cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k0080
title: Data from: Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes

description: Trait decoupling, wherein evolutionary release of constraints permits
 specialization of formerly integrated structures, represents a major
 conceptual framework for interpreting patterns of organismal diversity.
 However, few empirical tests of this hypothesis exist. A central
 prediction, that the tempo of morphological evolution and ecological
 diversification should increase following decoupling events, remains
 inadequately tested. In damselfishes (Pomacentridae), a ceratomandibular
 ligament links the hyoid bar and lower jaws, coupling two main
 morphofunctional units directly involved in both feeding and sound
 production. Here, we test the decoupling hypothesis by examining the
 evolutionary consequences of the loss of the ceratomandibular ligament in
 multiple damselfish lineages. As predicted, we find that rates of
 morphological evolution of trophic structures increased following the loss
 of the ligament. However, this increase in evolutionary rate is not
 associated with an increase in trophic breadth, but rather with
 morphofunctional specialization for the capture of zooplanktonic prey.
 Lineages lacking the ceratomandibular ligament also shows different
 acoustic signals (i.e. higher variation of pulse periods) from others,
 resulting in an increase of the acoustic diversity across the family. Our
 results support the idea that trait decoupling can increase morphological
 and behavioural diversity through increased specialization rather than the
 generation of novel ecotypes.
description: TableS1Electronic Supplemental MaterialAll ESM except Table S1 (i.e. Table S2, Fig. S1, Fig. S2).
DOI: 10.5061/dryad.f50h2
title: Data from: Life history costs make perfect sprouting maladaptive in two herbaceous perennials

description: 1.Why some herbaceous plant species refrain from sprouting in some years
 is a longstanding puzzle in plant ecology. When vegetatively “dormant”,
 the plant lives as a rootstock, but does not produce or maintain
 photosynthetic tissue. During this time, energy may be remobilized from
 resource reserves, or acquired from mycorrhizal fungi, although the
 mechanisms are still poorly understood. If vegetative dormancy is
 adaptive, it may be in response to a harsh environment, to life history
 costs, or as a bet-hedge against unpredictable environmental variability.
 2.We tested whether vegetative dormancy is adaptive via game theoretical
 analysis of deterministic and stochastic ahistorical and historical life
 history models parameterized with long-term census data for two long-lived
 plants, Anemone americana and Cypripedium parviflorum. The ahistorical
 deterministic model provided a test of the hypothesis that dormancy is
 adaptive in response to a generally harsh environment and/or short-term
 life history costs, while the historical model tested whether long-term
 costs drove the evolution of dormancy. The stochastic ahistorical model
 provided a test of whether dormancy is a bet-hedging trait. 3.We found
 that vegetative dormancy is an adaptive consequence of life history costs
 of growth to survival, and that these costs may be operating under a
 variable but generally harsh environment. Such costs led to sprouting and
 survival probabilities that generally increased with size in adults but
 never reached unity, and decreased with size in juveniles. Historical
 deterministic models particularly predicted observed sprouting
 frequencies, while deterministic ahistorical and stochastic models did
 not, suggesting although the environment is likely stressful and
 fluctuates between harsh and mild states, short-term costs and temporal
 stochasticity alone do not explain observed sprouting frequencies.
 4.Synthesis. Life history costs can drive the evolution of seemingly
 paradoxical traits. In particular, growth can lead to survival costs that
 may become significant in future years. These costs may be incurred via
 the use of stored reserves that, once used, cannot be used in the next
 several years. Such costs are the currency favoring the evolutionary
 maintenance of vegetative dormancy in two distantly related perennial
 plant species, and may account for dormancy throughout the Plant Kingdom.
description: Matrices.For.DryadExcel file containing spreadsheet with ahistorical and historical demographic matrices used in deterministic and stochastic invasibility analyses.
DOI: 10.5061/dryad.n63q1
title: Data from: Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora

