cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.51g4t
title: Data from: Exploring the hidden landscape of female preferences for complex signals

description: A major challenge in evolutionary biology is explaining the origins of
 complex phenotypic diversity. In animal communication, complex signals may
 evolve from simpler signals because novel signal elements exploit
 preexisting biases in receivers’ sensory systems. Investigating the shape
 of female preference functions for novel signal characteristics is a
 powerful, but underutilized, method to describe the adaptive landscape
 potentially guiding complex signal evolution. We measured female
 preference functions for characteristics of acoustic appendages added to
 male calling songs in the grasshopper Chorthippus biguttulus, which
 naturally produces only simple songs. We discovered both hidden
 preferences for and biases against novel complex songs, and identified
 rules governing song attractiveness based on multiple characteristics of
 both the base song and appendage. The appendage's temporal position
 and duration were especially important: long appendages preceding the song
 often made songs less attractive, while following appendages were neutral
 or weakly attractive. Appendages had stronger effects on songs of shorter
 duration, but did not restore the attractiveness of very unattractive
 songs. We conclude that sensory biases favor, within predictable limits,
 the evolution of complex songs in grasshoppers. The function-valued
 approach is an important tool in determining the generality of these
 limits in other taxa and signaling modalities.
description: Female Response
 dataRaw data of female
 response to each stimulusData.txtStimulus ListList of the experimental stimuli with a short description. Stimulus numbers correspond to stimulus ID in "Data.txt" file. See ReadMe for further details.StimulusList.txt
DOI: 10.5061/dryad.mn36c
title: Data from: Information use and resource competition: an integrative framework

description: Organisms may reduce uncertainty regarding how best to exploit their
 environment by collecting information about resource distribution. We
 develop a model to demonstrate how competition can facilitate or constrain
 an individual’s ability to use information when acquiring resources. Since
 resource distribution underpins both selection on information use and the
 strength and nature of competition between individuals, we demonstrate
 interdependencies between the two that should be common in nature.
 Individuals in our model can search for resources either personally or by
 using social information. We explore selection on social information use
 across a comprehensive range of ecological conditions, generalising the
 producer-scrounger framework to a wide diversity of taxa and resources. We
 show that resource ecology – defined by scarcity, depletion rate, and
 monopolisability – determines patterns of individual differences in social
 information use. These differences suggest co-evolutionary processes
 linking dominance systems and social information use, with implications
 for the evolutionary demography of populations.
description: Mean group-level
 scrounging probabilitiesMean group-level
 scrounging probabilities (column 5) for different, fixed values of N
 (column 1), a/F (column 2), c (column 3), and lambda (column 4). Data
 generated in R, representing numerical approximations of analytical
 solutions provided in manuscript.mean_tactic_group_level.csvMean individual-level scrounging probabilities and relative fitnessMean probabilities of scrounging behaviour (column 8), amount of resource consumed (column 7), and relative fitness (see manuscript for definition) (column 6) for individuals of different social ranks (column 5) across different fixed values of N (column 1), a/F (column 2), c (column 3) and lambda (column 4). Data generated in R. Probabilities, consumption rates, and fitnesses are computational approximations of analytical solutions provided in manuscript.means_individual_level.csv
DOI: 10.5061/dryad.q5rs8
title: Data from: Comanaging fresh produce for nature conservation and food safety

description: Fresh produce has become the primary cause of foodborne illness in the
 United States. A widespread concern that wildlife vector foodborne
 pathogens onto fresh produce fields has led to strong pressure on farmers
 to clear noncrop vegetation surrounding their farm fields. We combined
 three large datasets to demonstrate that pathogen prevalence in fresh
 produce is rapidly increasing, that pathogens are more common on farms
 closer to land suitable for livestock grazing, and that vegetation
 clearing is associated with increased pathogen prevalence over time. These
 findings contradict widespread food safety reforms that champion
 vegetation clearing as a pathogen mitigation strategy. More generally, our
 work indicates that achieving food safety and nature conservation goals in
 produce-growing landscapes is possible.
description: Pathogen Survey
 DataPlease see read file for
 data file descriptor.Karpetal_DryadData.xlsx
DOI: 10.5061/dryad.574s4
title: Data from: A field test of a model for the stability of androdioecy in the freshwater shrimp, Eulimnadia texana

