Analyzing Beta Diversity: Partitioning the Spatial Variation of Community Composition Data

Legendre, Pierre; Borcard, Daniel; Peres‐Neto, Pedro R.

doi:10.1890/05-0549

Cited by 1,109 publications

(1,129 citation statements)

References 80 publications

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“…MEM and AEM analyses are recognized as a relevant way to capture the spatial structure in data (Legendre, Borcard, & Peres‐Neto, 2005) while accounting for different scales of spatial dependence (Borcard & Legendre, 2002). However, MEM and AEM analyses sometimes overestimate the importance of spatial variables when the eigenvectors account for random spatial variations (Gilbert & Bennett, 2010).…”

Section: Discussionmentioning

confidence: 99%

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Dalongeville

Andrello

Mouillot

et al. 2018

Evolutionary Applications

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Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on single nucleotide polymorphism (SNP) allele frequencies. We used Moran's eigenvector maps (db‐MEMs) and asymmetric eigenvector maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (>1,000 km), while larval dispersal was the major predictor at smaller spatial scale (<1,000 km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history, or multigenerational stepping‐stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected area network that would efficiently enhance protection and persistence capacity of marine species.

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Section: Discussionmentioning

confidence: 99%

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Dalongeville

Andrello

Mouillot

et al. 2018

Evolutionary Applications

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show abstract

“…Pyrosequence data provided a semiquantitative assessment of the a-diversity for each of the wells, and these data were used to establish whether variations in relative community changes at each well (i.e., b-diversity) corresponded to environmental variables and overall carbonate geochemistry (see, e.g., Legendre et al, 2005). Presence and absence results at the levels of phyla through genera, where classification was possible, were collated.…”

Section: Discussionmentioning

confidence: 99%

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

Gray

Engel

2012

The ISME Journal

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Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.

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“…The relative importance of residual spatial autocorrelation, pedoclimatic characteristics and land-use in determining community composition turnover was tested by db-RDA (Legendre et al, 2005;Legendre and Fortin, 2010). Quantitative data were centered and scaled.…”

Section: Statistical Analysesmentioning

confidence: 99%

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding

et al. 2014

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The evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.

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Analyzing Beta Diversity: Partitioning the Spatial Variation of Community Composition Data

Cited by 1,109 publications

References 80 publications

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding

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