Reliability analysis of fish traits reveals discrepancies among databases

1. Trait-based approaches are commonly used in ecology to understand the relationship between biodiversity and ecosystem functioning, environmental filtering or biotic responses to anthropogenic perturbations. However, little is known about the reliability of assigned traits and the consistency of trait information among different databases currently in use.
2. Using 99 native and alien Iberian inland fish species, we investigated a total of 27 biological and ecological traits for their consistency among 19 different databases and identified less reliable traits, that is, traits with high disagreement among databases. Specifically, we used generalised linear models and inter-rater reliability statistics (Krippendorff's α) to test for differences in trait values among databases. We also identified well-studied versus data-deficient traits and species.
3. Our results show notable discrepancies and low reliability for several biological and ecological traits such as microhabitat preference, omnivory, invertivory, rheophily, and limnophily. Least reliable traits were mainly categorical (rather than continuous) and established by expert judgment and without a clear definition or a common methodology. Interestingly, categorical traits such as rheophily or limnophily, which showed significantly lower reliability, concurrently showed higher data availability and use than continuously scaled traits.
4. Such uncertainties in trait assignments could affect bioassessment and other ecological analyses. Species with smaller distributional ranges and those that have been described more recently, presented lower coverage and data availability in trait databases.
5. We encourage further standardisation of fish trait measurement protocols to help improve the robust application of bioassessment indices and trait-based approaches.

     

Chironomidae of the Holarctic region: a comparison of ecological and functional traits between North America and Europe

Chironomidae (Diptera) are widespread, abundant, diverse and ubiquitous, and include genera and species that are distributed across the Holarctic region. However, the geographical barriers between continents should have resulted in intraspecific population differentiation with reflection on individual biological and ecological traits. Our aim was to test for potential differences in Chironomidae species/genus and traits between the Nearctic and Palearctic regions. We compared the Chironomidae trait information gathered in two databases; one database was developed in Europe and the other in North America. Common genera and species of both databases were selected, and the common traits were adjusted into the same trait categories. Data were transformed into presence/absence and divided into Eltonian (biological/functional) and Grinnellian (ecological) traits. Common genera and common species were analyzed using Fuzzy correspondence analysis (FCA). Differences between databases occur for all trait domains. Yet, Eltonian traits showed lower level of concordance than Grinnellian traits at the species level. Different biological characteristics in the Nearctic and Palearctic regions may indicate that Chironomidae have different adaptions to similar ecological environments due to intraspecific variability or even trait plasticity.     

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete‐case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete‐case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.     

Frugivoria: A trait database for birds and mammals exhibiting frugivory across contiguous Neotropical moist forests

Motivation

Biodiversity in many areas is rapidly declining because of global change. As such, there is an urgent need for new tools and strategies to help identify, monitor and conserve biodiversity hotspots. This is especially true for frugivores, species consuming fruit, because of their important role in seed dispersal and maintenance of forest structure and health. One way to identify these areas is by quantifying functional diversity, which measures the unique roles of species within a community and is valuable for conservation because of its relationship with ecosystem functioning. Unfortunately, the functional trait information required for these studies can be sparse for certain taxa and specific traits and difficult to harmonize across disparate data sources, especially in biodiversity hotspots. To help fill this need, we compiled Frugivoria, a trait database containing ecological, life-history, morphological and geographical traits for mammals and birds exhibiting frugivory. Frugivoria encompasses species in contiguous moist montane forests and adjacent moist lowland forests of Central and South America—the latter specifically focusing on the Andean states. Compared with existing trait databases, Frugivoria harmonizes existing trait databases, adds new traits, extends traits originally only available for mammals to birds also and fills gaps in trait categories from other databases. Furthermore, we create a cross-taxa subset of shared traits to aid in analysis of mammals and birds. In total, Frugivoria adds 8662 new trait values for mammals and 14,999 for birds and includes a total of 45,216 trait entries with only 11.37% being imputed. Frugivoria also contains an open workflow that harmonizes trait and taxonomic data from disparate sources and enables users to analyse traits in space. As such, this open-access database, which aligns with FAIR data principles, fills a major knowledge gap, enabling more comprehensive trait-based studies of species in this ecologically important region.

Main Types of Variable Contained

Ecological, life-history, morphological and geographical traits.

