cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fxpnvx0sc
title: Visual recognition and coevolutionary history drive responses of amphibians to an invasive predator

description: During biotic invasions, native prey are abruptly exposed to novel
 predators and are faced with unprecedented predatory pressures. Under
 these circumstances, the lack of common evolutionary history may hamper
 predator recognition by native prey, undermining the expression of
 effective anti-predatory responses. Nonetheless, mechanisms allowing prey
 to overcome evolutionary naïveté exist. For instance, in naïve prey,
 history of coevolution with similar native predators or recognition of
 general traits characterizing predators can favor recognition of stimuli
 released by invasive predators. However, few studies assessed how these
 mechanisms shape prey response at the community level. Here, we evaluated
 behavioral responses in naïve larvae of 13 amphibian species to chemical
 and visual cues associated with an invasive predator, the American red
 swamp crayfish (Procambarus clarkii). Moreover, we investigated how
 variation among species responses was related to their coexistence with a
 similar native crayfish predator. Amphibian larvae altered their behavior
 in presence of visual stimuli of the alien crayfish, while chemical cues
 elicited feeble and contrasting behavioral shifts. Activity reduction was
 the most common and stronger response, whereas in some species we detected
 more heterogeneous strategies also involving distancing and rapid escape
 response. Interestingly, species sharing coevolutionary history with the
 native crayfish were able to finely tune their response to the invasive
 one, performing bursts to escape. These results suggest native prey can
 respond to invasive predators through recognition of generic risk cues
 (e.g., approaching large shapes), still the capability of modulating
 anti-predator strategies may also depend on their coevolutionary history
 with similar native predators.
description: Some tests were excluded from the analysis due to low quality of
 the video (see column "analyzed" in the dataset).
DOI: 10.5061/dryad.0vt4b8h0h
title: Conformity to Bergmann’s rule in birds depends on nest design and migration

description: Ecogeographical rules attempt to explain large-scale spatial patterns in
 biological traits. One of the most enduring examples is Bergmann’s rule,
 which states that species should be larger in colder climates due to the
 thermoregulatory advantages of larger body size. Support for Bergmann’s
 rule, however, is not consistent across taxonomic groups, raising
 questions about what factors may moderate its effect. Behaviour may play a
 crucial, yet so far underexplored, role in mediating the extent to which
 species are subject to environmental selection pressures in colder
 climates. Here, we tested the hypothesis that nest design and migration
 influence conformity to Bergmann’s rule in a phylogenetic comparative
 analysis of the birds of the Western Palearctic, a group encompassing
 dramatic variation in both climate and body mass. We predicted that
 migratory species and those with more protected nest designs would conform
 less to the rule than sedentary species and those with more exposed nests.
 We find that sedentary, but not short- or long-distance migrating species,
 are larger in colder climates. Among sedentary species, conformity to
 Bergmann’s rule depends, further, on nest design: species with open nests,
 in which parents and offspring are most exposed to adverse climatic
 conditions during breeding, conform most strongly to the rule. Our
 findings suggest that enclosed nests and migration enable small birds to
 breed in colder environments than their body size would otherwise allow.
 Therefore, we conclude that behaviour can substantially modify species’
 responses to environmental selection pressures.
description: Please see Methods section in associated Manuscript. We also
 include the R code and phylogeny used for the analyses.
description: Please see associated ReadMe file.
DOI: 10.5061/dryad.z08kprrd7
title: Data from: Ongoing habenular activity is driven by forebrain networks and modulated by olfactory stimuli

description: The data was collected using volumetric two-photon calcium imaging of the
 forebrain and habenula of juvenile zebrafish expressing a transgenic
 calcium indicator. The data provided is organized according to the figures
 of our manuscript and contains the necessary codes and data to replicate
 the figures presented. In short, included repository contains 6
 datasets of experiments. Data structure includes neuronal data as
 normalised to the baseline fluorescence for each neuron over time (DF/F),
 2 or 3 dimensional coordinates of each cell and information about duration
 and samplings rate of experiments, and appropriate information about
 stimulation either microstimulation or odor stimulation (if any was
 performed within the experiment).
description: This repository explains the
 code and data for the publication “Ongoing habenular activity is driven by
 forebrain networks and modulated by olfactory stimuli” in
 <em>Current Biology</em>.  Please see READ ME file for more
 information.
DOI: 10.7291/d1f68r
title: Lewontin 1972 The Apportionment of Human Diversity Apportionment Check and Recalculation Winther 2022