description: Ctenophores are a phylum of non-bilaterian marine (mostly planktonic)
 animals, characterised by several unique synapomorphies (e.g. comb rows,
 apical organ). Relationships between and within the nine recognised
 ctenophore orders are far from understood, notably due to a paucity of
 phylogenetically-informative anatomical characters. Previous attempts to
 address ctenophore phylogeny using molecular data (18S rRNA) led to poorly
 resolved trees but demonstrated the paraphyly of the order Cydippida. Here
 we compiled an updated 18S rRNA data set, notably including a few
 newly-sequenced species representing previously unsampled families
 (Lampeidae, Euryhamphaeidae), and we built up an additional more
 rapidly-evolving ITS1+5.8SrRNA+ITS2 alignment. These data sets have been
 analysed separately and in combination under a probabilistic framework,
 using different methods (Maximum Likelihood, Bayesian inference) and
 models (e.g. doublet model to accommodate secondary structure; data
 partitioning). An important lesson from our exploration of these datasets
 is that the fast-evolving ITS regions are useful markers for
 reconstructing high-level relationships within ctenophores. Our results
 confirm the paraphyly of the order Cydippida (and thus a “cyddipid-like”
 ctenophore common ancestor) and suggest that the family Mertensiidae could
 be the sister-group of all other ctenophores. The family Lampeidae (also
 part of the former “Cydippida”) is probably the sister-group of the order
 Platyctenida (benthic ctenophores). The order Beroida might not be
 monophyletic, due to the position of Beroe abyssicola outside of a clade
 grouping the other Beroe species and members of the “Cydippida” family
 Haeckeliidae. Many relationships (i.e. between Pleurobrachiidae, Beroida,
 Cestida, Lobata, Thalassocalycida) remain unresolved. Future progress in
 understanding ctenophore phylogeny will come from the use of additional
 rapidly-evolving markers and improvement of taxonomic sampling.
description: 18SAlignment of 18S
 sequences of Ctenophores and other metazoans18S_GBAlignment of 18S
 sequences of Ctenophores and other metazoans after use of
 G-blocks.ITSAlignment of ITS region
 (ITS1, 5.8SrRNA, ITS2) of Ctenophores.ITS_GBAlignment of ITS region
 (ITS1, 5.8SrRNA, ITS2) of Ctenophores after use of
 G-blocks.
DOI: 10.5061/dryad.82br3
title: Data from: Adaptive genetic divergence along narrow environmental gradients in four stream insects

description: A central question linking ecology with evolutionary biology is how
 environmental heterogeneity can drive adaptive genetic divergence among
 populations. We examined adaptive divergence of four stream insects from
 six adjacent catchments in Japan by combining field measures of habitat
 and resource components with genome scans of non-neutral Amplified
 Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was
 used to measure gene flow and non-neutral genetic variation was used to
 test for adaptive divergence. We identified the environmental
 characteristics contributing to divergence by comparing genetic distances
 at non-neutral loci between sites with Euclidean distances for each of 15
 environmental variables. Comparisons were made using partial Mantel tests
 to control for geographic distance. In all four species, we found strong
 evidence for non-neutral divergence along environmental gradients at
 between 6 and 21 loci per species. The relative contribution of these
 environmental variables to each species' ecological niche was
 quantified as the specialization index, S, based on ecological data. In
 each species, the variable most significantly correlated with genetic
 distance at non-neutral loci was the same variable along which each
 species was most narrowly distributed (i.e., highest S). These were
 gradients of elevation (two species), chlorophyll-a, and ammonia-nitrogen.
 This adaptive divergence occurred in the face of ongoing gene flow (Fst =
 0.01–0.04), indicating that selection was strong enough to overcome
 homogenization at the landscape scale. Our results suggest that adaptive
 divergence is pronounced, occurs along different environmental gradients
 for different species, and may consistently occur along the narrowest
 components of species' niche.
description: AFLP data of 4 stream
 insects and environment data in JapanAFLP_binary_Environment_data_Watanabe et at.2014.xlsx
DOI: 10.5061/dryad.25kn0
title: Data from: Effects of epistasis on infectivity range during host-parasite coevolution

