A quantitative null model of additive diversity partitioning: examining the response of beta diversity to extinction

Paleobiology ◽  
2007 ◽  
Vol 33 (1) ◽  
pp. 116-124 ◽  
Author(s):  
Karen M. Layou

Paleobiological diversity is often expressed as α (within-sample), β (among-sample), and γ (total) diversities. However, when studying the effects of extinction on diversity patterns, only variations in α and γ diversities are typically addressed. A null model that examines changes in β diversity as a function of percent extinction is presented here.The model examines diversity in the context of a hierarchical sampling strategy that allows for the additive partitioning of γ diversity into mean α and β diversities at varying scales. Here, the sampling hierarchy has four levels: samples, beds, facies, and region; thus, there are four levels of α diversity (α1, α2, α3, α4) and three levels of β diversity (β1, β2, and β3). Taxa are randomly assigned to samples within the hierarchy according to probability of occurrence, and initial mean α and β values are calculated. A regional extinction is imposed, and the hierarchy is resampled from the remaining extant taxa. Post-extinction mean α and β values are then calculated.Both non-selective and selective extinctions with respect to taxon abundance yield decreases in α, β, and γ diversities. Non-selective extinction with respect to taxon abundance shows little effect on diversity partitioning except at the highest extinction magnitudes (above 75% extinction), where the contribution of α1 to total γ increases at the expense of β3, with β1 and β2 varying little with increasing extinction magnitude. The pre-extinction contribution of α1 to total diversity increases with increased probabilities of taxon occurrence and the number of shared taxa between facies. Both β1 and β2 contribute equally to total diversity at low occurrence probabilities, but β2 is negligible at high probabilities, because individual samples preserve all the taxonomic variation present within a facies. Selective extinction with respect to rare taxa indicates a constant increase in α1 and constant decrease in β3 with increasing extinction magnitudes, whereas selective extinction with respect to abundant taxa yields the opposite pattern of an initial decrease in α1 and increase in β3. Both β1 and β2 remain constant with increasing extinction for both cases of selectivity. By comparing diversity partitioning before and after an extinction event, it may be possible to determine whether the extinction was selective with respect to taxon abundances, and if so, whether that selectivity was against rare or abundant taxa.Field data were collected across a Late Ordovician regional extinction in the Nashville Dome of Tennessee, with sampling hierarchy similar to that of the model. These data agree with the abundant-selective model, showing declines in α, β, and γ diversities, and a decrease in α1 and increase in β3, which suggests this extinction may have targeted abundant taxa.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e16016-e16016
Author(s):  
Jing Zuo ◽  
Wenjing Lv ◽  
Yudong Wang ◽  
Zhisong Fan ◽  
Li Feng ◽  
...  

e16016 Background: Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. Immune checkpoint–oriented immunotherapies have shown considerable promise and the advent of esophageal microbiome provides researchers with new ideas. Methods: DNA was extracted from blood, oral mucosal, saliva, urine, fecal samples from 20 ESCC patients before and after immunotherapy. Total microbial genomic DNA samples were extracted using an OMEGA Soil DNA Kit (D5625-01). The V3–V4 regions of bacterial 16S rRNA genes were amplified by PCR using the forward primer and the reverse primer and were sequenced with Illumina MiSeq platform. In order to comprehensively evaluate the α diversity of microbial communities, we used Chao1 and Observed Species indices to characterize the richness, Shannon and Simpson indices to characterize the diversity. PCoA were used to analyze differences in β diversity. Functions of 16S rRNA sequences were predicted using the PICRUSt2 and KEGG databases. Results: A comparison of blood, oral mucosal, saliva, urine, fecal samples of ESCC patients before and after immunotherapy showed that α diversity was not statistically significant. In terms of β diversity, no statistically significant differences were detected within blood, oral mucosal, saliva, urine, fecal samples of ESCC patients before and after immunotherapy. In ESCC patients treated before immunotherapy, the α diversity and β diversity of blood, oral mucosal, saliva, urine, fecal samples were different, and in ESCC patients treated after immunotherapy had the same rule. At the phylum level, the top 5 microbes in ESCC patients before and after immunotherapy were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria. At the genus level, the top 5 microbes in ESCC patients before immunotherapy were Aquabacterium, Streptococcus, Prevotella, Veillonella, Bacteroides, and in ESCC patients after immunotherapy were Aquabacterium, Streptococcus, Prevotella, Faecalibacterium, Veillonella. In terms of the microbial functions in ESCC patients before and after immunotherapy, the metabolic pathways accounted for the most. Conclusions: This study is conducive to exploring new mechanisms for tumor cells to evade host immune surveillance, providing new ideas and new strategies for the microecology-based immunotherapy of ESCC.


