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opencc-by-4.0May 2022View details →

Growth rate and life history shape plant resistance.

Premise: Plant defenses are shaped by many factors, including herbivory, lifespan, and mating system. Predictions about plant defense and resistance are often based on resource allocation trade‐offs with plant growth and reproduction. Additionally, two types of plant resistance, constitutive and induced resistance, are predicted to be evolutionary alternatives or redundant strategies. Given the variety of plant trait combinations and non‐mutually exclusive predictions, examining resistance strategies in related species with different combinations of growth and reproductive traits is important to tease apart roles of plant traits and evolutionary history on plant resistance. Methods: Phylogenetic comparative methods were used to examine the potentially interacting influences of life history (annual/perennial), mating system (self‐compatible/self-incompatible), and species growth rates on constitutive resistance and inducibility (additional resistance following damage) across Physalis species (Solanaceae). Results: Resistance was evolutionarily labile, and there was no correlation between constitutive resistance and inducibility. Annual species with fast growth rates displayed higher constitutive resistance, but growth rate did not affect constitutive resistance in perennials. In contrast, inducibility was negatively associated with species growth rate regardless of life history or mating system. Conclusions: The different effects of plant life history and growth rate on constitutive resistance and inducibility indicate that defensive evolution is unconstrained by a trade‐off between resistance types. The interactions among plant life history, growth, and herbivore resistance show that plant defense is shaped not only by herbivore environment, but also by plant traits that reflect a plant's evolutionary history and local selective pressures.

opencc-zeroJun 2022View details →

Does mast seeding shape mating time in wild boar? A comparative study

In seasonal environments, the timing of reproduction often matches with the peak of food resources. One well-known effect of global warming is an earlier phenology of resources, leading to a possible mismatch between timing of reproduction for consumers and food peak. However, global warming may also change the dynamics of food resources, such as the intensity and frequency of pulsed mast seeding. How quantitative changes in mast seeding influence the timing of reproduction of seed consumers remains unexplored. Here, we assess how yearly variation in mast seeding influences mating time in wild boar (Sus scrofa), a widespread seed consumer species. We took advantage of the intensive monitoring of both female reproduction (1,636 females) and acorn production over 6 consecutive years across 15 populations of wild boar in the wild. We found that mating time occurs earlier when acorn production increases in most but not all populations. In three out of fifteen populations, heavy females mated earlier than light ones. Our findings demonstrate that mast seeding does shape mating time in wild boar females, but differently across populations. This high plasticity of mating times in wild boar indicates that females locally adapt to environmental conditions.

opencc-zeroJun 2022View details →

Data from: Preston's universal formula for avian egg shape

The main data are 50 photographs of eggs, one from each of 50 species. 25 of these species have pyriform eggs, based on the traditional usage of this descriptive term. The photographs were taken to allow an investigation of egg shape, so they are lit from behind to provide a clear silhouete and were arranged to have the plane containing their longest axis parallel to the 'film' plane. A csv file contains basic information about each egg. A second csv file contains the results of processing these photographs (using the script GetErrors.R) to assess the error associated with various methods of summarising egg shape, including Preston's universal formula. A third csv file conatins some summary information on many more eggs obtained from a different study.

CESM2 data for "Ocean complexity shapes sea surface temperature variability in a CESM2 coupled model hierarchy" - submitted to JCLI

CESM2 Experiment names: <ul> <li>FC = fully coupled model, CESM2 (variables freely available on https://esgf-node.llnl.gov/search/cmip6/)</li> <li>MD = mechanically decoupled model, CESM2</li> <li>SOM = slab ocean model, CESM2</li> </ul> All datasets are for pre-industrial forcing (e.g., piControl), nominal 1-degree horizontal resolution  --- Decoding the files names: <ul> <li>climatology_monthly = 12 month climatology </li> <li>climatology_annual = time mean climatology</li> <li>variance = anomaly variance computed over time</li> </ul> --- Variables: <ul> <li>PRECL = large-scale convective precipitation</li> <li>PRECC = convective precipitation</li> <li>total precipitation (not provided but can be calculated) = PRECC + PRECL</li> <li>HMXL = mixed layer depth</li> <li>SST = sea surface temperature </li> </ul> Files for the CESM2 MD piControl run: <ol> <li>forcing_coupled.F90: POP2 (ocean) source code changes for cesm2.1.4-rc08 (search for "slarson" throughout code to find our changes</li> <li>cesm2.1.4-exp03-CTRL_B1850_f09_g17_hourlyclim_TAUX.nc: 6 hourly climatology for TAUX, from a FC run of CESM2. This file and the TAUY climatology are opened and read in the "rotate wind stress" subroutine in forcing_coupled.F90. This file is named "x2oavg_Foxx_taux_6hourly.nc" in forcing_coupled (we wanted a shorter file name in the code)</li> <li>cesm2.1.4-exp03-CTRL_B1850_f09_g17_hourlyclim_TAUY.nc: 6 hourly climatology for TAUY. This file is named "x2oavg_Foxx_tauy_6hourly.nc" in forcing_coupled (we wanted a shorter file name in the code) </li> </ol>