description: Data and recalculations of Lewontin (1972), per Winther, R.G. 2022.
 Lewontin (1972). In Lorusso, L and Winther, RG. Remapping Race in
 a Global Context. London: Routledge. In redoing all of his
 calculations, I find that Lewontin made calculation errors (including
 rounding errors or omitting diversity component values) for all the genes
 he analyzed, and understated the among races diversity component,
 according to even just his own calculations. I show that “Lewontin’s
 Distribution” of, respectively, within populations, among populations but
 within races, and among races diversity apportionment is properly
 86%/7%/7%.
description: 1. Description of methods used for collection/generation of
 data: Original tables for the allele frequencies of each of the 17 genes
 were consulted and checked. Especially Giblett (1969) and Mourant (1954)
 were useful. Moreover, values of various measures were also taken from
 Table 3 of Lewontin (1972).  Based on this data, all
 diversity apportionments for the 17 genes/loci of Lewontin’s classic study
 were recalculated. Recalculation methodology is described in two sections
 of Winther (2022): “The Measure of Diversity” and “The Results.”  
   2. Methods for processing the data: Basic Excel
 functions (e.g., average; binary logarithm) greatly helped in redoing all
 of Lewontin’s original calculations and checking them for accuracy.
    3. Instrument- or software-specific information
 needed to interpret the data: Excel.  4. All data was
 solely handled by the author.
DOI: 10.5061/dryad.fn2z34tv3
title: Data for: Marking through moults: An evaluation of visible implant elastomer to permanently mark individuals in a lower termite species

description: 1. Advances in individual marking methods have facilitated detailed
 studies of animal populations and behaviour as they allow tracking of
 individuals through time and space. Hemimetabolous insects, representing a
 wide range of commonly-used model organisms, present a unique challenge to
 individual marking as they are not only generally small-bodied, but also
 moult throughout development, meaning that traditional surface marks are
 not persistent. 2. Visible implant elastomer (VIE) offers a potential
 solution as small amounts of the inert polymer can be implanted under the
 skin or cuticle of an animal. VIE has proved useful for individually
 marking fish, crustaceans and amphibians in both field and laboratory
 studies, and has recently been successfully trialled in laboratory
 populations of worms and fly larvae. We trialled VIE in the single-piece
 nesting termite Zootermopsis angusticollis, a small hemimetabolous insect.
 3. We found that there was no effect of VIE on survival and that marks
 persisted following moulting. However, we found some evidence that marked
 termites performed less allogrooming and trophallaxis than controls,
 although effect sizes were very small. 4. Our study suggests that VIE is
 an effective technique for marking small hemimetabolous insects like
 termites but we advocate that caution is applied, particularly when
 behavioural observation is important.
description: Data were collected as described in the publication: Padget, R.
 F. B. and Thompson, F. J. (2021) Marking through moults: An evaluation of
 visible implant elastomer to permanently mark individuals in a lower
 termite species. <i>Ecology and Evolution.</i>
 We conducted a trial of visible implant elastomer in termites
 with one treatment and one control group. The treatment group was injected
 with visible implant elastomer, while the control group was not. We then
 censused both groups for 63 days and recorded the behaviour of each group
 on days 2, 4 and 10 following treatment. Census data
 (formatted_census_data.csv) show the number of days that termites from
 each housing survived. This was collected by direct observation of
 termites on each census day. Behaviour data (behaviour_data.csv) show
 either the proportion of time or the number of times that six behaviours
 (allogrooming, antennation, butting, environment manipulation,
 self-grooming, and trophallaxis) were recorded during a ten-minute video
 of each housing, which was coded using BORIS (Friard  & Gamba,
 2016).
description: The README file can be found as a .docx file uploaded to this
 repository, this contains details of how to use the dataset. The full R
 code for the analysis of these datasets can be found
 at: https://github.com/beckypadget/vie-trials. This is linked in the
 README and as associated software.
DOI: 10.5061/dryad.37pvmcvkz
title: Data from: Nitrification is a minor source of nitrous oxide (N2O) in an agricultural landscape and declines with increasing management intensity

