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opencc-by-4.0Jul 2023View details →

Datasets to compute species traits for Neotropical anurans

This dataset has harmonized data for modeling three species traits: phenology, physiology, and acoustic characteristics. The selected variables express intraspecific trait variation across the species' geographic range and provide a deeper understanding of the species-level capacity to deal with climate change. Besides, they supply data to document key, primarily unknown, life-history traits of a highly endangered group of vertebrates in a hyperdiverse region.

opencc-zeroJul 2023View details →

Data from: The quest for good genes: epigamic traits, fitness, MHC and multilocus heterozygosity in the guppy

The "good genes" hypothesis for the evolution of male secondary sexual traits poses that female preferences for such traits are driven by indirect genetic benefits. However, support for the hypothesis remains ambiguous, and, in particular, the genetic basis for the benefits has rarely been investigated. Here, we use semi-natural populations of Trinidadian guppies to investigate whether sexually selected traits (orange, black and iridescent colouration, gonopodium length and body size) predict fitness measured as the number of grandoffspring, a metric that integrates across fitness components and sexes. Furthermore, we tested whether two potential sources of genetic benefits – major histocompatibility complex (MHC) genotypes and multilocus heterozygosity (MLH) – are significant predictors of fitness and of the size of sexually selected traits. We found a significant, non-linear effect of the area of black pigmentation and male body size on the number of grandoffspring, suggesting stabilising selection on black area, and non-linear selection favouring small body size. MLH was heritable (h2 = 0.14) and significantly predicted the number of grandoffspring, indicating the potential for genetic benefits based on heterozygosity. We also found support for local heterozygosity effects, which may reflect a non-even distribution of genetic load across the genome. MHC genotype was not significantly associated with any tested fitness component, or with the load of Gyrodactylus parasites. Neither MHC nor MLH was a significant predictor of sexually selected traits. Overall, our results highlight the role of heterozygosity in determining fitness but do not provide support for male sexually selected traits being indicators of genetic quality.

opencc-zeroJul 2023View details →

The role of phylogenetic structure on Canidae lineage distribution and trait variation across the globe

Aim: Understanding the spatial structuring of ecological communities requires us to consider the interplay between evolutionary history and environmental factors. In this study, we investigated the influence of Canidae phylogenetic structure on the distribution and trait patterns of lineages across the planet. Location: Americas, Africa, Eurasia. Time period: 12 million years ago - present. Major taxa studied: Canidae. Methods: Using distribution data and phylogenetic information for 37 Canidae species, we employed phylogenetic fuzzy-weighting to compare assemblages based on their phylogenetic similarity. Results: Our results revealed distinct global patterns of body size, body mass, range size, habitat type, and evolutionary distinctiveness among lineages. We also identified the shared contributions of phylogenetic structure and temperature to trait variation using variance partitioning analysis. The PCPS axes highlighted the influence of phylogenetic relationships on Canidae assemblages, particularly in South America. Main conclusions: Notably, the study challenges the applicability of Bergmann's and Rapoport's rules in explaining canids' sizes and range sizes geographic variation across continents, emphasizing the importance of phylogenetic information. The unique diversification history of Canidae in South America and Africa and their diverse environmental conditions likely contribute to the observed trait patterns that make both continents so distinguished when compared to N. America and Eurasia. Our findings underscore the need to incorporate phylogenetic information in models assessing trait variation across geographic scales for unbiased estimations.

opencc-by-4.0Jul 2023View details →

Voltinism and life-history traits of the invasive fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) feeding on corn

Voltinism and life-history traits of the invasive fall armyworm (FAW) Spodoptera frugiperda were investigated under semi-natural conditions for a period of two years. The FAW invaded the corn field in the suburbs of Nanchang (28° 46′ N, 115° 50′ E) in early summer and produced six complete generations. The FAW had the characteristics of short developmental time, high survival rates and strong fecundity. The development time of female pupae was significantly faster than that of male pupae, resulting in the emergence of female pupae earlier than male pupae. Except for the sixth generation in 2021, there was no significant difference between female and male sex ratio, which was close to 1:1. The FAW showed male-bias sexual size dimorphism with male pupae being significantly larger than female pupae. Unlike pupal weight, in most generations, male adult weighed significantly less than females, because the weight loss of male pupae during metamorphosis was significantly greater than that of female pupae. The seasonal variation of pupal weight did not conform to the temperature–size rule. Compared with 22.8 °C, the 29.2 °C high temperature not only significantly reduced the development time of larvae but also significantly increased pupal weight. The adult fecundity feeding on fresh corn leaves was higher than that feeding on live corn plants in most generations. In most generations, pupal weight was positively correlated with larval development time and adult weight was positively correlated with fecundity. These results add to the understanding of the evolution of life-history traits in the FAW and may have important implications for predicting population dynamics of the FAW and optimizing control strategies.