Complex floral traits shape pollinator attraction to ornamental plants

Background and Aims Ornamental flowering plant species are often used in managed greenspaces to attract and support pollinator populations. In natural systems, selection by pollinators is hypothesized to result in convergent multimodal floral phenotypes that are more attractive to specific pollinator taxa. In contrast, ornamental cultivars are bred via artificial selection by humans, and exhibit diverse and distinct phenotypes. Despite their prevalence in managed habitats, the influence of cultivar phenotypic variation on plant attractiveness to pollinator taxa is not well resolved. Methods We used a combination of field and behavioural assays to evaluate how variation in floral visual, chemical and nutritional traits impacted overall attractiveness and visitation by pollinator taxonomic groups and bee species to 25 cultivars of five herbaceous perennial ornamental plant genera. Key results Despite significant phenotypic variation, cultivars tended to attract a broad range of pollinator species. Nonetheless, at the level of insect order (bee, fly, butterfly, beetle), attraction was generally modulated by traits consistent with the pollination syndrome hypothesis. At the level of bee species, the relative influence of traits on visitation varied across plant genera, with some floral phenotypes leading to a broadening of the visitor community, and others leading to exclusion of visitation by certain bee species. Conclusions Our results demonstrate how pollinator choice is mediated by complex multimodal floral signals. Importantly, the traits that had the greatest and most consistent effect on regulating pollinator attraction were those that are commonly selected for in cultivar development. Though variation among cultivars in floral traits may limit the pollinator community by excluding certain species, it may also encourage interactions with generalist taxa to support pollinator diversity in managed landscapes.

Imaging data (part 1) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"

This archive contains part 1 of the raw imaging data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".

Imaging data (part 2) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"

This archive contains part 2 of the raw imaging data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".

openother-openSep 2021View details →

Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest

This is the first release of the final data and code for the article accepted for publication in Evolutionary Applications journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.

Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation

Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. However, adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood and processes for surmounting fitness valleys remain controversial. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically novel pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. We leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, estimate genotypic fitness networks, and measure the accessibility of adaptive walks on the fitness landscape. We identified 132 SNPs that were significantly associated with fitness in field enclosures. Six out of the 13 regions most strongly associated with fitness contained differentially expressed genes and fixed SNPs between trophic specialists; one gene (mettl21e) was also misexpressed in lab-reared hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that scale-eating specialists are the most isolated of the three species on these networks. Intriguingly, introgressed and de novo variants reduced fitness landscape ruggedness as compared to standing variation, increasing the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and de novo mutations alter the shape of the fitness landscape, providing key connections in adaptive walks circumventing fitness valleys and triggering the evolution of novelty during adaptive radiation.

Raw data for the manuscript entitled "Forest age and topographic position jointly shape the species richness and composition of vascular plants in karstic habitats"

Doline surveys from the Mecsek Mountains, Hungary. Transects were established with north to south orientation across each doline, traversing their deepest point. Transects began and ended on doline rims, and consisted of 1 m  × 1 m plots spaced at 2 m intervals (94, 89, 90 and 99 plots in the different forest age classes, respectively; 372 plots in total). We recorded the presence/absence data of shrubs and herbs in each plot. Fieldwork was carried out between 2007 and 2019 from June to August, at the peak of the growing season.

Data for 'Warming and predation risk only weakly shape size-mediated priority effects in a cannibalistic damselfly'

In a laboratory experiment, we studied effects of warming (low and high temperature) and predation risk (presence and absence of predator cues of perch) on SMPE in life history and physiological traits in the cannibalistic damselfly Ischnura elegans. We induced SMPE by manipulating hatching dates, thereby creating four groups: non-mixed phenology early (E) and late (L) hatchlings, and mixed phenology early (E+L) and late (L+E) hatchlings. This data set includes: <ul> <li>hatch date</li> <li>emergence date</li> <li>survival until emergence and emergence success data</li> <li>mass of adult insects</li> <li>development time (from hatching to emergence, in days)</li> <li>growth rate (mass of adult insect/development time in days)</li> <li>protein content (μg of protein/μl of prepared homogenate)</li> <li>fat content (μg of fat/μl of prepared homogenate)</li> <li>phenoloxidase activity (PO, value of activity curve slope)</li> <li>PO activity/protein (value of activity curve slope/(μg of protein/μl of prepared homogenate)</li> </ul>

