cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sm32j
title: Data from: TLR and IMD signaling pathways from Caligus rogercresseyi (Crustacea: Copepoda): in silico gene expression and SNPs discovery

description: The Toll and IMD signaling pathways represent one of the first lines of
 innate immune defense in invertebrates like Drosophila. However, for
 crustaceans like Caligus rogercresseyi, there is very little genomic
 information and, consequently, understanding of immune mechanisms. Massive
 sequencing data obtained for three developmental stages of C.
 rogercresseyi were used to evaluate in silico the expression patterns and
 presence of SNPs variants in genes involved in the Toll and IMD pathways.
 Through RNA-seq analysis, which used 20 contigs corresponding to relevant
 genes of the Toll and IMD pathways, an overexpression of genes linked to
 the Toll pathway, such as toll3 and Dorsal, were observed in the copepod
 stage. For the chalimus and adult stages, overexpression of genes in both
 pathways, such as Akirin and Tollip and IAP and Toll9, respectively, were
 observed. On the other hand, PCA statistical analysis inferred that in the
 chalimus and adult stages, the immune response mechanism was more
 developed, as evidenced by a relation between these two stages and the
 genes of both pathways. Moreover, 136 SNPs were identified for 20 contigs
 in genes of the Toll and IMD pathways. This study provides transcriptomic
 information about the immune response mechanisms of Caligus, thus
 providing a foundation for the development of new control strategies
 through blocking the innate immune response.
description: immune_caligus20 contigs corresponding to relevant genes of the Toll and IMD pathways
DOI: 10.5281/zenodo.18382935
title: dataset for Generative Causal Agents in synthetic etiology
DOI: 10.5281/zenodo.18382936
title: dataset for Generative Causal Agents in synthetic etiology
DOI: 10.5061/dryad.11ng449
title: Data from: Nesting success and nest-site selection of white-rumped vultures (Gyps bengalensis) in western Maharashtra, India

description: A few breeding populations of White-rumped Vultures Gyps bengalensis still
 survive in pockets of their original vast range in India, having weathered
 a diclofenac induced population decline of 99.9% since the early 1990s.
 These breeding populations are potential sources of recruits, now that the
 overall population appears to be stabilising or even recovering in some
 areas. We studied two White-rumped Vulture nesting colonies in the Raigad
 district of coastal Maharashtra in 2013-14, to investigate site-specific
 nesting success and nest site choice. Our aim was to broadly understand
 the capability of these remnant populations to contribute to the stability
 of vulture populations at a landscape scale. We found that vultures
 preferred to nest on taller trees. Nest mortality was high before hatching
 but declined thereafter. Overall nesting outcome was unrelated to nesting
 near areas of disturbance, but may have been influenced by characteristics
 of nest trees. Proportion of successful nests was higher in the smaller
 colony, suggesting that colony size may not be the only best criterion for
 targeting conservation efforts.
description: Majgaonkar et al.
 Journal of Raptor research data filesThese files list the raw
 data which was used to perform the analysis in the article. It contains
 the following: (i) Nest status at each visit for both nesting colonies
 (ii) Nesting and unused tree characteristics for both colonies (ii) Model
 fit assessment through comparing observed vs. predicted for the top models
 relative to global and simplified model. For any information on sampling
 techniques, analysis and covariates used, refer to the
 manuscript.
DOI: 10.5061/dryad.n5n37
title: Data from: Selection for sex in finite populations

