cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.863s0
title: Data from: Segregation of male sterility alleles across a species boundary

description: Hybrid zones may serve as bridges permitting gene flow between species,
 including alleles influencing the evolution of breeding systems. Using
 greenhouse crosses, we assessed the likelihood that a hybrid zone could
 serve as a conduit for transfer of nuclear male-sterility alleles between
 a gynodioecious species and a hermaphroditic species with very rare
 females in some populations. Segregation patterns in progeny of crosses
 between rare females of hermaphroditic Schiedea menziesii and
 hermaphroditic plants of gynodioecious Schiedea salicaria heterozygous at
 the male-sterility locus, and between female S. salicaria and
 hermaphroditic plants from the hybrid zone, were used to determine whether
 male-sterility was controlled at the same locus in the parental species
 and the hybrid zone. Segregations of females and hermaphrodites in
 approximately equal ratios from many of the crosses indicate that the same
 nuclear male-sterility allele occurs in the parent species and the hybrid
 zone. These rare male-sterility alleles in S. menziesii may result from
 gene flow from S. salicaria through the hybrid zone, presumably
 facilitated by wind pollination in S. salicaria. Alternatively, rare
 male-sterility alleles might result from a reversal from gynodioecy to
 hermaphroditism in S. menziesii, or possibly de novo evolution of male
 sterility. Phylogenetic analysis indicates that some species of Schiedea
 have probably evolved separate sexes independently, but not in the lineage
 containing S. salicaria and S. menziesii. High levels of selfing and
 expression of strong inbreeding depression in S. menziesii, which together
 should favour females in populations, argue against a reversal from
 gynodioecy to hermaphroditism in S. menziesii.
description: DryadFile shows segregations
 of sex phenotypes from crosses between two species and a hybrid
 zone
DOI: 10.5061/dryad.h7k26
title: Data from: Combined effects of night warming and light pollution on predator-prey interactions

description: Interactions between multiple anthropogenic environmental changes can
 drive non-additive effects in ecological systems, and the non-additive
 effects can in turn be amplified or dampened by spatial covariation among
 environmental changes. We investigated the combined effects of night-time
 warming and light pollution on pea aphids and two predatory ladybeetle
 species. As expected, neither night-time warming nor light pollution
 changed the suppression of aphids by the ladybeetle species that forages
 effectively in darkness. However, for the more-visual predator, warming
 and light had non-additive effects in which together they caused much
 lower aphid abundances. These results are particularly relevant for
 agriculture near urban areas that experience both light pollution and
 warming from urban heat islands. Because warming and light pollution can
 have non-additive effects, predicting their possible combined consequences
 over broad spatial scales requires knowing how they co-occur. We found
 that night-time temperature change since 1949 covaried positively with
 light pollution, which has the potential to increase their non-additive
 effects on pea aphid control by 70% in US alfalfa. Our results highlight
 the importance of non-additive effects of multiple environmental factors
 on species and food webs, especially when these factors co-occur.
description: Miller et al data
 ProcBData on aphid abundances
 and lady beetle predationMiller data
 ProcB.xlsx
DOI: 10.5061/dryad.r5f30
title: Data from: Avoidable errors in the modeling of outbreaks of emerging pathogens, with special reference to Ebola

description: As an emergent infectious disease outbreak unfolds, public health response
 is reliant on information on key epidemiological quantities, such as
 transmission potential and serial interval. Increasingly, transmission
 models fit to incidence data are used to estimate these parameters and
 guide policy. Some widely used modelling practices lead to potentially
 large errors in parameter estimates and, consequently, errors in
 model-based forecasts. Even more worryingly, in such situations,
 confidence in parameter estimates and forecasts can itself be far
 overestimated, leading to the potential for large errors that mask their
 own presence. Fortunately, straightforward and computationally inexpensive
 alternatives exist that avoid these problems. Here, we first use a
 simulation study to demonstrate potential pitfalls of the standard
 practice of fitting deterministic models to cumulative incidence data.
 Next, we demonstrate an alternative based on stochastic models fit to raw
 data from an early phase of 2014 West Africa Ebola virus disease outbreak.
 We show not only that bias is thereby reduced, but that uncertainty in
 estimates and forecasts is better quantified and that, critically, lack of
 model fit is more readily diagnosed. We conclude with a short list of
 principles to guide the modelling response to future infectious disease
 outbreaks.
description: Model and
 dataConstructs the pomp
 object encoding the model and the data.ebola.RSimulation studyThese codes perform the simulation study described in the text.simstudy.RParameter estimationThese codes estimate for the model from the data in Sierra Leone, Guinea, and Liberia, as well as for the regional aggregation ("West Africa").profiles.RDiagnosticsThese codes compute various diagnostics on the fitted models.diagnostics.RForecasting codesThese codes compute the forecasts described in the text.forecasts.R
DOI: 10.5061/dryad.pf420
title: Data from: Onset of autumn shapes the timing of birth in Pyrenean chamois more than onset of spring

