cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3bn27
title: Data from: Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture recapture data

description: 1.Temporary migration – where individuals can leave and re-enter a sampled
 population – is a feature of many capture–mark–recapture (CMR) studies of
 mobile populations which, if unaccounted for, can lead to biased estimates
 of population capture probabilities and consequently biased estimates of
 population abundance. 2. We present a method for incorporating
 radiotelemetry data within a CMR study to eliminate bias due to temporary
 migration using a Bayesian state-space model. 3. Our results indicate that
 using a relatively small number of telemetry tags, it is possible to
 greatly reduce bias in estimates of capture probabilities using telemetry
 data to model transition probabilities in and out of the sampling area. In
 a capture–recapture data set for trout Cod in the Murray river, Australia,
 accounting for temporary migration led to overall higher estimates of
 capture probabilities than models assuming permanent or zero migration.
 Also, individual heterogeneity in detectability can be managed through
 explicit modelling. We show how accounting for temporary migration when
 estimating capture probabilities can be used to estimate the abundance and
 size distribution of a population as though it were closed. 4. Our model
 provides a basis for more complex models that might integrate telemetry
 data into other CMR scenarios, thus allowing for greater precision in
 estimates of vital rates that might otherwise be biased by temporary
 migration. Our results highlight the importance of accounting for
 migration in survey design and parameter estimation, and the potential
 scope for supplementing large-scale CMR data sets with a subset of
 auxiliary data that provide information on processes that are hidden to
 primary sampling processes.
description: Data from: Estimating
 population size in the presence of temporary migration using a joint
 analysis of telemetry and capture recapture dataThe file Data.R is a
 script file that will build Capture recapture matrices over 6 years of
 sampling in the Murray River, Australis. The first part of the script
 provides the raw data, which are then processed into matrices for use in
 the CMR model.Data.R
DOI: 10.5061/dryad.1m104
title: Data from: Differential selection between the sexes and selection for sex

description: Anisogamy is known to generate an important cost for sexual reproduction
 (the famous "twofold cost of sex"). However, male-female
 differences may have other consequences on the evolution of sex, due to
 the fact that selective pressures may differ among the sexes. On the one
 hand, intralocus sexual conflict should favor asexual females, which can
 fix female-beneficial, male-detrimental alleles. On the other hand, it has
 been suggested repeatedly that sexual selection among males may help to
 purge the mutation load, providing an advantage to sexual females.
 However, no analytical model has computed the strength of selection acting
 on a modifier gene affecting the frequency of sexual reproduction when
 selection differs between the sexes. In this paper we analyze a two-locus
 model using two approaches: a QLE analysis and a local stability analysis,
 whose predictions are verified using a multilocus simulation. We find that
 costly sex can be maintained when selection is stronger in males than in
 females, but acts in the same direction in both. Complete asexuality,
 however, evolves under any other form of selection. Finally, we discuss
 how experimental measurements of fitness variances and covariances between
 sexes could be used to determine the overall direction and strength on
 selection for sex arising from differences in selection between males and
 females.
description: C++
 programC++ simulation program
 for evolution of sex with differences in selection in males and
 femalesprogram.tar
DOI: 10.5061/dryad.9m0f7
title: Data from: Male-male aggression is unlikely to stabilize a poison frog polymorphism

