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opencc-by-4.0Oct 2022View details →

The confluence of traits and environmental factors driving diversification and niche expansion in the globally distributed order Myrtales

Supplementary files for the article: The confluence of traits and environmental factors driving diversification and niche expansion in the globally distributed order Myrtales

opencc-zeroOct 2022View details →

Mycorrhizae influence plant vegetative and floral traits and intraspecific trait variation

Premise. Arbuscular mycorrhizal fungi (AMF) can strongly influence host plant vegetative growth, but less is known about AMF effects on other plant traits, the relative impacts of AMF on vegetative growth versus floral traits, or AMF-induced intraspecific variation in traits. Key results. AMF species varied in their effects on host plants, from negative to positive effects. AMF often had inconsistent effects on vegetative biomass versus floral traits, and therefore quantifying one or the other may provide a misleading representation of potential AMF effects. AMF treatments generated key variation in plant traits, especially floral traits, with potential consequences for plant-pollinator interactions. Given increased intraspecific trait variation in Linum lewisii plants across AMF species compared to uninoculated individuals or single AMF treatments, local AMF diversity and their host plant associations may scale up to influence community-wide patterns of trait variation and species interactions. Conclusions. These results have implications for predicting how aboveground communities are affected by belowground communities. Including AMF effects on not just host plant biomass but also functional traits and trait variation will deepen our understanding of community structure and function, including pollination.

opencc-by-4.0Aug 2017View details →

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness

This archive includes the final summary tables used for the analyses.

opencc-by-4.0Aug 2017View details →

SurEau database : A database of hydraulic and stomatal traits for modelling drought resistance in plants

This file contains a database of hydraulic and stomatal traits that accompanies the paper untitled "Pant resistance to drought relies on timely stomatal closure" publish in Ecology Letters. This database was used to built the Figure of this manuscript. > The first page ("Stem_VCurves") contains the parameter of vulnerability curve to embolism for 150 species. Family, genus and species names as well as original reference are provided. > The second page ("Pgs90") contains a first proxy for the water potential causing stomatal closure, it is the value of water potential causing 90% stomatal closure computed from gs versus water potential. Family, genus and species names as well as original reference are provided. > The third page (Ptlp) contains a second proxy for the water potential causing stomatal closure, it is the turgor loss point computed from pressure volume curves. Family, genus and species names as well as original reference are provided. > The fourth page (ALL) contains all the three previous pages together, allowing to reconstruct Figure 1. > The fifth page (PitlpAdultSeedlings) contains values of turgor loss point for adults and seedilngs for 15 species. > The sixth page (P50AdultSeedlings) contains values of embolism resistance for adults and seedilngs for 14 species. > The seventh page (Emin) contains values of minimum (i.e. cuticular) conductance and minimum transpiration for 33 species as well as embolism resistance values for theese species.

opencc-by-4.0Apr 2024View details →

Harnessing interactions between traits and the environment to improve predictions of ecosystem functioning

The data correspond to the manuscript entitled "Harnessing interactions between traits and the environment to improve predictions of ecosystem functioning". Data needed to reproduce the figure 2 about springtails colonisation of defaunated soil blocks, from two different environments (forest or meadow), with the springtail species classified according to the supposed dispersal ability. Species with long legs and antennae, a well-developed jumping apparatus (furcula), and a complete visual apparatus were considered to be able to disperse more rapidly on their own and were thus categorized as “fast” dispersers. Other species with reduced locomotor and vision organs were categorized as “slow” dispersers (Ponge et al. 2006a). The "number of individuals" corresponds to the number of individuals found in each defaunated soil block after one week in the initial data set (Auclarc et al., 2009). Ponge J-F, Dubs F, Gillet S, et al. 2006a. Decreased biodiversity in soil springtail communities: the importance of dispersal and landuse history in heterogeneous landscapes. Soil Biol Biochem 38: 1158–61. Auclerc A, Ponge JF, Barot S, and Dubs F. 2009. Experimental assessment of habitat preference and dispersal ability of soil springtails. Soil Biol Biochem 41: 1596–604.

Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity

Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity. Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments. Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.

Data from: Genetic variation in growth and leaf traits associated with local adaptation to climate in yellow birch (Betula alleghaniensis Britton)

Understanding patterns of variation in functional traits of hardwood trees is crucial for conserving and managing North American temperate forests under climate change. This study examined provenance variation of yellow birch (Betula alleghaniensis Britton) in growth, biomass allocation, leaf morphology, and stable carbon isotope composition. Trees were grown from ten seed sources originating from across Canada and the northern USA. Height and diameter were not significantly related to climate at seed origin, suggesting that variation may be better explained by site factors, such as soil pH and soil moisture. In contrast, carbon isotope composition and leaf morphological traits were significantly correlated to climate variables including temperature, precipitation, and solar radiation. Provenances from warmer, drier localities tended to have higher stable carbon isotope ratio (δ13C), greater specific leaf area, and narrower leaf width than their counterparts from cooler, wetter climates. Thus, variation in leaf morphological traits appears to be involved in adaptation of yellow birch to variation in temperature and moisture availability across the species' range. Our results suggest that there may exist potential for selection and breeding of drought resistant yellow birch genotypes to aid in reforestation under climate change.

The scaling of metabolic traits differs among larvae and juvenile colonies of scleractinian corals

Body size profoundly affects organism fitness and ecosystem dynamics through the scaling of physiological traits. This study tests for variation in metabolic scaling and its potential drivers among corals differing in life history strategies and taxonomic identity. Data were compiled from published sources and augmented with empirical measurements of corals in Moorea, French Polynesia. The data compilation revealed metabolic isometry in broadcasted larvae, but size-independent metabolism in brooded larvae; empirical measures of Pocillopora acuta larvae also supported size-independent metabolism in brooded coral larvae. In contrast, for juvenile colonies (i.e., 1–4 cm diameter), metabolic scaling was isometric for Pocillopora spp. and negatively allometric for Porites spp. The scaling of biomass with surface area was isometric for Pocillopora spp., but positively allometric for Porites spp., suggesting the surface area:biomass ratio mediates metabolic scaling in these corals. The scaling of tissue biomass and metabolism was not affected by light treatment (i.e., either natural photoperiods or constant darkness) in both juvenile taxa. However, biomass was reduced by 9–15% in the juvenile corals from the light treatments and this coincided with higher metabolic scaling exponents, thus supporting the causal role of biomass in driving variation in scaling. This study shows that metabolic scaling is plastic in the early life stages of corals, with intrinsic differences between life history strategy (i.e., brooded and broadcasted larvae) and taxa (i.e., Pocillopora spp. and Porites spp.), and acquired differences attributed to changes in area-normalized biomass.

opencc-by-4.0Apr 2024View details →

Phylogenetic conservatism and coordination in traits of Chinese woody endemic flora

The dataset contains 5 files, including: (1)   “HLS. new” is a phylogenetic tree constructed with 1,387 species, we used Taxa01, Taxa02 in the phylogenetic tree construction process (refer to Taxa match species file). Please note that I marked outgroups (9 species) in yellow color, you may use “drop tips” function in R to delete them if it’s extra info for you; (2)   “Taxa match species” , Taxa name are corresponding to “HLS. new”; (3)   “OGU” is a species occurrence file, each gridcell could be regard as “community”, which we can use to analysis species assembling; Gridcell in this file corresponding to the Operational Geographic Units (OGUs). Species occurrence matrix were prepared according to Silva et al.'s (Cardoso da Silva, Cardoso de Sousa, & Castelletti, 2004) method: (a) To leverage the size effect, study area was divided into 50*50 km2 grid cells, covering the land area of China including Taiwan; (b) assign species occurrence into each grid cell; (c) delimit OGUs where contains at least two endemic species and land area covered more than half of grid cells (1,250 km2). (4)   “Climate”. bio 1-19 were download from CHELSA: https://chelsa-climate.org/timeseries/; (Karger et al., 2017; Karger, Nobis, Normand, Graham, & Zimmermann, 2021). I also attached the description for chelsa.   (5)   “Trait”. We tried our best to access to the information regarding to leaf length, height and seed diameter. For few cases, you may still find N.A. data. I believe it’s very common in macroecology research.

