Much ado about nothings: using zero similarity points in distance-decay curves

Millar, Russell B.; Anderson, Marti J.; Tolimieri, Nick

doi:10.1890/11-0029.1

Cited by 36 publications

(62 citation statements)

References 23 publications

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“…As a small number of our sample sites had no bacterial OTUs in common, we plotted distancedecay relationships between bacterial community composition or function, and geographic distance, using the generalised dissimilarity model of (Millar et al, 2011). As we detected significant spatial variability in bacterial communities, we also chose to determine an optimal sampling intensity for alpine ponds based on this study data using a multivariate Mantel correlogram approach (the 'mantel.correlog' function in the R package 'vegan'; Oksanen et al, 2012).…”

Section: Statistical Analysesmentioning

confidence: 99%

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

et al. 2014

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The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100 þ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNAfingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located 420 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24-38% and 17-39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17-32% and 15-20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally 'redundant'. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of 420 m may be dispersal limited, even within the highly continuous environment of lentic water.

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Section: Statistical Analysesmentioning

confidence: 99%

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

et al. 2014

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“…a difference of 100 mm in annual precipitation is likely to have a much bigger effect on biological composition in a desert than in a rainforest). Second, if compositional similarity is log-transformed, then parameter estimates can be highly sensitive to assemblages that share no species in common because the log of zero is undefined [13].…”

Section: Introductionmentioning

confidence: 99%

Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients

et al. 2013

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A common approach for analysing geographical variation in biodiversity involves using linear models to determine the rate at which species similarity declines with geographical or environmental distance and comparing this rate among regions, taxa or communities. Implicit in this approach are weakly justified assumptions that the rate of species turnover remains constant along gradients and that this rate can therefore serve as a means to compare ecological systems. We use generalized dissimilarity modelling, a novel method that accommodates variation in rates of species turnover along gradients and between different gradients, to compare environmental and spatial controls on the floras of two regions with contrasting evolutionary and climatic histories: southwest Australia and northern Europe. We find stronger signals of climate history in the northern European flora and demonstrate that variation in rates of species turnover is persistent across regions, taxa and different gradients. Such variation may represent an important but often overlooked component of biodiversity that complicates comparisons of distance-decay relationships and underscores the importance of using methods that accommodate the curvilinear relationships expected when modelling beta diversity. Determining how rates of species turnover vary along and between gradients is relevant to understanding the sensitivity of ecological systems to environmental change.

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“…D h indicates the distance at which S 0 halves, and provides relevant information regarding the spatial scale of species turnover. Pair-wise Jaccard similarities (S ij = 1 -d ij ) (Anderson et al 2013) were plotted against least-cost distance with distance decay relationships estimated by generalised linear models (GLMs) with binomial observation error and a loglink function (Millar et al 2011), taking the form:…”

Section: Spatial Analysismentioning

confidence: 99%

“…As pairwise similarities are not independent, parameter estimates and their standard errors for α, β and D h were obtained by a leave-one-out jackknife procedure using 9999 permutations (Millar et al 2011). Because species turnover was positively related to protection status (Table 2), we performed a sensitivity analysis to evaluate the potential confounding effect due to having a larger number of sites within MPAs in the western than in the eastern region.…”

Section: Spatial Analysismentioning

confidence: 99%

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Geographic distance, water circulation and environmental conditions shape the biodiversity of Mediterranean rocky coasts

Rattray¹,

Andrello²,

Asnaghi³

et al. 2016

Mar. Ecol. Prog. Ser.

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Ecological connectivity is important for effective marine planning and biodiversity conservation. Our aim was to identify factors important in influencing variation in benthic community structure on shallow rocky reefs in 2 regions of the Mediterranean Sea with contrasting oceanographic regimes. We assessed beta (β) diversity at 146 sites in the littoral and shallow sublittoral from the Adriatic/Ionian Seas (eastern region) and Ligurian/Tyrrhenian Seas (western region) using a null modelling approach to account for variation in species richness. The distance decay relationship between species turnover within each region and geographic distance by sea was determined using generalised linear models. Mantel tests were used to examine correlations between β diversity and connectivity by ocean currents, estimated from Lagrangian dispersal simulations. Variation in β diversity between sites was partitioned according to environmental and spatial components using a distance-based redundancy approach. Species turnover along a gradient of geographic distance was greater by a factor of 3 to 5 in the western region than the eastern region, suggesting lower connectivity between sites. β diversity was correlated with connectivity by ocean currents at both depths in the eastern region but not in the western region. The influ-

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Much ado about nothings: using zero similarity points in distance-decay curves

Cited by 36 publications

References 23 publications

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients

Geographic distance, water circulation and environmental conditions shape the biodiversity of Mediterranean rocky coasts

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