No evidence for environmental filtering of cavity-nesting solitary bees and wasps by urbanization using trap nests.

Spatial patterns in biodiversity are used to establish conservation priorities and ecosystem management plans. The environmental filtering of communities along urbanization gradients has been used to explain biodiversity patterns but demonstrating filtering requires precise statistical tests to link suboptimal environments at one end of a gradient to lower population sizes via ecological traits. Here, we employ a three-part framework on observational community data to test: (I) for trait clustering (i.e., phenotypic similarities among co-occurring species) by comparing trait diversity to null expectations, (II) if trait clustering is correlated with an urbanization graient, and (III) if species' traits relate to environmental conditions. If all criteria are met, then there is evidence that urbanization is filtering communities based on their traits. We use a community of 46 solitary cavity-nesting bee and wasp species sampled across Toronto, a large metropolitan city, over 3 years to test these hypotheses. None of the criteria were met, so we did not have evidence for environmental filtering. We do show that certain ecological traits influence which species perform well in urban environments. For example, cellophane bees (Hylaeus: Colletidae) secrete their own nesting material and were overrepresented in urban areas, while native leafcutting bees (Megachile: Megachilidae) were most common in greener areas. For wasps, prey preference was important, with aphid-collecting (Psenulus and Passaloecus: Crabronidae) and generalist spider-collecting (Trypoxylon: Crabronidae) wasps overrepresented in urban areas and caterpillar- and beetle-collecting wasps (Euodynerus and Symmorphus: Vespidae, respectively) overrepresented in greener areas. We emphasize that changes in the prevalence of different traits across urban gradients without corresponding changes in trait diversity with urbanization do not constitute environmental filtering. By applying this rigorous framework, future studies can test whether urbanization filters other nesting guilds (i.e., ground-nesting bees and wasps) or larger communities consisting of entire taxonomic groups.

Limiting similarity shapes the functional and phylogenetic structure of root neighborhoods in a subtropical forest.

Environmental filtering and limiting similarity mechanisms can simultaneously structure community assemblages. However, how they shape the functional and phylogenetic structure of root neighborhoods remains unclear, hindering the understanding of belowground community assembly processes and diversity maintenance. In a 50-ha plot in a subtropical forest, China, we randomly sampled > 2700 root clusters from 625 soil samples. Focusing on 10 root functional traits measured on 76 woody species, we examined the functional and phylogenetic structure of root neighborhoods and linked their distributions with environmental cues. Functional overdispersion was pervasive among individual root traits (50% of the traits) and accentuated when different traits were combined. Functional clustering (20% of the traits) seemed to be associated with a soil nutrient gradient with thick roots dominating fertile areas whereas thin roots dominated infertile soils. Nevertheless, such traits also were sorted along other environmental cues, showing multidimensional adaptive trait syndromes. Species relatedness also was an important factor defining root neighborhoods, resulting in significant phylogenetic overdispersion. These results suggest that limiting similarity may drive niche differentiation of coexisting species to reduce competition, and that alternative root strategies could be crucial in promoting root neighborhood resource use and species coexistence.

covRNA: discovering covariate associations in large-scale gene expression data.

OBJECTIVE: The biological interpretation of gene expression measurements is a challenging task. While ordination methods are routinely used to identify clusters of samples or co-expressed genes, these methods do not take sample or gene annotations into account. We aim to provide a tool that allows users of all backgrounds to assess and visualize the intrinsic correlation structure of complex annotated gene expression data and discover the covariates that jointly affect expression patterns. RESULTS: The Bioconductor package covRNA provides a convenient and fast interface for testing and visualizing complex relationships between sample and gene covariates mediated by gene expression data in an entirely unsupervised setting. The relationships between sample and gene covariates are tested by statistical permutation tests and visualized by ordination. The methods are inspired by the fourthcorner and RLQ analyses used in ecological research for the analysis of species abundance data, that we modified to make them suitable for the distributional characteristics of both, RNA-Seq read counts and microarray intensities, and to provide a high-performance parallelized implementation for the analysis of large-scale gene expression data on multi-core computational systems. CovRNA provides additional modules for unsupervised gene filtering and plotting functions to ensure a smooth and coherent analysis workflow.

Use of functional traits to assess changes in stream fish assemblages across a habitat gradient

Functional traits are important for understanding the links between species occurrence and environmental conditions. Identifying these links makes it possible to predict changes in species composition within communities under specific environmental conditions. We used functional traits related to habitat use and trophic ecology in order to assess the changes in fish community composition between streams with varying habitat structure. The relationship between the species traits and habitat characteristics was analyzed using an RLQ ordination analysis. Although species were widely distributed in habitats with different structures, physical conditions did favor some species based on their functional characteristics. Eight functional traits were found to be associated with stream habitat structure, allowing us to identify traits that may predict the susceptibility of fish species to physical habitat degradation.

