species abundances
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2022 ◽  
Author(s):  
Mingjie Luo ◽  
Yinqiu Ji ◽  
Douglas W. Yu

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet reconstruction and quantitative food webs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, capture bias, capture noise, species pipeline biases, and pipeline noise all combine to inject error into DNA-based datasets. We focus on methods for correcting the latter two error sources, as the first two are addressed extensively in the ecological literature. To extract abundance information, it is useful to distinguish two concepts. (1) Across-species quantification describes relative species abundances within one sample. (2) In contrast, within-species quantification describes how the abundance of each individual species varies from sample to sample, as in a time series, an environmental gradient, or different experimental treatments. Firstly, we review methods to remove species pipeline biases and pipeline noise. Secondly, we demonstrate experimentally (with a detailed protocol) how to use a 'DNA spike-in' to remove pipeline noise and recover within-species abundance information. We also introduce a statistical estimator that can partially remove pipeline noise from datasets that lack a physical DNA spike-in.


2021 ◽  
Author(s):  
Alex Akins ◽  
Panagiotis Vergados ◽  
Tatiana Bocanegra-Bahamon ◽  
Chi Ao ◽  
Robert Preston ◽  
...  

2021 ◽  
Vol 8 ◽  
Author(s):  
Madeline P. B. C. Anderson ◽  
Phillip B. Fenberg ◽  
Huw J. Griffiths ◽  
Katrin Linse

In 2018 RRS James Clark Ross investigated the marine benthic biodiversity of the Prince Gustav Channel area which separates the eastern coast of the Antarctic Peninsula from James Ross Island. The southern end of this channel had been covered by the Prince Gustav Ice Shelf until its collapse in 1995. Benthic samples were collected by an epibenthic sledge at six stations (200–1,200 m depth) in the channel and adjacent Duse Bay. In total 20,307 live collected mollusc specimens belonging to 50 species and 4 classes (Solenogastres, Bivalvia, Gastropoda, and Scaphopoda) were identified. The area may be characterised by it’s low species richness (ranging from 7 to 39 species per station) but high abundances (specifically of the Scaphopods with 11,331 specimens). The functional traits of the community were dominated by motile development and mobility type. Assemblage analyses of the molluscan species abundances within the Prince Gustav Channel stations sit distinct, with no pattern by depth or location. However, when bivalve assemblages were analysed with reference to the wider Weddell Gyre region (15 stations from 300 to 2,000 m depth), the Prince Gustav Channel sits distinct from the other Weddell Gyre stations with a higher dissimilarity between the deeper or more geographically distant areas. The Prince Gustav Channel is undergoing colonisation following the recent ice shelf collapse. With many Antarctic ice shelves threatened under climate warming, this area, with future monitoring, may serve as a case study of benthic faunal succession.


2021 ◽  
Vol 17 (12) ◽  
pp. e1008906
Author(s):  
Icíar Civantos-Gómez ◽  
Javier García-Algarra ◽  
David García-Callejas ◽  
Javier Galeano ◽  
Oscar Godoy ◽  
...  

Prediction is one of the last frontiers in ecology. Indeed, predicting fine-scale species composition in natural systems is a complex challenge as multiple abiotic and biotic processes operate simultaneously to determine local species abundances. On the one hand, species intrinsic performance and their tolerance limits to different abiotic pressures modulate species abundances. On the other hand there is growing recognition that species interactions play an equally important role in limiting or promoting such abundances within ecological communities. Here, we present a joint effort between ecologists and data scientists to use data-driven models to predict species abundances using reasonably easy to obtain data. We propose a sequential data-driven modeling approach that in a first step predicts the potential species abundances based on abiotic variables, and in a second step uses these predictions to model the realized abundances once accounting for species competition. Using a curated data set over five years we predict fine-scale species abundances in a highly diverse annual plant community. Our models show a remarkable spatial predictive accuracy using only easy-to-measure variables in the field, yet such predictive power is lost when temporal dynamics are taken into account. This result suggests that predicting future abundances requires longer time series analysis to capture enough variability. In addition, we show that these data-driven models can also suggest how to improve mechanistic models by adding missing variables that affect species performance such as particular soil conditions (e.g. carbonate availability in our case). Robust models for predicting fine-scale species composition informed by the mechanistic understanding of the underlying abiotic and biotic processes can be a pivotal tool for conservation, especially given the human-induced rapid environmental changes we are experiencing. This objective can be achieved by promoting the knowledge gained with classic modelling approaches in ecology and recently developed data-driven models.


