence for a focused set of traits offer promising avenues to understand mechanisms of community response to environmental change.

The contemporary moss assemblages of a high arctic upland, northern Ellesmere Island, N.W.T., Canada

1989 ◽  
Vol 67 (2) ◽  
pp. 491-504 ◽  
Author(s):  
Catherine LaFarge-England
Keyword(s):  
Environmental Gradients ◽  
Specific Conductivity ◽  
Detrended Correspondence Analysis ◽  
Distribution Patterns ◽  
High Arctic ◽  
Organic Content ◽  
Ellesmere Island ◽  
Physical Parameters ◽  
Major Species ◽  
Species Groups

A quantitative analysis of contemporary moss assemblages is presented for a fault block at the southern end of Piper Pass, northern Ellesmere Island, N.W.T. (82°12′N, 68°31′W). Twenty-eight stands are analyzed using the two-way indicator species analysis, resulting in seven major species groups and five major stand groups. Physical parameters correlated with the stand data show soil moisture and slope to be the most important factors influencing the distribution of moss assemblages. Sodium, organic content, and specific conductivity are also correlated with the vegetation data. Detrended correspondence analysis confirms these stand relationships. The interdependence of physical, chemical, and vegetation data is also discussed. Distribution patterns of the species groups within the stand groups are analyzed by means of a percent frequency diagram. A direct gradient analysis of the vegetation below a late-lying snowbank also demonstrates the selective distribution of species in terms of environmental gradients.

scholarly journals Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5643 ◽  
Author(s):  
Fiona Chong ◽  
Matthew Spencer
Keyword(s):  
Data Analysis ◽  
Regression Model ◽  
Compositional Data ◽  
Environmental Gradients ◽  
Compositional Data Analysis ◽  
Multinomial Regression ◽  
Point Count ◽  
Compositional Approach ◽  
Multinomial Regression Model ◽  
Relative Abundances

Ecologists often analyze relative abundances, which are an example of compositional data. However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We fit a quadratic multivariate regression model with multinomial observations to point count data obtained from video transects. As well as being an appropriate observation model in this case, the multinomial deals with the problem of zeros, which often makes compositional data analysis difficult. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data.

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.

scholarly journals Gene Rearrangements in the Mitochondrial Genomes of Whiteflies (Hemiptera: Aleyrodinae): Plesiomorphies, Synapomorphies and Autapomorphies

2021 ◽  
Author(s):  
Avas Pakrashi ◽  
VIKAS KUMAR ◽  
Dhirti Banerjee ◽  
Kaomud Tyagi ◽  
C. M. Kalleshwaraswamy
Keyword(s):  
Phylogenetic Analyses ◽  
Species Level ◽  
Individual Species ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Gene Block ◽  
Level Data ◽  
The Family ◽  
Codon Positions ◽  
Complete Mitogenome

Abstract Mitochondrial genome rearrangements have been used for defining historical relationships, but there have been incidences of convergences at different taxonomic levels. Here, we sequenced complete mitogenome of Aleurodicus rugioperculatus (Aleyrodidae: Aleurodicinae) to examine gene rearrangements and phylogenetic relationships within the family Aleyrodidae. We identified five gene blocks (I-V) in the whitefly ancestor that are shared plesiomorphies retained in different whitefly lineages. Gene block I is conserved in all whiteflies except three species (Tetraleurodes acaciae and two Bemisia species). Conversely, we detected 83 derived gene boundaries within the family. Mapping these gene boundaries onto a phylogenetic tree revealed that 16 were symplesiomorphies for two subfamilies; 9 were synapomorphies at different taxonomic levels, and 28 autapomorphies for individual species. Bayesian Inference (BI) and Maximum Likelihood (ML) phylogenetic analyses yielded similar topologies supporting the monophyly of Aleyrodinae and Aleurodicinae. Exclusion of PCG third codon positions from phylogenetic analyses improved both node support and consistency with prior analyses. To understand the significance of gene order convergence on phylogeny of the whiteflies, more species-level data is required.

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