cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n15m7
title: Data from: Signal architecture: temporal variability and individual consistency of multiple sexually selected signals

description: 1. Multiple signals should be favoured when the benefit of additional
 signals outweigh their costs. Despite increased attention on
 multiple-signalling systems, few studies have focused on signal
 architecture to understand the potential information content of multiple
 signals. 2. To understand the patterns of signal plasticity and
 consistency over the lifetime of individuals we conducted a longitudinal
 study of multiple signals known to be under sexual selection in male lark
 buntings, Calamospiza melanocorys. 3. Within years, we found extensive
 among-individual variation in all four plumage ornaments we measured.
 Surprisingly, there were few correlations among these signals, suggesting
 that individuals contain a mosaic of signals. Signals were only moderately
 repeatable across years, which indicates some signal plasticity or age
 related change. In some years, the direction of change in particular
 signals relative to the previous year was consistent for most individuals
 in the population, suggesting that broad scale ecological factors affected
 the ornament phenotype. Different ornaments were affected by different
 ecological or social factors because the population-wide shift in a given
 signal was independent of change in other signals. 4. Our combined results
 suggest that different signals—including different components of the same
 color patch in some cases—provide diverse and independent information
 about the individual to signal receivers in the context of sexual
 selection.
description: Plumage and body size
 traits for lark buntings from 1999-2003. Chaine and Lyon; Functional
 Ecology 2015Data includes 3 tables:
 1) ID and traits for all males caught from 1999-2003. This includes raw
 data for body size, patch color, and patch area. It also includes the
 principal component scores extracted from raw data which were used in the
 published analyses. Comments in the data header line provide additional
 information. 2) Data used to estimate repeatability of spectrometry data.
 3) Measures of birds from the UC Berkeley Museum for repeatability of
 plumage.ChaineLyon_BuntingTraits_DRYAD.xlsx
DOI: 10.5061/dryad.4j169
title: Data from: Sex-chromosome differentiation and ‘sex races’ in the common frog (Rana temporaria)

description: Sex-chromosome differentiation was recently shown to vary among common
 frog populations in Fennoscandia, suggesting a trend of increased
 differentiation with latitude. By rearing families from two contrasted
 populations (respectively, from northern and southern Sweden), we show
 this disparity to stem from differences in sex-determination mechanisms
 rather than in XY-recombination patterns. Offspring from the northern
 population display equal sex ratios at metamorphosis, with phenotypic
 sexes that correlate strongly with paternal LG2 haplotypes (the sex
 chromosome); accordingly, Y haplotypes are markedly differentiated, with
 male-specific alleles and depressed diversity testifying to their smaller
 effective population size. In the southern population, by contrast, a
 majority of juveniles present ovaries at metamorphosis; only later in
 development do sex ratios return to equilibrium. Even at these later
 stages, phenotypic sexes correlate only mildly with paternal LG2
 haplotypes; accordingly, there are no recognizable Y haplotypes. These
 distinct patterns of gonadal development fit the concept of ‘sex races’
 proposed in the 1930s, with our two populations assigned to the
 ‘differentiated’ and ‘semi-differentiated’ races, respectively. Our
 results support the suggestion that ‘sex races’ differ in the genetic
 versus epigenetic components of sex determination. Analysing populations
 from the ‘undifferentiated race’ with high-density genetic maps should
 help to further test this hypothesis.
description: Table S2 - raw LG2-15
 genotypes dryadRaw genotypic data for
 the 62 adults and 594 offspring from the two Swedish populations of
 Ammarnäs and Tvedöra.
DOI: 10.5061/dryad.26qd7
title: Data from: Beyond magic traits: multimodal mating cues in Heliconius butterflies

