Community ecologists are active in describing species by their functional traits, quantifying the functional structure of plant and animal assemblages and inferring community assembly processes with ...null-model analyses of trait distribution and functional diversity indices. Intraspecific variation in traits and effects of spatial scale are potentially important in these analyses.
Here, we introduce the R package cati (Community Assembly by Traits: Individuals and beyond) available on CRAN, for the analysis of community assembly with functional traits. cati builds on a recent approach to community assembly that explicitly incorporates individual differences in community assembly analyses and decomposes phenotypic variations across scales and organizational levels, based on three phenotypic variance ratios, termed the T-statistics. More generally, the cati package 1) calculates a variety of single-trait and multi-trait indices from interspecific and intraspecific trait measures; 2) it partitions functional trait variation among spatial and taxonomic levels; 3) it implements a palette of flexible null models for detecting non-random patterns of functional traits. These patterns can be used to draw inferences about hypotheses of community assembly such as environmental filtering and species interactions.
The basic input for cati is a data frame in which columns are traits, rows are species or individuals, and entries are the measured trait values. The cati package can also incorporate a square distance matrix into analyses, which could include phylogenetic or genetic distances among individuals or species. Users select from a variety of functional trait metrics and analyze these relative to a null model that specifies trait distributions in a regional source pool.
AIM: The Hutchinsonian hypervolume is the conceptual foundation for many lines of ecological and evolutionary inquiry, including functional morphology, comparative biology, community ecology and ...niche theory. However, extant methods to sample from hypervolumes or measure their geometry perform poorly on high‐dimensional or holey datasets. INNOVATION: We first highlight the conceptual and computational issues that have prevented a more direct approach to measuring hypervolumes. Next, we present a new multivariate kernel density estimation method that resolves many of these problems in an arbitrary number of dimensions. MAIN CONCLUSIONS: We show that our method (implemented as the ‘hypervolume’ R package) can match several extant methods for hypervolume geometry and species distribution modelling. Tools to quantify high‐dimensional ecological hypervolumes will enable a wide range of fundamental descriptive, inferential and comparative questions to be addressed.
emergence and promise of functional biogeography Violle, Cyrille; Reich, Peter B.; Pacala, Stephen W. ...
Proceedings of the National Academy of Sciences - PNAS,
09/2014, Letnik:
111, Številka:
38
Journal Article
Recenzirano
Odprti dostop
Understanding, modeling, and predicting the impact of global change on ecosystem functioning across biogeographical gradients can benefit from enhanced capacity to represent biota as a continuous ...distribution of traits. However, this is a challenge for the field of biogeography historically grounded on the species concept. Here we focus on the newly emergent field of functional biogeography: the study of the geographic distribution of trait diversity across organizational levels. We show how functional biogeography bridges species-based biogeography and earth science to provide ideas and tools to help explain gradients in multifaceted diversity (including species, functional, and phylogenetic diversities), predict ecosystem functioning and services worldwide, and infuse regional and global conservation programs with a functional basis. Although much recent progress has been made possible because of the rising of multiple data streams, new developments in ecoinformatics, and new methodological advances, future directions should provide a theoretical and comprehensive framework for the scaling of biotic interactions across trophic levels and its ecological implications.
Ensuring the temporal stability of national food production is crucial for avoiding sharp drops in domestic food availability. The average stability of individual crop yields and asynchrony among ...crop yield fluctuations are two candidate mechanisms to stabilize national food production. However, the quantification of their respective influence on the stability of national food production is lacking, as is the identification of the factors regulating both mechanisms. Using yield data for 138 crops and 115 countries over a 50-year period, we first show that the stability of total national yield mostly relies on the fluctuations of the yield of crops covering the largest share of cropland. The average yield stability of these crops exert a stabilizing effect on national food production that is twice as important as the one of the asynchronous yield fluctuations among them. Climate variability reduces the stability of national food production by synchronizing yield fluctuations among crops and destabilizing the yield of individual crops. However, our results suggest that increasing crop diversity can counteract the synchronizing effects of climate variability by enhancing asynchronous dynamics among crops. Irrigation can promote the average stability of individual crop yields but cannot compensate for the destabilizing effect of climate variability. Considering both the response of each crop to climatic variations and the dynamics emerging from crop baskets will help agricultural policies to ensure stable food supply at the national level.
Plant domestication through an ecological lens Milla, Rubén; Osborne, Colin P.; Turcotte, Martin M. ...
Trends in ecology & evolution (Amsterdam),
08/2015, Letnik:
30, Številka:
8
Journal Article
Recenzirano
•Ecology is an underexploited science in the study of crop evolution.•A framework is provided to analyze ecological causes and effects of domestication.•Single traits and whole phenotypes react to ...natural selection under cultivation.•Domesticates exert relevant effects on ecosystem processes and co-occurring species.