description: Finite population size generates interference between selected loci, which
 has been shown to favour increased rates of recombination. In this
 article, I present different analytical models exploring selection acting
 on a ‘sex modifier locus’ (that affects the relative investment into
 asexual and sexual reproduction) in a finite population. Two forms of
 selective forces act on the modifier: direct selection due to intrinsic
 costs associated with sexual reproduction and indirect selection generated
 by one or two other loci affecting fitness. The results show that indirect
 selective forces differ from those acting on a recombination modifier even
 in the case of a haploid population: in particular, a single selected
 locus generates indirect selection for sex, while two loci are required in
 the case of a recombination modifier. This effect stems from the fact that
 modifier alleles increasing sex escape more easily from low-fitness
 genetic backgrounds than alleles coding for lower rates of sex.
 Extrapolating the results from three-locus models to a large number of
 loci at mutation–selection balance indicates that in the parameter range
 where indirect selection is strong enough to outweigh a substantial cost
 of sex, interactions between selected loci have a stronger effect than the
 sum of individual effects of each selected locus. Comparisons with
 multilocus simulation results show that such extrapolations may provide
 correct predictions for the evolutionarily stable rate of sex, unless the
 cost of sex is high.
description: integrationProgram to integrate numerically the selection gradient on a sex modifier locus over a linear genetic map (C++ program)simulation programHaploid sex modifier simulation program (C++ program)simulation_program.tar
DOI: 10.5061/dryad.2fp14fg
title: Data from: Hindered and constrained: limited potential for thermal adaptation in post-metamorphic and adult Rana temporaria along elevational gradients

description: Adaptation to warming climates could counteract the effects of global
 warming. Thus, understanding how species cope with contrasting climates
 may inform us about their potential for thermal adaptation and which
 processes may hamper that ability (e.g. evolutionary trade-offs,
 phenology, or behavioural thermoregulation). In addition to temperature,
 time constraints may also exert important selective pressures. Here we
 compare the thermal sensitivity of locomotion of metamorphic and adult
 European common frogs (Rana temporaria) originating from populations along
 an elevational gradient. We employed the template mode of variation (TMV)
 analysis to decompose the thermal sensitivity of locomotion and explore
 the existence of trade-offs (‘hotter is better’ and
 ‘specialist-generalist’) and the degree of local adaptation. To that end,
 we studied the relationship between TMV parameters and local environmental
 conditions. Further, we compared preferred temperatures to assess whether
 behavioral thermoregulation could dampen the effects of thermal variation,
 reducing the intensity of selection and limiting thermal adaptation (i.e.
 ‘Bogert effect’). We suggest that behavioral thermoregulation has promoted
 the conservatism of thermal sensitivity in R. temporaria. Yet, we observed
 a trend towards narrower thermal niches shifted towards warmer temperature
 in populations with severe temporal constraints, conforming to the
 ‘generalist-specialist’ trade-off. Apparently, this enables
 time-constrained populations – especially in the case of metamorphs – to
 effectively exploit resources during the warmest periods. The limited
 potential of R. temporaria for thermal adaptation suggests that forecasts
 of global warming should incorporate thermoregulation and explore its
 potential to buffer species from rising temperatures.
description: morphologylocom_adultslocom_metasgradients_adultsgradients_metasREADMEInformation about provided data filesREAD_ME.txt
DOI: 10.5061/dryad.1sr5c
title: Data from: Ecological and genetic factors influencing the transition between host-use strategies in sympatric Heliconius butterflies

description: Shifts in host-plant use by phytophagous insects have played a central
 role in their diversification. Evolving host-use strategies will reflect a
 trade-off between selection pressures. The ecological niche of herbivorous
 insects is partitioned along several dimensions, and if populations remain
 in contact, recombination will break down associations between relevant
 loci. As such, genetic architecture can profoundly affect the coordinated
 divergence of traits and subsequently the ability to exploit novel
 habitats. The closely related species Heliconius cydno and H. melpomene
 differ in mimetic colour pattern, habitat and host-plant use. We
 investigate the selection pressures and genetic basis underlying host-use
 differences in these two species. Host-plant surveys reveal that H.
 melpomene specializes on a single species of Passiflora. This is also true
 for the majority of other Heliconius species in secondary growth forest at
 our study site, as expected under a model of interspecific competition. In
 contrast, H. cydno, which uses closed-forest habitats where both
 Heliconius and Passiflora are less common, appears not to be restricted by
 competition and uses a broad selection of the available Passiflora.
 However, other selection pressures are likely involved, and field
 experiments reveal that early larval survival of both butterfly species is
 highest on Passiflora menispermifolia, but most markedly so for H.
 melpomene, the specialist on that host. Finally, we demonstrate an
 association between host-plant acceptance and colour pattern amongst
 interspecific hybrids, suggesting that major loci underlying these
 important ecological traits are physically linked in the genome. Together,
 our results reveal ecological and genetic associations between shifts in
 habitat, host use and mimetic colour pattern that have likely facilitated
 both speciation and coexistence.
description: Raw host use data: H.
 melpomene, H. cydno and hybridsRaw data collected from
 insectary host use assays as described in the
 manuscript.supplementary
 materials_revised.docx
DOI: 10.5061/dryad.c8290
title: Data from: Wnt5a regulates the assembly of human adipose-derived stromal vascular fraction-derived microvasculatures