description: Species coexistence involves the evolution of reproductive barriers
 opposing gene flow. Heliconius butterflies display colorful patterns
 affecting mate choice and survival through warning signaling and mimicry.
 These patterns are called “magic traits” for speciation because divergent
 natural selection may promote mimicry shifts in pattern whose role as
 mating cue facilitates reproductive isolation. By contrast, between
 comimetic species, natural selection promotes pattern convergence. We
 addressed whether visual convergence interferes with reproductive
 isolation by testing for sexual isolation between two closely related
 species with similar patterns, H. timareta thelxinoe and H. melpomene
 amaryllis. Experiments with models confirmed visual attraction based on
 wing phenotype, leading to indiscriminate approach. Nevertheless, mate
 choice experiments showed assortative mating. Monitoring male behavior
 toward live females revealed asymmetry in male preference, H. melpomene
 males courting both species equally while H. timareta males strongly
 preferred conspecifics. Experiments with hybrid males suggested an
 important genetic component for such asymmetry. Behavioral observations
 support a key role for short-distance cues in determining male choice in
 H. timareta. Scents extracts from wings and genitalia revealed
 interspecific divergence in chemical signatures, and hybrid female scent
 composition was significantly associated with courtship intensity by H.
 timareta males, providing candidate chemical mating cues involved in
 sexual isolation.
description: Raw data for behaviour
 and chemical signatureData are provided for
 male choice on models, male choice on virgin females, female hybrid
 success as well as wing and genital chemical signature from both sexes.
 Each set of data ison a separate sheet of the excel file with all relevant
 information. Please refer to the methods and Table S1 if
 neededArchived_data.xlsx
DOI: 10.5061/dryad.jq362
title: Data from: Different response-effect trait relationships underlie contrasting responses to two chemical stressors

description: 1. Trait-based approaches predict ecosystem functioning under
 environmental change by relating traits predicting changes in species
 densities (response traits) to traits driving ecosystem functioning
 (effect traits). Stressors can however affect ecosystem functioning not
 only by altering species densities, but also by directly changing species
 effect traits. 2. We first identified the response traits predicting the
 cell density of 18 marine benthic diatom strains along gradients of two
 chemical stressors (a pesticide and a metal, atrazine and copper). We then
 tested if response traits could predict stressor-induced changes in
 ecosystem functioning, i.e. changes in the effect traits driving the
 diatoms’ potential contribution to primary production, sediment
 stabilization and energy content in intertidal systems. Finally, we
 examined if changes in density and changes in ecosystem functioning were
 correlated, to assess whether species capable of growing under stressful
 conditions could maintain their contribution to ecosystem functioning. 3.
 The relationship between response traits and stressor-induced changes in
 density and ecosystem functioning was different depending on stressor
 type: a set of intercorrelated morphological traits predicted changes in
 both density and ecosystem functioning under metal stress, with large
 cells being more stress-resistant. Changes in density and changes in
 ecosystem functioning were positively related: diatoms whose density was
 least affected by the metal were also able to sustain functioning under
 metal exposure. 4. In contrast, the capacity for mixotrophic growth
 predicted changes in density, but not changes in ecosystem functioning
 under pesticide stress. Pesticide effects on density and on ecosystem
 functioning were negatively related for energy content and sediment
 stabilization, indicating a limited capacity of pesticide-tolerant diatoms
 to maintain their contribution to ecosystem functioning. Synthesis.
 Ecosystem functioning under stress can depend on whether response traits
 driving changes in density also predict direct stress effects on the
 species’ contribution to ecosystem functioning. Based on our results, we
 expect a disproportionate loss of functioning when traits driving species
 densities do not allow to maintain ecosystem functioning under stress.
description: data_package_MensensEtAl2017_JournalOfEcologyThis data package contains data from the publication: Mensens, C., De Laender, F., Janssen, C.R., Sabbe, K. & De Troch M. (2017) Different response-effect trait relationships underlie contrasting responses to two chemical stressors. Journal of Ecology. Details about the content of the package can be found in the Readme.txt file in the zip folder.MensensEtAl2017JEcol.zip
DOI: 10.5061/dryad.67n14
title: Data from: Differential octopaminergic modulation of olfactory receptor neuron responses to sex pheromones in Heliothis virescens