Our understanding of domestication comes largely from archeology and genetics. Here, we advocate using current ecological theory and methodologies to provide novel insights into the causes and limitations of evolution under cultivation, as well as into the wider ecological impacts of domestication. We discuss the importance of natural selection under cultivation, that is, the forces promoting differences in Darwinian fitness between plants in crop populations and of constraints, that is, limitations of diverse nature that, given values for trait X, shorten the range of variation of trait Y, during the domestication process. Throughout this opinion paper, we highlight how ecology can yield insight into the effects of domestication on plant traits, on crop feedback over ecological processes, and on how species interactions develop in croplands.
1. Trait-based approaches applied to community ecology have led to a considerable advance in understanding the effect of environmental filters on species assembly. Although plant traits are known to ...vary both between and within species, little is known about the role of intraspecific trait variability in the non-random assembly mechanisms controlling the coexistence of species, including habitat filtering and niche differentiation. 2. We investigate the role of intraspecific variability in three key functional traits - specific leaf area (SLA), leaf dry matter content (LDMC) and height - in structuring grassland communities distributed along a flooding gradient. We quantified the contribution of intraspecific variability relative to interspecific differences in the trait-gradient relationship, and we used a null model approach to detect patterns of habitat filtering and niche differentiation, with and without intraspecific variability. 3. Community mean SLA and height varied significantly along the flooding gradient and intraspecific variability accounted for 44% and 32%, respectively, of these trait-gradient relationships. LDMC did not vary along the gradient, with and without accounting for intraspecific variability. Our null model approach revealed significant patterns of habitat filtering and niche differentiation for SLA and height, but not for LDMC. More strikingly, considering intraspecific trait variability greatly increased the detection of habitat filtering and was necessary to detect niche differentiation processes. 4. Synthesis. Our study provides evidence for a strong role of intraspecific trait variability in community assembly. Our findings suggest that intraspecific trait variability promotes species coexistence, by enabling species to pass through both abiotic and biotic filters. We argue that community ecology would benefit from more attention to intraspecific variability.
Plants respond to resource stress by changing multiple aspects of their biomass allocation, morphology, physiology and architecture. To date, we lack an integrated view of the relative importance of ...these plastic responses in alleviating resource stress and of the consistency/variability of these responses among species.
We subjected nine species (legumes, forbs and graminoids) to nitrogen and/or light shortages and measured 11 above-ground and below-ground trait adjustments critical in the alleviation of these stresses (plus several underlying traits).
Nine traits out of 11 showed adjustments that improved plants’ potential capacity to acquire the limiting resource at a given time. Above ground, aspects of plasticity in allocation, morphology, physiology and architecture all appeared important in improving light capture, whereas below ground, plasticity in allocation and physiology were most critical to improving nitrogen acquisition. Six traits out of 11 showed substantial heterogeneity in species plasticity, with little structuration of these differences within trait covariation syndromes.
Such comprehensive assessment of the complex nature of phenotypic responses of plants to multiple stress factors, and the comparison of plant responses across multiple species, makes a clear case for the high (but largely overlooked) diversity of potential plastic responses of plants, and for the need to explore the potential rules structuring them.
1. Plant phenotypic diversity is shaped by the interplay of trade-offs and constraints in evolution. Closely integrated groups of traits (i.e. trait dimensions) are used to classify plant phenotypic ...diversity into plant strategies, but we do not know the degree of interdependence among trait dimensions. To assess how selection has shaped the phenotypic space, we examine whether trait dimensions are independent. 2. We gathered data on saplings of 24 locally coexisting tree species in a temperate forest, and examined the correlation structure of 20 leaf, branch, stem and root traits. These traits fall into three well-established trait dimensions (the leaf economic spectrum, the wood spectrum and Corner's Rules) that characterize vital plant functions: resource acquisition, sap transport, mechanical support and canopy architecture. Using ordinations, network analyses and Mantel tests, we tested whether the sapling phenotype of these tree species is organized along independent trait dimensions. 3. Across species, the sapling phenotype is not structured into clear trait dimensions. The trait relationships defining trait dimensions are either weak or absent and do not dominate the correlation structure of the sapling phenotype as a whole. Instead traits from the three commonly recognized trait dimensions are organized into an integrated trait network. The effect of phylogeny on trait correlations is minimal. 4. Our results indicate that trait dimensions apparent in broad-based interspecific surveys do not hold up among locally coexisting species. Furthermore, architectural traits appear central to the phenotypic network, suggesting a pivotal role for branching architecture in linking resource acquisition, mechanical support and hydraulic functions. 5. Synthesis. Our study indicates that local and global patterns of phenotypic integration differ and calls into question the use of trait dimensions at local scales. We propose that a network approach to assessing plant function more effectively reflects the multiple trade-offs and constraints shaping the phenotype in locally co-occurring species.
Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric ...bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations.
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