cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tn715
title: Data from: Local adaptation and the potential effects of a contaminant on predator avoidance and antipredator responses under global warming: a space-for-time substitution approach

description: The ability to deal with temperature-induced changes in interactions with
 contaminants and predators under global warming is one of the outstanding,
 applied evolutionary questions. For this, it is crucial to understand how
 contaminants will affect activity levels, predator avoidance and
 antipredator responses under global warming and to what extent gradual
 thermal evolution may mitigate these effects. Using a space-for-time
 substitution approach, we assessed the potential for gradual thermal
 evolution shaping activity (mobility and foraging), predator avoidance and
 antipredator responses when Ischnura elegans damselfly larvae were exposed
 to zinc in a common-garden warming experiment at the mean summer water
 temperatures of shallow water bodies at these latitudes (24 and 20°C,
 respectively). Zinc reduced mobility and foraging, predator avoidance and
 escape swimming speed. Importantly, high-latitude populations showed
 stronger zinc-induced reductions in escape swimming speed at both
 temperatures, and in activity levels at the high temperature. The latter
 indicates that local thermal adaptation may strongly change the ecological
 impact of contaminants under global warming. Our study underscores the
 critical importance of considering local adaptation along natural
 gradients when integrating biotic interactions in ecological risk
 assessment, and the potential of gradual thermal evolution mitigating the
 effects of warming on the vulnerability to contaminants.
description: Behaivours and escape
 swimming speed of Ischnura elegans damselfly larvaeThe activity levels and
 escape swimming speed of Ischnura elegans damselfly larvae during the
 6-day exposure period as a function of zinc concentrations, temperature
 and latitude.Janssens
 EVA-2013-144-OA.xlsx
DOI: 10.5061/dryad.4r5p1
title: Data from: Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)

description: Premise of the study: Despite the extensive phenotypic variation that
 characterizes the Gesneriaceae family, there is a lack of genomic
 resources to investigate the molecular basis of their diversity. We
 developed and compared the transcriptomes for two species of the
 Neotropical lineage of the Gesneriaceae. Methods and Results: Illumina
 sequencing and de novo assembly of floral and leaf samples were used to
 generate multigene sequence data for Sinningia eumorpha and S. magnifica,
 two species endemic to the Brazilian Atlantic Forest. A total of 300
 million reads were used to assemble the transcriptomes, with an average of
 92,038 transcripts and 43,506 genes per species. The transcriptomes showed
 good quality metrics, with the presence of all eukaryotic core genes, and
 an equal representation of clusters of orthologous groups (COG)
 classifications between species. The orthologous search produced 8602
 groups, with 15–20% of them annotated using BLAST tools. Discussion: This
 study provides the first step toward a comprehensive multispecies
 transcriptome characterization of the Gesneriaceae family. These resources
 are the basis for comparative analyses in this species-rich Neotropical
 plant group; they will also allow the investigation of the evolutionary
 importance of multiple metabolic pathways and phenotypic diversity, as
 well as developmental programs in these nonmodel species.
description: Trimmed_SE_TrinityFasta file with the Trinity assembly for Sinningia eumorphaTrimmed_SM_TrinityFasta file with Trinity assembly for Sinningia magnificanewBLASTX_allgenesSESMBlastX for all genes assembled for S. eumorpha (SE_) and S. magnifica (SM_)newBLASTP_allgenes_SESMBlastP for all genes assembled for S. eumorpha (SE_) and S. magnifica (SM_)ORF_SESM_CDSFasta file with the predicted ORF (Open Reading Frame) in S. eumorpha and S. magnificaOrthGroups_SE_SMOrthoMLC ortholog groups between S. eumorpha and S. magnifica. Input file the predicted ORF.ORF_SE_SM_CDS.fastaPredicted SSR makers (Single Sequence Repeat) in S. eumorpha and S. magnifica. Input file the predicted ORF.
DOI: 10.5061/dryad.16049f4
title: Data from: Pre- and post-natal effects of experimentally manipulated maternal corticosterone on growth, stress reactivity, and survival of nestling house wrens