description: Octopamine is an important neuromodulator of neural function in
 invertebrates. Octopamine increases male moth sensitivity to female sex
 pheromones, however, relatively little is known as to the role of
 octopamine in the female olfactory system, nor its possible effects on the
 reception of non-pheromone odorants. The purpose of this study was to
 determine relative effects of octopamine on the sensitivity of the
 peripheral olfactory system in male and female Heliothis virescens. Single
 sensillum recording was conducted in both sexes following injection with
 octopamine or Ringer solution, and during odorant stimulation with
 conspecific female sex pheromone or host plant volatiles. Results indicate
 that octopamine plays a significant modulatory role in female sex
 pheromone detection in female moths; and that male and female pheromone
 detection neurons share distinct pharmacological and physiological
 similarities in H. virescens despite sexual dimorphism at the antennal
 level.
description: Kavanagh and Hillier
 2015 Data Nov 2015Summary of Single
 sensillum recording data from male and female H. virescens following
 injection of octopamine or salineOA SSR
 2015.xlsx
DOI: 10.5061/dryad.8d3r7
title: Data from: Concordance analysis in mitogenomic phylogenetics

description: Here I advocate the utility of Bayesian concordance analysis as a
 mechanism for exploring the magnitude and source of phylogenetic signal in
 concatenated mitogenomic phylogenetic studies. While typically applied to
 the study of independently evolving gene trees, Bayesian concordance
 analysis can also be applied to linked, but individually analyzed, gene
 regions using a prior probability that reflects the expectation of similar
 phylogenetic reconstructions. For true branches in the mitogenomic tree,
 concordance factors should represent the number of gene regions that
 contain phylogenetic signal for a particular clade. As a demonstration of
 the application of Bayesian concordance analysis to empirical data, I
 analyzed two different salamander (Hynobiidae and Plethodontidae)
 mitogenomic data sets using a gene-based partitioning strategy. The
 results revealed many strongly supported clades in the concatenated trees
 that have high concordance factors, permitting the inference that these
 are robustly resolved through phylogenetic signal distributed across the
 mitogenome. In contrast, a number of strongly supported clades in the
 concatenated tree received low concordance factors, indicating that their
 reconstruction is either driven primarily by phylogenetic signal in a
 small number of gene regions, or that they are inconsistent
 reconstructions influenced by properties of the data that can produce
 inaccurate trees (e.g., compositional bias, selection, etc.). Exploration
 of the Bayesian joint posterior distribution of trees highlighted
 partitions that contribute phylogenetic information to similar clade
 reconstructions. This approach was particularly insightful in the hynobiid
 data, where different combinations of genes were identified that support
 alternative tree reconstructions. Concatenated analysis of these different
 subsets of genes highlighted through Bayesian concordance analysis
 produced strongly supported and contrasting trees, demonstrating the
 potential for inconsistency in concatenated mitogenomic phylogenetics. The
 overall results presented here suggest that Bayesian concordance analysis
 can serve as an effective exploration of the influence of different gene
 regions in mitogenomic (and other organellar genomic) phylogenetic
 studies.
description: Hynobiidae
 alignmentsThese are the hynobiid
 mitochondrial gene alignments used in my study. These data were previously
 published and were retrieved from GenBank. Accession numbers are listed in
 my paper.Plethodontidae
 alignmentsThese are the 16 aligned
 plethodontid mitochondrial gene regions used in my study. These data were
 previously published and were retrieved from GenBank. Accession numbers
 are provided in my paper.
DOI: 10.5061/dryad.cc3km5t
title: Data from: No measurable fitness cost to experimentally evolved host defense in the Caenorhabditis elegans-Serratia marcescens host-parasite system