description: 1. In seasonal environments, birth dates are a central component for a
 species’ life history, with potential long-term fitness consequences. Yet
 our understanding of selective pressures of environmental changes on birth
 dates is limited in wild mammals due to the difficulty of data collection.
 In a context of rapid climate change, the question of a possible mismatch
 between plant phenology and birth phenology also remains unanswered for
 most species. 2. We assessed whether and how the timing of birth in a
 mountain mammal (isard, Rupicapra pyrenaica) tracked changes in plant
 growing season, accounting for maternal traits, individual heterogeneity,
 and population density. We not only focused on spring conditions but also
 assessed to what extent onset of autumn can be a driver of phenological
 biological events and compared the magnitude of the response to the
 magnitude of the environmental changes. We relied on a 22-year study based
 on intensively monitored marked individuals of known age. 3. Births were
 highly synchronized (80% of kids born within 25 days) and highly
 repeatable (84%; among-females variation of 9.6 days, withinfemale
 variation of 4.2 days). Individual phenotypic plasticity allows females to
 respond rapidly to inter-annual changes in plant phenology but did not
 prevent the existence of a mismatch: a 10-day advance in the autumn or
 spring plant phenology led to 3.9 and 1.3 days advance in birth dates,
 respectively. 4. Our findings suggest that plant phenology may act as a
 cue to induce important stages of the reproductive cycle (e.g., conception
 and gestation length), subsequently affecting parturition dates, and
 stressed the importance of focusing on long-term changes during spring for
 which females may show much lower adaptive potential than during autumn.
 These results also question the extent to which individual plasticity
 along with high heterogeneity among individuals will allow species to cope
 with demographic consequences of climate changes.
description: Births_isardDataset collected from a long-term monitoring of individually marked female isard. For details regarding variables included see Table 1. For more details and use, please contact the authors.birth_isard.csv
DOI: 10.5061/dryad.04s6s
title: Data from: Diagnostic accuracy study of an oscillometric ankle-brachial index in peripheral arterial disease: the influence of oscillometric errors and calcified legs

description: Background. Peripheral arterial disease (PAD) is an indicator of
 widespread atherosclerosis. However, most individuals with PAD, in spite
 of being at high cardiovascular risk, are asymptomatic. This fact,
 together with the limitations of the Doppler ankle-brachial index (ABI),
 contributes to PAD underdiagnose. The aim of this study was to compare
 oscillometric ABI and Doppler ABI to diagnose peripheral arterial disease,
 and also to examine the influence of oscillometric errors and calcified
 legs on the PAD diagnoses. Methods and Findings. We measured the
 ankle-brachial indexes of 90 volunteers (n = 180 legs, age 70 ± 14 years,
 43% diabetics) using both oscillometer OMRON-M3 and Doppler. For
 concordance analyses we used the Bland and Altman method, and also
 estimated the intraclass correlation coefficient. Receiver Operating
 Characteristic Curves were used to examine the diagnostic performance of
 both methods. The ABI means were 1.06 ± 0.14 and 1.04 ± 0.16 (p = 0.034)
 measured by oscillometer and Doppler ABIs respectively, with limits of
 agreement of ± 0.20 and intraclass correlation coefficient = 0.769.
 Oscillometer yielded 23 "error" measurements, and also
 overestimated the measurements in low ankle pressures. Using Doppler as
 gold standard, oscillometer performance for diagnosis of PAD showed an
 Area Under Curve = 0.944 (sensitivity: 66.7%, specificity: 96.8%).
 Moreover, when considered calcified legs and oscillometric
 "error" readings as arteriopathy equivalents, sensitivity rose
 to 78.2%, maintaining specificity in 96%. The best oscillometer cut-off
 point was 0.96 (sensitivity: 87%, specificity: 91%, positive likelihood
 ratio: 9.66 and negative likelihood ratio: 0.14). Conclusion. Despite its
 limitations, oscillometric ABI could be a useful tool for the diagnosis of
 PAD, particularly when considering calcified legs and oscillometric
 "errors" readings as peripheral arterial disease equivalents.
description: Ankle Brachial Index
 Plos OneData file has two pages.
 1Read_me contains an explanation about the data. Hoja2 contains data with
 self-explanatory titles.
DOI: 10.5061/dryad.r86n4
title: Data from: Genetic evidence of hybridization between the critically endangered Cuban crocodile and the American crocodile: implications for population history and in situ/ex situ conservation