Spatial Location and Grain

Neotropical countries (Mexico, Guatemala, Costa Rica, Panama, El Salvador, Belize, Nicaragua, Ecuador, Colombia, Peru, Bolivia, Argentina, Venezuela and Chile) with contiguous montane regions.

Time Period and Grain

IUCN spatial data: obtained February 2023, spanning range maps collated from 1998 to 2022. IUCN species data: obtained June 2019–September 2022. Newly included traits: span 1924 to 2023.

Major Taxa and Level of Measurement

Classes Mammalia and Aves; 40,074 species-level traits; 5142 imputed traits for 1733 species (mammals: 582; birds: 1147) and 16 sub-species (mammals).

Software Format

.csv; R.     

Phylogenetic imputation of plant functional trait databases

Continental‐scale maps of plant functional diversity are a fundamental piece of data of interest to ecosystem modelers and ecologists, yet such maps have been exceedingly hard to generate. The large effort to compile global plant functional trait databases largely for the purpose of mapping and analyzing the spatial distribution of function has resulted in very sparse data matrices thereby limiting progress. Identifying robust methodologies to gap fill or impute trait values in these databases is an important objective. Here I argue that existing statistical tools from phylogenetic comparative methods can be used to rapidly impute values into global plant functional trait databases due to the large amount of phylogenetic signal often in trait data. In particular, statistical models of phylogenetic signal in traits can be generated from existing data and used to predict missing values of closely related species often with a high degree of accuracy thereby facilitating the continental‐scale mapping of plant function. Despite the promise of this approach, I also discuss potential pitfalls and future challenges that will need to be addressed.     

Revisiting the Holy Grail: using plant functional traits to understand ecological processes

One of ecology's grand challenges is developing general rules to explain and predict highly complex systems. Understanding and predicting ecological processes from species' traits has been considered a ‘Holy Grail’ in ecology. Plant functional traits are increasingly being used to develop mechanistic models that can predict how ecological communities will respond to abiotic and biotic perturbations and how species will affect ecosystem function and services in a rapidly changing world; however, significant challenges remain. In this review, we highlight recent work and outstanding questions in three areas: (i) selecting relevant traits; (ii) describing intraspecific trait variation and incorporating this variation into models; and (iii) scaling trait data to community‐ and ecosystem‐level processes. Over the past decade, there have been significant advances in the characterization of plant strategies based on traits and trait relationships, and the integration of traits into multivariate indices and models of community and ecosystem function. However, the utility of trait‐based approaches in ecology will benefit from efforts that demonstrate how these traits and indices influence organismal, community, and ecosystem processes across vegetation types, which may be achieved through meta‐analysis and enhancement of trait databases. Additionally, intraspecific trait variation and species interactions need to be incorporated into predictive models using tools such as Bayesian hierarchical modelling. Finally, existing models linking traits to community and ecosystem processes need to be empirically tested for their applicability to be realized.     

Intra-Specific Leaf Trait Variation: Management and Fertility Matter More than the Climate at Continental Scales

Plant functional traits have contributed to the understanding of how vegetation responds to management, community assembly and how vegetation controls ecosystem processes. As traits are time consuming to measure – and it may not always be feasible or practical to measure all traits within a study – great reliance has been put on using trait values from databases. This ignores intraspecific trait variability and the traits’ responses to the environment. This study uses trait values measured as part of a large-scale investigation of land use impacts on vegetation to assess how environmental factors, specifically climate, soil and management, control inter-population level intra-specific variation in key traits. There was clear evidence that intra-specific variation in leaf carbon content, leaf dry matter content, leaf nitrogen content and specific leaf area were all sensitive to edaphic factors and to management, but only leaf dry matter content was linearly affected by the climate (rainfall). There were also significant interactions between climate and species identity for leaf dry matter content and leaf nitrogen content, suggesting that species responses to the climate are not uniform or simple. The results of this study suggest that site fertility and management ought to be associated with trait data in databases to allow for the incorporation of intra-specific variation in analyses and that more research is needed to identify the shape of trait:climate relationships.     

Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.     