description: Host susceptibility to parasites can vary over space and time. Costs
 associated with the maintenance of host defense are thought to account for
 a portion of this variation. Specifically, tradeoffs wherein elevated
 defense is maintained at the cost of fitness in the absence of the
 parasite may cause levels of host defense to change over time and differ
 between populations. In previous studies we found that populations of the
 host nematode, Caenorhabditis elegans evolved greater levels of parasite
 avoidance and resistance against the bacterial parasite, Serratia
 marcescens. Here, we passaged these host populations either in the
 presence or absence of the parasite to test for a cost of elevated host
 defenses. After 16 generations, we found that elevated levels of host
 defense were maintained during evolution in both the presence and absence
 of the parasite. Further, this maintenance of defense was not the result
 of limited standing genetic variation, but rather the absence of a
 measurable cost associated with defense. Therefore, costs associated with
 host defense may not broadly account for differences in host
 susceptibility across space and time.
description: Host fitness data after
 experimental evolutionCOREE fitness
 data.xlsAncestral host mortality
 dataCOREE
 ancestors.xls
DOI: 10.5061/dryad.705q4
title: Data from: Bat species comparisons based on external morphology: a test of traditional versus geometric morphometric approaches

description: External morphology is commonly used to identify bats as well as to
 investigate flight and foraging behavior, typically relying on simple
 length and area measures or ratios. However, geometric morphometrics is
 increasingly used in the biological sciences to analyse variation in shape
 and discriminate among species and populations. Here we compare the
 ability of traditional versus geometric morphometric methods in
 discriminating between closely related bat species – in this case European
 horseshoe bats (Rhinolophidae, Chiroptera) – based on morphology of the
 wing, body and tail. In addition to comparing morphometric methods, we
 used geometric morphometrics to detect interspecies differences as shape
 changes. Geometric morphometrics yielded improved species discrimination
 relative to traditional methods. The predicted shape for the variation
 along the between group principal components revealed that the largest
 differences between species lay in the extent to which the wing reaches in
 the direction of the head. This strong trend in interspecific shape
 variation is associated with size, which we interpret as an evolutionary
 allometry pattern.
description: dataset_geometric
 morphometric_raw coordinatesDataset containing
 geometric morphometric raw coordinates and centroid
 size.dataset_traditional
 morphometricDataset including all
 traditional morphometric measures and ratios used for methods 1-3. The
 four residuals were used for method 3. The length measures were obtained
 from two wing pictures of the same individual and therefore the averaged
 measures are shown in the dataset. Similarly for calculating the ratios
 averaged length and area measures (not included in the dataset) were taken
 from two wing pictures per individual. Because the measurement error was
 low we only took measurements from one wing picture for individuals from
 2014.
DOI: 10.5061/dryad.123
title: Data from: Combining data sets with different phylogenetic histories

description: The possibility that two data sets may have different underlying
 phylogenetic histories (such as gene trees that deviate from species
 trees) has become an important argument against combining data in
 phylogenetic analysis. However, two data sets sampled for a large number
 of taxa may differ in only part of their histories. This is a realistic
 scenario and one in which the relative advantages of combined, separate,
 and consensus analysis become much less clear. I suggest a simple
 methodology for dealing with this situation that involves (1) partitioning
 the available data to maximize detection of different histories, (2)
 performing separate analyses of the data sets, and (3) combining the data
 but considering questionable or unresolved those parts of the combined
 tree that are strongly contested in the separate analyses (and which
 therefore may have different histories), until a majority of unlinked data
 sets supports one resolution over another. In support of this methodology,
 computer simulations suggest that (1) the accuracy of combined analysis at
 recovering the true species phylogeny may exceed that of either of two
 separately analyzed data sets under some conditions, particularly when the
 mismatch between phylogenetic histories is small and the estimates of the
 underlying histories are imperfect (few characters and/or high homoplasy),
 and (2) combined analysis provides a poor estimate of the species tree in
 areas of the phylogenies with different histories but an improved estimate
 in regions that share the same history. Thus, when there is a localized
 mismatch between the histories of two data sets, separate, consensus, and
 combined analysis may all give unsatisfactory results in certain parts of
 the phylogeny. Similarly, approaches that allow data combination only
 after a global test of heterogeneity will suffer from the potential
 failings of either separate or combined analysis, depending on the outcome
 of the test. Excision of conflicting taxa is also problematic in that it
 may obfuscate the position of conflicting taxa within a larger tree, even
 when their placement is congruent between data sets. Application of the
 proposed methodology to molecular and morphological data sets for
 Sceloporus lizards is discussed.
description: Wiens
 Appendiceswiensapp.html
DOI: 10.5061/dryad.mp44794
title: Data from: Functional integration for enrolment constrains evolutionary variation of phacopid trilobites despite developmental modularity