description: 1. Corticosterone plays a central role in maintaining homeostasis,
 promoting energy acquisition, and regulating the stress response in birds.
 Exposure to elevated levels of corticosterone during development can
 profoundly alter offspring behaviour and physiology, but the effects of
 elevated maternal corticosterone on offspring development remain poorly
 understood. 2. We tested two competing hypotheses concerning the effect of
 maternally derived corticosterone on growth and development of free-living
 house wrens: i) elevated maternal corticosterone causes damaging effects
 on nestling phenotype and fitness (collateral damage hypothesis) and (ii)
 increased maternal corticosterone enhances offspring fitness by preparing
 nestlings for the environment experienced by their mother
 (environmental/maternal-matching hypothesis). 3. We used a non-invasive
 means to increase maternal corticosterone by providing females with
 corticosterone-injected mealworms prior to and during egg production in
 the absence of any overt pre-natal maternal stress. To disentangle pre-
 and post-natal effects of this elevation in maternal corticosterone, we
 cross-fostered young in two experiments: i) nestlings of control and
 experimental females were reared by unmanipulated, natural females in a
 uniform maternal environment; ii) a split-brood design that enabled us to
 assess the interaction between the mother’s corticosterone treatment and
 that of the nestlings. 4. There were significant pre-natal effects of
 increased maternal corticosterone on nestling growth and survival.
 Offspring of females experiencing experimentally increased corticosterone
 were heavier and larger than offspring of control females. There also was
 a significant interaction between maternal corticosterone treatment and
 the corticosterone treatment to which young were exposed within the egg in
 their effect on nestling survival while in the nest; experimental young
 exhibited greater survival than control young, but only when reared by
 control mothers. There was also a significant effect of maternal
 corticosterone treatment on nestling stress reactivity and, in both
 experiments, on the eventual recruitment of offspring as breeding adults
 in the local population. 5. These patterns are broadly consistent with the
 environmental/maternal-matching hypothesis, and highlight the importance
 of disentangling pre- and post-natal effects of manipulations of maternal
 hormone levels on offspring phenotype.
description: Clutch size, both
 experimentsDryad data Weber et
 al..xlsx
DOI: 10.5061/dryad.2ff04
title: Data from: Curvature-induced stiffening of a fish fin

description: How fish modulate their fin stiffness during locomotive manoeuvres remains
 unknown. We show that changing the fin's curvature modulates its
 stiffness. Modelling the fin as bendable bony rays held together by a
 membrane, we deduce that fin curvature is manifested as a misalignment of
 the principal bending axes between neighbouring rays. An external force
 causes neighbouring rays to bend and splay apart, and thus stretches the
 membrane. This coupling between bending the rays and stretching the
 membrane underlies the increase in stiffness. Using three-dimensional
 reconstruction of a mackerel (Scomber japonicus) pectoral fin for
 illustration, we calculate the range of stiffnesses this fin is expected
 to span by changing curvature. The three-dimensional reconstruction shows
 that, even in its geometrically flat state, a functional curvature is
 embedded within the fin microstructure owing to the morphology of
 individual rays. As the ability of a propulsive surface to transmit force
 to the surrounding fluid is limited by its stiffness, the fin curvature
 controls the coupling between the fish and its surrounding fluid. Thereby,
 our results provide mechanical underpinnings and morphological predictions
 for the hypothesis that the spanned range of fin stiffnesses correlates
 with the behaviour and the ecological niche of the fish.
description: Mackerel Fin CT
 ReconstructionContains data for a
 micro CT scan of a dissected Mackerel (S. japonicus) pectoral
 fin.Dryad_submission.zip
DOI: 10.5061/dryad.9q510
title: Data from: Genetic drift linked to heterogeneous landscape and ecological specialization drives diversification in the Alpine endemic columbine Aquilegia thalictrifolia