description: Human adipose-derived stromal vascular fraction (hSVF) cells are an easily
 accessible, heterogeneous cell system that can spontaneously self-assemble
 into functional microvasculatures in vivo. However, the mechanisms
 underlying vascular self-assembly and maturation are poorly understood,
 therefore we utilized an in vitro model to identify potential in vivo
 regulatory mechanisms. We utilized passage one (P1) hSVF because of the
 rapid UEA1+ endothelium (EC) loss at even P2 culture. We exposed hSVF
 cells to a battery of angiogenesis inhibitors and found that the pan-Wnt
 inhibitor IWP2 produced the most significant hSVF-EC networking decrease
 (~25%). To determine which Wnt isoform(s) and receptor(s) may be involved,
 hSVF was screened by PCR for isoforms associated with angiogenesis, with
 only WNT5A and its receptor, FZD4, being expressed for all time points
 observed. Immunocytochemistry confirmed Wnt5a protein expression by hSVF.
 To see if Wnt5a alone could restore IWP2-induced EC network inhibition,
 recombinant human Wnt5a (0–150 ng/ml) was added to IWP2-treated cultures.
 The addition of rhWnt5a significantly increased EC network area and
 significantly decreased the ratio of total EC network length to EC network
 area compared to untreated controls. To determine if Wnt5a mediates in
 vivo microvascular self-assembly, 3D hSVF constructs containing an IgG
 isotype control, anti-Wnt5a neutralizing antibody or rhWnt5a were
 implanted subcutaneously for 2w in immune compromised mice. Compared to
 IgG controls, anti-Wnt5a treatment significantly reduced vessel length
 density by ~41%, while rhWnt5a significantly increased vessel length
 density by ~62%. However, anti-Wnt5a or rhWnt5a did not significantly
 affect the density of segments and nodes, both of which measure vascular
 complexity. Taken together, this data demonstrates that endogenous Wnt5a
 produced by hSVF plays a regulatory role in microvascular self-assembly in
 vivo. These findings also suggest that manipulating Wnt signaling could
 enhance control of hSVF vascularization in tissue engineering
 applications.
description: Wnt5a
 DataVascular morphometry
 data
DOI: 10.5061/dryad.cq814
title: Data from: Increase in multiple paternity across the reproductive lifespan in a sperm-storing, hermaphroditic freshwater snail

description: Polyandry is a common phenomenon and challenges the traditional view of
 stronger sexual selection in males than in females. In simultaneous
 hermaphrodites, the physical proximity of both sex functions was long
 thought to preclude the operation of sexual selection. Laboratory studies
 suggest that multiple mating and polyandry in hermaphrodites may actually
 be common, but data from natural populations are sparse. We therefore
 estimated the rate of multiple paternity and its seasonal variability in
 the annual, sperm-storing, simultaneously hermaphroditic freshwater snail
 Radix balthica for the entire duration of the reproductive lifespan. We
 also tested whether multiple paternity was associated with clutch size or
 embryonic development. To obtain these data, we measured and genotyped 60
 field-collected egg clutches using nine highly polymorphic microsatellite
 markers. Overall, 50% of the clutches had multiple fathers, and both the
 frequency (20–93% of clutches) and magnitude of multiple paternity (mean
 1.3–3.8 fathers per clutch) substantially increased over time, probably
 because of extensive sperm storage. Most multiply sired clutches (83%) had
 a dominant father, but neither clutch size nor the proportion of developed
 embryos per clutch was associated with levels of multiple paternity. Both
 the evident promiscuity and the frequent skew of paternity shares suggest
 that sexual selection may be an important evolutionary force in the study
 population.
description: Characteristics of 201
 field-collected egg clutchesThis file provides for
 each of 201 field-collected egg clutches the collection date, number of
 eggs, number of developed and undeveloped embryos, and (for clutches of
 which embryos were genotyped) two estimates of the number of fathers that
 sired the clutch, one obtained from using the parentage analysis software
 COLONY version 2.0.5.9 and one obtained from simple allele
 counting.Shell lengths of 1013
 field-collected snailsThis file provides the
 collection date and shell length for each of 1013 adult field-collected
 snails.
DOI: 10.5061/dryad.5n4np5df
title: Data from: Linking genetic diversity and temporal fluctuations in population abundance of the introduced feral cat (Felis silvestris catus) on the Kerguelen Archipelago.

