What do beta diversity components reveal from presence-absence community data? Let us connect every indicator to an indicandum!

Schmera, Dénes; Podani, János; Legendre, Pierre

doi:10.1016/j.ecolind.2020.106540

Cited by 32 publications

(58 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As data are restricted to site-by-species presence matrices, we use the Jaccard family of indices [ 59 , 60 ]. Using the POD and SET frameworks [ 12 , 13 , 61 ], we identify the diversity patterns in each vent system by quantifying the pairwise pattern components (PPCs) using the ‘beta.div.comp’ function in the ‘adespatial’ R package [ 62 , 63 ]. The PPCs are represented as species overlap (O J ), richness difference (D J ) and replacement (R J ), which can occur singly or in combination [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

“…Using the POD and SET frameworks [ 12 , 13 , 61 ], we identify the diversity patterns in each vent system by quantifying the pairwise pattern components (PPCs) using the ‘beta.div.comp’ function in the ‘adespatial’ R package [ 62 , 63 ]. The PPCs are represented as species overlap (O J ), richness difference (D J ) and replacement (R J ), which can occur singly or in combination [ 13 ]. As they correspond with the SDR-simplex indices developed by Podani and Schmera [ 61 ], we generated simplex plots for each vent system using the ‘TernaryPlot’ function in the ‘Ternary’ R package [ 64 ].…”

Section: Methodsmentioning

confidence: 99%

“…By separating β-diversity into its components, ecologists can both describe diversity patterns and test hypotheses regarding mechanisms that shape them [ 7 – 9 ]. The specific formulation to identify components is debated (e.g., [ 10 – 12 ]), but we find the recent SET framework [ 13 ] derives a clear scenario. This framework introduces the concept of pairwise pattern components (PPCs) that isolate the community response pattern between every pair of sites examined for species presence/absence.…”

Section: Introductionmentioning

confidence: 90%

See 2 more Smart Citations

Beta diversity differs among hydrothermal vent systems: Implications for conservation

Giguère

Tunnicliffe

2021

PLoS ONE

View full text Add to dashboard Cite

Deep-sea hydrothermal vent habitats are small, rare and support unique species through chemosynthesis. As this vulnerable ecosystem is increasingly threatened by human activities, management approaches should address biodiversity conservation. Diversity distribution data provide a useful basis for management approaches as patterns of β-diversity (the change in diversity from site to site) can guide conservation decisions. Our question is whether such patterns are similar enough across vent systems to support a conservation strategy that can be deployed regardless of location. We compile macrofaunal species occurrence data for vent systems in three geological settings in the North Pacific: volcanic arc, back-arc and mid-ocean ridge. Recent discoveries in the Mariana region provide the opportunity to characterize diversity at many vent sites. We examine the extent to which diversity distribution patterns differ among the systems by comparing pairwise β-diversity, nestedness and their additive components. A null model approach that tests whether species compositions of each site pair are more or less similar than random provides insight into community assembly processes. We resolve several taxonomic uncertainties and find that the Mariana arc and back-arc share only 8% of species despite their proximity. Species overlap, species replacement and richness differences create different diversity distributions within the three vent systems; the arc system exhibits much greater β-diversity than both the back-arc and mid-ocean ridge systems which, instead, show greater nestedness. The influence of nestedness on β-diversity also increased from the arc to back-arc to ridge. Community assembly processes appear more deterministic in the arc and ridge systems while back-arc site pairs deviate little from the null expectation. These analyses reflect the need for a variety of management strategies that consider the character of diversity distribution to protect hydrothermal vents, especially in the context of mining hydrothermal deposits.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 90%

See 1 more Smart Citation

Beta diversity differs among hydrothermal vent systems: Implications for conservation

Giguère

Tunnicliffe

2021

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…Species replacement indicates the turnover of species among samples, for example due to environmental filtering or competition (Legendre 2014). On the other hand, richness differences may reflect the different coexistence parameters in different locations and/or dispersal limitation independently of species replacement (Schmera et al 2020). Nestedness, for example, is a type of richness difference characterized by subsets of species from the richer site (Legendre 2014).…”

