cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f6s45p7
title: Data from: Neotropical frogs and mating songs: the evolution of advertisement calls in glassfrogs.

description: Anurans emit advertisement calls with the purpose of attracting mates and
 repelling conspecific competitors. The evolution of call traits is
 expected to be associated with the evolution of anatomical and behavioral
 traits due to the physics of call emission and transmission. Additionally,
 since vocalizing might imply a trade-off with investment in parental care,
 the evolution of calls is expected to trade-off with parental care. Here,
 we investigated the association between body size, calling site, parental
 care and call properties (call duration, number of notes, peak frequency,
 frequency bandwidth and call structure) of the advertisement calls of
 glassfrogs (Centrolenidae)—a family of Neotropical, leaf-dwelling
 anurans—using phylogenetic comparative methods. We also explored the tempo
 and mode of evolution of these traits and compared them with those of
 three morphological traits associated with body size, locomotion and
 feeding. We generated and compiled acoustic data for 72 glassfrog species
 (46% of total species richness), including representatives of all genera.
 We found that almost all acoustic traits have significant, but generally
 modest, phylogenetic signal. Peak frequency of calls is significantly
 associated with body-size, while call structure is significantly
 associated with calling site and paternal care. Thus, the evolution of
 body size and calling site could constrain call evolution. The estimated
 disparity of acoustic traits was larger than that of morphological traits
 and the peak in disparity of acoustic traits generally occurred later in
 the evolution of glassfrogs, indicating a historically recent outset of
 the acoustic divergence in this clade.
description: Acoustic, morphometric,
 and ecological data of glassfrogs (Centrolenida)We obtained acoustic
 data from analyses of audio recordings gathered from personal and museum
 collections for 67 species and from the bibliography for 5 species. We
 obtained morphometric data for 67 glassfrog species from the literature,
 and for 11 species from fellow researchers. We compiled the predominant
 calling site of each species from the literature (72 species) and
 complemented it with field observations provided by fellow researchers. We
 compiled parental care (i.e., prolonged attendance) data from Delia et al.
 (2017). See Escalona et al., Journal of Evolutionary Biology, for more
 details.Data_Escalona_et_al_JEB.csvDataset S1. Sound records analyzed per species, with the corresponding authorship, locality, and coordinates with its source.Dataset_S1.docxDataset S2. Sound data for those species for which literature data was used.Dataset S2.docxDataset S3. Morphometric and natural history data for Centrolenidae species considered in the phylogenetic comparative analysis with corresponding sources.Dataset S3.docx
DOI: 10.5061/dryad.mb1vd
title: Data from: Do high-impact invaders have the strongest negative effects on abundant and functionally similar resident species?

description: 1.Although invasive plants may outcompete and cause local-scale
 extirpations of resident species, it is widely observed that they cause
 few extinctions at larger spatial scales. 2.One possible explanation is
 that highly successful invaders tend to be functionally similar to, and
 therefore compete most strongly with, resident species that are also
 relatively successful and widespread. High abundance may then protect
 these functionally similar residents from complete extinction over large
 areas despite their stronger competition with the invader. 3.We tested
 this idea in a native-rich grassland where a novel invader, Aegilops
 triuncialis (barb goatgrass), strongly affects community diversity at the
 local scale. We compared resident species abundances in paired invaded and
 uninvaded plots with similar soil and community characteristics and
 invasibility as assayed by experimentally planted Aegilops. 4.We found
 that the negative effects of the invader on abundance were strongest on
 resident species belonging to the same functional group as the invader
 (annual grasses). Within grasses, multivariate functional similarity to
 the invader also predicted decline in abundance under invasion. 5.However,
 we did not find the predicted general relationship between abundance,
 functional similarity to the invader, and tendency to decline under
 invasion. 6.Additional factors, such as spatial heterogeneity in the
 invaded community, must contribute to the relative scarcity of large-scale
 extinctions under invasion.
description: Community by Species
 MatrixRows are sites and
 columns are species names; Values are visual estimations of %
 cover.Year1.21Jan2015.csvPairing StructureIdentifies paired plots.Pairing.csvSoil DataSoil analysis dataSoilforRCompile2.csvFunctional TraitsTraits.2Feb2015.csv
DOI: 10.5061/dryad.b02h0
title: Data from: Problems with using rock outcrop area as a paleontological sampling proxy: rock outcrop and exposure area compared with coastal proximity, topography, land use, and lithology.