Rigid Shell Rolling on a Dimpled Bowl-shaped Rigid Surface Example 2

The computations use zero-mass particles--the first use of such particles in nonrelativistic classical mechanics—to perform these animations. The four animation files deal with simulations for Cases A, B, C, and D of Example 2, in the above-mentioned paper in the Special Issue. Each file shows an animation for 25 s of the shell rolling on the surface, without slipping. Each animation shows the dimpled surface and the complex motion of the shell as it finds its path over the dimpled surface. The different cases (A to D) relate to the different orientations of the non-uniform shell at the start of the animation with respect to the surface. At the beginning of each animation the shell is shown for a few extra seconds so that its initial orientation can be observed. The location of the point on the sphere that touches the surface at the start of the animation is the same for all the 4 different animations; the initial velocity of the geometric center of the shell is also the same in all the animations. As seen, the motion of the non-uniform shell and the path it takes on the surface is highly sensitive to its orientation at the start of the animation with respect to the surface. The motion is slowed in these animations so that the extremely complex motion of the shell can be seen better. For details of each case (A to D) see the paper.

Data from: Mosaic adaptive peak shifts underlie body shape diversification in Pelagiaria fishes (Acanthomorpha: Percomorpha)

Extreme body elongation in fishes is a major evolutionary transformation that extends the boundaries of morphological diversity and alters aspects of function, behavior, and ecology. Prior studies have identified features of the cranial and axial skeleton that characterize elongate fishes, but a lack of detailed reconstructions of anatomical evolution has limited inferences about factors that underlie major shifts in body shape. In this study, we fit multi-peak adaptive (Ornstein-Uhlenbeck) evolutionary models to species body shape and anatomical dimensions in Pelagiaria, a radiation of open-ocean fishes whose species span a continuum from deep-bodied to highly elongate. We inferred an ancestral fusiform adaptive peak that is retained by several major pelagiarian lineages (e.g., Scombridae) and found robust support for multiple transitions to deep-bodied (in the families Stromateidae, Bramidae, and Caristiidae) and elongate-bodied optima (within Trichiuroidei), including two instances of sequential shifts toward increasingly elongate optima that followed distinct paths of anatomical evolution. Within Trichiuridae, initial increases in head length and vertebral number were followed by changes in head and vertebral shape. Within an elongate-bodied subclade of taxa traditionally identified as 'gempylids', shifts in head and vertebral shape as well as number of precaudal vertebrae preceded an increase in number of caudal vertebrae. Altogether, this mosaic of anatomical peak shifts suggests that body shape transformations were associated with differing selective demands and developmental changes.

Burrowing Constrains Patterns of Skull Shape Evolution in Wrasses

The evolution of behavioral and ecological specialization can have marked effects on the tempo and mode of phenotypic evolution. Head-first burrowing has been shown to exert powerful selective pressures on the head and body shapes of many vertebrate and invertebrate taxa. In wrasses, burrowing behaviors have evolved multiple times independently, and are commonly used in foraging and predator avoidance behaviors. While recent studies have examined the kinematics and body shape morphology associated with this behavior, no study to-date has examined the macroevolutionary implications of burrowing on patterns of phenotypic diversification in this clade. Here, we use three-dimensional geometric morphometrics and phylogenetic comparative methods to study the evolution of skull shape in fossorial wrasses and their relatives. We test for skull shape differences between burrowing and non-burrowing wrasses and evaluate hypotheses of shape convergence among the burrowing wrasses. We also quantify rates of skull shape evolution between burrowing and non-burrowing wrasses to test for whether burrowing constrains or accelerates rates of skull shape evolution in this clade. We find that while burrowing and non-burrowing wrasses exhibit similar degrees of morphological disparity, for burrowing wrasses, it took nearly twice as long to amass this disparity. Furthermore, while the disparities between groups are evenly matched, we find that most burrowing species are confined to a particular region of shape space with most species exhibiting narrower heads than many non-burrowing species. These results suggest head-first burrowing constrains patterns of skull shape diversification in wrasses by potentially restricting the range of phenotypes that can perform this behavior.

Data from: Signal detection shapes ornament allometry in functionally convergent Caribbean Anolis and Southeast Asian Draco lizards

Visual ornaments have long been assumed to evolve hyper-allometry as an outcome of sexual selection. Yet growing evidence suggests many sexually-selected morphologies can exhibit other scaling patterns with body size, including hypo-allometry. The large conspicuous throat fan, or dewlap, of arboreal Caribbean Anolis lizards was one ornament previously thought to conform to the classical expectation of hyper-allometry. We re-evaluated this classic example alongside a second arboreal group of lizards that has also independently evolved a functionally equivalent dewlap, the Southeast Asian Draco lizards. Across multiple closely-related species in both genera, the Anolis and Draco dewlaps were either isometric or had hypo-allometric scaling patterns. In the case of the Anolis dewlap, variation in dewlap allometry was predicted by the distance of conspecifics and the light environment in which the dewlap was typically viewed. Signal efficacy therefore appears to have driven the evolution of hypo-allometry in what was originally thought to be a sexually-selected ornament with hyper-allometry. Our findings suggest that other elaborate morphological structures used in social communication might similarly exhibit isometric or hypo-allometric scaling patterns because of environmental constraints on signal detection.