description: The evolution of hermaphroditism from dioecy is a poorly studied
 transition. Androdioecy (the coexistence of males and hermaphrodites) has
 been suggested as an intermediate step in this evolutionary transition or
 could be a stable reproductive mode. Freshwater crustaceans in the genus
 Eulimnadia have reproduced via androdioecy for 24+ million years and thus
 are excellent organisms to test models of the stability of androdioecy.
 Two related models that allow for the stable maintenance of males and
 hermaphrodites rely on the counterbalancing of three life history
 parameters. We tested these models in the field over three field seasons
 and compared the results to previous laboratory estimates of these three
 parameters. Male and hermaphroditic ratios within years were not well
 predicted using either the simpler original model or a version of this
 model updated to account for differences between hermaphroditic types
 (‘monogenic’ and ‘amphigenic’ hermaphrodites). Using parameter estimates
 of the previous year to predict the next year's sex ratios revealed a
 much better fit to the original relative to the updated version of the
 model. Therefore, counter to expectations, accounting for differences
 between the two hermaphroditic types did not improve the fit of these
 models. At the moment, we lack strong evidence that the long-term
 maintenance of androdioecy in these crustaceans is the result of a
 balancing of life history parameters; other factors, such as
 metapopulation dynamics or evolutionary constraints, may better explain
 the 24+ million year maintenance of androdioecy in clam shrimp.
description: Raw gel
 scoresAllozyme scores for the
 shrimp used in this study.RMES
 dataAllozyme gel data
 transcribed into the RMES format.Monogenics vs
 amphigenicsData used to distinguish
 the monogenic from amphigenic hermaphrodites.Relative male
 survivalPopulation data used to
 calculate relative male survival.Eggs &
 LengthSize and egg number data
 by individual shrimp used to calculate inbreeding
 depression.
DOI: 10.5061/dryad.6jq11
title: Data from: Evolutionary relationships among pollinators and repeated pollinator sharing in sexually deceptive orchids

description: The mechanism of pollinator attraction is predicted to strongly influence
 both plant diversification and the extent of pollinator sharing between
 species. Sexually deceptive orchids rely on mimicry of species-specific
 sex pheromones to attract their insect pollinators. Given that sex
 pheromones tend to be conserved among related species, we predicted that
 in sexually deceptive orchids, (i) pollinator sharing is rare, (ii)
 closely related orchids use closely related pollinators and (iii) there is
 strong bias in the wasp lineages exploited by orchids. We focused on
 species that are pollinated by sexual deception of thynnine wasps in the
 distantly related genera Caladenia and Drakaea, including new field
 observations for 45 species of Caladenia. Specialization was extreme with
 most orchids using a single pollinator species. Unexpectedly, seven cases
 of pollinator sharing were found, including two between Caladenia and
 Drakaea, which exhibit strikingly different floral morphology.
 Phylogenetic analysis of pollinators using four nuclear sequence loci
 demonstrated that although orchids within major clades primarily use
 closely related pollinator species, up to 17% of orchids within these
 clades are pollinated by a member of a phylogenetically distant wasp
 genus. Further, compared to the total diversity of thynnine wasps within
 the study region, orchids show a strong bias towards exploiting certain
 genera. Although these patterns may arise through conservatism in the
 chemical classes used in sex pheromones, apparent switches between wasp
 clades suggest unexpected flexibility in floral semiochemical production.
 Alternatively, wasp sex pheromones within lineages may exhibit greater
 chemical diversity than currently appreciated.
description: Phillips et al CAD
 DRYADAlignment of the CAD
 sequence locus. Used for phylogenetic analysisPhillips et al COI
 DRYADAlignment of the COI
 sequence locus. Used for DNA barcoding analysis of thynnine
 waspsPhillips et al Rhodopsin
 DRYADAlignment of the LW
 Rhodopsin sequence locus. Used in phylogenetic analysis of thynnine
 waspsPhillips et al RNA pol2
 DRYADDNA sequence alignment
 of the RNA poly2 sequence locus. Used in phylogenetic analysis of thynnine
 waspsPhillips et al Wingless
 DRYADDNA sequence alignment
 of the Wingless sequence locus. Used in phylogenetic analysis of thynnine
 wasps
DOI: 10.5061/dryad.p9h8g
title: Data from: Transgenerational effects of sexual interactions and sexual conflict: non-sires boost the fecundity of females in the following generation