2010 ◽  
Vol 16 ◽  
pp. 95-116 ◽  
Author(s):  
Thomas D. Olszewski

Diversity (the variety of different types of organisms) of an ecological or paleoecological system reflects processes and history operating across a range of hierarchically related scales. For example, the diversity of a biofacies is the sum of the diversity in all the local patches composing the biofacies, the diversity of a depositional system is composed of all the biofacies composing the depositional system, and the diversity of a biotic province is composed of all the landscapes composing the province. Diversity at a larger scale (γ-diversity) incorporates both the average inventory diversity of units of the next smaller scale (α-diversity) and the compositional differences, or differentiation diversity, among the smaller units (β-diversity). Many familiar means of measuring diversity can be mathematically partitioned to determine the relative contribution of different diversity components at any hierarchical level. When using richness (the number of taxa in an ecological system) as a measurement of diversity, it is necessary to use rarefaction to correct for differences in sample size. The divergence between sample-based and individual-based rarefaction curves of a composite collection (γ-diversity) incorporating all the samples (α-diversity) contributing to a given hierarchical level reflects the degree of non-random compositional difference among the smaller scale units (β-diversity). Alternatively, Shannon's entropy can be partitioned additively: β-entropy equals γ-entropy (based on a composite sample) minus average α-entropy of the constituent samples. A useful property of entropy is that it can be converted to effective richness, the number of taxa that would result in the same entropy value if all were equally abundant. Effective richness can be thought of as a unit conversion from non-intuitive entropy units to more easily understood richness units. Effective richness derived from Shannon's entropy partitions diversity multiplicatively – i.e., β-diversity is the number of compositionally distinct smaller units that contribute to the total diversity at the higher level. Diversity partitioning is rapidly becoming adopted as a tool for directly addressing how the structure of higher-level ecological and paleoecological systems reflects interactions among lower-level units in response to environmental and evolutionary changes.


Author(s):  
Robert E. Danczak ◽  
Rosalie K. Chu ◽  
Sarah J. Fansler ◽  
Amy E. Goldman ◽  
Emily B. Graham ◽  
...  

AbstractEnvironmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis ‘meta-metabolome ecology’ and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed α-diversity and β-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and βNTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.


Web Ecology ◽  
2014 ◽  
Vol 14 (1) ◽  
pp. 51-60 ◽  
Author(s):  
H.-R. Gregorius

Abstract. It is routinely understood that the total diversity within a metacommunity (γ-diversity) can be partitioned into one component summarizing the diversity within communities (α-diversity) and a second component representing the contribution of diversity (or differences) between communities (β-diversity). The underlying thought is that merging differentiated communities should raise the total diversity above the average level of diversity within the communities. The crucial point in this partitioning criterion is set by the notion of "diversity within communities" (DWC) and its relation to the total diversity. The common approach to summarizing DWC is in terms of averages. Yet there are many different ways to average diversity, and not all of these averages stay below the total diversity for every measure of diversity, corrupting the partitioning criterion. This raises the question of whether conceptual properties of diversity measures exist, the fulfillment of which implies that all measures of DWC obey the partitioning criterion. It is shown that the straightforward generalization of the plain counting of types (richness) leads to a generic diversity measure that has the desired properties and, together with its effective numbers, fulfills the partitioning criterion for virtually all of the relevant diversity measures in use. It turns out that the classical focus on DWC (α) and its complement (β as derived from α and γ) in the partitioning of total diversity captures only the apportionment perspective of the distribution of trait diversity over communities (which implies monomorphism within communities at the extreme). The other perspective, differentiation, cannot be assessed appropriately unless an additional level of diversity is introduced that accounts for differences between communities (such as the joint "type-community diversity"). Indices of apportionment IA (among which is GST and specially normalized versions of β) and differentiation ID are inferred, and it is demonstrated that conclusions derived from IA depend considerably on the measure of diversity to which it is applied, and that in most cases an assessment of the distribution of diversity over communities requires additional computation of ID.