Trait means,trait plasticity and trait differences to other species jointly explain species performances in grasslands of varying diversity

Functional traits may help to explain the great variety of species performances in plant communities, but it is not clear whether the magnitude of trait values of a focal species or trait differences to co‐occurring species are key for trait‐based predictions. In addition, trait expression within species is often plastic, but this variation has been widely neglected in trait‐based analyses. We studied functional traits and plant biomass of 59 species in 66 experimental grassland mixtures of varying species richness (Jena Experiment). We related mean species performances (species biomass and relative yield RY) and their plasticities along the diversity gradient to trait‐based pedictors involving mean species traits (T_mean), trait plasticities along the diversity gradient (T_slope), extents of trait variation across communities (T_CV; coefficient of variation) and hierarchical differences (T_diff) and trait distances (absolute values of trait differences T_dist) between focal and co‐occurring species. T_mean (30–55%) and T_diff (30–33%) explained most variation in mean species performances and their plasticities, but T_slope (20–25%) was also important in explaining mean species performances. The mean species traits and the trait differences between focal species and neighbors with the greatest explanatory power were related to plant size and stature (shoot length, mass:height ratios) and leaf photosynthetic capacity (specific leaf area, stable carbon isotopes and leaf nitrogen concentration). The contribution of trait plasticities in explaining species performances varied in direction (positive or negative) and involved traits related to photosynthetic capacity, nitrogen acquisition (nitrogen concentrations and stable isotopes) as well as structural stability (shoot carbon concentrations). Our results suggest that incorporating plasticity in trait expression as well as trait differences to co‐occurring species is critical for extending trait‐based analyses to understand the assembly of plant communities and the contribution of individual species in structuring plant communities.     

The biogeography and filtering of woody plant functional diversity in North and South America

Aim In recent years evidence has accumulated that plant species are differentially sorted from regional assemblages into local assemblages along local‐scale environmental gradients on the basis of their function and abiotic filtering. The favourability hypothesis in biogeography proposes that in climatically difficult regions abiotic filtering should produce a regional assemblage that is less functionally diverse than that expected given the species richness and the global pool of traits. Thus it seems likely that differential filtering of plant traits along local‐scale gradients may scale up to explain the distribution, diversity and filtering of plant traits in regional‐scale assemblages across continents. The present work aims to address this prediction. Location North and South America. Methods We combine a dataset comprising over 5.5 million georeferenced plant occurrence records with several large plant functional trait databases in order to: (1) quantify how several critical traits associated with plant performance and ecology vary across environmental gradients; and (2) provide the first test of whether the woody plants found within 1° and 5° map grid cells are more or less functionally diverse than expected, given their species richness, across broad gradients. Results The results show that, for many of the traits studied, the overall distribution of functional traits in tropical regions often exceeds the expectations of random sampling given the species richness. Conversely, temperate regions often had narrower functional trait distributions than their smaller species pools would suggest. Main conclusion The results show that the overall distribution of function does increase towards the equator, but the functional diversity within regional‐scale tropical assemblages is higher than that expected given their species richness. These results are consistent with the hypothesis that abiotic filtering constrains the overall distribution of function in temperate assemblages, but tropical assemblages are not as tightly constrained.     

The influence of variability in species trait data on community‐level ecological prediction and inference

Species trait data have been used to predict and infer ecological processes and the responses of biological communities to environmental changes. It has also been suggested that, in lieu of trait, data niche differences can be inferred from phylogenetic distance. It remains unclear how variation in trait data may influence the strength and character of ecological inference. Using species‐level trait data in community ecology assumes intraspecific variation is small in comparison with interspecific variation. Intraspecific variation across species ranges or within populations may lead to variability in trait data derived from different scales (i.e., local or regional) and methods (i.e., mean or maximum values). Variation in trait data across species can affect community‐level relationships. I examined variability in body size, a key trait often measured across taxa. I collected 12 metrics of fish species length (including common and maximum values) for 40 species from literature, online databases, museum collections, and field data. I then tested whether different metrics of fish length could consistently predict observed species range boundary shifts and the impacts of an introduced predator on inland lake fish communities across Ontario, Canada. I also investigated whether phylogenetic signal, an indicator of niche‐conservativism, changed among measures. I found strong correlations between length metrics and limited variation across metrics. Accordingly, length was a consistently significant predictor of the response of fish communities to environmental change. Additionally, I found significant evidence of phylogenetic signal in fish length across metrics. Limited variation in length across metrics (within species), in comparison with variation within metrics (across species), made fish species length a reliable predictor at a community‐level. When considering species‐level trait data from different sources, researchers should examine the potential influence of intraspecific trait variation on data derived by different metrics and at different scales.     