description: Fossil specimens can be recovered easily only from exposed localities, so
 rock exposure area should represent a better proxy for rock availability
 than the frequently used outcrop (i.e., map) area. Data collected via
 remote sensing and GIS show that map area does not consistently correlate
 with exposure area in different regions. Proportional rock exposure is not
 geographically consistent and is influenced by a number of variables that
 are independent of outcrop area, including proximity to the coast,
 elevation, bedrock age, land use and lithology. These variables appear to
 be non-independent in their influence on rock exposure, and are not
 consistent in their effects across continents. The inconsistency in the
 correlation between outcrop and exposure area, and the variability in the
 influence of different factors on rock exposure, suggests that using
 outcrop area as a sampling proxy is poorly supported. The weaknesses in
 using outcrop area as a sampling proxy, highlighted by the lack of
 correlation with exposure area, suggest that a single accurate global
 sampling proxy may never be attained and it is premature to assume that
 paleodiversity curves can be corrected using such proxies. It is therefore
 preferable to work on a regional scale, comparing regional fossil
 collection data with a number of proxies representing all aspects of
 sampling. The lack of correlation between outcrop and exposure area
 suggests that the covariance detected between outcrop area and
 paleodiversity might be better explained by a common-cause model, and that
 geological megabiases may not have had as profound an effect on
 paleodiversity curves as previously thought.
description: Appendix S1 10062 AM
 DUNHILLAppendix S1 referenced
 in article.Appendix S2 10062 AM
 DUNHILLAppendix S2 referenced
 in article.Appendix S3 10062 AM
 DUNHILLAppendix S3 referenced
 in article.Appendix S4 10062 AM
 DUNHILLAppendix S4 referenced
 in article.10062 AM DUNHILL RAW
 DATARemote sensing and GIS
 data used in the study. Including outcrop area, exposure area, lithology,
 elevation, bedrock age etc.
DOI: 10.5061/dryad.4kd16
title: Data from: Local interactions and global properties of wild, free-ranging stickleback shoals

description: Collective motion describes the global properties of moving groups of
 animals and the self-organized, coordinated patterns of individual
 behaviour that produce them. We examined the group-level patterns and
 local interactions between individuals in wild, free-ranging shoals of
 three-spine sticklebacks, Gasterosteus aculeatus. Our data reveal that the
 highest frequencies of near-neighbour encounters occur at between one and
 two body lengths from a focal fish, with the peak frequency alongside a
 focal individual. Fish also show the highest alignment with these
 laterally placed individuals, and generally with animals in front of
 themselves. Furthermore, fish are more closely matched in size, speed and
 orientation to their near neighbours than to more distant neighbours,
 indicating local organization within groups. Among the group-level
 properties reported here, we find that polarization is strongly influenced
 by group speed, but also the variation in speed among individuals and the
 nearest neighbour distances of group members. While we find no
 relationship between group order and group size, we do find that larger
 groups tend to have lower nearest neighbour distances, which in turn may
 be important in maintaining group order.
description: Group-level
 DataThis data was used for
 the analysis of global group patternsGroupdata.xlsxPosition and distance to centroid dataThis data was used for the analysis of spatial positioning of the individuals within shoalsPosition and distance to centroid.xlsxFocaltoNearNeighbourDifferencesThis file was used for the analysis of the relationship between topological distance and the size, speed and orientation of individuals within groups
DOI: 10.5061/dryad.6kt60
title: Data from: Reproductive ecology and isolation of Psittacanthus calyculatus and P. auriculatus mistletoes (Loranthaceae)