description: The long-term contribution of nitrification to nitrous oxide (N2O)
 emissions from terrestrial ecosystems is poorly known and thus poorly
 constrained in biogeochemical models. Here, using Bayesian inference to
 couple 25 years of in situ N2O flux measurements with site-specific
 Michaelis-Menten kinetics of nitrification-derived N2O, we test the
 relative importance of nitrification-derived N2O across six cropped and
 unmanaged ecosystems along a management intensity gradient in the U.S.
 Midwest. We found that the maximum potential contribution from
 nitrification to in situ N2O fluxes was 13-17% in a conventionally
 fertilized annual cropping system, 27-42% in a low-input cover-cropped
 annual cropping system, and 52-63% in perennial systems including a late
 successional deciduous forest. Actual values are likely to be less than
 10% of these values because of low N2O yields in cultured nitrifiers
 (typically 0.04 to 8% of NH3 oxidized) and competing sinks for available
 NH4+ in situ. Most nitrification-derived N2O was produced by ammonia
 oxidizing bacteria (AOB) rather than archaea (AOA), who appeared
 responsible for no more than 30% of nitrification-derived N2O production
 in all but one ecosystem. Although the proportion of nitrification-derived
 N2O production was lowest in annual cropping systems, these ecosystems
 nevertheless produced more nitrification-derived N2O (higher Vmax) than
 perennial and successional ecosystems. We conclude that nitrification is
 minor relative to other sources of N2O in all ecosystems examined.
description: Please see Materials and Methods in published paper.
DOI: 10.5061/dryad.wpzgmsbnj
title: Many roads to success: Different combinations of life-history traits provide accurate germination timing in seasonally dry environments

description: Germination timing is determined by several plant life-history traits.
 Seed dormancy regulates the time and place of early plant development and
 spreads recruitment risks over time. Dispersal phenology and syndrome can
 influence germination timing and buffer spatial heterogeneity. The
 ecological requirements for germination (the germination niche) can also
 influence when and where germination takes place. To date, the relative
 importance of each of these four traits to ensure the phenological
 adaptation of individual species in diverse communities remains
 unexplored. Here, we investigated the functional interactions among them
 and their relevance in heterogenous, seasonally dry environments. We
 collected seed dispersal phenology and syndrome for 82 species of the
 Brazilian savanna (cerrado) and evaluated the dormancy and germination
 behavior of the seeds of every taxon. Based on these data, we developed
 two new ecological indexes to estimate the likelihood of a non-dormant
 seed to germinate upon dispersal (∆G) and the overall variability of
 germination through time (σT). We then evaluated the influence of each
 trait on germination timing within a phylogenetically controlled
 framework. Our results show that even though germination is concentrated
 at the beginning of the rainy season, seed dispersal takes place
 year-round. Non-dormant seeds released during the dry season were
 characterized by high ∆G values that delayed their germination until the
 onset of the favorable season. Simultaneously, seed dormancy and spatial
 dispersal (i.e., the two risk-reduction mechanisms) were negatively
 correlated as dormancy and high σT values were only prevalent in seeds
 with reduced spatial dispersal ability. We conclude that the timing of
 seed germination is ultimately the net outcome of adaptive interactions
 among life-history traits, which can result in multiple functionally
 equivalent phenotypes. It is possible that this might contribute to
 community diversity by providing opportunities for the coexistence of
 different species.
DOI: 10.5061/dryad.v6wwpzgwk
title: Glue genes are subjected to diverse selective forces in Drosophila during Drosophila development