Oikos ◽  
2021 ◽  
Author(s):  
Werner Ulrich ◽  
Markus Klemens Zaplata ◽  
Nicholas J. Gotelli

2021 ◽  
Vol 8 ◽  
Author(s):  
Liyan Zhang ◽  
Jing Zhang ◽  
Shigang Liu ◽  
Rui Wang ◽  
Jiali Xiang ◽  
...  

The Ninety East Ridge is a submarine north–south oriented volcanic ridge in the eastern Indian Ocean. Surface-layer ichthyoplankton collected in this area from September to October were identified by combined morphological and molecular (DNA barcoding) techniques, and their species composition, diversity, and abundance, and correlations with environmental variables were described. Collections comprised 109 larvae and 507 eggs, which were identified to 37 taxa in 7 orders, 20 families, and 27 genera, and were dominated by the order Perciformes and species Vinciguerria sp., Oxyporhamphus micropterus, and Decapterus macarellus. Species abundances at each station and of each species were relatively low, suggesting that this area or the time of sampling were not of major importance for fish spawning. Waters above Ninety East Ridge had lower species diversity but higher species richness than waters further offshore. A generalized additive model revealed that high abundance of ichthyoplanktonic taxa occurred in areas with low sea surface height and high sea surface salinity, temperature, and chlorophyll a concentration. Of these, sea surface height was most correlated with ichthyoplankton abundance. We provided baseline data on surface-dwelling ichthyoplankton communities in this area to aid in development of pelagic fishery resources in waters around the Ninety East Ridge.


2021 ◽  
Vol 17 (10) ◽  
pp. e1008899
Author(s):  
Susanne Pettersson ◽  
Martin Nilsson Jacobi

Understanding ecosystem stability and functioning is a long-standing goal in theoretical ecology, with one of the main tools being dynamical modelling of species abundances. With the help of spatially unresolved (well-mixed) population models and equilibrium dynamics, limits to stability and regions of various ecosystem robustness have been extensively mapped in terms of diversity (number of species), types of interactions, interaction strengths, varying interaction networks (for example plant-pollinator, food-web) and varying structures of these networks. Although many insights have been gained, the impact of spatial extension is not included in this body of knowledge. Recent studies of spatially explicit modelling on the other hand have shown that stability limits can be crossed and diversity increased for systems with spatial heterogeneity in species interactions and/or chaotic dynamics. Here we show that such crossing and diversity increase can appear under less strict conditions. We find that the mere possibility of varying species abundances at different spatial locations make possible the preservation or increase in diversity across previous boundaries thought to mark catastrophic transitions. In addition, we introduce and make explicit a multitude of different dynamics a spatially extended complex system can use to stabilise. This expanded stabilising repertoire of dynamics is largest at intermediate levels of dispersal. Thus we find that spatially extended systems with intermediate dispersal are more robust, in general have higher diversity and can stabilise beyond previous stability boundaries, in contrast to well-mixed systems.


Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 489
Author(s):  
M. Teresa Farriols ◽  
Francesc Ordines ◽  
Enric Massutí

Species diversity in a community is mainly related to the number and abundance of species that form it. N90 is a recently developed diversity index based on the results of the similarity percentage (SIMPER) analysis that represents the number of species contributing up to ninety percent of within-group similarity in a group of samples. The calculation of N90 is based on the Bray–Curtis similarity index and involves the number of species and abundances in a group of samples. We have explored the properties of N90 compared to other alpha, beta and gamma diversity indices and to beta diversity measures accounting for nestedness and turnover. We have used a non-real data set to compare the values of all indices with N90 and two real data sets of demersal fish communities along large and short depth gradients with higher influence of turnover and nestedness, respectively, to correlate the same indices with N90. The sensitivity of N90 to reductions in the frequency of occurrence and the evenness of the distribution of species abundances among samples allows the detection of diversity loss due to the fishing-induced retreatment of species populations to localities presenting the most favorable ecological conditions. This property, both in the identification of species replacement and species loss through SIMPER analysis, make N90 a useful indicator to support the Ecosystem Approach to Fisheries within the current context of global change.


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