description: Phenotypic polymorphism is common in animals, and the maintenance of
 multiple phenotypes in a population requires forces that act against
 homogenizing drift and selection. Male-male competition can contribute to
 the stability of a polymorphism when males compete primarily with males of
 the same phenotype. In and around a contact zone between red and blue
 lineages of the poison frog Oophaga pumilio, we used simulated territorial
 intrusions to test the non-exclusive predictions that males would direct
 more aggression toward males of (i) their own phenotype and/or (ii) the
 phenotype that is most common in their population. Males in the
 monomorphic red and blue populations that flank the contact zone were more
 aggressive toward simulated intruders that matched the local coloration.
 However, males in the two polymorphic populations biased aggression toward
 neither their own color nor the color most common in their population. In
 sympatry, the rarer color morph gains no advantage via reduced male-male
 aggression from territorial males in these O. pumilio populations, and so
 male aggression seems unlikely to stabilize color polymorphism on its own.
 More broadly, these results suggest that the potential for divergent male
 aggression biases to maintain phenotypic diversity depends on the
 mechanism(s) that generate the biases and the degree to which these
 mechanisms persist in sympatry.
description: Yang_JEB_ESM_StatAnalysisR markdown document (.Rmd) of all analyses described in the manuscript. Necessary descriptions of the variables and statistical details are included in the commentsYang_JEB_ESM_rawdataRaw data file for input to the R markdown document
DOI: 10.5061/dryad.j182q
title: Data from: Unraveling conflicting density- and distance-dependent effects on plant reproduction using a spatially-explicit approach

description: 1. Density- and distance-dependent (DDD) mechanisms are important
 determinants of plant reproductive success (PRS). Different components of
 sequential PRS can operate either in the same or in different directions
 and thus reinforce or neutralize each other, and they may also operate at
 different spatial scales. Thus, spatially-explicit approaches are needed
 to detect such complex DDD effects across multiple PRS components and
 spatial scales. 2. To reveal DDD effects of different components of early
 PRS of the Iberian pear (Pyrus bourgaeana) sampled over three consecutive
 years, we used marked point pattern analysis. Our special interest is to
 identify conflicting processes that regulate populations at different
 spatial scales, e.g. whether DDD on fruit initiation and on fruit
 development acted in opposite directions. To evaluate the significance of
 observed mark correlation functions based on empirical data (e.g. fruiting
 success) we compared them to expectations given by spatially-explicit null
 models. 3. Diverse DDD processes affected several aspects of PRS in a
 variable extent over the three seasons. First, early fruit set was higher
 for individuals with more neighbors at small distances (i.e. up to 40m).
 However, late P. bourgaeana fruit set decreased with increasing number of
 nearby neighbors, but these effects canceled for overall fruit set that
 did not show DDD effects. Second, the absolute number of fruits produced
 (crop sizes) by trees showed positive density dependence in 2011 and 2012
 but not in 2013. Finally, the total number of seeds produced did not show
 DDD effects, indicating that conflicting demographic processes can disrupt
 the initial spatial pattern of tree investment in reproduction. 4.
 Synthesis: Understanding complex spatial effects of density- and
 distance-dependent (DDD) processes requires dissection of component
 processes to attain the complete picture since contrasting DDD processes
 may be hidden behind a single cumulative measure of reproductive success.
 The combination of novel and classic mark correlation functions used here
 constitute a powerful spatially-explicit tool that can be broadly applied
 to unravel conflicting mechanisms of DDD regulating the persistence of
 sessile organisms at a range of spatial scales. Our findings help to
 explain why some authors failed to find expected DDD of PRS and highlight
 the importance of detailed multi-year field studies on plant reproductive
 success.
description: crop
 sizesThis file contains data
 concerning tree location and crop size during 2011, 2012, and
 2013.fruit
 initiationThis file contains data
 concerning tree locations and fruit initiation successes during 2012 and
 2013.fruit
 developmentThis files contains data
 concerning tree locations and fruiting development successes during 2011,
 2012, and 2013.seed set
 2011This file contains data
 on tree locations and total seed number per tree during
 2011.
DOI: 10.5061/dryad.p2k02
title: Data from: Field evidence for a rapid adaptive plastic response in morphology and growth of littoral and pelagic brook charr: a reciprocal transplant experiment