2016 ◽  
Vol 67 (2) ◽  
pp. 238 ◽  
Author(s):  
Raiane S. Costa ◽  
Joseline Molozzi ◽  
Luiz U. Hepp ◽  
Renato M. Rocha ◽  
José E. L. Barbosa

Salterns consist of a series of interconnected evaporators that form sectors in the salterns. Their operation generates an increasing saline gradient, which influences species diversity. The present study was conducted in three salterns, with the goal of evaluating the diversity partitioning of phytoplankton along the saline gradient. We identified 65 taxa; the species richness was similar among the salterns, with higher values occurring in initial sectors and a downward trend with increasing salinity. In the partitioning analysis, the α diversity contributed 33.8% of the total diversity. The diversity variance showed a strong reduction from the α to β1 (33.8–6.3%). At higher scales, the highest species richness was found between salt marshes; however, there was lower diversity and a decrease in similarity from the lower to the higher scale. Therefore, we demonstrated that the greater variance in phytoplankton richness was at higher scales.


2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.


2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.


2004 ◽  
Vol 94 (2) ◽  
pp. 111-121 ◽  
Author(s):  
P.A.V. Borges ◽  
V.K. Brown

AbstractThe arthropod species richness of pastures in three Azorean islands was used to examine the relationship between local and regional species richness over two years. Two groups of arthropods, spiders and sucking insects, representing two functionally different but common groups of pasture invertebrates were investigated. The local–regional species richness relationship was assessed over relatively fine scales: quadrats (= local scale) and within pastures (= regional scale). Mean plot species richness was used as a measure of local species richness (= α diversity) and regional species richness was estimated at the pasture level (= γ diversity) with the ‘first-order-Jackknife’ estimator. Three related issues were addressed: (i) the role of estimated regional species richness and variables operating at the local scale (vegetation structure and diversity) in determining local species richness; (ii) quantification of the relative contributions of α and β diversity to regional diversity using additive partitioning; and (iii) the occurrence of consistent patterns in different years by analysing independently between-year data. Species assemblages of spiders were saturated at the local scale (similar local species richness and increasing β-diversity in richer regions) and were more dependent on vegetational structure than regional species richness. Sucking insect herbivores, by contrast, exhibited a linear relationship between local and regional species richness, consistent with the proportional sampling model. The patterns were consistent between years. These results imply that for spiders local processes are important, with assemblages in a particular patch being constrained by habitat structure. In contrast, for sucking insects, local processes may be insignificant in structuring communities.


1984 ◽  
Vol 57 (6) ◽  
pp. 1742-1748 ◽  
Author(s):  
T. R. Bai ◽  
B. J. Rabinovitch ◽  
R. L. Pardy

Because of its potential relevance to heavy exercise we studied the ventilatory muscle function of five normal subjects before, during, and after shortterm near-maximal voluntary normocapnic hyperpnea. Measurements of pleural and abdominal pressures and diaphragm electromyogram (EMG) during hyperpnea and of maximum respiratory pressures before and after hyperpnea were made at four levels of ventilation: 76, 79, and 86% maximal voluntary ventilation (MVV) and at MVV. Measurements of pleural and abdominal pressures and diaphragm electromyogram (EMG) during hyperpnea and of maximum respiratory pressures before and after hyperpnea were made. The pressure-stimulation frequency relationship of the diaphragm obtained by unilateral transcutaneous phrenic nerve stimulation was studied in two subjects before and after hyperpnea. Decreases in maximal inspiratory (PImax) and transdiaphragmatic (Pdimax) strength were recorded posthyperpnea at 76 and 79% MVV. Decreases in the pressure-frequency curves of the diaphragm and the ratio of high-to-low frequency power of the diaphragm EMG occurred in association with decreases in Pdimax. Analysis of the pressure-time product (P X dt) for the inspiratory and expiratory muscles individually indicated the increasing contribution of expiratory muscle force to the attainment of higher levels of ventilation. Demonstrable ventilatory muscle fatigue may limit endurance at high levels of ventilation.


2007 ◽  
Vol 4 (3) ◽  
pp. 1069-1094
Author(s):  
M. Rivas-Casado ◽  
S. White ◽  
P. Bellamy

Abstract. River restoration appraisal requires the implementation of monitoring programmes that assess the river site before and after the restoration project. However, little work has yet been developed to design effective and efficient sampling strategies. Three main variables need to be considered when designing monitoring programmes: space, time and scale. The aim of this paper is to describe the methodology applied to analyse the variation of depth in space, scale and time so more comprehensive monitoring programmes can be developed. Geostatistical techniques were applied to study the spatial dimension (sampling strategy and density), spectral analysis was used to study the scale at which depth shows cyclic patterns, whilst descriptive statistics were used to assess the temporal variation. A brief set of guidelines have been summarised in the conclusion.


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