description: The European Alpine system is an extensive mountain range, whose
 heterogeneous landscape together with Quaternary climatic oscillations
 significantly affected organismal diversity and distribution in Europe.
 The model genus Aquilegia represents a textbook example of a rapid and
 recent radiation through the Northern hemisphere, with the majority of the
 European taxa occuring in the Alpine system. However, the processes
 governing genetic differentiation of the genus in this complex geographic
 area are still widely unexplored. In this work, we used nine
 microsatellite loci to study the genetic structure and diversity of 11
 populations of Aquilegia thalictrifolia Schott & Kotschy, an
 alpine taxon characterized by a marked ecological specificity. We found
 that, despite the endemic and fragmented distribution, A. thalictrifolia
 has overall high levels of heterozigosity, which is consistent to the
 substantial inbreeding depression that characterizes the genus. Strong
 spatial genetic structuring of populations suggests a historical
 prevalence of genetic drift over gene flow, with natural barriers and
 ecological niche hindering migration. An analytical comparison of fixation
 (GST) and population differentiation (Dest) indexes allowed us to infer
 hypotheses of the post-glacial history and more recent demographic events
 that have influenced the genetics of the species. Overall, our results
 indicate allopatry as a major force of differentiation in the European
 scenario, likely to underlie the development of taxonomic boundaries in a
 broader geographic context. This adds to previous notions on the primary
 evolutionary forces shaping the Aquilegia radiation in Europe.
description: Lega_et_al_2014_Aquilegia_thalictrifolia_SSR_GenotypesThis file contains the genotypes of 9 SSR loci for 295 A. thalictrifolia individuals from 11 sampling localities. Missing data are indicated by '?'.
DOI: 10.5061/dryad.8k57d86
title: Data from: Invasive plants differentially affect soil biota through litter and rhizosphere pathways: a meta-analysis

description: Invasive plants affect soil biota through litter and rhizosphere inputs,
 but the direction and magnitude of these effects are variable. We
 conducted a meta-analysis to examine the different effects of litter and
 rhizosphere of invasive plants on soil communities and nutrient cycling.
 Our results showed that invasive plants increased bacterial biomass by
 16%, detritivore abundance by 119% and microbivore abundance by 89%
 through litter pathway. In the rhizosphere, invasive plants reduced
 bacterial biomass by 12%, herbivore abundance by 55% and predator
 abundance by 52%, but increased AM fungal biomass by 36%. Moreover, CO2
 efflux, N mineralization rate and enzyme activities were all higher in
 invasive than native rhizosphere soils. These findings indicate that
 invasive plants may support more decomposers that in turn stimulate
 nutrient release via litter effect, and enhance nutrient uptake by
 reducing root grazing but forming more symbioses in the rhizosphere. Thus,
 we hypothesize that litter- and root-based loops are probably linked to
 generate positive feedback of invaders on soil systems through stimulating
 nutrient cycling, consequently facilitating plant invasion. Our findings
 from limited cases with diverse contexts suggest that more studies are
 needed to differentiate litter and rhizosphere effects within single
 systems to better understand invasive plant-soil interactions.
description: yi and vi values of
 meta-analysisIn this data file, yi
 means ln RR, vi means variances of log response ratio.data
 archived.xlsx
DOI: 10.5061/dryad.t5jp7
title: Data from: Ejaculate evolution in external fertilizers: influenced by sperm competition or sperm limitation?