Evolution of species trait through resource competition

To understand the evolution of diverse species, theoretical studies using a Lotka–Volterra type direct competition model had shown that concentrated distributions of species in continuous trait space often occurs. However, a more mechanistic approach is preferred because the competitive interaction of species usually occurs not directly but through competition for resource. We consider a chemostat-type model where species consume resource that are constantly supplied. Continuous traits in both consumer species and resource are incorporated. Consumers utilize resource whose trait values are similar with their own. We show that, even when resource-supply has a continuous distribution in trait space, a positive continuous distribution of consumer trait is impossible. Self-organized generation of distinct species occurs. We also prove global convergence to the evolutionarily stable distribution.     

Ecological constraints from incumbent clades drive trait evolution across the tree‐of‐life of freshwater macroinvertebrates

The rates of species and trait diversification vary across the Tree‐of‐Life and over time. Whereas species richness and clade age generally are decoupled, the correlation of accumulated trait diversity of clades (trait disparity) with clade age remains poorly explored. Total trait disparity may be coupled with clade age if the growth of disparity (disparification) within and across clades is continuous with time in an additive niche expansion process (linear‐cumulative model), or alternatively if the rate of trait disparification varies over time and decreases as ecological space becomes gradually saturated (disparity‐dependent model). Using a clock‐calibrated phylogenetic tree for 143 freshwater macroinvertebrate families and richness and trait databases covering > 6400 species, we measured trait disparity in 18 independent clades that successively transitioned to freshwater ecosystems and analyzed its relation with clade age. We found a positive correlation between clade age and total disparity within clades, but no relationship for most individual traits. Traits unique to freshwater lifestyle were highly variable within older clades, while disparity in younger clades shifted towards partially terrestrial lifestyles and saline tolerance to occupy habitats previously inaccessible or underutilized. These results argue that constraints from incumbent lineages limit trait disparity in younger clades that evolved for filling unoccupied regions of the trait space, which suggests that trait disparification may follow a disparity‐dependent model. Overall, we provide an empirical pattern that reveals the potential of the disparity‐dependent model for understanding fundamental processes shaping trait dynamics across the Tree‐of‐Life.     

Functional traits,convergent evolution,and periodic tables of niches

Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche ‘dimensions’, or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait‐value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification.     

Mycorrhizal traits and plant communities: perspectives for integration

Plant functional type‐ and trait‐based approaches to understanding vegetation dynamics are gradually gaining popularity. However, plant mycorrhizal traits are rarely considered in plant trait databases and are almost totally neglected in trait‐based plant community studies, despite more than 90% of the land flora being mycorrhizal. In this paper I describe and define the mycorrhizal traits of plant species, notably mycorrhizal type, mycorrhizal status, mycorrhizal flexibility and mycorrhizal dependency, which potentially influence plant distribution and community structure. I propose ways of using these traits for large‐scale synthetic studies for understanding the role of mycorrhizal symbiosis in vegetation dynamics. I suggest considering plant community mycorrhization – community means of mycorrhizal traits weighted by plant species abundances – and suggest an index of mycorrhization to describe the mycorrhizal trait composition of plant communities.     

Rising temperature reduces divergence in resource use strategies in coexisting parasitoid species

Coexistence of species sharing the same resources is often possible if species are phylogenetically divergent in resource acquisition and allocation traits, decreasing competition between them. Developmental and life-history traits related to resource use are influenced by environmental conditions such as temperature, but thermal trait responses may differ among species. An increase in ambient temperature may, therefore, affect trait divergence within a community, and potentially species coexistence. Parasitoids are interesting models to test this hypothesis, because multiple species commonly attack the same host, and employ divergent larval and adult host use strategies. In particular, development mode (arrested or continued host growth following parasitism) has been recognized as a major organiser of parasitoid life histories. Here, we used a comparative trait-based approach to determine thermal responses of development time, body mass, egg load, metabolic rate and energy use of the coexisting Drosophila parasitoids Asobara tabida, Leptopilina heterotoma, Trichopria drosophilae and Spalangia erythromera. We compared trait values between species and development modes, and calculated trait divergence in response to temperature, using functional diversity indices. Parasitoids differed in their thermal response for dry mass, metabolic rate and lipid use throughout adult life, but only teneral lipid reserves and egg load were affected by developmental mode. Species-specific trait responses to temperature were probably determined by their adaptations in resource use (e.g. lipogenesis or ectoparasitism). Overall, trait values of parasitoid species converged at the higher temperature. Our results suggest that local effects of warming could affect host resource partitioning by reducing trait diversity in communities.     