description: Linking temporal variations of genetic diversity, including allelic
 richness and heterozygosity, and spatio-temporal fluctuations in
 population abundance has emerged as an important tool for understanding
 demographic and evolutionary processes in natural populations. This
 so-called ‘genetic monitoring’ was conducted across 12 consecutive years
 (1996-2007) at three sites for the feral cat, introduced onto the
 Kerguelen Archipelago fifty years ago. Temporal changes in allelic
 richness and heterozygosity at 18 microsatellite DNA loci were compared to
 temporal changes in the adult population abundance index, obtained by
 typical demographic monitoring. No association was found at the island
 spatial scale but we observed an association between genetic diversity and
 adult population indices from year to year within each study site. More
 particularly, the magnitude of successive increases or decreases in the
 adult population abundance index appeared to be the major factor linking
 the trajectories of genetic diversity and adult population abundance
 indices. Natal dispersal and/or local recruitment, both facilitated by
 high juvenile survival when the adult population size is small, are
 proposed as the major demographic processes contributing to such an
 observed pattern. Finally, we suggested avoiding the use of the harmonic
 mean as an estimator of long-term population size to study the
 relationships between demographic fluctuations and heterozygosity in
 populations characterized by strong multi-annual density fluctuations.
description: Microsatellites and
 sample locationsMultilocus
 microsatellite genotypes, location and sampling year of n=271 feral cats
 on the Kerguelen Archipelago
DOI: 10.5061/dryad.12b0h
title: Data from: Shade tolerance and the functional trait - demography relationship in temperate and boreal forests

description: Despite being instrumental in forest ecology, the definition and nature of
 shade tolerance are complex and not beyond controversy. Moreover, the role
 it plays in the trait – demography relationship remains unclear. Here, we
 hypothesize that shade tolerance can be achieved by alternative
 combinations of traits depending on the species’ functional group
 (evergreen vs. deciduous species), and that its ability to explain the
 array of traits involved in demography will also vary between these two
 groups. We used dimension reduction to identify the main trait spectra for
 48 tree species, including 23 evergreens and 25 deciduous – dispersed
 across 21 genera and 13 families. We assessed the relationship between
 functional traits, shade tolerance and demographic performance at high and
 low light using structural equation modelling. The dimensions found
 corresponded to the trait spectra previously observed in the literature
 and were significantly related to measures of demography. However, our
 results support the existence of a divergence between evergreen and
 deciduous species in the way shade tolerance relates to the demography of
 species along light gradients. We show that shade tolerance can be
 attained through different combination of traits depending on the
 functional and geographical context, and thus its utilization as a
 predictor of forest dynamics and species coexistence requires previous
 knowledge on the role it plays in the demographic performance of the
 species under study.
description: Demography_LifeHistoriesLife histories values for each species and site, as obtained from the parameterization carried out in studies that used the model SORTIE. The data include growth at full light (Growth-L), defined as the time (in years) needed for a sapling with DBH= 1cm to become an adult (DBH=7.5 cm) when light = 100%; growth in shade (Growth-D), as the time (in years) needed for a sapling with DBH= 1cm to become an adult (DBH=7.5 cm) when light = 1%; and survival in shade (Surv-D), defined as the 5-year survivorship of a sapling with DBH = 1cm when light = 1%. The data source of each value can be found in Appendix S2 in the manuscript.Demography_Dryad.xlsxFunctional_TraitsFunctional trait values for each of the 48 study species, including 23 evergreen and 25 deciduous. Traits include Leaf mass area (LMA), photosynthetic capacity per unit leaf mass (Amass), Leaf N content per unit mass (Nmass), Leaf P content per unit mass (Pmass), Leaf lifespan (LL), Leaf length (Llength), seed mass (SeM), wood density (WD) ad maximum tree height (MaxH).FunctionalTraits_Dryad.xlsx
DOI: 10.5061/dryad.g1228
title: Data from: Dispersal propensity, but not flight performance, explains variation in dispersal ability