description: Molecular evolutionary studies usually focus on genes with clear roles in
 adult fitness or on developmental genes expressed at multiple time points
 during the life of the organism. Here, we examine the evolutionary
 dynamics of Drosophila glue genes, a set of eight genes tasked with a
 singular primary function during a specific developmental stage: the
 production of glue that allows animal pupa to attach to a substrate for
 several days during metamorphosis. Using phenotypic assays and available
 data from transcriptomics, PacBio genomes, and genetic variation from
 global populations, we explore the selective forces acting on the glue
 genes within the cosmopolitan D. melanogaster species and its five closely
 related species, D. simulans, D. sechellia, D. mauritiana, D. yakuba, and
 D. teissieri. We observe a three-fold difference in glue adhesion between
 the least and the most adhesive D. melanogaster strain, indicating a
 strong genetic component to phenotypic variation. These eight glue genes
 are among the most highly expressed genes in salivary glands yet they
 display no notable codon bias. New copies of Sgs3 and Sgs7 are found in D.
 yakuba and D. teissieri with the Sgs3 coding sequence evolving rapidly
 after duplication in the D. yakuba branch. Multiple sites along the
 various glue genes appear to be constrained. Our population genetics
 analysis in D. melanogaster suggests signs of local adaptive evolution for
 Sgs3, Sgs5 and Sgs5bis and traces of recent selection for Sgs1, Sgs3, Sgs7
 and Sgs8. Our work shows that stage-specific genes can be subjected to
 various dynamic evolutionary forces.
description: <b>Dataset1.ods: Raw
 data</b> Sheet1: Stock_information: Information of the fly lines used for the analysis. Sheet2: adhesion_test: Results of the adhesion assay performed on pupae used in the analyses (including adhesion tests that were excluded from further analysis). Sheet3: glue_area: Pupa-substrate contact area measurements. Sheet4: codon_usage_and_expression: Expression level and codon adaptation index for genes expressed in salivary glands of wandering larva. Sheet5: PAML_dN_values: synonymous and non synonymous substitution rates obtained with PAML under M0 and free ratio models. Sheet6: FEL_results: raw results obtained by the Fixed Effect Likelihood method implemented in HyPhy via the datamonkey web platform.   <b>fasta_alignments.zip: </b>Sequence alignments used for the different analyses. <b>scripts.zip: </b>folder containing scripts used to do the analyses. <strong>circos_plot_revised.R</strong>: R script to produce the revised circos plot figure 4. <strong>Fst_distribution.R</strong>: R script to analyze Fst between <em>D. melanogaster</em> populations. <b>circos_raw_data.zip: </b>data used to produce circos plot figures. <b>glue_prints.zip: </b>folder containing pictures of prints left by pupae after detachment.
DOI: 10.5061/dryad.f7m0cfxwt
title: Semi-intensive Shrimp-Farms as Experimental Arenas for the Study of Predation Risk from Falcons to Shorebirds

description: Varying environmental conditions and energetic demands can affect habitat
 use by predators and their prey. Anthropogenic habitats may provide an
 opportunity to document both predation events and foraging activity by
 prey, and therefore enable an empirical evaluation how prey cope with
 trade-offs between starvation and predation risk in environments of
 variable foraging opportunities and predation danger. Here we use seven
 years of observational data of peregrine falcons Falco peregrinus and
 shorebirds at a semi-intensive shrimp-farm to determine how starvation and
 predation risk vary for shorebirds under a predictable variation in
 foraging opportunities. Attack rate (mean 0.1 attacks/hr, equating 1
 attack every ten hours) was positively associated with the total foraging
 area available for shorebirds at the shrimp-farm throughout the harvesting
 period, with tidal amplitude at the adjacent mudflat having a strong
 non-linear (quadratic) effect. Hunt success (mean 14%) was higher during
 low tides, and declined as the target flocks became larger. Finally,
 individual shorebird vigilance behaviours were more frequent when birds
 foraged in smaller flocks at ponds with poorer conditions. Our results
 provide empirical evidence of a risk threshold modulated by tidal
 conditions at the adjacent wetlands, where shorebirds trade-off risk and
 rewards to decide to avoid or forage at the shrimp-farm (a potentially
 dangerous habitat) depending on their need to meet daily energy
 requirements. We propose that semi-intensive shrimp farms serve as ideal
 ‘arenas’ for studying predator-prey dynamics of shorebirds and falcons,
 because harvest operations and regular tidal cycles create a mosaic of
 foraging patches with predictable food supply. In addition, the relatively
 low hunt success suggests that indirect effects associated to enhanced
 starvation risk are important in shorebird life-history decisions. --
DOI: 10.15468/dl.y2b7sc
title: Occurrence Download

description: A dataset containing 188 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sagina saginoides"
 ]
}