opencc-by-4.0Mar 2024View details →

European ancestry: 72 traits spanning multiple clinical domains (GRCh37)

<div> </div> <div> This collection of 72 traits contains a wide variety of traits including metabolic traits (e.g. lipid levels, glycemic traits…), immune system diseases (e.g. inflammatory bowel disease, celiac disease), cardiovascular outcomes and more. This collection allows experimenting with combination of traits from different clinical domains and searching for highly pleiotropic variants.  More details on GWAS summary statistics and their curation are available <a href="https://www.biorxiv.org/content/10.1101/2023.10.27.564319v1" target="_blank" rel="noreferrer noopener">here</a>.  </div>

Data from: Dine and dash: How trophic ecology and migration shape functional locomotory traits in Clupeiform fishes

Understanding how interactions between multiple selective forces influence traits at the macroevolutionary scale is key to understanding adaptive landscapes. Diadromy, an extreme form of migration between marine and freshwater environments, is thought to require locomotory traits conducive to long-distance migration. Yet, other selective forces, such as predator avoidance, habitat use, and prey acquisition, are also likely to shape locomotory adaptation in fishes. We examined how diadromy and trophic ecology together influenced locomotory trait diversity across Clupeiformes, a clade of fishes containing high trophic diversity and numerous transitions to diadromy. We found that both diadromy and trophic ecology influenced the pattern and pace of trait evolution. Diadromous taxa rapidly evolved traits characterized by high cruising efficiency, but the extent to which diadromous and non-diadromous taxa differed depended on their trophic ecology. Macropredators showed greater differences in locomotory traits between diadromous and non-diadromous taxa than phytodetritivores and micropredators, suggesting that traits conducive to migration might be most costly to consumers of evasive prey. This work shows that simultaneously characterizing the roles of multiple ecological or life-history factors in phenotypic evolution can bring the topography of adaptive landscapes into sharper focus and provide a more holistic view of the forces driving patterns of trait evolution.

opencc-zeroDec 2023View details →

Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows

Background Conducting genome-wide association studies (GWAS) for reproductive traits in Hanwoo cattle, including age at first calving (AFC), calving interval (CI), gestation length (GL), and number of artificial inseminations per conception (NAIPC), is of paramount significance. These analyses provided a thorough exploration of the genetic basis of these traits, facilitating the identification of key markers for targeted trait improvement. Breeders can optimize their selection strategies, leading to more efficient and sustainable breeding programs, by incorporating genetic insights. This impact extends beyond individual traits and contributes to the overall productivity and profitability of the Hanwoo beef cattle industry. Ultimately, GWAS is essential in ensuring the long-term genetic resilience and adaptability of Hanwoo cattle populations. The primary goal of this study was to identify significant single nucleotide polymorphisms (SNPs) or quantitative trait loci (QTLs) associated with the studied reproductive traits and subsequently map the underlying genes that hold promise for trait improvement. Results A genome-wide association study of reproductive traits identified 68 significant single nucleotide polymorphisms (SNPs) distributed across 29 Bos taurus autosomes (BTA). Among them, BTA14 exhibited the highest number of identified SNPs (25), whereas BTA6, BTA7, BTA8, BTA10, BTA13, BTA17, and BTA20 exhibited 8, 5, 5, 3, 8, 2, and 12 significant SNPs, respectively. Annotation of candidate genes within a 500 kb region surrounding the significant SNPs led to the identification of ten candidate genes relevant to age at first calving. These genes were: FANCG, UNC13B, TESK1, TLN1, and CREB3 on BTA8; FAM110B, UBXN2B, SDCBP, and TOX on BTA14; and MAP3K1 on BTA20. Additionally, APBA3, TCF12, and ZFR2, located on BTA7 and BTA10, were associated with the calving interval; PAX1, SGCD, and HAND1, located on BTA7 and BTA13, were linked to gestation length; and RBM47, UBE2K, and GPX8, located on BTA6 and BTA20, were linked to the number of artificial inseminations per conception in Hanwoo cows. Conclusions The findings of this study enhance our knowledge of the genetic factors that influence reproductive traits in Hanwoo cattle populations and provide a foundation for future breeding strategies focused on improving desirable traits in beef cattle. This research offers new evidence and insights into the genetic variants and genome regions associated with reproductive traits and contributes valuable information to guide future efforts in cattle breeding.

