cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.20650
title: Data from: Pathways to fitness: carry-over effects of late hatching and urbanisation on lifetime mating success

description: Life history theory and most empirical studies assume carry-over effects
 of larval conditions to shape adult fitness through their impact on
 metamorphic traits (age and mass at metamorphosis). Yet, very few formal
 tests of this connection across metamorphosis exist, because this entails
 longitudinal studies from the egg stage and requires measuring fitness in
 (semi)natural conditions. In a longitudinal one-year common-garden rearing
 experiment consisting of an outdoor microcosm part for the larval stage
 and a large outdoor insectary part for the adult stage, we studied the
 effects of two factors related to time constraints in the larval stage
 (egg hatching period and urbanisation) on life history traits and lifetime
 mating success in the males of the damselfly Coenagrion puella. We reared
 early- and late-hatched larvae from each of three rural and three urban
 populations from the egg stage throughout their adult life. Key findings
 were that both the hatching period and urbanisation shaped adult fitness,
 yet through different pathways. As expected, the more time-constrained
 late-hatched individuals accelerated their larval life history and this
 was associated with a lower lifetime mating success. A path analysis
 revealed this carry-over effect was mediated by the changes in the two
 metamorphic traits (reduced age and lower mass at emergence). Notably,
 urban males had a 50% lower lifetime mating success, which was not
 mediated by age and mass at emergence, and possibly driven by their
 shorter lifespan. Our results point to long-term carry-over effects of the
 usually ignored natural variation in egg hatching dates, and further
 contribute to the limited evidence showing fitness costs of adjusting to
 an urban lifestyle.
description: data_oikos_tuzun&stoks_2017Data used for the Tuzun & Stoks 2017 Oikos paper.
DOI: 10.5061/dryad.hm505
title: Data from: Poison frog color morphs express assortative mate preferences in allopatry but not sympatry

description: The concurrent divergence of mating traits and preferences is necessary
 for the evolution of reproductive isolation via sexual selection, and such
 coevolution has been demonstrated in diverse lineages. However, the extent
 to which assortative mate preferences are sufficient to drive reproductive
 isolation in nature is less clear. Natural contact zones between lineages
 divergent in traits and preferences provide exceptional opportunities for
 testing the predicted evolutionary consequences of such divergence. The
 strawberry poison frog (Oophaga pumilio) displays extreme color
 polymorphism in and around the young Bocas del Toro archipelago. In a
 transition zone between red and blue allopatric lineages, we asked whether
 female preferences diverged along with coloration, and whether any
 divergent preferences persist in a zone of sympatry. When choosing among
 red, blue and phenotypically intermediate males, females from monomorphic
 red and monomorphic blue populations both expressed assortative
 preferences. However, red, blue, and intermediate females from the contact
 zone all preferred red males, suggesting that divergent preferences may be
 insufficient to effect behavioral isolation. Our results highlight the
 complexity of behavioral isolation, and the need for studies that can
 reveal the circumstances under which divergent preferences do and do not
 contribute to speciation.
description: DB Lab Mate
 ChoiceMate choice behavioral
 assay done in the lab.
DOI: 10.5061/dryad.g8g20
title: Data from: Predator-guided sampling reveals biotic structure in the bathypelagic