Section: Methodsmentioning

confidence: 99%

Disentangling metacommunity processes using multiple metrics in space and time

Thompson

et al. 2020

Preprint

View full text Add to dashboard Cite

Metacommunity ecology has focused on using observational and analytical approaches to disentangle the role of critical assembly processes, such as dispersal limitation and environmental filtering. Many methods have been proposed for this purpose, most notably multivariate analyses of species abundance and its association with variation in spatial and environmental conditions. These approaches tend to focus on few emergent properties of metacommunities and have largely ignored temporal community dynamics. By doing so, these are limited in their ability to differentiate metacommunity dynamics. Here, we develop a 'virtual ecologist' approach to evaluate critical metacommunity assembly processes based on a number of summary statistics of community structure across space and time. Specifically, we first simulate metacommunities emphasizing three main processes that underlie metacommunity dynamics (density-independent responses to abiotic conditions, density-dependent biotic interactions, and dispersal). We then calculate a number of commonly used summary statistics of community structure in space and time, and use random forests to evaluate their utility for understanding the strength of these three processes. We found that: (i) time series are necessary to disentangle metacommunity processes, (ii) each of the three studied processes is distinguished with different descriptors, (iii) each summary statistic is differently sensitive to temporal and spatial sampling effort. Some of the most useful statistics include the coefficient of variation of abundances through time and metrics that incorporate variation in the relative abundances (evenness) of species. Surprisingly, we found that when we only used a single snapshot of community variation in space, the most commonly used approaches based on variation partitioning were largely uninformative regarding assembly processes, particularly, variation in dispersal. We conclude that a combination of methods and summary statistics will be necessary to understand the processes that underlie metacommunity assembly through space and time.

show abstract

“…Partitioning of Taxonomic and Functional β Diversity Regional differences in diversity (β diversity) were estimated from presence-absence data using Sørensen's (1948) dissimilarity. For each pair of cores, taxonomic β diversity and its two components, turnover and nestedness, were computed using the Baselga partitioning scheme (Baselga, 2017;Schmera et al, 2020). Functional β diversity was computed based on the multidimensional functional space from the Fuzzy Correspondence Analysis, where axes were synthetic components summarizing functional traits (Villéger et al, 2010).…”

Section: Subt Subtidal Speciesmentioning

confidence: 99%

Musical Chairs on Temperate Reefs: Species Turnover and Replacement Within Functional Groups Explain Regional Diversity Variation in Assemblages Associated With Honeycomb Worms

et al. 2021

View full text Add to dashboard Cite

Reef-building species are recognized as having an important ecological role and as generally enhancing the diversity of benthic organisms in marine habitats. However, although these ecosystem engineers have a facilitating role for some species, they may exclude or compete with others. The honeycomb worm Sabellaria alveolata (Linnaeus, 1767) is an important foundation species, commonly found from northwest Ireland to northern Mauritania, whose reef structures increase the physical complexity of the marine benthos, supporting high levels of biodiversity. Local patterns and regional differences in taxonomic and functional diversity were examined in honeycomb worm reefs from 10 sites along the northeastern Atlantic to explore variation in diversity across biogeographic regions and the potential effects of environmental drivers. While taxonomic composition varied across the study sites, levels of diversity remained relatively constant along the European coast. Assemblages showed high levels of species turnover compared to differences in richness, which varied primarily in response to sea surface temperatures and sediment content, the latter suggesting that local characteristics of the reef had a greater effect on community composition than the density of the engineering species. In contrast, the functional composition of assemblages was similar regardless of taxonomic composition or biogeography, with five functional groups being observed in all sites and only small differences in abundance in these groups being detected. Functional groups represented primarily filter-feeders and deposit-feeders, with the notable absence of herbivores, indicating that the reefs may act as biological filters for some species from the local pool of organisms. Redundancy was observed within functional groups that may indicate that honeycomb worm reefs can offer similar niche properties to its associated assemblages across varying environmental conditions. These results highlight the advantages of comparing taxonomic and functional metrics, which allow identification of a number of ecological processes that structure marine communities.

show abstract

What do beta diversity components reveal from presence-absence community data? Let us connect every indicator to an indicandum!

Cited by 32 publications

References 45 publications

Beta diversity differs among hydrothermal vent systems: Implications for conservation

Beta diversity differs among hydrothermal vent systems: Implications for conservation

Disentangling metacommunity processes using multiple metrics in space and time

Musical Chairs on Temperate Reefs: Species Turnover and Replacement Within Functional Groups Explain Regional Diversity Variation in Assemblages Associated With Honeycomb Worms

Contact Info

Product

Resources

About