description: The evolution of sperm quality and quantity is shaped by various selective
 processes, with sperm competition generally considered the primary
 selective agent. Particularly in external fertilizers, however, sperm
 limitation through gamete dispersal can also influence gamete investments,
 but empirical data examining this effect are limited. Here, we studied the
 relative importance of sperm competition and the spawning conditions in
 explaining the macroevolutionary patterns of sperm size and number within
 two taxa with external fertilization but differences in their reproductive
 biology. In frogs, sperm swim slowly but for up to hours as they penetrate
 the gelatinous egg coating, whereas fish sperm typically swim fast, are
 very short-lived (seconds to minutes), and often face a relatively higher
 risk of being moved away from the ova by currents. Our phylogenetic models
 and path analyses revealed different trajectories of ejaculate evolution
 in these two taxa. Sperm size and number responded primarily to variation
 in sperm competition in the anurans, but more strongly to egg number and
 water turbulence in the fishes. Whereas the results across anurans align
 with the general expectation that sexual selection is the main driver of
 ejaculate evolution, our findings across the fishes suggest that sperm
 limitation has been underappreciated.
description: Data
 frogsData of the 130 anuran
 species used in this study, including spawning site occurrence of foam
 nesting, mating system/amplexus, oviposition substrate site, oviposition
 type, egg capsule consistency, water type, male body mass (in g), combined
 testes mass (in mg), total sperm length (in µm), sperm head length (in
 µm), sperm flagellum length (in µm), sperm number (in million), female
 snout-vent length (in mm), clutch size, and egg diameter (in mm). OD in
 the references refers to own data.Data_frogs.txtData fishesData of the 57 fish species used in this study, including male body mass (in g), combined testes mass (in g), the presence or absence of hormonal induction of sperm production, sperm number (in billions), total sperm length (in µm), average-path sperm velocity (in µm/s), sperm longevity (in s), female body mass (in g), egg diameter (in mm), egg number (in thousands), the type of spawning water, spawning site, and mating system.Data_fishes.txtPhylogeny frogsPhylogenetic reconstruction for the 130 anurans used in this studyPhylogeny_frogs.nexPhylogeny fishesPhylogenetic reconstruction for the 57 fishes used in this studyPhylogeny_fish.nex
DOI: 10.5061/dryad.7005f
title: Data from: An edrioasteroid from the Silurian Herefordshire Lagerstätte of England reveals the nature of the water vascular system in an extinct echinoderm

description: Echinoderms are unique in having a water vascular system with tube feet,
 which perform a variety of functions in living forms. Here, we report the
 first example of preserved tube feet in an extinct group of echinoderms.
 The material, from the Silurian Herefordshire Lagerstätte, UK, is assigned
 to a new genus and species of rhenopyrgid edrioasteroid, Heropyrgus
 disterminus. The tube feet attach to the inner surface of compound
 interradial plates and form two sets, an upper and a lower, an arrangement
 never reported previously in an extant or extinct echinoderm. Cover plates
 are absent and floor plates are separated creating a large permanent
 entrance to the interior of the oral area. The tube feet may have captured
 food particles that entered the oral area and/or enhanced respiration. The
 pentameral symmetry of the oral surface transitions to eight columns in
 which the plates are vertically offset resulting in a spiral appearance.
 This change in symmetry may reflect flexibility in the evolutionary
 development of the axial and extraxial zones in early echinoderm
 evolution.
description: Virtual Models and Raw
 DataZip file containing (a)
 Raw serial-grinding tomograms (slice-images) for all datasets used in
 publication, and (b) VAXML/STL format 3D models of all datasets used in
 publication.Briggs_et_al_2017_Data.zip
DOI: 10.5061/dryad.bg49s
title: Data from: Species with a chemical defense, but not chemical offense, live longer

description: Evolutionary hypotheses for aging generally predict that delayed
 senescence should evolve in organisms that experience lower extrinsic
 mortality. Thus, one might expect species that are highly toxic or
 venomous (i.e., chemically protected) will have longer lifespans than
 related species that are not likewise protected. This remarkable
 relationship has been suggested to occur in amphibians and snakes. First,
 we show that chemical protection is highly conserved in several lineages
 of amphibians and snakes. Therefore, accounting for phylogenetic
 autocorrelation is critical when conservatively testing evolutionary
 hypotheses because species may possess similar longevities and defensive
 attributes simply through shared ancestry. Herein we compare maximum
 longevity of chemically protected and non-protected species, controlling
 for potential non-independence of traits among species using recently
 available phylogenies. Our analyses confirm that longevity is positively
 correlated with body size in both groups which is consistent with
 life-history theory. We also show that maximum lifespan was positively
 associated with chemical protection in amphibian species but not in
 snakes. Chemical protection is defensive in amphibians, but primarily
 offensive (involved in prey capture) in snakes. Thus, we find that while
 chemical defense in amphibians favours long life, there is no evidence
 that chemical offense in snakes does the same.
description: Data
 tablesData tables used in our
 analysis. Most of the data is originally from Blanco and Sherman (2005)
 Mech Ageing Dev 126: 794-803. Tables include data for maximum lifespan,
 presence/absence of chemical protection, and body size (snout-vent length
 for amphibians, total length for snakes).
DOI: 10.5061/dryad.05f81
title: Data from: A novel mechanism for grazing lawn formation: large herbivore-induced modification of the plant-soil water balance