 The dataset includes 188 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002907-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5tb2rbp4h
title: Data from: Occasional long-distance dispersal may not prevent inbreeding in a threatened butterfly

description: Background: To set up successful conservation measures, detailed knowledge
 on the dispersal and colonization capacities of the focal species and
 connectivity between populations is of high relevance. We developed
 species-specific nuclear microsatellite molecular markers for the grayling
 (Hipparchia semele), a butterfly endemic to Europe and of growing
 conservation concern in North-West Europe, and report on its population
 genetics, in a fragmented, anthropogenic landscape in Belgium. Our study
 included samples from 23 different locations nested in two regions and
 additional historical samples from two locations. We assessed
 contemporary, long-distance dispersal based on genetic assignment tests
 and investigated the effect of habitat loss and fragmentation on the
 population genetic structure and genetic variation using data of nine
 microsatellite loci. Results: Detected dispersal events covered remarkably
 long distances, which were up to ten times larger than previously reported
 colonisation distances, with the longest movement recorded in this study
 even exceeding 100 km. However, observed frequencies of long-distance
 dispersal were low. Our results point to the consequences of the strong
 population decline of the last decades, with evidence of inbreeding in 72%
 of the recently sampled populations and low estimates of effective
 population sizes (Ne) (ranging from 20 to 54 individuals). Conclusions:
 Our study shows low frequencies of long-distance dispersal, which is
 unable to prevent inbreeding in most of the local populations. We discuss
 the significance for species conservation including future translocation
 events and discuss appropriate conservation strategies to maintain viable
 grayling (meta)populations in highly fragmented, anthropogenic landscapes.
description: <strong><em>Hipparchia semele</em>
 microsatellite data</strong> The file Hipparchia
 semele microsatellite data includes the data from 15 microsatellites for
 653 unique genotypes of <em>Hipparchia semele</em> from in
 total 24 sampling locations located in Belgium. The data matrix also
 include the spatial coordinates of each sampled population and the sex of
 the sampled individuals, given in the three last columns.
DOI: 10.5061/dryad.j6q573nf8
title: Data From: Active sinking particles: Flow and transport dynamics due to sessile suspension feeders on sinking aggregates

description: Sinking or sedimentation of biological aggregates plays a critical role in
 carbon sequestration in the ocean and in vertical material fluxes in
 waste-water treatment plants. In both these contexts, the sinking
 aggregates are “active,” since they are biological hot-spots and are
 densely colonized by microorganisms including bacteria and sessile
 protists, some of which generate feeding currents. However, the effect of
 these feeding currents on the sinking rates, trajectories, and mass
 transfer to these "active sinking particles," has not previously
 been studied. Here we use a novel scale-free vertical-tracking microscope
 (a.k.a. Gravity Machine, Krishnamurthy et al. "Scale-free vertical
 tracking microscopy." Nature Methods (2020)) to follow model sinking
 aggregates (agar spheres) with attached protists (Vorticella convallaria),
 sinking over long distances while simultaneously measuring local flows. We
 find that activity due to attached \vortc causes significant changes to
 the flow around aggregates in a dynamic manner and reshapes mass transport
 boundary layers. Furthermore, we find that activity-mediated local flows
 along with sinking modify the encounter and plume cross-sections of the
 aggregate and induce sustained aggregate rotations. Overall our work shows
 the important role of biological activity in shaping the near-field flows
 around aggregates with potentially important effects on aggregate fate and
 material fluxes.
description: Detailed methods are in "Active Sinking Particles: Flow and
 transport dynamics due to sessile suspension feeders on sinking
 aggregates." Included in this dataset are Particle Image Velocimetry
 (PIV) flow fields for <em>Vorticella convallaria</em> on
 sinking aggregates.  
description: Please see README file.