cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1888
title: Data from: Species selection maintains self-incompatibility

description: Identifying traits that affect rates of speciation and extinction and
 hence explain differences in species diversity among clades is a major
 goal of evolutionary biology. Detecting such traits is especially
 difficult when they undergo frequent transitions between states.
 Self-incompatibility, the ability of hermaphrodites to enforce
 outcrossing, is frequently lost in flowering plants, enabling
 self-fertilization. We show, however, that in the nightshade plant family
 (Solanaceae), species with functional self-incompatibility diversify at a
 significantly higher rate than those without it. Apparent short-term
 advantages of potentially self-fertilizing individuals are therefore
 offset by strong species selection, which favors obligate outcrossing.
description: NicSolstatus.csvBreeding system data for species used in the analyses. See included text file for explanation.NicSolPLML.treRate-smoothed ML tree of 356 Solanaceae species.
DOI: 10.5061/dryad.46bq0
title: Data from: Differential sperm storage by female zebra finches Taeniopygia guttata

description: When females mate promiscuously, female sperm storage provides scope to
 bias the fertilization success towards particular males via the non-random
 acceptance and utilization of sperm. The difficulties observing
 post-copulatory processes within the female reproductive tract mean that
 the mechanisms underlying cryptic female choice remain poorly understood.
 Here, we use zebra finches Taeniopygia guttata, selected for divergent
 sperm lengths, combined with a novel technique for isolating and
 extracting sperm from avian sperm storage tubules (SSTs), to test the
 hypothesis that sperm from separate ejaculates are stored differentially
 by female birds. We show that sperm from different inseminations enter
 different SSTs in the female reproductive tract, resulting in almost
 complete segregation of the sperm of competing males. We propose that
 non-random acceptance of sperm into SSTs, reflected in this case by sperm
 phenotype, provides a mechanism by which long sperm enjoy enhanced
 fertilization success in zebra finches.
description: Hemmings Birkhead 2017
 PRSB Differential sperm storage dataThis data file contains
 data on the number of sperm from different male zebra finches with long or
 short sperm, stored in the sperm storage tubules of females who had mated
 with both males. It also contains data on the number of sperm from both
 males that reached the perivitelline layer of the ovum. See associated
 README file for further details.Hemmings Birkhead Differential
 sperm storage data.csv
DOI: 10.15468/dl.nbsxd8
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cavendishia cuatrecasasii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 116 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001239-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7vj52
title: Data from: Why is the giant panda black and white?

description: Although the external appearances of most mammals are drab browns and
 grays used to match their backgrounds, certain species stand out as
 exceptions, perhaps the most notable being the giant panda. Using a
 comparative phylogenetic approach, we examined associations between
 different pelage regions and socioecological variables across carnivores
 and ursid subspecies to shed light on the giant panda’s black and white
 pelage coloration. Analyses of fur color and background environments
 suggest that the giant panda’s white face, nape, dorsum, flank, belly, and
 rump are adapted for crypsis against a snowy background, whereas its black
 shoulders and legs are adapted for crypsis in shade. Dark markings on the
 head are not used in crypsis, however, but in communication: Dark ears may
 be involved with signaling intent about ferocity whereas dark eye marks
 may serve in individual recognition. There is no compelling support for
 their fur color being involved in temperature regulation, disrupting the
 animal’s outline, or in reducing eye glare. We infer that the giant
 panda’s unique pelage coloration serves a constellation of functions that
 enable it to match its background in different environments and to
 communicate using facial features.
description: SpeciesSupplementCarnivore species data filePandaSubSuppUrsid subspecies data file
DOI: 10.5061/dryad.p307vp1
title: Data from: How much starvation, desiccation and oxygen depletion can Drosophila melanogaster tolerate before its upper thermal limits are affected?