description: 1. Large herbivores play a key-role in creating spatial heterogeneity
 through the formation of grazing lawns. Recent research suggests that the
 currently accepted nutrient-based theory on the formation of these grazing
 lawns cannot universally explain their formation in all ecosystems where
 they are found. 2. We developed and investigated an alternative hypothesis
 on grazing lawn formation and maintenance based on herbivore effects on
 the plant-soil water balance. We propose that large herbivores change the
 soil water balance in grazing lawns through defoliation and soil
 compaction, causing a shift in vegetation composition towards a drought
 tolerant plant community. 3. Investigating this idea in a tropical
 savanna, we indeed found profound differences in grazing lawn soil
 properties and water balance. In particular, defoliation increased soil
 temperatures and potential evaporation rates while soil compaction
 increased bulk density and decreased water infiltration rates, especially
 on fine-textured soils. Soil moisture was therefore generally much lower
 in grazing lawns than in adjacent bunch grass areas. 4. Furthermore, we
 found that grazing lawn species show drought-tolerant traits, with higher
 leaf sodium levels, suggesting evolutionary adaptation to these
 herbivore-induced dry conditions. However, leaf water potentials did not
 differ between grazing lawn and bunch grass species. 5. Synthesis: This
 study shows that large herbivores might form grazing lawns through
 previously underestimated effects on water balance. Thus, future studies
 on large herbivore effects on vegetation should increasingly focus on
 additional pathways of soil compaction and defoliation. While
 nutrient-based processes driving grazing lawn formation may operate during
 the wet season in savannas, we suggest that water balance-based processes
 are additionally important during the dry season.
description: DataR_files
DOI: 10.5061/dryad.2tr22
title: Data from: Evolution of female multiple mating: a quantitative model of the "sexually-selected sperm" hypothesis

description: Explaining the evolution and maintenance of polyandry remains a key
 challenge in evolutionary ecology. One appealing explanation is the
 sexually-selected sperm (SSS) hypothesis, which proposes that polyandry
 evolves due to indirect selection stemming from positive genetic
 covariance with male fertilization efficiency, and hence with a
 male's success in post-copulatory competition for paternity. However,
 the SSS hypothesis relies on verbal analogy with ‘sexy-son’ models
 explaining co-evolution of female preferences for male displays, and
 explicit models that validate the basic SSS principle are surprisingly
 lacking. We developed analogous genetically-explicit individual-based
 models describing the SSS and ‘sexy-son’ processes. We show that the
 analogy between the two is only partly valid, such that the genetic
 correlation arising between polyandry and fertilization efficiency is
 generally smaller than that arising between preference and display,
 resulting in less reliable co-evolution. Importantly, indirect selection
 was too weak to cause polyandry to evolve in the presence of negative
 direct selection. Negatively-biased mutations on fertilization efficiency
 did not generally rescue runaway evolution of polyandry unless realized
 fertilization was highly skewed towards a single male, and co-evolution
 was even weaker given random mating-order effects on fertilization. Our
 models suggest that the SSS process is, on its own, unlikely to generally
 explain the evolution of polyandry.
description: SSS model source code:
 header fileSSS_model.hSSS model source code: cpp fileSSS_model.cppMate-choice model source code: header fileMateChoice_model.hMate-choice model source code: cpp fileMateChoice_model.cpp