opencc-by-4.0Jul 2023View details →

Raw data accompanying the manuscript "Uptake of microplastics and impacts on plant traits of savoy cabbage"

These are the raw datasets used to generate Figure 1 for the manuscript entitled "Uptake of microplastics and impacts on plant traits of savoy cabbage". The folders contain all raw CARS and SRS data that are needed to reproduce Figure 1 (TIFF format).

opencc-zeroJul 2023View details →

A theory of oligogenic adaptation of a quantitative trait

Rapid phenotypic adaptation is widespread in nature, but the underlying genetic dynamics remain controversial. Whereas population genetics envisages sequential beneficial substitutions, quantitative genetics assumes a collective response through subtle shifts in allele frequencies. This dichotomy of a monogenic and a highly polygenic view of adaptation raises the question of a middle ground, as well as the factors controlling the transition. Here, we consider an additive quantitative trait with equal locus effects under Gaussian stabilizing selection that adapts to a new trait optimum after an environmental change. We present an analytical framework based on Yule branching processes to describe how phenotypic adaptation is achieved by collective changes in allele frequencies at the underlying loci. In particular, we derive an approximation for the joint allele-frequency distribution at threshold levels of the trait mean as a comprehensive descriptor of the adaptive architecture. Depending on the model parameters, this architecture reproduces the well-known patterns of sequential, monogenic sweeps, or of subtle, polygenic frequency shifts. Between these endpoints, we observe oligogenic architecture types that exhibit characteristic patterns of partial sweeps. We find that a single compound parameter, the population-scaled background mutation rate Θbg, is the most important predictor of the type of adaptation, while selection strength, the number of loci in the genetic basis, and linkage only play a minor role.

Directional and stabilizing selection shaped morphological, reproductive, and physiological traits of the invader Solidago canadensis

Trait evolution in invasive plant species is important because it can impact demographic parameters key to invasion success. Invasive plant species often show phenotypic clines along geographic and climatic gradients. However, the relative contributions of natural selection and neutral evolutionary processes to phenotypic trait variation among populations of invasive plants remains unclear. A common method to assess whether a trait has been shaped by natural selection or neutral evolutionary processes is to compare the geographical pattern for the trait of interest to the divergence in neutral genetic loci (i.e., QST-FST comparisons). A redundancy analysis (RDA) can facilitate identification of putative agents of natural selection on the trait. Here, we employed both a QST-FST comparisons approach and RDA to infer whether natural selection shaped traits of invasive populations of S. canadensis in China and identify the potential environmental drivers of natural selection. We addressed two questions: (1) Does natural selection drive phenotypic trait variation among S. canadensis populations? (2) Do climatic, latitudinal, longitudinal, and altitudinal gradients drive patterns of genetic variation among S. canadensis populations? We found significant directional selection for several morphological and reproductive traits (i.e., QST >FST) and stabilizing selection for physiological traits (i.e., QST < FST). The RDA showed that stem biomass of S. canadensis was strongly positively correlated with longitude, while leaf width ratio and specific leaf area were significantly positively correlated with mean diurnal range. Stem biomass had a strong negative correlation with annual precipitation. Moreover, height of S. canadensis individuals was strongly positively correlated with altitude and precipitation of the wettest quarter. Precipitation seasonality that was associated with longitudinal shift in China likely selected for larger stem biomass in S. canadensis. Overall, these results suggest that longitudinal and altitudinal clines in climate exerted strong selection pressures that shaped phenotypic traits of S. canadensis.