description: Heat tolerance is commonly assessed as the critical thermal maximum
 (CTmax) using the dynamic method exposing organisms to a gradually
 increasing (ramping) temperature until organisms fall into a coma. The
 CTmax estimate is dependent on the ramping rate, with decreased rates
 leading to longer treatments and ultimately lower CTmax estimates. There
 is a current discussion surrounding the physiological dynamics of the
 effect of the time of exposure by temperature interaction on these
 estimates. Besides temperature the time of exposure to limited food
 (starvation), desiccation, and reduced levels of oxygen or increased
 levels of CO2 may, in interaction with ramping rate, act as confounding
 factors when assessing upper thermal limits using the dynamic method. Here
 we test the role of the different potentially confounding factors for
 assaying thermal tolerance using a ramping assay under four different
 ramping rates, varying from 0.01°C/min to 0.2°C/min. We find that CTmax
 values are higher at faster ramping rates and that oxygen or CO2
 concentration does not show any negative effect on the CTmax values
 obtained within the experimental pre-treatment period (32h). Both water
 (up to 6h) and food (up to 42h) deprivation prior to assay showed a
 negative correlation with thermal tolerance of the flies. For both traits,
 we found a significant interaction with ramping rate, most likely due to
 prolonged assays at lower rates. However, as little water was lost during
 the ramping assay and as food deprivation only modestly affected CTmax
 values, results were very robust to the conditions experienced during the
 assay (even at slow rates) and mainly affected by the conditions
 experienced prior to performing the assay. Thus, for the most commonly
 applied experimental conditions CTmax estimates are unlikely to be biased
 or confounded by ramping rate, starvation, desiccation or deteriorating
 atmospheric composition.
description: Read
 meOverview of associated
 data filesCTmax and
 oxygenHeat tolerance (CTmax)
 as a function of oxygen limitationoxygen.csvstarvation (Fig 1)Data on heat tolerance as a function of starvationdesiccation (Fig 2)Data on heat tolerance as a function of desiccationwater content (Fig 3A)Water content in flies exposed to ramping assay under different conditions (vial types)water content (Fig 3B)Water content in flies exposed to desiccation for different amounts of timelipid content (Fig 3C)Lipid content in flies exposed to starvation for different amounts of time
DOI: 10.71728/senscience.4f2j-8h1k
title: Atoll biodiversity and environments: an AI-ready, interactive data portal for Indo-Pacific atolls

description: This FAIR² data portal provides harmonized information on biodiversity and environments for Indo-Pacific atolls.
DOI: 10.5061/dryad.1q52r71
title: Data from: Flexible memory controls sperm competition responses to male Drosophila melanogaster

description: Males of many species use social cues to predict sperm competition and
 tailor their reproductive strategies, such as ejaculate or behavioural
 investment, accordingly. Whilst these plastic strategies are widespread,
 the underlying mechanisms remain largely unknown. Plastic behaviour
 requires individuals to learn and memorise cues associated with
 environmental change before using this experience to modify behaviour.
 Drosophila melanogaster respond to an increase in sperm competition threat
 by extending mating duration after exposure to a rival male. This
 behaviour shows lag times between environmental change and behavioural
 response suggestive of acquisition and loss of memory. Considering
 olfaction is important for a male’s ability to assess the sperm
 competition environment, we hypothesised that an olfactory learning and
 memory pathway may play a key role in controlling this plastic behaviour.
 We assessed the role of genes and brain structures known to be involved in
 learning and memory. We show that sperm competition responses depend on
 anaesthesia sensitive memory, specifically the genes rut and amn. We also
 show that the γ lobes of the mushroom bodies are integral to the control
 of plastic mating behaviour. These results reveal the genetic and neural
 properties required for reacting to changes in the sperm competition
 environment.
description: Data from:Flexible
 memory controls sperm competition responses in male Drosophila
 melanogasterRaw data from Rouse,
 Watkinson and Bretman 2018 Flexible memory controls sperm competition
 responses in male Drosophila melanogasterRouse et al 2018 raw
 data.xlsx
DOI: 10.15468/dl.cx8cv3
title: Occurrence Download

description: A dataset containing 25668 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sorex monticolus"
 ]
}

 The dataset includes 25668 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001238-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t3jp4
title: Data from: Impact of host nutritional status on infection dynamics and parasite virulence in a bird-malaria system