description: 1. Phenotypic plasticity, a process by which individuals modify their
 morphology, physiology, or behaviour in response to environmental changes,
 can be seen as the first step in adaptive evolution. Phenotypic plasticity
 is adaptive if two conditions are met: (i) the phenotype is associated
 with an environment (plastic response) and (ii) the phenotype–environment
 association increases individual fitness (adaptive response). 2. Using a
 reciprocal transplant experiment, we tested the hypothesis that functional
 morphological responses are correlated with growth at two organizational
 levels (between and within ecotypes) in brook charr. 3. Four-month-old
 individuals from four littoral and four pelagic families raised in the
 laboratory were transferred into eight littoral (3 m × 4 m × 1.5 m depth)
 and eight pelagic (3 m × 4 m × 6 m depth) lake enclosures for a period of
 12 weeks. 4. Fin length (the main discriminant trait of the littoral and
 pelagic ecotypes) was less plastic than body shape. Growth was higher in
 the pelagic than in the littoral habitat, but offspring from littoral and
 pelagic parental origins did not experience higher growth in their
 respective habitats (comparison between ecotypes). The body shape of most
 individuals transplanted to their reciprocal environment shifted toward
 the form expected in that environment. This plastic response in body shape
 was functionally correlated with growth within ecotypes, but only in the
 littoral habitat. Furthermore, the within-ecotype variance of both
 morphological traits and growth were higher in the littoral than in the
 pelagic habitat. 5. Small phenotypic differences could have direct
 consequences on fitness in the less favourable habitat, inducing higher
 inter-individual variance in growth and stronger phenotype–growth
 associations. We suggest that phenotypic accommodation and cryptic genetic
 variation, two mechanisms previously proposed as mechanisms involved in
 distinct situations, could be simultaneously involved to hasten the
 process of adaptive evolution in an unfavourable environment.
description: Pepino_et_al_Original_Data
DOI: 10.5061/dryad.529p4
title: Data from: The role of isoforms in the evolution of cryptic coloration in Peromyscus mice

description: A central goal of evolutionary biology is to understand the molecular
 mechanisms underlying phenotypic adaptation. While the contribution of
 protein-coding and cis-regulatory mutations to adaptive traits has been
 well documented, additional sources of variation – such as the production
 of alternative RNA transcripts from a single gene, or isoforms – have been
 understudied. Here, we focus on the pigmentation gene Agouti, known to
 express multiple alternative transcripts, to investigate the role of
 isoform usage in the evolution of cryptic colour phenotypes in deer mice
 (genus Peromyscus). We first characterize the Agouti isoforms expressed in
 the Peromyscus skin and find two novel isoforms not previously identified
 in Mus. Next, we show that a locally adapted light-coloured population of
 P. maniculatus living on the Nebraska Sand Hills shows an upregulation of
 a single Agouti isoform, termed 1C, compared with their ancestral
 dark-coloured conspecifics. Using in vitro assays, we show that this
 preference for isoform 1C may be driven by isoform-specific differences in
 translation. In addition, using an admixed population of wild-caught mice,
 we find that variation in overall Agouti expression maps to a region near
 exon 1C, which also has patterns of nucleotide variation consistent with
 strong positive selection. Finally, we show that the independent evolution
 of cryptic light pigmentation in a different species, P. polionotus, has
 been driven by a preference for the same Agouti isoform. Together, these
 findings present an example of the role of alternative transcript
 processing in adaptation and demonstrate molecular convergence at the
 level of isoform regulation.
description: dataaccessibility_FINAL
DOI: 10.5061/dryad.r6k64
title: Data from: An unusual new species of Bidens (Asteraceae, Coreopsideae) with its phylogenetic position and taxonomic notes