description: Inter-specific hybridization may be especially detrimental when one
 species is extremely rare and the other is abundant owing to the potential
 for genetic swamping. The Cuban crocodile (Crocodylus rhombifer) is a
 critically endangered island endemic largely restricted to Zapata Swamp,
 where it is sympatric with the widespread American crocodile (C. acutus).
 An on-island, C. rhombifer captive breeding program is underway with the
 goals of maintaining taxonomic integrity and providing a source of
 individuals for reintroduction, but its conservation value is limited by
 lack of genetic information. Here we collected mtDNA haplotypic and
 nuclear genotypic data from wild and captive C. rhombifer and C. acutus in
 Cuba to: (1) investigate the degree of inter-specific hybridization in
 natural (in situ) and captive (ex situ) populations; (2) quantify the
 extent, distribution and in situ representation of genetic variation ex
 situ; and (3) reconstruct founder relatedness to inform management. We
 found high levels of hybridization in the wild (49.1%) and captivity
 (16.1%), and additional evidence for a cryptic lineage of C. acutus in the
 Antilles. We detected marginally higher observed heterozygosity and
 allelic diversity ex situ relative to the wild population, with captive C.
 rhombifer exhibiting over twice the frequency of private alleles. Although
 mean relatedness was high in captivity, we identified 37 genetically
 important individuals that possessed individual mean kinship (MK) values
 lower than the population MK. Overall, these results will guide long-term
 conservation management of Cuban crocodiles for maintaining the genetic
 integrity and viability of this species of high global conservation value.
description: CubanCroc_Heredity_DRYAD
DOI: 10.5061/dryad.jm361
title: Data from: Is population structure in the European white stork determined by flyway permeability rather than translocation history?

description: European white stork are long considered to diverge to eastern and western
 migration pools as a result of independent overwintering flyways. In
 relatively recent times, the western and northern distribution has been
 subject to dramatic population declines and country-specific extirpations.
 A number of independent reintroduction programs were started in the mid
 1950s to bring storks back to historical ranges. Founder individuals were
 sourced opportunistically from the Eastern and Western European
 distributions and Algeria, leading to significant artificial mixing
 between eastern and western flyways. Here we use mitochondrial and
 microsatellite DNA to test the contention that prior to translocation,
 eastern and western flyways were genetically distinct. The data show a
 surprising lack of structure at any spatial or temporal scale suggesting
 that even though birds were moved between flyways, there is evidence of
 natural mixing prior to the onset of translocation activities. Overall a
 high retention of genetic diversity, high Nef, and an apparent absence of
 recent genetic bottleneck associated with early 20th century declines
 suggest that the species is well equipped to respond to future
 environmental pressures.
description: DRYAD stork microsat
 data
DOI: 10.5061/dryad.650fk
title: Data from: The importance of species identity and interactions on multifunctionality depends on how ecosystem functions are valued

description: Studies investigating how biodiversity affects ecosystem functioning
 increasingly focus on multiple functions measured simultaneously
 (‘multifunctionality’). However, few such studies assess the role of
 species interactions, particularly under alternative environmental
 scenarios, despite interactions being key to ecosystem functioning. Here
 we address five questions of central importance to ecosystem
 multifunctionality using a terrestrial animal system: 1) Does the
 contribution of individual species differ for different ecosystem
 functions?; 2) Do inter-species interactions affect the delivery of single
 functions and multiple functions?; 3) Does the community composition which
 maximises individual functions also maximise multifunctionality?; 4) Is
 the functional role of individual species, and the effect of interspecific
 interactions, modified by changing environmental conditions?; and 5) How
 do these roles and interactions change under varying scenarios where
 ecosystem services are weighted to reflect different societal preferences?
 We manipulated species’ relative abundance in dung beetle communities and
 measured 16 functions contributing to dung decomposition, plant
 productivity, nutrient recycling, reduction of greenhouse gases, and
 microbial activity. Using the Multivariate Diversity-Interactions
 framework, we assessed how changes in species identity, composition, and
 interspecific interactions affected these functions in combination with an
 environmental driver (increased precipitation). This allowed us to
 identify key species and interactions across multiple functions. We then
 developed a Desirability Function Approach to examine how individual
 species and species mixtures contribute to a desired state of overall
 ecosystem functioning. Species contributed unequally to individual
 functions, and to multifunctionality, and individual functions were
 maximised by different community compositions. Moreover, the species and
 interactions important for maintaining overall multifunctionality depended
 on the weight given to individual functions. This combination of
 methodological approaches allows us to resolve the interactions and
 indirect effects among species that drive ecosystem functioning, revealing
 how multiple aspects of biodiversity can simultaneously drive ecosystem
 functioning. Optimal multifunctionality is therefore context-dependent,
 and is sensitive to the valuation of services. Our results highlight the
 importance of a multifunctionality perspective for complete assessment of
 species’ functional contributions.
description: Data_Dyrad_Slade_et_al_EcologySee README fileSAS code for Slade_Kirwan et al_EcologySAS code for analyses
DOI: 10.5061/dryad.14k55m8
title: Data from: Pheromone-induced accuracy of nestmate recognition in carpenter ants: simultaneous decrease of Type I and Type II errors