description: Understanding how parasites adapt to changes in host resistance is crucial
 to evolutionary epidemiology. Experimental studies have demonstrated that
 parasites are more capable of adapting to gradual, rather than sudden
 changes in host phenotype, as the latter may require multiple mutations
 that are unlikely to arise simultaneously. A key, but as yet unexplored
 factor is precisely how interactions between mutations (epistasis) affect
 parasite evolution. Here, we investigate this phenomenon in the context of
 infectivity range, where parasites may experience selection to infect
 broader sets of genotypes. When epistasis is strongly positive, we find
 that parasites are unlikely to evolve broader infectivity ranges if hosts
 exhibit sudden, rather than gradual changes in phenotype, in close
 agreement with empirical observations. This is due to a low probability of
 fixing multiple mutations that individually confer no immediate advantage.
 When epistasis is weaker, parasites are more likely to evolve broader
 infectivity ranges if hosts make sudden changes in phenotype, which can be
 explained by a balance between mutation supply and selection. Thus, we
 demonstrate that both the rate of phenotypic change in hosts and the form
 of epistasis between mutations in parasites are crucial in shaping the
 evolution of infectivity range.
description: Simulation code and
 dataPlease see README file
 for full description.ashby2014_epistasis.zip
DOI: 10.5061/dryad.jh421
title: Data from: Theoretical and empirical perspectives in ecology and evolution: a survey

description: Scientific research is often conceptually divided into empirical and
 theoretical approaches, and researchers often specialize as empiricists or
 theorists. Both approaches are essential to scientific progress, but
 interactions between the two groups have at times seemed problematic. I
 present results from a recent survey of 614 scientists (predominantly
 ecologists and evolutionary biologists) regarding interactions between
 theoretical and empirical work. Some overall themes emerged from these
 results. One theme is a widespread and mutual lack of trust,
 understanding, and interaction between empiricists and theorists. Another
 is a general desire, among almost all of the respondents, for greater
 understanding, more collaboration, and closer interactions between
 empirical and theoretical work. The final theme is that institutions, such
 as journals, funding agencies, and universities, are often seen as
 hindering such interactions. These results provide a clear mandate for
 institutional changes to improve interactions between theorists and
 empiricists in ecology and evolutionary biology.
description: Survey
 resultsThe results form the
 survey conducted, except long-form responses, which are contained in other
 data filessurvey_results.csvGood interactionsLong-form responses to the question about "good interactions"good_interactions.csvBad interactionsLong-form responses to the question about "bad interactions"bad_interactions.csvOther thoughtsLong-form responses to the question about "other thoughts"other_thoughts.csvQuestionnaire problemsLong-form responses to the question about "questionnaire problems"questionnaire_problems.csvSurvey analysis scriptAn R script file with code for cleanup, simplification, and analysis of the main survey results given in survey_results.csvsurvey_analysis.RGood interaction papersA zip archive with the various papers mentioned by the respondents in the "good interactions" question, given in various file formatsgood_int_papers.zip
DOI: 10.5061/dryad.7kn5k
title: Data from: Evolutionary history and biogeographical patterns of barnacles endemic to deep-sea hydrothermal vents

description: The characterization of evolutionary and biogeographical patterns is of
 fundamental importance to identify factors driving biodiversity. Due to
 their widespread but discontinuous distribution, deep-sea hydrothermal
 vent barnacles represent an excellent model for testing biogeographic
 hypotheses regarding the origin, dispersal, and diversity of modern vent
 fauna. Here we characterize the global genetic diversity of vent barnacles
 to infer their time of radiation, place of origin, mode of dispersal, and
 diversification. Our approach was to target a suite of multiple loci in
 samples representing seven out of the eight described genera. We also
 performed restriction-site associated DNA sequencing on individuals from
 each species. Phylogenetic inferences and topology hypothesis tests
 indicate that vent barnacles have colonized deep-sea hydrothermal vents at
 least twice in history. Consistent with preliminary estimates, we find a
 likely radiation of barnacles in vent ecosystems during the Cenozoic. Our
 analyses suggest that the western Pacific was the place of origin of the
 major vent barnacle lineage, followed by circumglobal colonization
 eastward through the southern hemisphere during the Neogene. The inferred
 time of radiation rejects classic hypotheses of antiquity of vent taxa.
 The timing and the mode of origin, radiation and dispersal are consistent
 with recent inferences made for other deep-sea taxa, including non-vent
 species, and are correlated with the occurrence of major geological events
 and mass extinctions. Thus, we suggest that the geological processes and
 dispersal mechanisms discussed here can explain current distribution
 patterns of many other marine taxa and have played an important role
 shaping deep-sea faunal diversity. These results also constitute critical
 baseline data with which to assess potential effects of anthropogenic
 disturbances on deep-sea ecosystems.
description: Vent barnacle
 sanger-based phyloAlignment and tree files
 from maximum likelihood and bayesian inference phylogenetic analyses using
 sanger-based markers.vent_barnacle_sanger-based_phylo.zipVent barnacle sanger-based datingInput and tree files from bayesian inference phylogenetic/dating analyses using sanger-based markers.vent_barnacle_sanger-based_dating.zipVent barnacle pyRADCommand, output and statistics files from RAD-seq clustering using pyRAD. Phylogenetic trees and bootstrap consensus from maximum likelihood inferences.vent_barnacle_pyRAD.zip
DOI: 10.5061/dryad.5s63b
title: Data from: Consequences of multiple inflorescences and clonality for pollinator behavior and plant mating