description: An unusual new species of Bidens (Asteraceae) from Brazil is described and
 its placement within the genus is elucidated by phylogenetic analysis of
 ITS sequences. The new species, described as Bidens campanulata , is
 distinct in the genus based on its broadly campanulate corolla limb with
 long lobes, an extremely reduced involucre (shorter than the flower
 length), and the absence of awns on the pappus. This study presents a
 taxonomic treatment of the species of Bidens with discoid capitula endemic
 to the Brazilian Cerrado, including a key to the species, typification,
 and information on conservation status.
description: Concat_FEB-2016 (ITS
 1+2)This is an alignment
 matrix of ITS sequences of Coreopsideae (Compositae). Three new sequences
 are new and the other ones were gotten from Genbank. The 5.8 part of ITS
 was excluded from the alignment.BayConcat FEB (ITS 1-2)
 conBayesian consensus tree
 (50 % majority rule) from the analysis with ITS data of Bidens and closely
 related outgroups.PAUP 2 Concat_FEB-2016
 (ITS 1+2)Phylogram of strict
 consensus of 1260 most parsimonious trees based on ITS data matrix,
 showing the relationship of the new species described and closely related
 groups of Coreopsideae
DOI: 10.5061/dryad.cb060
title: Data from: Physiological effects of temperature do not explain prevalence of females in populations of gynodioecious Lobelia siphilitica growing in warmer climates

description: PREMISE OF THE STUDY: Gynodioecy is a sexual polymorphism whereby female
 and hermaphroditic plants co-occur within populations. In many
 gynodioecious species, stressful abiotic environments are associated with
 higher frequencies of females. This association suggests that abiotic
 stress affects the relative fitness of females and hermaphrodites and,
 thus, the maintenance of gynodioecy. METHODS:To test whether abiotic
 stress affects the fitness of females and hermaphrodites, we grew
 open-pollinated Lobelia siphilitica families in temperature regimes
 characteristic of the southern portion of the species' range (where
 females are common) and the northern portion of the range (where females
 are rare). We measured physiological and phenological traits that are
 indicative of heat stress, and fitness components of females and
 hermaphrodites that could affect the maintenance of gynodioecy. KEY
 RESULTS:Contrary to expectations if growth at high temperatures is
 stressful, we found that the hot treatment increased leaf chlorophyll
 content, decreased the percentage of plants that delayed flowering
 initiation, and did not affect the quantum efficiency of photosystem II.
 Growth at high temperatures did not affect the magnitude of the difference
 in rosette size (a correlate of flower number) between females and
 hermaphrodites, or the variance in pollen viability among hermaphrodites.
 CONCLUSIONS:We found that growing-season temperatures typical of high
 female L. siphilitica populations were not stressful and did not affect
 either the fitness of females compared to hermaphrodites or variation in
 fitness among hermaphrodites. Consequently, further research is necessary
 to explain correlations between abiotic environmental factors and the
 frequency of females in this and other gynodioecious species.
description: Bailey, Case, Caruso
 (2017) AJBphysiological data for
 lab-grown plants under different temperature regimesDryad
 submission.xlsx
DOI: 10.5061/dryad.hg686
title: Data from: Despite reproductive interference, the net outcome of reproductive interactions among spider mite species is not necessarily costly

description: Reproductive interference is considered a strong ecological force,
 potentially leading to species exclusion. This supposes that the net
 effect of reproductive interactions is strongly negative for one, or both,
 of the species involved. Testing this requires a comprehensive analysis of
 interspecific reproductive interactions, accounting for the order and
 timing of mating events, and for their effects on either fertility or
 fecundity. To this aim, we measured reproductive interactions among spider
 mites, using a focal species, Tetranychus urticae, and an invasive
 (T.evansi) and a resident (T. ludeni) species, varying the mating sequence
 and interval, and measuring the effect of such crosses on fecundity and
 offspring sex ratio (a measure of fertility, as these species are
 haplodiploid). We found that mating with heterospecifics affected
 fecundity and sex ratio negatively, but also positively, depending on the
 species involved, and on the order and timing of mating events. Overall,
 the net effect of reproductive interactions was weak despite strong
 effects of particular events. In natural situations, the outcome of
 reproductive interactions will thus hinge upon the frequency of each
 event.
description: Clemente-et-al_Data_BEHECO-2017-0362Excel file with 10 datasets corresponding to the analysis presented and described in the manuscript. A legend is provided.
DOI: 10.5061/dryad.mn652
title: Data from: Interspecific competition alters leaf stoichiometry in 20 grassland species