description: The ecological and evolutionary success of social insects relies on their
 ability to efficiently discriminate between group members and aliens.
 Nestmate recognition occurs by phenotype matching, the comparison of the
 referent (colony) phenotype to the one of an encountered individual. Based
 on the level of dissimilarity between the two, the discriminator accepts
 or rejects the target. The tolerated degree of mismatch is predicted by
 the acceptance threshold model, which assumes adaptive threshold shifts
 depending on the costs of discrimination errors. Inherent in the model is
 that rejection (Type I) and acceptance (Type II) errors are reciprocally
 related: if one type decreases, the other increases. We studied whether
 alarm pheromones modulate the acceptance threshold. We exposed Camponotus
 aethiops ants to formic acid and subsequently measured aggression towards
 nestmates and non-nestmates. Formic acid induced both more non-nestmate
 rejection and more nestmate acceptance than a control treatment, thus
 uncovering an unexpected effect of an alarm pheromone on responses to
 nestmates. Nestmate discrimination accuracy was improved via a decrease of
 both types of errors, a result that cannot be explained by a shift in the
 acceptance threshold. We propose that formic acid increases the amount of
 information available to the ants, thus decreasing the perceived
 phenotypic overlap between nestmate and non-nestmate recognition cues.
 This mechanism for improved discrimination reveals a novel function of
 alarm pheromones in recognition processes and may have far-reaching
 implications in our understanding of the modus operandi of recognition
 systems in general.
description: Original
 dataBORIS software was used
 to extract the occurrence and duration of aggressive behaviors in
 Experiment 2: one-to-two encounters.
DOI: 10.5061/dryad.854g1
title: Data from: Morphological and colour morph clines along an altitudinal gradient in the meadow grasshopper Pseudochorthippus parallelus

description: Many animals show altitudinal clines in size, shape and body colour.
 Increases in body size and reduction in the length of body appendices in
 colder habitats are usually attributed to improved heat conservation at
 lower surface-to-volume ratios (known as Bergmann's and Allen's
 rule, respectively). However, the patterns are more variable and sometimes
 reversed in small ectotherms that are affected by shortened growing
 seasons. Altitude can also affect colouration. The thermal melanism
 hypothesis predicts darker colours under cooler conditions because of a
 thermoregulatory advantage. Darker colours may also be favoured at high
 altitudes for reasons of UV protection or habitat-dependent crypsis. We
 studied altitudinal variation in morphology and colour in the
 colour-polymorphic meadow grasshopper Pseudochorthippus parallelus based
 on 563 individuals from 17 populations sampled between 450 and 2,500 m
 asl. Pronotum length did not change with altitude, while postfemur length
 decreased significantly in both sexes. Tegmen (forewing) length decreased
 in males, but not in females. The results indicate that while body size,
 as best quantified by pronotum length, was remarkably constant, extended
 appendices were reduced at high altitudes. The pattern thus follows
 Allen's rule, but neither Bergmann's nor converse
 Bergmann's rule. These results indicate that inference of converse
 Bergmann's rule based on measurements from appendices should be
 treated with some caution. Colour morph ratios showed significant changes
 in both sexes from lowland populations dominated by green individuals to
 high-altitude populations dominated by brown ones. The increase of brown
 morphs was particularly steep between 1,500 and 2,000 m asl. The results
 suggest shared control of colour in males and females and local adaptation
 along the altitudinal gradient following the predictions of the thermal
 melanism hypothesis. Interestingly, both patterns, the reduction of body
 appendices and the higher frequency of brown individuals, may be explained
 by a need for efficient thermoregulation under high-altitude conditions.
description: Data on sampling
 sitesThe tab separated file
 contains sampling site information. The data is the same as in Table 1 of
 the manuscript.ParallelusSites.txtData on individualsThe tab separated file contains information sex, morphology and morph identity of all individuals recording in the Nadig collection. Each row represents a single individual.ParallelusIndividuals.txt