description: We targeted habitat used differentially by deep-diving, air-breathing
 predators to empirically sample their prey’s distributions off southern
 California. Fine-scale measurements of the spatial variability of
 potential prey animals from the surface to 1200 m were obtained using
 conventional fisheries echosounders aboard a surface ship and uniquely
 integrated into a deep-diving autonomous vehicle. Significant spatial
 variability in the size, composition, total biomass, and spatial
 organization of biota was evident over all spatial scales examined and was
 consistent with the general distribution patterns of foraging Cuvier’s
 beaked whales (Ziphius cavirostris) observed in separate studies. Striking
 differences were found in prey characteristics between regions at depth,
 however, did not reflect differences observed in surface layers. These
 differences in deep pelagic structure horizontally and relative to surface
 structure, absent clear physical differences, change our long-held views
 of this habitat as uniform. The revelation that animals deep in the water
 column are so spatially heterogeneous at scales from 10 m to 50 km
 critically affects our understanding of the processes driving
 predator-prey interactions, energy transfer, biogeochemical cycling and
 other ecological processes in the deep sea, and the connections between
 the productive surface mixed layer and the deep water column.
description: Target relative
 frequency responseThe frequency response
 (38-120 kHz) of single targets identified between 900 and 1200 m for each
 transect type (low, alternate, high Ziphius use).Relative frequency
 response.xlsxTarget
 strengthThe target strength
 distribution of single targets consistent with squid between 900 and 1200
 m within three sampling zones (high, alternate, and low Ziphius
 use).
DOI: 10.5061/dryad.44p35
title: Data from: Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs

description: Zoonotic diseases are a looming threat to global populations, and nearly
 75% of emerging infectious diseases can spread among wildlife, domestic
 animals and humans. A ‘One World, One Health’ perspective offers us an
 ideal framework for understanding and potentially mitigating the spread of
 zoonoses, and the island of Madagascar serves as a natural laboratory for
 conducting these studies. Rapid habitat degradation and climate change on
 the island are contributing to more frequent contact among humans,
 livestock and wildlife, increasing the potential for pathogen spillover
 events. Given Madagascar's long geographical isolation, coupled with
 recent and repeated introduction of agricultural and invasive species, it
 is likely that a number of circulating pathogens remain uncharacterized in
 lemur populations. Thus, it is imperative that new approaches be
 implemented for de novo pathogen discovery. To this end, we used
 non-targeted deep sequencing of blood transcriptomes from two species of
 critically endangered wild lemurs (Indri indri and Propithecus diadema) to
 characterize blood-borne pathogens. Our results show several undescribed
 vector-borne parasites circulating within lemurs, some of which may cause
 disease in wildlife, livestock and humans. We anticipate that advanced
 methods for de novo identification of unknown pathogens will have broad
 utility for characterizing other complex disease transmission systems.
description: Consensus sequences of
 Babesia, Borrelia, C. Neoehrlichia, Plasmodium, and
 TrypanosomaThis data file contains
 consensus sequences of ribosomal and mitochondrial genes for Babesia,
 Borrelia, C. Neoehrlichia, Plasmodium, and Trypansosoma identified in
 lemur blood samples from Madagascar.Larsen_etal_2016_ConsensusSequences.zip
DOI: 10.5061/dryad.742fp
title: Data from: Effect of winter cold duration on spring phenology of the orange tip butterfly, Anthocharis cardamines

description: The effect of spring temperature on spring phenology is well understood in
 a wide range of taxa. However, studies on how winter conditions may affect
 spring phenology are underrepresented. Previous work on Anthocharis
 cardamines (orange tip butterfly) has shown population-specific reaction
 norms of spring development in relation to spring temperature and a
 speeding up of post-winter development with longer winter durations. In
 this experiment, we examined the effects of a greater and ecologically
 relevant range of winter durations on post-winter pupal development of A.
 cardamines of two populations from the United Kingdom and two from Sweden.
 By analyzing pupal weight loss and metabolic rate, we were able to
 separate the overall post-winter pupal development into diapause duration
 and post-diapause development. We found differences in the duration of
 cold needed to break diapause among populations, with the southern UK
 population requiring a shorter duration than the other populations. We
 also found that the overall post-winter pupal development time, following
 removal from winter cold, was negatively related to cold duration, through
 a combined effect of cold duration on diapause duration and on
 post-diapause development time. Longer cold durations also lead to higher
 population synchrony in hatching. For current winter durations in the
 field, the A. cardamines population of southern UK could have a reduced
 development rate and lower synchrony in emergence because of short
 winters. With future climate change, this might become an issue also for
 other populations. Differences in winter conditions in the field among
 these four populations are large enough to have driven local adaptation of
 characteristics controlling spring phenology in response to winter
 duration. The observed phenology of these populations depends on a
 combination of winter and spring temperatures; thus, both must be taken
 into account for accurate predictions of phenology.
description: a_card.txtana_hatch.Rana_prop_dia.Rana_rd.Rana_t0.Rana_tp.R
DOI: 10.5061/dryad.6t1f2
title: Data from: Maternal programming of offspring antipredator behavior in a seabird