description: 1. Host resources can drive the optimal parasite exploitation strategy by
 offering a good or a poor environment to pathogens. Hosts living in
 resource-rich habitats might offer a favourable environment to developing
 parasites because they provide a wealth of resources. However, hosts
 living in resource-rich habitats might afford a higher investment into
 costly immune defences providing an effective barrier against infection.
 Understanding how parasites can adapt to hosts living in habitats of
 different quality is a major challenge in the light of the current
 human-driven environmental changes. 2. We studied the role of nutritional
 resources as a source of phenotypic variation in host exploitation by the
 avian malaria parasite Plasmodium relictum. We investigated how the
 nutritional status of birds altered parasite within-host dynamics and
 virulence, and how the interaction between past and current environments
 experienced by the parasite accounts for the variation in the infection
 dynamics. Experimentally-infected canaries were allocated to control or
 supplemented diets. Plasmodium parasites experiencing the two different
 environments were subsequently transmitted in a full-factorial design to
 new hosts reared under similar control or supplemented diets. 3. Food
 supplementation was effective since supplemented hosts gained body mass
 during a 15 day period that preceded the infection. Host nutrition had
 strong effects on infection dynamics and parasite virulence. Overall
 parasites were more successful in control non-supplemented birds, reaching
 larger population sizes and producing more sexual (transmissible) stages.
 However, supplemented hosts paid a higher cost of infection, and when
 keeping parasitaemia constant had lower haematocrit than control hosts. 4.
 Parasites grown on control hosts were better able to exploit the
 subsequent hosts since they reached higher parasitaemia than parasites
 originating from supplemented hosts. They were also more virulent since
 they induced higher mass and haematocrit loss. 5. Our study highlights
 that parasite virulence can be shaped by the host nutritional status and
 that parasite can adapt to the environment provided by their hosts,
 possibly through genetic selection.
description: Data from: Impact of
 host nutritional status on infection dynamics and parasite virulence in a
 bird-malaria systemRepeated measurements of
 body mass, haematocrit and blood parasitaemia (RQ) taken over a -15/17
 day-period in birds infected by Plasmodium relictum and fed with control
 or supplemented diets (experiment 1). Parasites originating from
 control/supplemented hosts were inoculated to new birds that were also fed
 either control or supplemented diet (experiment 2). For more details,
 refer to the Materials and Methods section of the
 manuscript.Cornet_DataArchiving.txt
DOI: 10.5061/dryad.2t4gv
title: Data from: Strong, nonlinear selection against fluctuating asymmetry in wild populations of a marine fish

description: Theoretical links between fluctuating asymmetry (FA) and fitness have led
 many to use FA as a proxy for average fitness. However, studies examining
 whether asymmetry actually correlates with individual fitness in wild
 populations are relatively rare and often use simple measures of
 association (e.g., correlation coefficients). Consequently, the pattern of
 selection on asymmetry in the wild is seldom clear. We examined selection
 on FA of pectoral fin morphology in two wild populations of a marine fish
 (the kelp perch; Brachyistius frenatus). As expected, variance in signed
 FA in each initial sample was significantly greater than that found in the
 surviving population, indicating selection against FA. Our estimate of the
 fitness surface confirmed perfect symmetry as the phenotypic optimum and
 indicated strong, nonlinear selection against asymmetry. No difference in
 the form of selection was detected between populations. However, the level
 of FA in the initial samples varied among populations, leading to an
 overall difference in the level of selective mortality. Our results
 suggest that selection on asymmetry in wild populations may be strongly
 nonlinear, and indicate that the demographic costs of asymmetry may play a
 substantial role in the dynamics of populations.
description: surfperch FA
 dataRaw data collected from
 images of kelp perch used to calculate FA. Namely, the number of fin rays
 counted on the left and right pectoral fins of each fish, organized by
 location (Palos Verdes Peninsula or Catalina Island), and by collection
 (initial or survivors). There are two sets of counts for each fish because
 the fin rays were counted by two independent observers (ARC and
 DRC).bootstrap estimates of
 corrected FAThis is the R code used
 to calculate FA (Left-Right) based on counted fin rays in right and left
 pectoral fins of all four samples (two from the Palos Verdes Peninsula:
 initial and survivors, and two from Catalina Island: initial and
 survivors). There are two independent counts and therefore two estimates
 of FA. The variance between these two estimates was used to correct for
 measurement error. The corrected FA estimate was then also corrected for
 the presence of directional asymmetry, and the samples were bootstrapped
 to give a statistically significant estimate of the relative size of FA
 between the two populations at the time of the two different sampling
 events.
DOI: 10.5061/dryad.3mf68
title: Data from: Compensatory life history responses of a mesopredator may undermine carnivore management efforts