description: Modularity and integration are variational properties expressed at various
 levels of the biological hierarchy. Mismatches among these levels, for
 example developmental modules that are integrated in a functional unit,
 could be informative of how evolutionary processes and trade‐offs have
 shaped organismal morphologies as well as clade diversification. In the
 present study, we explored the full, integrated and modular spaces of two
 developmental modules in phacopid trilobites, the cephalon and the
 pygidium, and highlight some differences among them. Such contrasts reveal
 firstly that evolutionary processes operating in the modular spaces are
 stronger in the cephalon, probably due to a complex regime of selection
 related to the numerous functions ensured by this module. Secondly, we
 demonstrate that the same pattern of covariation is shared among species,
 which also differentiate along this common functional integration. This
 common pattern might be the result of stabilizing selection acting on the
 enrolment and implying a coordinate variation between the cephalon and the
 pygidium in a certain direction of the morphospace. Finally, we noticed
 that Austerops legrandi differs slightly from other species in that its
 integration is partly restructured in the way the two modules interact.
 Such a divergence can result from the involvement of the cephalon in
 several vital functions that may have constrained the response of the
 features involved in enrolment and reorganized the covariation of the
 pygidium with the cephalon. Therefore, it is possible that important
 evolutionary trade‐offs between enrolment and other functions on the
 cephalon might have partly shaped the diversification of trilobites.
description: Supp. Table
 1Results of angular
 comparisons between species PLS1 and the common PLS for each species
 (sample size &gt;20), on the cephalon (top of the table) and the pygidium
 (bottom of the table).Supplementary
 Information - cephala procrusted landmarksProcrusted landmarks
 from the cephalon of each individual.Supplementary
 Information - pygidia procrusted landmarksProcrusted landmarks
 from the pygidium of each individual.Supplementary
 Information - Rcodes for modular spaceR script for the
 computation of the modular space.
DOI: 10.5061/dryad.3c153
title: Data from: Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes beetles on La Réunion Island

description: Insects and nematodes represent the most species-rich animal taxa and they
 occur together in a variety of associations. Necromenic nematodes of the
 genus Pristionchus are found on scarab beetles with more than 30 species
 known from worldwide samplings. However, little is known about the
 dynamics and succession of nematodes and bacteria during the decomposition
 of beetle carcasses. Here, we study nematode and bacterial succession of
 the decomposing rhinoceros beetle Oryctes borbonicus on La Réunion Island.
 We show that Pristionchus pacificus exits the arrested dauer stage seven
 days after the beetles´ deaths. Surprisingly, new dauers are seen after 11
 days, suggesting that some worms return to the dauer stage after one
 reproductive cycle. We used high-throughput sequencing of the 16S rRNA
 genes of decaying beetles, beetle guts and nematodes to study bacterial
 communities in comparison to soil. We find that soil environments have the
 most diverse bacterial communities. The bacterial community of living and
 decaying beetles are more stable but one single bacterial family dominates
 the microbiome of decaying beetles. In contrast, the microbiome of
 nematodes is relatively similar even across different families. This study
 represents the first characterization of the dynamics of
 nematode-bacterial interactions during the decomposition of insects.
description: microbiomeThe data contains tables in txt format with read counts for bacterial phyla (Phylum_level_readsCountTable.txt) and families (Family_level_readsCountTable.txt) in pooled samples from five different environments (nematodes, beetle gut, decaying beetle, native soil, and decaying beetle). Zero read counts (no reads mapping to a taxonomic group) has been replaced by a value of 1e-5 to facilitate downstream analysis, such as taking the logarithm. We pooled the reads of technical replicates into one single sample by adding up the read counts, including 1e-5 values. For this reason some entries are floating point values rather than integers. Tables contain detailed information about each sample such as environment, sequencing year, decaying status, species and beetle parts information for nematode gut samples.