description: Predation risk is an important environmental factor for animal
 populations, expected to trigger maternal effects to prepare offspring for
 living in an environment with predators. Yet, evidence of adaptive
 anticipatory maternal effects in wild animals is still weak. Here, we
 explored this question in a wild colony of yellow-legged gulls, Larus
 michahellis. To this aim, prior to laying we exposed mothers to either
 mink decoys or non-predator rabbit decoys and explored the antipredator
 behavior of 118 chicks at the age of two days. We found that chicks from
 second-laid eggs by predator-exposed mothers crouched faster after hearing
 a playback with adult alarm calls than chicks from second-laid eggs by
 control mothers. Besides, chicks from third-laid eggs by predator-exposed
 mothers were lighter than control chicks, but this was not due to
 differences in egg volume. Our results suggest that predator-exposed
 mothers modified offspring phenotype via eggs to cope with predators,
 although only in chicks from second-laid eggs. Maternal transference of
 corticosterone could underlie chick behavioral plasticity. Results support
 the role of maternal effects as a form of phenotype programming to
 forewarn offspring about environmental hazards.
description: behavior_dataThis file contains chick anti-predator behavioral data, offspring growth and other relevant variables (treatment, foster nest, date and area of origin)
DOI: 10.5061/dryad.454ss
title: Data from: Calculating competitive intransitivity: computational challenges

description: Intransitive, or 'rock-paper-scissors' competition is compelling
 because it promotes species coexistence and because recent work suggests
 it may be common in natural systems. One class of intransitivity indices
 works by considering s, the minimum number of competitive reversals to
 convert a given competitive community (i.e., a 'tournament') to
 a hierarchy. The most straightforward example of such
 'reversal-based' indices is Petraitis' index, t = 1 - s/M,
 where M is the maximum s across all possible n-species tournaments. Using
 exhaustive searches, we prove that Petraitis' formula for M (and,
 therefore, t) does not hold for n ≥ 7. Furthermore, the determination of s
 for even moderate values of n may prove difficult, as the equivalent
 graph-theoretical problem is NP-hard; there is no known computationally
 feasible way to compute an exact answer for anything but small values of
 n, let alone a closed-form solution. Petraitis' t is a valuable index
 of intransitivity; however, at present its use is limited to relatively
 species-poor systems. More broadly, reversal-based indices, while
 intuitive, may be problematic because of this computability issue.
description: find_sA Matlab MEX function,
 written in C++, which finds the minimum number of competitive reversals
 required to change a given tournament to a hierarchy (s in Petraitis
 1979).find_MA Matlab MEX function,
 written in C++, which, given n, provides a list of all n-species
 tournaments, gives the minimum number of reversals required to change them
 into their respective minimally distant hierarchies (s in Petraitis 1979),
 and also gives the maximum minimum number of reversals (M in Petraitis
 1979).
DOI: 10.5061/dryad.h0246
title: Data from: Sperm number trumps sperm size in mammalian ejaculate evolution