Data from: Trait interactions effects on tropical tree demography depend on the environmental context

Although functional traits are defined based on their impact on demographic parameters, trait-demography relationships are often reported as weak. These weak relationships might be due to disregarding trait interactions and environmental contexts, which should modulate species trait-demography relationships. We applied different models, including boosted regression tree (BRT) models, to investigate changes in the relationship between traits and demographic rates of tropical tree species in plots along an elevational gradient and among time intervals between censuses, analyzing the effect of a strong drought event. Based on a large dataset of 18,000 tree individuals from 133 common species, distributed among twelve 1-ha plots (habitats) in the Atlantic Forest (Brazil), we evaluated how trait interactions and the environmental context influence the demographic rates (growth, mortality, and recruitment). Functional traits, trait-trait, and trait-habitat interactions predicted demography with a good fit through either BRTs or linear mixed-models. Changes in growth rates were best related to size (diameter), and mortality rates to habitats, while changes in recruitment rates were best related to the specific leaf area. Moreover, the influence of traits differed among time intervals, and for demographic parameters, habitat affected growth and mortality by interacting with diameter. Here, we provide evidence that trait-demography relationships can be improved when considering the environmental context (space and time) and trait interactions to cope with the complexity of changes in the demography of tropical tree communities. Thus, to expand predictions of demography based on functional traits, we show that it is useful to fully incorporate the concept of multiple trait-fitness optima, resulting from trait interactions in different habitats and growth conditions.

Data from: Freshwater fishes maintain multi-trait phenotypic stability across an environmental gradient in aqueous calcium

Reductions in a limiting nutrient might be expected to necessitate compromises in the functional traits that depend on that nutrient; yet populations existing in locations with low levels of such nutrients often do not show the expected degradation of functional traits. Indeed, we previously found that fish of three species, Logperch (Percina caprodes),Pumpkinseed Sunfish (Lepomis gibbosus), and Yellow Perch (Perca flavescens) residing in low-calcium water in the Upper St. Lawrence River nevertheless maintained levels of scale calcium comparable to those of conspecific populations in high-calcium water. However, it remains possible that the maintenance of one functional trait under nutrient-limited conditions could come at the expense of maintaining other functional traits that depend on that same nutrient. Hence, we here extend prior work by examining other calcium-dependent traits: skeletal element sizes and bone densities in the same fish species in the same area. Using radiographs of 101 fish from the three species across four locations (two in high-calcium water and two in low-calcium water), we document multi-trait "homeostasis" along the gradient of water calcium. That is, we did not detect any effect of calcium regime (low-calcium versus high-calcium) on any of the measured variables. Further, effect sizes for the skeletal traits were very low – lower even than effect sizes previously documented for scale calcium. Our results thus show that native fishes maintain phenotype stability across a suite of functional traits linked to calcium regulation, perhaps pointing to an "organismal-level homeostasis" scenario rather than a "trait-level homeostasis" scenario.

Predicting plant species climate preferences on the basis of mechanistic traits

Improved estimation of climate niches is critical, given climate change. Plant adaptation to climate depends on their physiological traits and their distributions, yet traits are rarely used to inform the estimation of species climate niches, and the power of a trait-based approach has been controversial, given the many ecological factors and methodological issues that may result in decoupling of species' traits from their native climate. For 107 species across six ecosystems of California, we tested the hypothesis that mechanistic leaf and wood traits can robustly predict the mean of diverse species' climate distributions, when combining methodological improvements from previous studies, including standard trait measurements and sampling plants growing together at few sites. Further, we introduce an approach to quantify species' trait-climate mismatch. We demonstrate a strong power to predict species' mean climate from traits. As hypothesized, the prediction of species' mean climate is stronger (and mismatch lower) when traits are sampled for individuals closer to species' mean climates. Improved resolution of species' climate niches based on mechanistic traits can importantly inform conservation of vulnerable species under the threat of climatic shifts in upcoming decades.

opencc-by-4.0Aug 2023View details →

The Anatomy of Conspirators: Unveiling Traits using a Comprehensive Twitter Dataset

This repository contains the Twitter dataset used to investigate the traits of 7,394 conspiracy users and 7,394 random users. Both the profile's info and the most recent 3,200 tweets (until Jun 13th, 2022) are provided.

Cytoplasmic male sterility and abortive seed traits generated through mitochondrial genome editing coupled with allotopic expression of atp1 in tobacco

Genome editing tools have recently been developed that are capable of generating deletions and/or rearrangements in plant mitochondrial genomes. We utilized custom-designed meganuclease constructs targeting the essential mitochondrial gene atp1 in tobacco plants carrying a version of atp1 that had been repurposed to function as a nuclear gene. Leaf extracts enriched in mitochondria from three independent genome editing events were evaluated by PacBio sequencing and analysis. Contigs that display sequence homology to the reference mitochondrial genome BA000042 are deposited here. Some of the contigs correspond to the tobacco mitochondrial genome as expected, while others corresponded to sequences from the nucleus where the ancient transfer of portions of the mitochondrial genome became incorporated into the nuclear genome. Still other contigs correspond to the chloroplast genome, or pieces of the chloroplast genome anciently transferred to the nucleus, as small fragments of the chloroplast genome are interspersed in plant mitochondrial genomes. Analysis of contigs of genuine mitochondrial origin demonstrated that the double-strand breaks imposed by the genome editing enzymes resulted in the deletion of atp1 and neighboring sequences, along with rearrangements in overall genome structure.