description: Lethal carnivore management, aimed at reducing carnivore impacts, is a
 global phenomenon threatening the persistence of many carnivores.
 Black-backed jackals Canis mesomelas, the dominant cause of livestock
 predation in southern Africa, are widely hunted to reduce livestock
 predation. Despite centuries of lethal management, jackals persist.
 Smaller canids, like jackals, are highly adaptable and display variable
 responses to mortality sources, which may affect management outcomes. The
 effects of killing carnivores will depend on their behaviour, social
 organization, reproduction and dispersal patterns. We predicted that
 hunted jackals will alter demographic and reproductive patterns to
 compensate for increased mortality. Here, we collected demographic and
 reproductive information from harvested jackals and compared it between
 continually hunted (farms) and unmanaged populations (reserves). The
 removal of jackals from farms results in a decrease in median age from 5–6
 years (reserves) to 2–3 years (farms). Hunting also changed the age
 structure of jackal populations from a stable population to an expanding
 population. This may be ascribed to the compensatory immigration of
 individuals from neighbouring unmanaged areas, suggesting the formation of
 a source–sink system. Unmanaged areas may act as source populations
 exporting young, dispersing individuals to hunted areas which may act as
 sinks. This is likely driven by disruptions in the normal, mutually
 exclusive territorial system resulting in low densities of conspecifics on
 farms. The low density of conspecifics allows younger individuals that
 would be socially precluded from reproducing to reproduce. Jackals on
 farms compensated for increased mortality by increasing the pregnancy rate
 of young individuals and increasing the litter size at younger ages,
 thereby increasing reproductive output. Synthesis and applications. The
 lethal management of predators is the prevailing strategy to reduce
 livestock predation. However, the highly adaptable nature of jackals and
 the combination of compensatory mechanisms such as increased reproduction
 and potential for immigration allow these predators to persist in the face
 of severe anthropogenic mortality, possibly through the formation of a
 source–sink system. These compensatory processes will continue to counter
 population management actions as long as recruitment from unmanaged areas
 persists.
description: Jackal demographic and
 reproduction dataData used for the
 analyses of demographic and reproduction of jackals on hunted farms and
 unmanaged reserves. Data include: Treatment, age class, sex, body
 condition indices (body mass and renal fat index), and female reproduction
 parameters (pregnant, lactating, litter size,
 fecundity).Demo_repr.csvJackal foetus dataData used for the analyses of female reproduction of jackals on hunted farms and unmanaged reserves. Data include: Treatment, number of foetuses per female, and sex of foetus.Foetus.csv
DOI: 10.5061/dryad.32r30
title: Data from: Coinfection outcome in an opportunistic pathogen depends on the inter-strain interactions

description: Background In nature, organisms are commonly coinfected by two or more
 parasite strains, which has been shown to influence disease virulence.
 Yet, the effects of coinfections of environmental opportunistic pathogens
 on disease outcome are still poorly known, although as host-generalists
 they are highly likely to participate in coinfections. We asked whether
 coinfection with conspecific opportunistic strains leads to changes in
 virulence, and if these changes are associated with bacterial growth or
 interference competition. We infected zebra fish (Danio rerio) with three
 geographically and/or temporally distant environmental opportunist
 Flavobacterium columnare strains in single and in coinfection. Growth of
 the strains was studied in single and in co-cultures in liquid medium, and
 interference competition (growth-inhibiting ability) on agar. Results: The
 individual strains differed in their virulence, growth and ability for
 interference competition. Number of coinfecting strains significantly
 influenced the virulence of infection, with three-strain coinfection
 differing from the two-strain and single infections. Differences in
 virulence seemed to associate with the identity of the coinfecting
 bacterial strains, and their pairwise interactions. This indicates that
 benefits of competitive ability (production of growth-inhibiting
 compounds) for virulence are highest when multiple strains co-occur,
 whereas the high virulence in coinfection may be independent from in vitro
 bacterial growth. Conclusions: Intraspecific competition can lead to
 plastic increase in virulence, likely caused by faster utilization of host
 resources stimulated by the competitive interactions between the strains.
 However, disease outcome depends both on the characteristics of individual
 strains and their interactions. Our results highlight the importance of
 strain interactions in disease dynamics in environments where various
 pathogen genotypes co-occur.
description: Virulence
 dataVirulence data for the
 confection experimentvirulence
 data.xlsxculturedataBacterial growth parameters in the co-culture experiments
DOI: 10.5061/dryad.qb4m0
title: Data from: Enhanced flight performance by genetic manipulation of wing shape in Drosophila

description: Insect wing shapes are remarkably diverse and the combination of shape and
 kinematics determines both aerial capabilities and power requirements.
 However, the contribution of any specific morphological feature to
 performance is not known. Using targeted RNA interference to modify wing
 shape far beyond the natural variation found within the population of a
 single species, we show a direct effect on flight performance that can be
 explained by physical modelling of the novel wing geometry. Our data show
 that altering the expression of a single gene can significantly enhance
 aerial agility and that the Drosophila wing shape is not, therefore,
 optimized for certain flight performance characteristics that are known to
 be important. Our technique points in a new direction for experiments on
 the evolution of performance specialities in animals.
description: Individual flight
 performance and wing shape metricsFruit fly flight
 performance and wing shape morphometrics. Trajectory analysis metrics.
 Principal component scores for left and right wings, where available, for
 each genotype described in Ray et al.(2016).data
 archive.xlsx