description: The consequences of sexual interactions extend beyond the simple
 production of offspring. These interactions typically entail direct
 effects on female fitness, but may also impact the life histories of later
 generations. Evaluating the cross-generational effects of sexual
 interactions provides insights into the dynamics of sexual selection and
 conflict. Such studies can elucidate whether offspring fitness optima
 diverge across sexes upon heightened levels of sexual interaction among
 parents. Here, we found that, in Drosophila melanogaster, components of
 reproductive success in females, but not males, were contingent on the
 nature of sexual interactions experienced by their mothers. In particular,
 maternal sexual interactions with non-sires enhanced female fecundity in
 the following generation. This highlights the importance of non-sire
 influences of sexual interactions on the expression of offspring life
 histories.
description: All data for
 Transgenerational Effects manuscriptAll data for the
 manuscript in an Excel file. Details can be found in the first spreadsheet
 and ESM.DRYAD
 Transgenerational_effects_Drosophila.xlsx
DOI: 10.5061/dryad.43t7r
title: Data from: The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals

description: Background: G protein-coupled receptors (GPCRs) play a central role in
 eukaryotic signal transduction. However, the GPCR component of this
 signalling system, at the early origins of metazoans is not fully
 understood. Here we aim to identify and classify GPCRs in Amphimedon
 queenslandica (sponge), a member of the Porifera (one of the earliest
 diverging metazoan lineages). Furthermore, phylogenetic comparisons of
 sponge GPCRs with eumetazoan and bilaterian GPCRs will be essential to our
 understanding of the GPCR system at the roots of metazoan evolution.
 Results: We present a curated list of 220 GPCRs in the sponge genome after
 excluding incomplete sequences and false positives from our initial
 dataset of 282 predicted GPCR sequences obtained using Pfam search.
 Phylogenetic analysis reveals that the sponge contains members belonging
 to four of the five major GRAFS families including Glutamate (33),
 Rhodopsin (126), Adhesion (40), and Frizzled (3). Interestingly, the
 sponge Rhodopsin family sequences lack orthologous relationships with
 those found in eumetazoan and bilaterian lineages, since they clustered
 separately to form sponge specific groups in the phylogenetic analysis.
 This suggests that sponge Rhodopsins diverged considerably from that found
 in other basal metazoans. A few Adhesion GPCRs clustered basal to Adhesion
 subfamilies that are commonly found in most of the vertebrates, suggesting
 some Adhesion subfamilies may have diverged prior to the divergence of
 Bilateria. Furthermore, at least eight of the sponge Adhesion members have
 a Hormone binding motif (HRM domain) in their N-termini, although hormones
 have yet to be identified in sponges. We also phylogenetically clarified
 that sponge has homologs of metabotropic glutamate (mGluRs) and GABA
 receptors. Conclusion: Our phylogenetic comparisons of sponge GPCRs with
 other metazoan genomes suggest that sponge contains a significantly
 diversified set of GPCRs. This is evident at the family/subfamily level
 comparisons for most GPCR families, in particular for the Rhodopsin family
 of GPCRs. In summary, this study provides a framework to perform future
 experimental and comparative studies to further verify and understand the
 roles of GPCRs that predates the divergence of bilaterian and eumetazoan
 lineages.
description: Raw alignments and
 phylogenetic tree files (Krishnan et al BMC evolutionary
 Biology)Alignments and Trees (Krishnan
 et al BMC evolutionary Biology).rar
DOI: 10.5061/dryad.kv358
title: Data from: Local adaptation and divergence in colour signal conspicuousness between monomorphic and polymorphic lineages in a lizard