description: Angiosperms engage in distributed reproduction, producing sex organs in
 multiple flowers on one or more inflorescences, including on different
 physical individuals of clonal plants. We investigated the effects of
 alternative deployments of artificial flowers for pollinator behavior and
 simulated pollen dispersal. Plants presented 18 flowers on either one
 inflorescence (1-I plants) or three inflorescences (3-I plants) spaced
 either closely or widely. Bees often skipped inflorescences on 3-I plants,
 visiting an average of 1.5 fewer flowers overall than on 1-I plants. In
 simulations with all flowers receiving and donating pollen, this behavior
 caused 7% less geitonogamy for 3-I plants, contradicting a common
 supposition that clonality increases geitonogamy. Bees generally moved
 upward within inflorescences and downward between inflorescences.
 Consequently, in simulations, segregation of pollen receipt to lower
 flowers and pollen donation to upper flowers reduced self-pollination and
 enhanced pollen export much more for 1-I plants. Nectar volume per flower
 had little relevant influence on bee behavior. The observed bee responses
 and simulated mating results suggest that production of multiple
 inflorescences and clonality promote pollination quality when flowers
 simultaneously receive and donate pollen, whereas a single large
 inflorescence is advantageous when segregation of sex roles among flowers
 reduces geitonogamy effectively.
description: Liao & Harder visit
 dataObservations of bumble
 bee behavior on artificial 18-flowered plants with one inflorescence,
 three closely spaced inflorescences, or three widely spaced
 inflorescences. See "Variables" worksheet for explanation of
 columns in "Visit" worksheet.Liao & Harder
 simulation dataResults of simulations
 of plant mating based on observed bee behavior on artificial 18-flowered
 plants with one large inflorescence, three closely spaced 6-flowered
 inflorescences, or three widely spaced 6-flowered inflorescences. Results
 in the "bisexual" worksheet are from a simulation in which all
 flowers both donated and received pollen, whereas those in the
 "protandry" worksheet are from a simulation in which lower
 flowers received pollen and upper flowers donated pollen. See the
 "Variables" worksheet for descriptions of the data in the
 columns of the "bisexual" and "protandry"
 worksheets.
DOI: 10.5061/dryad.dd815
title: Data from: Ecological causes of multi-level covariance between size and first-year survival in a wild bird population

description: 1. Estimates of selection in natural populations are frequent but our
 understanding of ecological causes of selection, and causes of variation
 in the direction, strength and form of selection, is limited. 2. Here, we
 apply a multi-level framework to partition effects of great tit fledging
 mass on first-year survival to hierarchical levels and quantify their
 ecological dependence using a data set spanning 51 years. 3. We show that
 estimates of the effect of fledging mass on first-year survival decline
 three-fold from year- to brood- to individual-level, so that estimates of
 selection depend strongly on the level at which they are calculated. 4. We
 identify variables related to summer and winter food availability as
 underlying higher-level effects of fledging mass on first-year survival,
 and show experimentally that brood-level effects originate early in
 development. Further, we show that predation and conspecific density
 modulate individual-level effects of fledging mass on first-year survival.
 5. These analyses demonstrate how correlations between traits, fitness and
 environment influence estimates of selection, and show how partitioning
 trait-effects between levels of selection and environmental factors is a
 promising approach to identify potential agents of selection.
description: 1960-2010 data fledging
 massLongitudinal dataset
 used to study effects of fledging mass on local first-year survival in
 great tits.exp data fledging
 massExperimental data used
 to analyse effects of fledging mass on first-year survival in great
 tits.
DOI: 10.5061/dryad.v7f7r
title: Data from: The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia

description: Next generation sequencing (NGS) platforms are replacing traditional
 molecular biology protocols like cloning and Sanger sequencing. However,
 accuracy of NGS platforms has rarely been measured when quantifying
 relative frequencies of genotypes or taxa within populations. Here we
 developed a new bioinformatic pipeline (QRS) that pools similar sequence
 variants and estimates their frequencies in NGS data sets from populations
 or communities. We tested whether the estimated frequency of
 representative sequences, generated by 454 amplicon sequencing, differs
 significantly from that obtained by Sanger sequencing of cloned PCR
 products. This was performed by analysing sequence variation of the highly
 variable first internal transcribed spacer (ITS1) of the ichthyosporean
 Caullerya mesnili, a microparasite of cladocerans of the genus Daphnia.
 This analysis also serves as a case example of the usage of this pipeline
 to study within-population variation. Additionally, a public Illumina data
 set was used to validate the pipeline on community-level data. Overall,
 there was a good correspondence in absolute frequencies of C. mesnili ITS1
 sequences obtained from Sanger and 454 platforms. Furthermore, analyses of
 molecular variance (amova) revealed that population structure of C.
 mesnili differs across lakes and years independently of the sequencing
 platform. Our results support not only the usefulness of amplicon
 sequencing data for studies of within-population structure but also the
 successful application of the QRS pipeline on Illumina-generated data.
description: Caullerya_ITSalignment.GonzalezTortuero_etal_2014DNA alignment of 3,700 Caullerya's ITS1 sequences in FASTA format
DOI: 10.5061/dryad.qf6t5
title: Data from: Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

description: Willows (Salix: Salicaceae) form a major ecological component of Holarctic
 floras, and consequently are an obvious target for a DNA-based
 identification system. We surveyed two to seven plastid genome regions
 (~3.8 kb; ~3% of the genome) from 71 Salix species across all five
 subgenera, to assess their performance as DNA barcode markers. Although
 Salix has a relatively high level of interspecific hybridization, this may
 not sufficiently explain the near complete failure of barcoding that we
 observed: only one species had a unique barcode. We recovered 39 unique
 haplotypes, from more than 500 specimens, that could be partitioned into
 six major haplotype groups. A unique variant of group I (haplotype 1*) was
 shared by 53 species in three of five Salix subgenera. This unusual
 pattern of haplotype sharing across infrageneric taxa is suggestive of
 either a massive non-random coalescence failure (incomplete lineage
 sorting), or of repeated plastid capture events, possibly including a
 historical selective sweep of haplotype 1* across taxonomic sections. The
 former is unlikely as molecular dating indicates that haplotype 1*
 originated recently, and is nested in the oldest major haplotype group in
 the genus. Further, we detected significant non-neutrality in the
 frequency spectrum of mutations in group I, but not outside group I, and
 demonstrated a striking absence of geographic structure to the haplotype
 distributions in this group. The most likely explanation for the patterns
 we observed involves recent repeated plastid capture events, aided by
 widespread hybridization and long-range seed dispersal, but primarily
 propelled by one or more trans-species selective sweeps.
description: bold salix
 samplesspecies, specimen,
 location listsSALIX_matKmatK sequence alignmentSALIX_rbcLrbcL sequence alignmentSALIX_rpoBrpoB sequence alignmentSALIX_rpoC1rpoC1 sequence alignmentSALIX_trnHtrnH-psbA sequence alignmentSALIX_psbKpsbK-psbI sequence alignmentSALIX_atpFatpF-atpH sequence alignmentSALIX_COICOI sequence alignment