Trait value of Stipa krylovii populations in control and drought treatments

Understanding patterns of intraspecific trait variation can help us understand plant adaptability to environmental changes. To explore the underlying adaptation mechanisms of zonal plant species, we selected seven populations of Stipa krylovii, a dominant species in the Inner Mongolia Steppe of China, and evaluated the effects of phenotypic plasticity and genetic differentiation, the effects of climate variables on population trait differentiation, and traits coordinated patterns under each soil moisture treatment. We selected seeds from seven populations of S. krylovii in the Inner Mongolia Steppe, China, and carried out a soil moisture (2) × population origin (7) common garden experiment at Tianjin City, China, and measured ten plant traits of S. krylovii. General linear analyses were used to analyze how soil moisture and population origin affect each trait variation, Mantel tests were used to analyze population trait differentiation - geographic distance (or climatic difference) relationships, regression analyses were used to evaluate the trait-climatic variable relationships, and plant trait networks (PTNs) were used to evaluate the traits coordinated patterns. Both soil moisture and population origin showed significant effects on most of the traits. Aboveground biomass, root-shoot ratio, leaf width, specific leaf area, and leaf nitrogen (N) content were significantly correlated with climate variables under the control condition. Specific leaf area and leaf N content were significantly correlated with climate variables under drought conditions. By PTNs, the hub trait(s) was plant height under the control treatment and were aboveground biomass, root length, and specific leaf area under drought conditions. This study indicates that both phenotypic plasticity and genetic differentiation can significantly affect the adaptability of S. krylovii. In addition, soil moisture treatments show significant effects on trait-climate relationships and trait-coordinated patterns. These findings provide new insights into the adaptive mechanisms of zonal species in the semi-arid grassland region.

Winners and losers of reef flattening: An assessment of coral reef fish species and traits

Anthropogenic stressors are causing widespread coral mortality, leading to loss of coral cover and decreased structural complexity that threatens reef biodiversity, functioning, and ecosystem services. Reef fishes are intimately linked to coral reef complexity, but we lack a generic understanding of which species are particularly affected by reef flattening and what traits make them susceptible. We used extensive species- and trait-based analyses to build a framework for western Atlantic fish association with both structural complexity and coral cover to better understand the implications of reef degradation. These analyses also investigated the relative importance of live coral versus the value of the structure it provides to reef fishes. We modeled how 25 biophysical and anthropogenic factors correlated with the densities of 109 fish species across 3292 Floridian reef sites. The importance of a metric of structural complexity and coral cover to the abundance of each species was then isolated. Species with positive associations were categorized as likely future 'losers' and negative associations as 'winners'. We showed that structure loss was more critical than loss of coral cover, as 53% of species were predicted as losers on low-relief reefs, while only 11% were losers with decreased coral cover. We found morphological, behavioral, and ecological traits mediate species' responses to reef degradation, and shared evolutionary history is unlikely to be a strong driver of trait relationships. Eight traits explained 79.7% of variation in species' associations with relief and six traits explained 27.8% of associations with coral cover. Smaller, streamlined, habitat and trophic generalists are more likely winners on flattened reefs and large-bodied predators and species with deeper bodies and intermediate caudal fin shapes are likely losers. Identifying these important traits provides insight into mechanisms that may link fish and complex habitats, which allows us to better predict assemblage-wide responses to future reef flattening.

Tackling local ecological homogeneity: Finding intraspecific trait variability in local populations of Mediterranean plants

Local homogeneity, in ecology, is the often undisclosed assumption that variability within populations is negligible or mostly distributed evenly. In large areas, this can lead to the aggregation of different populations without regard for their unique needs and characteristics, such as drought sensitivity and functional traits distributions. Here we discuss whether this assumption can be justified, and we hypothesize that discerning the source of variation between plasticity and adaptation could be a feasible approach to formulate an informed decision. We test this hypothesis on plants, resorting to a common garden experiment to determine the source of variation of several plant functional traits at a local scale (~60 Km) of three wild species: Quercus ilex, Pistacia lentiscus and Cistus salviifolius. Individuals of each species were sourced from three key sites chosen along a local aridity gradient. Our approach led to the rejection of the local homogeneity assumption for Q. ilex and C. salviifolius at this scale due to the adaptive divergence observed among neighbouring populations. This case study provides evidence that addressing local homogeneity can highlight diverging populations in a relatively simple way. We conclude that gathering empirical evidence on intraspecific variability is a feasible approach that can provide researchers with solid bases to decide whether to adopt the local homogeneity assumption or not.