Demographic history shapes genomic ancestry in hybrid zones

Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries), as well as heterogenicity (the genomic proportion heterozygous for ancestry), are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.

ddRAD data for: Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps

Aedes albopictus originates from Southeast Asia and is considered one of the most invasive species globally. This mosquito is a nuisance and a disease vector of significant public health relevance. In Europe, Ae. albopictus is firmly established and widespread south of the Alps, a mountain range that forms a formidable biogeographic barrier to many organisms. Recent reports of Ae. albopictus north of the Alps raise questions of 1) the origins of its recent invasion, and 2) if this mosquito has established overwintering populations north of the Alps. To answer these questions, we analyzed population genomic data from >4000 genome-wide SNPs obtained through double digest restriction-site associated DNA sequencing. We collected SNPs data from specimens from 6 sites in Switzerland, north and south of the Alps, and analyzed them together with specimens from other 33 European sites, 5 from the Americas, and 5 from its Asian native range. At a global level, we detected 4 genetic clusters with specimens from Indonesia, Brazil and Japan as the most differentiated, whereas specimens from Europe, Hong Kong and USA largely overlapped. Across the Alps, we detected a weak genetic structure and high levels of genetic admixture, supporting a scenario of rapid and human-aided dispersal along transportation routes. While the genetic pattern suggests frequent re-introductions from Italian sources into Switzerland, the recovery of a pair of full siblings in two consecutive years in Strasbourg, France, suggests the presence of an overwintering population north of the Alps. The finding of overwintering populations of Ae. albopictus north of the Alps and the expansion patterns points to an increased risk of further northwards expansion and the need for increased surveillance of mosquito populations in northern Europe.

Sex, landscape diversity and primary productivity shape the seasonal space use of a migratory European raptor

Intrinsic and extrinsic drivers shape the space use of wide-ranging raptors. A large proportion of raptors are migrants that shift their activity ranges between summer and winter habitats, where they encounter different environmental conditions. Analysing the effects of intrinsic and extrinsic drivers on the space use in summer and winter habitats provides crucial insights into the ecology of migratory raptors. Here, we investigated the seasonal space use by 43 red kites (Milvus milvus) tracked by GPS-transmitters across central and south-western Europe over seven years. We compared space use patterns, i.e., activity range sizes and mean daily distances of the birds between summer and winter, and analysed the influence of extrinsic (landscape diversity, primary productivity) and intrinsic factors (sex). Within summer, we investigated the influence of breeding success and sex on activity range sizes. We further analysed differences in habitat availability and habitat selection between seasons. We found that space use was smaller in summers than in winters. When compared to those of males, activity ranges of female red kites were larger in summers and smaller in winters, with shorter mean daily distances in both seasons. Within summer, successfully breeding red kites had smaller activity range sizes in both sexes, but this effect was stronger in females than in males. Regardless of the season, landscape diversity was positively correlated with space use, whereas primary productivity was negatively correlated with it. The habitat use differed between seasons, with agricultural landscapes being less proportionally used in summers than in winters. Overall, we showed that both intrinsic and extrinsic drivers shaped space use in both the seasons, leading to differences in space use patterns and habitat use in migratory raptors between their summer and winter habitats. Our findings underline the importance of consideration of the entire annual cycle of migratory species for conservation management.

opencc-zeroAug 2022View details →

Seeing shapes in clouds: the fallacy of deriving ecological hypotheses from statistical distributions

The explanations behind observations of global patterning in species diversity pre-date the field of ecology itself. The generation of new species-area theories, in particular, far outpaces their falsification, resulting in a centuries-old accumulation in species diversity theories. We use historical assessment and new data analysis to argue that one of the earliest recognized and most consistent patterns in species diversity is not strictly an ecological phenomenon and, when ecological mechanism is invoked, the range of potential mechanisms is too numerous for tractable hypothesis falsification. We provide a historical parallel in that the normal distribution once was treated as a pattern assuming a biological mechanism rather than a statistical distribution that can be generated by biological and non-biological forces. Similarly, power law distributions are ubiquitous in aggregated data, such as the species-area relationship. That nearly identical broad-scale aggregation patterns are observed for both ecological and non-ecological data as a function of area suggest that these broad-scale patterns reflect a statistical distribution that, in itself, cannot be used to discern between or among ecological and non-ecological mechanisms. We argue that by seeking processes in such a ubiquitous pattern, ecologists may read ecological mechanism into statistical patterns, and we suggest that falsifying broad-scale diversity distribution hypotheses should be a greater priority than generating or parameterizing new ones.