Below- and aboveground traits explain local abundance,and regional,continental and global occurrence frequencies of grassland plants

Plants vary widely in how common or rare they are, but whether commonness of species is associated with functional traits is still debated. This might partly be because commonness can be measured at different spatial scales, and because most studies focus solely on aboveground functional traits. We measured five root traits and seed mass on 241 central European grassland species, and extracted their specific leaf area, height, mycorrhizal status and bud-bank size from databases. Then we tested if trait values are associated with commonness at seven spatial scales, ranging from abundance in 16-m² grassland plots, via regional and European-wide occurrence frequencies, to worldwide naturalization success. At every spatial scale, commonness was associated with at least three traits. The traits explained the greatest proportions of variance for abundance in grassland plots (42%) and naturalization success (41%) and the least for occurrence frequencies in Europe and the Mediterranean (2%). Low root tissue density characterized common species at every scale, whereas other traits showed directional changes depending on the scale. We also found that many of the effects had significant non-linear effects, in most cases with the highest commonness-metric value at intermediate trait values. Across scales, belowground traits explained overall more variance in species commonness (19.4%) than aboveground traits (12.6%). The changes we found in the relationships between traits and commonness, when going from one spatial scale to another, could at least partly explain the maintenance of trait variation in nature. Most importantly, our study shows that within grasslands, belowground traits are at least as important as aboveground traits for species commonness. Therefore, belowground traits should be more frequently considered in studies on plant functional ecology.     

Correlated evolution between climate and suites of traits along a fast–slow continuum in the radiation of Protea

Evolutionary radiations are responsible for much of Earth's diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as “adaptive” or not. Across many groups of plants, trait–climate relationships suggest that traits are an important indicator of how plants adapt to different climates. In particular, analyses of plant functional traits in global databases suggest that there is an “economics spectrum” along which combinations of functional traits covary along a fast–slow continuum. We examine evolutionary associations among traits and between trait and climate variables on a strongly supported phylogeny in the iconic plant genus Protea to identify correlated evolution of functional traits and the climatic‐niches that species occupy. Results indicate that trait diversification in Protea has climate associations along two axes of variation: correlated evolution of plant size with temperature and leaf investment with rainfall. Evidence suggests that traits and climatic‐niches evolve in similar ways, although some of these associations are inconsistent with global patterns on a broader phylogenetic scale. When combined with previous experimental work suggesting that trait–climate associations are adaptive in Protea, the results presented here suggest that trait diversification in this radiation is adaptive.     

Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)

Several prominent evolutionary theories propose mechanisms whereby the evolution of a defensive trait or suite of traits causes significant shifts in species diversification rate and niche evolution. We investigate the role of cuticular spines, a highly variable morphological defensive trait in the hyperdiverse ant genus Polyrhachis, on species diversification and geographic range size. Informed by key innovation theory and the escape-and-radiate hypothesis, we predicted that clades with longer spines would exhibit elevated rates of diversification and larger range sizes compared to clades with shorter spines. To address these predictions, we estimated phylogenetic relationships with a phylogenomic approach utilizing ultraconserved elements and compiled morphological and biogeographic trait databases. In contrast to the first prediction, we found no association between diversification rate and any trait (spine length, body size and range size), with the sole exception of a positive association between range size and diversification in one of three trait-based diversification analyses. However, we recovered a positive phylogenetic correlation between spine length and geographic range size, suggesting that spines promote expanded geographic range. Notably, these results were consistent across analyses using different phylogenetic inference approaches and spine trait measurement schemes. This study provides a rare investigation of the role of a defensive trait on geographic range size, and ultimately supports the hypothesis that defensive spines are a factor in increased range size in Polyrhachis ants. Furthermore, the lack of support for an association between spines and diversification, which contrasts with previous work demonstrating a positive association between spines and diversification rate, is intriguing and warrants further study.