Os atributos funcionais são importantes para entender a ligação entre ocorrência das espécies e condições ambientais, permitindo predizer sobre as mudanças na composição de espécies em comunidades submetidas a condições ambientais específicas. Utilizamos atributos funcionais relacionados com o uso de habitat e ecologia trófica para avaliar as mudanças na composição de espécies de peixes em riachos com diferenças na estrutura física. O relacionamento entre os atributos das espécies e as variáveis ambientais foi avaliado por meio da análise de ordenação RLQ. Embora algumas espécies tenham sido amplamente distribuídas em hábitats com diferentes características, outras foram restritas por essas condições e este relacionamento está associado com as características morfológicas. Oito atributos funcionais foram capazes de detectar as variações na estrutura física do hábitat em riachos, permitindo a identificação de atributos que podem predizer a suscetibilidade das espécies de peixes para a degradação física do hábitat.

The influence of environmental variables on the functional structure of headwater stream fish assemblages: a study of two tropical basins in Central Brazil

We investigated functional patterns of fish assemblages of two adjacent basins (Araguaia and Tocantins) to test whether their headwater stream fish assemblages are more functionally (dis)similar than expected by chance and whether these (dis)similarities are related to differences of environmental conditions between basins. We used an analysis of similarities (ANOSIM) on a functional dissimilarity matrix to test for (dis)similarities between fish assemblages of both basins. We performed RLQ and fourth-corner analyses to determine fish species trait-environment relationship. Our results revealed functional dissimilarities between fish assemblages of both basins and significant species trait-environment relationships, suggesting that environmental conditions are driving such dissimilarities. Inter-basin dissimilarities are mainly driven by altitudinal and water temperature gradients, whereas dissimilarities among streams within the basins are influenced by channel depth, turbidity and conductivity. These five environmental variables mostly affected six fish species traits (body mass, water column position, substrate preference, parental care, foraging locality and migration) in different manners. This study is an attempt to understand functional trends of fish assemblages in a tropical region that remains poorly known but severely threatened.

Nós investigamos os padrões funcionais das assembleias de peixes de duas bacias adjacentes (Araguaia and Tocantins) para testar se as assembleias de peixes de seus riachos de cabeceira são funcionalmente mais (dis)similares do que o esperado ao acaso e se estas (dis)similaridades estão relacionadas a diferenças nas condições ambientais entre as bacias. Nós utilizamos uma análise de similaridades (ANOSIM) sobre uma matriz de dissimilaridade funcional para testar por (dis)similaridades entre as assembleias de peixes das duas bacias. Nós realizamos análises de RLQ e fourth-corner para determinar a relação entre o ambiente e a estrutura funcional das assembleias de peixes. Nossos resultados revelaram dissimilaridades funcionais entre as assembleias de peixes de ambas as bacias e relações significativas entre atributos das espécies e o ambiente, sugerindo que as condições ambientais estão direcionando tais dissimilaridades. As dissimilaridades entre bacias são influenciadas principalmente pelos gradientes de altitude e temperatura da água, enquanto as dissimilaridades entre os riachos na bacia pela profundidade do canal, turbidez e condutividade. Estas cinco variáveis ambientais afetaram principalmente seis atributos das espécies de peixes (massa corporal, posição na coluna de água, preferência por substrato, cuidado parental, local de forrageio e migração) de diferentes maneiras. Este estudo é uma tentativa para entender os padrões funcionais das assembleias de peixes de uma região ainda pouco conhecida, mas, seriamente ameaçada.

Let's go beyond taxonomy in diet description: testing a trait-based approach to prey-predator relationships.

Understanding 'Why a prey is a prey for a given predator?' can be facilitated through trait-based approaches that identify linkages between prey and predator morphological and ecological characteristics and highlight key functions involved in prey selection. Enhanced understanding of the functional relationships between predators and their prey is now essential to go beyond the traditional taxonomic framework of dietary studies and to improve our knowledge of ecosystem functioning for wildlife conservation and management. We test the relevance of a three-matrix approach in foraging ecology among a marine mammal community in the northeast Atlantic to identify the key functional traits shaping prey selection processes regardless of the taxonomy of both the predators and prey. Our study reveals that prey found in the diet of marine mammals possess functional traits which are directly and significantly linked to predator characteristics, allowing the establishment of a functional typology of marine mammal-prey relationships. We found prey selection of marine mammals was primarily shaped by physiological and morphological traits of both predators and prey, confirming that energetic costs of foraging strategies and muscular performance are major drivers of prey selection in marine mammals. We demonstrate that trait-based approaches can provide a new definition of the resource needs of predators. This framework can be used to anticipate bottom-up effects on marine predator population dynamics and to identify predators which are sensitive to the loss of key prey functional traits when prey availability is reduced.