Data from: Extinction selectivity obscures patterns of trait-dependent endangerment in Columbiformes

Understanding how extinction has occurred in the recent past is crucial to unravel its main drivers as well as to implement effective conservation practices to minimize global biodiversity loss. It has long been hypothesized that extinction risk is not randomly distributed among traits of species. However, the actual traits making species more prone to extinction may have been overlooked because already extinct species are often not considered in comparative analyses of extinction risk. We characterized the drivers of extinction in a cosmopolitan bird clade, including Holocene and contemporary extinctions potentially related to human impacts, and provided evidence of an 'extinction selectivity' in species traits. We constructed a new phylogenetic hypothesis of the Columbiformes, a cosmopolitan bird clade consisting of 33 recently extinct and 351 extant species. Then, we integrated data on geography, behaviour, and morphology to reveal the drivers of extinction risk. We used phylogenetic generalized least square models to test the effect of geography, behaviour, and morphology on the risk of extinction and identified differences in the drivers of extinction when including vs. excluding recently extinct species. Our analysis revealed that Columbiformes endemic from islands with ground-foraging habits, weak flying abilities, migratory behaviour, and larger body sizes are more vulnerable to extinction. Our results also show that excluding recently extinct species identifies extinction drivers differently from those when including recently extinct species. Only by accurately identifying the traits that increase extinction risk can we develop targeted conservation measures that promote the long-term persistence of threatened species. Extinction selectivity has important implications for the conservation of biological communities and ultimately ecosystem functioning, considering the critical role Columbiformes often play as seed dispersers.

Clinal variation in quantitative traits but not in evolutionary potential along elevational and latitudinal gradients in the widespread Anthyllis vulneraria

Premise of the study Strong elevational and latitudinal gradients allow the study of genetic differentiation in response to similar environmental changes. However, it is uncertain whether the environmental changes along the two types of gradients result in similar genetically based changes in quantitative traits. Peripheral arctic and alpine populations are thought to have a lower evolutionary potential than more central ones. Methods We studied quantitative traits of the widespread Anthyllis vulneraria in a common garden. Plants originated from 20 populations along a 2000 m elevational gradient from the lowlands to the elevational limit of the species in the Alps, and from 20 populations along a 2400 km latitudinal gradient from the centre of the distribution of the species in Central Europe to its northern distributional margin. Key results Several traits showed similar clinal variation with elevation and latitude of origin. Higher QST-values than FST-values in some traits indicated divergent selection. The same traits were subject to strongly diversifying selection among populations (high QST) and strong stabilising selection within populations (low evolvability). Genetic diversity of most quantitative traits and neutral molecular markers was only weakly correlated. Plasticity in response to benign conditions declined with both increasing elevation and latitude of origin, but the evolvability of most traits did not. Conclusions The clinal variation suggests adaptive differentiation of quantitative traits along the two gradients. Our results indicate that the evolutionary potential of peripheral populations is not necessarily reduced. However, lower plasticity may threaten their survival under rapidly changing climatic conditions.