description: Enhanced dispersal ability may lead to accelerated range expansion and
 increased rates of population establishment, thereby affecting population
 genetic structure and evolutionary potential. Morphological, behavioural
 and physiological traits that characterize dispersive individuals from
 residents are poorly understood for many invertebrate systems, especially
 in non-polymorphic pterygote species. Here we examined phenotypic
 differences between dispersal-prone and philopatric individuals from
 repeated mark-release-recapture (MRR) experiments using an invasive
 agricultural pest, Ceratitis capitata. Comprehensive morphometric
 assessment and subsequent minimal adequate modelling using an information
 theoretic approach identified thorax mass : body mass ratio as a key
 predictor of disperser flies under semi-natural conditions. Performance
 differences in flight ability were then examined under controlled
 laboratory conditions to assess whether greater thorax mass : body mass
 ratio was associated with enhanced flight ability. The larger thorax :
 body mass ratio was associated with measurable differences in mean flight
 duration, most predominantly in males, and also by their willingness to
 disperse, scored as the number and duration of voluntary flights. No other
 measures of whole-animal flight performance (e.g. mean and peak vertical
 force, total or maximum flight duration) differed. Variation in voluntary
 behaviour may result in significant alterations of movement behaviour and
 realized dispersal in nature. This phenomenon may help explain
 intraspecific variation in the dispersal ability of insects.
description: Steyn et al. Data
 file
DOI: 10.5061/dryad.7fq4j
title: Data from: Host nutritional status mediates degree of parasitoid virulence

description: Parasitic organisms rely on the resources of their hosts to obtain
 nutrients essential for growth and reproduction. Insect parasitoids
 constitute an extreme condition since they develop in a single host from
 which they typically consume all available resources. As a result, the
 host is killed following parasitism. However, a few intriguing cases of
 host survival have been reported wherein hosts resume foraging and may
 even reproduce following parasitoid emergence. Yet, the ultimate and
 proximate mechanisms responsible for host recovery remain unresolved. We
 tested the impact of host nutrition on host fate and parasitoid fitness,
 using the association between Dinocampus coccinellae and the spotted lady
 beetle Coleomegilla maculata. Under laboratory conditions, we fed
 parasitized ladybirds on different aphid diets, with or without pollen. In
 the field, we followed the fate of parasitized ladybirds during seasonal
 variations in pollen and aphid abundance. We found that ladybirds fed on
 aphids or a combination of aphids and pollen recovered more frequently
 from parasitism (from 65 to 81%) than those eating only pollen (48%).
 Field data suggest that the fate of parasitized ladybirds is also related
 to food availability. On the other hand, when hosts fed on a combination
 of aphids and pollen, consequences for parasitoid fitness were often
 ‘all-or-nothing’: parasitoid emergence rate was the lowest of all host
 nutrition regimes (˜50%), but parasitoids that did emerge were larger than
 individuals emerging from other host nutrition regimes. Laboratory and
 field results concur to show that host nutritional status during
 parasitoid development significantly influences both host fate and
 parasitoid fitness.
description: Diet experiment
 dataData collected in the
 laboratory in Montreal, Quebec (Canada). "Ladybirds" =
 Coleomegilla maculata; "Parasitoid" = Dinocampus
 coccinellae.Diet
 data_Dryad.xlsx