description: The extensive use of traits in ecological studies over the last few
 decades to predict community functions has revealed that plant traits are
 plastic and respond to various environmental factors. These plant traits
 are assumed to predict how plants compete and capture resources. Variation
 in stoichiometric ratios both within and across species reflects resource
 capture dynamics under competition. However, the impact of local plant
 diversity on species-specific stoichiometry remains poorly studied. Here,
 we analyze how spatial and temporal diversity in resource-acquisition
 traits affects leaf elemental stoichiometry of plants (i.e., the result of
 resource capture) and how flexible this stoichiometry is depending on the
 functional composition of the surrounding community. Therefore, we
 assessed inter- and intraspecific variations of leaf carbon (C), nitrogen
 (N), and phosphorus (P) (and their ratios) of 20 grassland species in a
 large trait-based plant diversity experiment located in Jena (Germany) by
 measuring leaf elemental concentrations at the species-level along a
 gradient in plant trait dissimilarity. Our results show that plants showed
 large intra- and interspecific variation in leaf stoichiometry, which was
 only partly explained by the functional group identity (grass or herb) of
 the species. Elemental concentrations (N, P, but not C) decreased with
 plant species richness, and species tended to become more deviant from
 their monoculture stoichiometry with increasing trait dissimilarity in the
 community. These responses differed among species, some consistently
 increased or decreased in P and N concentrations; for other species, the
 negative or positive change in P and N concentrations increased with
 increasing trait difference between the target species and the remaining
 community. The strength of this relationship was significantly associated
 to the relative position of the species along trait gradients related to
 resource acquisition. Trait-difference and trait-diversity thus were
 important predictors of how species’ resource capture changed in
 competitive neighbourhoods.
description: Data on plant
 stoichiometry from Jena Trait-based experimentThe data set contains
 the lemental composition of plants in the Jena trait-based experiment,
 including derived variables. The columns are explained in the read me
 file.guiz
 data.xlsx
DOI: 10.5061/dryad.975m1
title: Data from: The interaction between predation risk and food ration on behavior and morphology of Eurasian perch

description: Both the risk of predation and food level have been shown to affect
 phenotypic development of organisms. However, these two factors also
 influence animal behavior that in turn may influence phenotypic
 development. Hence, it might be difficult to disentangle the behavioral
 effect from the predator or resource level effects. This is because the
 presence of predators and high resource levels usually results in a lower
 activity, which in turn affects energy expenditure that is used for
 development and growth. It is therefore necessary to study how behavior
 interacts with changes in body shape with regard to resource density and
 predators. Here, we use the classic predator induced morphological defense
 in fish to study the interaction between predator cues, resource
 availability and behavioral activity with the aim to determine their
 relative contribution to changes in body shape. We show that all three
 variables; the presence of a predator, food level and activity, both
 additively and interactively, affected the body shape of perch. In
 general, the presence of predators, lower swimming activity and higher
 food levels induced a deep body shape, with predation and behavior having
 similar effect and food treatment the smallest effect. The shape changes
 seemed to be mediated by changes in growth rate since body condition
 showed a similar effect as shape with regard to food level and predator
 treatments. Our results suggests that shape changes in animals to one
 environmental factor, for example predation risk, can be context
 dependent, and depend on food levels or behavioral responses. Theoretical
 and empirical studies should further explore how this context dependence
 affect fitness components such as resource gain and mortality and their
 implications for population dynamics.
description: behavioral
 databehavioral data from the
 start and the end of the experimentdigitized
 landmarkslandmark data on each
 individual perch at the end of the experimentindividual
 dataindividual length and
 weight data at the end of the experiment