opencc-by-4.0May 2024View details →

The Relationship between Self-Perception of Smile Aesthetics and Personality Traits of University Students: A Cross-Sectional Study

Los documentos contienen la base de datos que se obtuvo del estudio "The Relationship between Self-Perception of Smile Aesthetics and Personality Traits of University Students: A Cross-Sectional Study", siendo datos reales de estudiantes de una universidad nacional de Perú. Luego se encuentra el documento con los instrumentos, en formato como se presentó para la ejecución.

Traits mediate environmental responses of benthic ciliates in dynamic coastal habitats

Aim: Understanding how species' traits mediate environmental responses provides a mechanistic perspective on community assembly processes. Although traits that influence the response of multicellular organisms to environments have been studied, the identification of such traits in unicellular organisms, like ciliates, is underexplored. Since ciliates are dominate animals at coastal sandy sediments and contribute significantly to interstitial community respiration, identifying links between their occurrence and sandy-coast characteristics is crucial for conserving biodiversity and protecting coastal habitats. Location: Coasts of China. Methods: We used Hierarchical Modeling of Species Communities, a trait-based joint species distribution model, to analyze ciliate community data collected from 344 sites belonging to 31 beaches across the Chinese coastline. Results: We found that physical variables play the most important role in determining ciliate occurrence. The beach index which combines the tidal range, sediment grain size and beach slope of beach selected species based on body size as well as feeding type, while sediment grain size constrained different mobility types, with swimming species favoring fine sandy sediments. The significant contribution of phylogeny in explaining the residual variation among species responses indicates that there are phylogenetically conserved but unmeasured traits too that influence species' responses. Species richness of benthic ciliates was higher in dissipative beaches with high primary productivity. Main conclusions: Based on our research, ciliate occurrence in coastal beaches is mediated by their traits which are filtered by local environmental variables. The beach index is essential in predicting distribution patterns and species richness of benthic ciliates. Nevertheless, further research is needed to identify additional traits that will enhance the accuracy of predicting ciliate niches. Our study provides insights into the mechanisms driving ciliate community assembly processes and has implications for the conservation of biodiversity in sandy coastal habitats.

opencc-zeroDec 2023View details →

Data from: Dispersal-related plant traits are associated with range size in the Atlantic Forest

Aim: The efficiency of animal-mediated seed dispersal is threatened by declines of animal populations, especially in tropical forests. We hypothesise that large-seeded plants with animal-mediated dispersal tend to have limited geographic ranges and face an increased risk of extinction due to the potential decline in seed dispersal by large-bodied fruit-eating and seed-dispersing animals (frugivores) Location: Atlantic Forest, Brazil, South America Taxon: Angiosperms Methods: First, we collected dispersal-related trait (dispersal syndrome, fruit size, seed size), growth form (tree, climber, other) and preferred vegetation type (open, closed) data for 1,052 Atlantic Forest plant species. Next, we integrated these with occurrence records, extinction risk assessments, and phylogenetic trees. Finally, we performed phylogenetic generalized least squares (PGLS) regressions to test the direct and interactive effects of dispersal-related traits and vegetation type on geographical range size. Results: Large-seeded species had smaller range sizes than small-seeded species, but only for species with animal-mediated dispersal, not for those dispersed by abiotic mechanisms. However, plants with abiotic dispersal had overall smaller range sizes than plants with animal-mediated dispersal. Furthermore, we found that species restricted to forests had smaller ranges than those occurring in open or mixed vegetation. Finally, at least 29% of the Atlantic Forest flora is threatened by extinction, but this was not related to plant dispersal syndromes. Main Conclusions: Large-seeded plants with animal-mediated dispersal may be suffering from dispersal limitation, potentially due to past and ongoing defaunation of large-bodied frugivores, leading to small range sizes. Other factors, such as deforestation and fragmentation, will probably modulate such effects of dispersal on range size, and ultimately extinction. Our study sheds light on the relationship between plant traits, mutualistic interactions and distribution that are key to the functioning of tropical forests.