description: Postcopulatory sexual selection is widely accepted to underlie the
 extraordinary diversification of sperm morphology. However, why does it
 favour longer sperm in some taxa but shorter in others? Two recent
 hypotheses addressing this discrepancy offered contradictory explanations.
 Under the sperm dilution hypothesis, selection via sperm density in the
 female reproductive tract favours more but smaller sperm in large, but the
 reverse in small, species. Conversely, the metabolic constraint hypothesis
 maintains that ejaculates respond positively to selection in small
 endothermic animals with high metabolic rates, whereas low metabolic rates
 constrain their evolution in large species. Here, we resolve this debate
 by capitalizing on the substantial variation in mammalian body size and
 reproductive physiology. Evolutionary responses shifted from sperm length
 to number with increasing mammalian body size, thus supporting the sperm
 dilution hypothesis. Our findings demonstrate that body-size-mediated
 trade-offs between sperm size and number can explain the extreme
 diversification in sperm phenotypes.
description: Phylogeny of the 100
 mammalian speciesPhylogeny in NEXUS
 format of the 100 mammalian species used in the study.size.number.phylo.nexData of the 100 mammalian speciesData on sperm number (in millions), sperm length (um), combined testes mass (g) and male and female body mass (g) of all 100 mammalian species used in this study.size.number.data.txtsize.number.referencesReferences of the data sources.
DOI: 10.5061/dryad.52mb6
title: Data from: Revisiting Brownian motion as a description of animal movement: a comparison to experimental movement data

description: Characterization of patterns of animal movement is a major challenge in
 ecology with applications to conservation, biological invasions and pest
 monitoring. Brownian random walks, and diffusive flux as their mean field
 counterpart, provide one framework in which to consider this problem.
 However, it remains subject to debate and controversy. This study presents
 a test of the diffusion framework using movement data obtained from
 controlled experiments. Walking beetles (Tenebrio molitor) were released
 in an open circular arena with a central hole and the number of
 individuals falling from the arena edges was monitored over time. These
 boundary counts were compared, using curve fitting, to the predictions of
 a diffusion model. The diffusion model is solved precisely, without using
 numerical simulations. We find that the shape of the curves derived from
 the diffusion model is a close match to those found experimentally.
 Furthermore, in general, estimates of the total population obtained from
 the relevant solution of the diffusion equation are in excellent agreement
 with the experimental population. Estimates of the dispersal rate of
 individuals depend on how accurately the initial release distribution is
 incorporated into the model. We therefore show that diffusive flux is a
 very good approximation to the movement of a population of Tenebrio
 molitor beetles. As such, we suggest that it is an adequate
 theoretical/modelling framework for ecological studies that account for
 insect movement, although it can be context specific. An immediate
 practical application of this can be found in the interpretation of trap
 counts, in particular for the purpose of pest monitoring.
description: Experimental data and
 MATLAB codeThis archive contains
 the experimental data and MATLAB code used in the publication named. Three
 folders are included containing: raw and processed data files; MATLAB
 functions for parameter estimation; and MATLAB functions for the
 generation of power law random walks. The README file provides additional
 information about these folders and the files contained
 within.supplementary
 data.zip
DOI: 10.5061/dryad.63f26
title: Data from: Genetic evolution, plasticity and bet-hedging as adaptive responses to temporally autocorrelated fluctuating selection: a quantitative genetic model

description: Adaptive responses to autocorrelated environmental fluctuations through
 evolution in mean reaction norm elevation and slope and an independent
 component of the phenotypic variance is analysed using a quantitative
 genetic model. Analytic approximations expressing the mutual dependencies
 between all three response modes are derived and solved for the joint
 evolutionary outcome. Both genetic evolution in reaction norm elevation
 and plasticity are favored by slow temporal fluctuations, with plasticity,
 in the absence of microenvironmental variability, being the dominant
 evolutionary outcome for reasonable parameter values. For fast
 fluctuations, tracking of the optimal phenotype through genetic evolution
 and plasticity is limited. If residual fluctuations in the optimal
 phenotype are large and stabilizing selection is strong, selection then
 acts to increase the phenotypic variance (bet-hedging adaptive).
 Otherwise, canalizing selection occurs. If the phenotypic variance
 increases with plasticity through the effect of microenvironmental
 variability, this shifts the joint evolutionary balance away from
 plasticity in favor of genetic evolution. If microenvironmental deviations
 experienced by each individual at the time of development and selection
 are correlated, however, more plasticity evolves. The adaptive
 significance of evolutionary fluctuations in plasticity and the phenotypic
 variance, transient evolution, and the validity of the analytic
 approximations are investigated using simulations.
description: mismatch-uv.rR-functions for simulating the process, solving for the joint evolutionary outcome and for generating the different plots in the paper.dryad-examplesExample R-code generating Figs. 1, 2 and 3 in the paper, a contourplot of the joint evolutionary outcome, as well as code solving for the joint evolutionary outcome and simulating the process. Calls the functions in mismatch-uv.r which needs to be in the working directory.
DOI: 10.5061/dryad.5q27k
title: Data from: Local perspectives on environmental insecurity and its influence on illegal biodiversity exploitation