description: Population differences in visual environment can lead to divergence in
 multiple components of animal coloration including signalling traits and
 colour patterns important for camouflage. Divergence may reflect selection
 imposed by different receivers (conspecifics, predators), which depends in
 turn on the location of the colour patch. We tested for local adaptation
 of two genetically and phenotypically divergent lineages of a
 rock-inhabiting lizard, Ctenophorus decresii, by comparing the visual
 contrast of colour patches to different receivers in native and non-native
 environments. The lineages differ most notably in male throat coloration,
 which is polymorphic in the northern lineage and monomorphic in the
 southern lineage, but also differ in dorsal and lateral coloration, which
 is visible to both conspecifics and potential predators. Using models of
 animal colour vision, we assessed whether lineage-specific throat, dorsal
 and lateral coloration enhanced conspicuousness to conspecifics, increased
 crypsis to birds or both, respectively, when viewed against the
 predominant backgrounds from each lineage. Throat colours were no more
 conspicuous against native than non-native rock but contrasted more
 strongly with native lichen, which occurs patchily on rocks inhabited by
 C. decresii. Conversely, neck coloration (lateral) more closely matched
 native lichen. Furthermore, although dorsal coloration of southern males
 was consistently more conspicuous to birds than that of northern males,
 both lineages had similar absolute conspicuousness against their native
 backgrounds. Combined, our results are consistent with local adaptation of
 multiple colour traits in relation to multiple receivers, suggesting that
 geographic variation in background colour has influenced the evolution of
 lineage-specific coloration in C. decresii.
description: Spectral Reflectance and
 Irradiance DataSpectral reflectance of
 the throat, dorsum, head, bright neck coloration and dark lateral stripe
 of male tawny dragon lizards, and predominant background colours. Each
 column is the reflectance of a given colour patch averaged across three
 measurements. Reflectance data were smoothed by averaging over each 5nm
 interval within the range 300–700nm (visual spectrum of birds and most
 diurnal lizards), and the mean irradiance across all sites was normalised
 to a maximum of one. Note that mean reflectance of backgrounds were used
 in subsequent analyses.reflectance_data.xlsxVisual Contrast DataChromatic and achromatic contrasts of lizard colour patches against predominant backgrounds, and the internal contrast between constituent throat colour patches. Contrasts are from the perspective of conspecific lizards, likely predators (birds), or both.contrast_data.xlsx
DOI: 10.5061/dryad.3nr95
title: Data from: The origin of the serpentine endemic Minuartia laricifolia subsp. ophiolitica by vicariance and competitive exclusion

description: Serpentine soils harbour a unique flora that is rich in endemics. We
 examined the evolution of serpentine endemism in Minuartia laricifolia,
 which has two ecologically distinct subspecies with disjunct
 distributions: subsp. laricifolia on siliceous rocks in the western Alps
 and eastern Pyrenees and subsp. ophiolitica on serpentine in the northern
 Apennines. We analysed AFLPs and chloroplast sequences from 30 populations
 to examine their relationships and how their current distributions and
 ecologies were influenced by Quaternary climatic changes. Minuartia
 laricifolia was divided into four groups with a BAPS cluster analysis of
 the AFLP data, one group consisted only of subsp. ophiolitica, while three
 groups were found within subsp. laricifolia: Maritime Alps, north-western
 Alps and central Alps. The same groups were recovered in a
 neighbour-joining tree, although subsp. ophiolitica was nested within the
 Maritime Alps group of subsp. laricifolia. Subspecies ophiolitica
 contained three different chloroplast haplotypes, which were also found in
 the Maritime Alps group of subsp. laricifolia. Given its high genetic
 diversity, subsp. ophiolitica appears to have arisen from subsp.
 laricifolia by vicariance instead of by long-distance dispersal. Genetic
 and geographic evidence point to the Maritime Alps populations of subsp.
 laricifolia as the closest relatives of subsp. ophiolitica. We hypothesize
 that M. laricifolia was also able to grow on nonserpentine rocks in the
 northern Apennines during glacial periods when the vegetation was more
 open, but that only the serpentine-adapted populations were able to
 persist until the present due to their competitive exclusion from more
 favourable habitats.
description: M50_54combined_20120701_DryadThe AFLP data for all individuals sampled of Minuartia laricifolia subspp. laricifolia (all remaining populations) and ophiolitica (populations OG1, OG2, OMP) as well as M. capillacea (populations CSM and CBR).cp_haplotypesThe aligned sequences of the eight chloroplast haplotypes recovered in the study.indel_codingThe key to the indel codes in the cp haplotypes file. (The ReadMe file is the same for both.)voucher_tableFurther ecological and locality information for the sampled populations.
DOI: 10.5061/dryad.7b185
title: Data from: How diverse is Mitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman

description: Mitopus morio is a widespread harvestman species occurring in most of
 Europe and in moderate and cold-moderate zones of Asia and North America.
 The species is characterized by extreme variability in body size and leg
 length. As leg length is correlated with habitat temperature, M. morio has
 been considered as an example of Allen's rule. Recently, observations
 for a single location in Tyrol, Austria, indicated the absence of mating
 between short- and long-legged individuals. This study examines for signs
 of putative cryptic species in M. morio using an integrative approach that
 combines mating trials, amplified fragment length polymorphism
 whole-genome scans, mitochondrial sequences and morphometrics. The mating
 trials did not corroborate the initial hypothesis of a reproductive
 barrier associated with leg size. Both types of genetic data revealed the
 existence of three distinct groups, in line with the mating results but
 largely unrelated to leg morphology and geographical origin of specimens.
 Morphometric characters supporting the findings of the other disciplines
 were identified using a supervised approach. We infer from all data
 together the existence of strongly diverged cryptic lineages among the
 analysed individuals, cautiously interpret them as three sympatric species
 and conclude that in these harvestmen Allen's rule applies at
 different levels. Due to the unexpected amount of differentiation found
 within a geographical scale very small compared with the distribution of
 M. morio, we suggest a thorough revision of the genus prior to formal
 taxonomic changes. Our case study underlines the general applicability of
 the integrative taxonomic protocol used and highlights the relevance of
 several rationales implemented in the protocol.
description: cytBcompleteClustalX alignment of cytochrome B mtDNA16ScompleteClustalX alignment of 16S mtDNAMitopus AFLP genotypesIndividual 0/1 genotype matrices in FASTA formatMitopus AFLP genotype.fasoptiFLP resultsRaw log and result files generated with optiFLPBAPS resultsInput and result files from BAPS analysis
DOI: 10.5061/dryad.mc8jp7p
title: Data from: Shifts to earlier selfing in sympatry may reduce costs of pollinator sharing

description: Coexisting plant congeners often experience strong competition for
 resources. Competition for pollinators can result in direct fitness costs
 via reduced seed set or indirect costs via heterospecific pollen transfer
 (HPT), causing subsequent gamete loss and unfit hybrid offspring
 production. Autonomous selfing may alleviate these costs, but to preempt
 HPT, selfing should occur early, before opportunities for HPT occur (i.e.
 “preemptive selfing hypothesis”). We evaluated conditions for this
 hypothesis in Collinsia sister species, C. linearis and C. rattanii. In
 field studies, we found virtually identical flowering times and pollinator
 sharing between congeners in sympatric populations. Compared to allopatric
 populations, sympatric C. linearis populations enjoyed higher pollinator
 visitation rates, whereas visitation to C. rattanii did not differ in
 sympatry. Importantly, the risk of HPT to each species in sympatry was
 strongly asymmetrical; interspecies visits comprised 40% of all
 flower-to-flower visits involving C. rattanii compared to just 4%
 involving C. linearis. Additionally, our greenhouse experiment
 demonstrated a strong cost of hybridization, when C. rattanii was the
 pollen donor. Together, these results suggest that C. rattanii pays the
 greatest cost of pollinator sharing. Matching predictions of the
 preemptive selfing hypothesis, C. rattanii exhibit significantly earlier
 selfing in sympatric relative to allopatric populations.
description: FloralPhenology_Randle_Spigler_KaliszFloral Phenology data for C. linearis and C. rattanii in sympatryHybridCrossF1Germination_RandleSpiglerKaliszGermination data from hybrid crosses of C. rattanii and C. linearisHybridCrossFruit&SeedSet_RandleSpiglerKaliszFruit and seed-set data from hybrid crosses of C. linearis and C. rattaniiPollinatorData_RandleSpiglerKaliszPollinator visitation data to C. linearis and C. rattanii in sympatric and allopatric sites in Oregon.TOS_RandleSpiglerKaliszThe timing of self-pollination in C. linearis and C. rattanii populations in sympatry and allopatry. The timing of selfing experiment was conducted on plants grown in a common greenhouse from seed collected from either sympatric or allopatric sites.