Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community

Hardy, Olivier J.

doi:10.1111/j.1365-2745.2008.01421.x

Cited by 263 publications

(392 citation statements)

References 40 publications

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“…r-project.org) and Vegan v2.0-2 Finally, we inferred the underlying processes following the three steps listed in the Introduction section. For instance, the variation in the magnitude of ses.betaMNTD should be driven primarily by variation in the influence of deterministic processes as deviations from the betaMNTD null model expectation are primarily due to niche-based processes (Hardy, 2008). Significant increases in ses.betaMNTD with increasing environmental distances therefore implies that the influence of niche-based processes grows with increasingly large shifts in measured environmental conditions (Fine and Kembel, 2011;Stegen et al, 2012).…”

Section: Statistical Analysesmentioning

confidence: 99%

“…In this case, the partial Mantel coefficient related to spatial distance should reflect deterministic processes governed by unmeasured environmental variables. The reason is twofold: (i) the influence of measured environmental variables has already been accounted for because we are dealing with partial Mantel coefficients; and (ii) the magnitude of phylogenetic null model departures (that is, ses.betaMNTD) should only be influenced by deterministic processes; stochastic processes should have no influence (Hardy, 2008).…”

Section: Phylogenetic Signal Varies With Phylogenetic Distancementioning

confidence: 99%

“…For each habitat, a standardized effect size (ses.betaMNTD) was computed as the number of standard deviations that observed betaMNTD departed from the mean of null distribution (999 null iterations) based on random shuffling of OTU labels across the tips of the phylogeny (Hardy, 2008;Fine and Kembel, 2011;Stegen et al, 2012). This randomization holds constant observed species richness, species occupancy and species turnover.…”

Section: Statistical Analysesmentioning

confidence: 99%

“…A significant relationship with spatial distances, after controlling for environmental distances, suggests that unmeasured environmental variables impose deterministic processes that overwhelm any influences of stochastic processes. This is because stochastic processes should not cause phylogenetic null model deviations (Hardy, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

et al. 2013

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Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

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Section: Statistical Analysesmentioning

confidence: 99%

Section: Phylogenetic Signal Varies With Phylogenetic Distancementioning

confidence: 99%

Section: Statistical Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

et al. 2013

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“…In this model, the tips (individual taxa) are shuffled throughout the phylogeny and the resulting metrics were compared with the observed value with a ¼ 0.05. The tip shuffling model was determined to be robust for Phylocom analysis with a low level of Type I error (false positives; Hardy, 2008). We used the net relatedness index (NRI) metric to compare phylogenetic clustering of microbial communities across the distinct gut regions.…”

Section: Phylogenetic Community Analysismentioning

confidence: 99%

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut ofOdontotaenius disjunctus

et al. 2013

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Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by 15 N 2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni-Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N 2 that is important for this beetle to subsist on woody biomass.

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Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

Marx

Richards

Johnson

et al. 2019

American J of Botany

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PREMISE: At the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high alpine flora in the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities. METHODS:We used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assessed whether maximum elevation explains phylogenetic structure. To evaluate similarities between summits, we quantified phylogenetic turnover, taking into consideration microhabitats (talus vs. meadows). RESULTS:We found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely not different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: overdispersion degraded as elevation increased. Between summits, we found high phylogenetic turnover driven by greater niche heterogeneity on summits with alpine meadows. CONCLUSIONS:Our results provide further evidence that stochastic processes may also play an important role in the assembly of vascular plant communities in high alpine habitats at regional scales. However, order-specific patterns suggest that adaptations are still important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important in disentangling the interplay of ecoevolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.

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Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community

Cited by 263 publications

References 40 publications

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut ofOdontotaenius disjunctus

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

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