description: Environmental insecurity is a source and outcome of biodiversity declines
 and social conflict. One challenge to scaling insecurity reduction
 policies is that empirical evidence about local attitudes is
 overwhelmingly missing. We set three objectives: determine how local
 people rank risk associated with different sources of environmental
 insecurity; assess perceptions of environmental insecurity, biodiversity
 exploitation, myths of nature and risk management preferences; and explore
 relationships between perceptions and biodiversity exploitation. We
 conducted interviews (N = 88) with residents of Madagascar’s Torotorofotsy
 Protected Area, 2014. Risk perceptions had a moderate effect on
 perceptions of environmental insecurity. We found no effects of
 environmental insecurity on biodiversity exploitation. Results offer one
 if not the first exploration of local perceptions of illegal biodiversity
 exploitation and environmental security. Local people’s perception of risk
 seriousness associated with illegal biodiversity exploitation such as
 lemur hunting (low overall) may not reflect perceptions of policy-makers
 (considered to be high). Discord is a key entry point for attention.
description: Madagascar insecurity
 dataThe data instrument is
 attached to the manuscript file as supplementary information. Michigan
 State University’s Committee on Research Involving Human Subjects IRB#
 x10-394 reviewed and approved all methods and procedures used in this
 research. A committee-approved informed consent was obtained in verbal
 form due to potential participant illiteracy. In instances where
 participants approved use of a digital voice recorder, consent was
 documented digitally. In all instances, participants had to verbally
 consent to participate in the study before data collection
 commenced.Mada2014Dryad.sav
DOI: 10.15468/dl.3wzp47
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Psychroteuthis glacialis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 34 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001233-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t5n3t
title: Data from: Negative effects of pesticides on wild bee communities can be buffered by landscape context

description: Wild bee communities provide underappreciated but critical agricultural
 pollination services. Given predicted global shortages in pollination
 services, managing agroecosystems to support thriving wild bee communities
 is, therefore, central to ensuring sustainable food production. Benefits
 of natural (including semi-natural) habitat for wild bee abundance and
 diversity on farms are well documented. By contrast, few studies have
 examined toxicity of pesticides on wild bees, let alone effects of
 farm-level pesticide exposure on entire bee communities. Whether
 beneficial natural areas could mediate effects of harmful pesticides on
 wild bees is also unknown. Here, we assess the effect of conventional
 pesticide use on the wild bee community visiting apple (Malus domestica)
 within a gradient of percentage natural area in the landscape. Wild bee
 community abundance and species richness decreased linearly with
 increasing pesticide use in orchards one year after application; however,
 pesticide effects on wild bees were buffered by increasing proportion of
 natural habitat in the surrounding landscape. A significant contribution
 of fungicides to observed pesticide effects suggests deleterious
 properties of a class of pesticides that was, until recently, considered
 benign to bees. Our results demonstrate extended benefits of natural areas
 for wild pollinators and highlight the importance of considering the
 landscape context when weighing up the costs of pest management on crop
 pollination services.
description: Data_Park et
 alExcel file containing
 list of orchards surveyed for bees, with environmental, landscape and
 pesticide information included for each farm and collection event.
 Worksheet 2 provides a meta data/notes of each column's
 meaning.