Data from: Vertical niche usage and trait associations in Gabonese amphibians

Tropical forests are vertically complex, and offer unique niche opportunities in the form of resource, climate, and habitat-gradients from the forest floor to the canopy. Rainforest amphibians organize within this vertical space and the highest levels of vertical stratification occur in structurally complex and climatically stable tropical rainforests. Amphibians have diversified into numerous habitat and climatic niches, which has led to the development of a wide variety of morphological, behavioural, physiological, and reproductive traits. However, a lack of data regarding the vertical niche space used by amphibian species has prevented a nuanced analysis of traits and vertical height. We performed 74 ground-to-canopy surveys for amphibians at Baposso Village, Ngounie Province, Gabon, and describe the vertical stratification patterns of the assemblage in terms of richness, abundance, and species specific vertical niche usage. We analyse the relationships between amphibian traits with vertical height using linear mixed effects models, finding strong support that frogs with bigger toes in relation to their length access greater height in the canopy. We also see differences in the vertical heights of species according to their reproductive modes, highlighting the importance of reproductive mode diversity for the vertical stratification of amphibian assemblages.

Data from: A comparative study of body size evolution in moths: Evidence of correlated evolution with feeding and phenology-related traits

Interspecific variation in body size is one of the most popular topics in comparative studies. Despite recent advances, little is still known about the patterns and processes behind the evolution of body size in insects. Here, we used a robust data set comprising all geometrid moth species occurring in Northern Europe to examine the evolutionary associations involving body size and several life-history traits under an explicitly phylogenetic framework. We provided new insights into the interactive effects of life-history traits on body size and evidence of correlated evolution. We further established the sequence of trait evolution linking body size with the life-history traits correlated with it. We found that most (but not all) of the studied life-history traits, to some extent, interfered with interspecific variation in body size, but interactive effects were uncommon. Both bi- and multivariate phylogenetic analyses indicated that larger species tend to be nocturnal flyers, overwinter in the larval stage, feed on the foliage of trees rather than herbs, and have a generalist feeding behavior. We found evidence of correlated evolution involving body size with overwintering stage, host-plant growth form, and dietary specialization. The examination of evolutionary transitions within the correlated models signaled that overwintering as larvae preceded the evolution of large sizes, as did feeding on tree foliage and the generalist feeding behavior. By showing that both body size and all life-history traits correlated with it evolve at very slow rates, we caution against uncritical attempts to propose causal explanations for respective associations based on contemporary ecological settings.

Data from: Sexually discordant selection is associated with trait specific morphological changes and a complex genomic response

Sexes often have differing fitness optima, potentially generating intra-locus sexual conflict, as each sex bears a genetic 'load' of alleles beneficial to the other sex. One strategy to evaluate conflict in the genome is to artificially select populations discordantly, against established sexual dimorphism, reintroducing attenuated conflict. We investigate a long-term artificial selection experiment reversing sexual size dimorphism in Drosophila melanogaster during ~350 generations of sexually discordant selection. We explore morphological and genomic changes to identify loci under selection between the sexes in discordantly and concordantly size selected treatments. Despite substantial changes to overall size, concordant selection maintained ancestral sexual dimorphism. However, discordant selection altered size dimorphism in a trait-specific manner. We observe multiple, possible soft selective sweeps in the genome, with size related genes showing signs of selection. Patterns of genomic differentiation between the sexes within lineages identified potential sites maintained by sexual conflict. One discordant selected lineage shows a pattern of elevated genomic differentiation between males and females, on chromosome 3L, consistent with the maintenance of sexual conflict. Our results suggest visible signs of conflict and differentially segregating alleles between the sexes due to discordant selection.