Heat-induced maternal effects shape avian eggshell traits and embryo development and phenotype at high incubation temperatures

Phenotypic plasticity is an important avenue by which organisms may persist in the face of rapid environmental change. Environmental cues experienced by the mother can also influence the phenotype of offspring, a form of plasticity called maternal effects. Maternal effects can adaptively prepare offspring for the environmental conditions they will experience, however, their ability to buffer offspring against environmental stressors as embryos is understudied. Using captive zebra finches, we performed a maternal-offspring environmental match-mismatch experiment utilizing a 2x2x2 factorial design. Mothers were exposed to a mild heat conditioning (38 °C) or control (22 °C) treatment as juveniles, an acute high heat (42 °C) or control (22 °C) treatment as adults, then paired for breeding. The eggs produced by those females were incubated at a hyperthermic (38.5 °C) or optimal temperature (37.2 °C). We found that when mothers were exposed to a mild heat conditioning as juveniles, their embryos exhibited reduced water loss, longer development times, and produced hatchlings with heavier pectoralis muscles when incubated at high incubation temperatures, compared to embryos from control mothers. Mothers exposed to both the mild heat conditioning as juveniles and a high heat stressor as adults produced eggs with a higher density of shell pores, and embryos with lower heart rates during development. However, there was a cost when there was a mismatch between maternal and embryo environment. Embryos from these conditioned and heat-stressed mothers had reduced survival at control incubation temperatures, indicating the importance of offspring environment when interpreting potential adaptive effects.

Root functional traits and growth rates in savanna trees and grasses

Root-based functional traits are relatively overlooked as drivers of savanna plant community dynamics, an important gap in water-limited ecosystems. Recent work has shed light on patterns of trait coordination in roots, but less is known about the relationship between root functional traits, water acquisition, and plant demographic rates. Here, we investigated how fine-root vascular and morphological traits are related in two dominant PFTs (C3 trees and C4 grasses from the savanna biome), whether root traits can predict plant relative growth rate (RGR), and whether root trait relationships differ in trees and grasses. We used root data from 21 tree and 18 grass species grown under greenhouse conditions, and quantified a suite of vascular and morphological root traits. We used a principal components analysis (PCA) to identify common axes of trait variation, compared trait correlation matrices between the two PFTs, and investigated the relationship between PCA axes and individual traits and RGR. We found that there was no clear single axis integrating vascular and morphological traits, but found that vascular anatomy predicted RGR in both trees and grasses. Trait correlation matrices differed in trees and grasses, suggesting potentially divergent patterns of trait coordination between the two functional types. Our results suggested that, despite differences in trait relationships between trees and grasses, root conductivity may constrain maximum growth rate in both PFTs, highlighting the critical role that water relations play in savanna vegetation dynamics and suggesting that root water transport capacity is an important predictor of plant performance in the savanna biome.

Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.

Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population

Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances, and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.

Propagule phenotypic traits of Kandelia obovata and sampling sites information in China

Increasing studies have shown the importance of intraspecific trait variation (ITV) on the ecological process. However, the patterns and sources of ITV are still unclear, especially in the propagule of coastal vegetation. Here, we measured fresh weight (FW), fresh length (FL), maximum transverse diameter (TDmax), minimum transverse diameter (TDmin) and the ratio of TDmax to TDmin (RTD) of the hypocotyl (propagule) of Kandelia obovata for 66 genealogies across 26 sites. By combining multiple factors of climate, ocean and maternal tree to analyze their effects on the intraspecific trait variation of mangrove hypocotyl. The results showed that value of establishment traits (FW, FL, TDmax and TDmin which are related to mass) decreased along increasing latitudinal gradients and they were directly positively regulated by temperature. ITV of dispersal trait (RTD) was unstructured along latitudinal gradients, which was constrained by fitness tradeoff. Our findings indicate that establishment traits mainly varied between populations, whereas dispersal traits mainly varied between individuals. This study provides insights into the ITV of propagule in different functional dimensions on a broad scale and that may help integrate ITV into future analyses of mangrove protection.