description: Background: Relationships between floral biology and pollinator behavior
 are important to understanding species diversity of hemiparasitic
 Psittacanthus mistletoes (c. 120 species). We aimed to investigate trait
 divergence linked to pollinator attraction and reproductive isolation (RI)
 in two hummingbird-pollinated and bird-dispersed Psittacanthus species
 with range overlap. Methods: We investigated the phylogenetic
 relationships, floral biology, pollinator assemblages, seed dispersers and
 host usage, and the breeding system and female reproductive success of two
 sympatric populations of P. calyculatus and P. auriculatus, and one
 allopatric population of P. calyculatus. Flowers in sympatry were also
 reciprocally pollinated to assess a post-mating component of RI. Results:
 Hummingbird assemblages differed between calyculatus populations, while
 allopatric plants of calyculatus opened more but smaller flowers with
 longer lifespans and produced less nectar than those in sympatry.
 Bayesian-based phylogenetic analysis indicated monophyly for calyculatus
 populations (i.e. both populations belong to the same species). In
 sympatry, calyculatus plants opened more and larger flowers with longer
 lifespans and produced same nectar volume than those of auriculatus;
 populations shared pollinators but seed dispersers and host usage differed
 between species. Nectar standing crops differed between sympatric
 populations, with lower visitation in calyculatus. Hand pollination
 experiments indicated a predominant outcrossing breeding system, with
 fruit set after interspecific pollination two times higher from
 calyculatus to auriculatus than in the opposite direction. Conclusions:
 Given the low genetic differentiation between calyculatus populations,
 observed trait divergence could have resulted from changes regarding the
 local communities of pollinators and, therefore, expected divergence for
 peripheral, allopatric populations. Using RI estimates, there were fewer
 heterospecific matings than expected by chance in P. calyculatus (RI4A =
 0.629) as compared to P. auriculatus (RI4A = 0.20). When considering other
 factors of ecological isolation that affect co-occurrence, the RI4C values
 indicate that isolation by hummingbird pollinators was less effective
 (0.20) than isolation by host tree species and seed dispersers (0.80 and
 0.60, respectively), suggesting that host usage is the most important
 ecological isolation factor between the two species. Accordingly, the
 absolute and relative cumulative strength values indicated that the host
 tree species’ barrier is currently contributing the most to maintaining
 these species in sympatry.
description: Diaz Infante et
 al_ITSITS_File: Psittacanthus
 sequences of the internal transcribed spacer (ITS) region of the nuclear
 ribosomal DNA (nrDNA) sequences.Diaz Infante et
 al_trnLFtrnL-F_File:
 Psittacanthus sequences of the trnL-F intergenic spacer region from the
 chloroplast genome (cpDNA).
DOI: 10.5061/dryad.24bn2
title: Data from: The impact of reproductive investment and early-life environmental conditions on senescence: support for the disposable soma hypothesis

description: Several hypotheses have been put forward to explain the evolution of
 senescence. One of the leading hypotheses, the disposable soma hypothesis,
 predicts a trade-off, whereby early-life investment in reproduction leads
 to late-life declines in survival (survival senescence). Testing this
 hypothesis in natural populations is challenging, but important for
 understanding the evolution of senescence. We used the long-term data set
 from a contained, predator-free population of individually marked
 Seychelles warblers (Acrocephalus sechellensis) to investigate how
 age-related declines in survival are affected by early-life investment in
 reproduction and early-life environmental conditions. The disposable soma
 hypothesis predicts that higher investment in reproduction, or
 experiencing harsh conditions during early life, will lead to an earlier
 onset, and an increased rate, of senescence. We found that both sexes
 showed similar age-related declines in late-life survival consistent with
 senescence. Individuals that started breeding at a later age showed a
 delay in survival senescence, but this later onset of breeding did not
 result in a less rapid decline in late-life survival. Although survival
 senescence was not directly related to early-life environmental
 conditions, age of first breeding increased with natal food availability.
 Therefore, early-life food availability may affect senescence by
 influencing age of first breeding. The disposable soma hypothesis of
 senescence is supported by delayed senescence in individuals that started
 breeding at a later age and therefore invested less in reproduction.
description: SurvivalAbbreviations: Bird = individual identifier; LayYear = year of birth; AFR = age of first reproduction as a dominant; ELGS = early-life group size; ELYearQual = early-life year quality; ELTQ = early-life territory quality; year = year of observation; survival = survived until the next year or notDryad_Survival.xlsxReproductive lifespan and age of first reproductionAbbreviations: BirdID = individual identifier; LayYear = year of birth; AFR = age of first reproduction as a dominant; RLS = reproductive lifespan; event = whether an individual died before the end of the study period; NatalGS = natal group size; NatalYQ = natal year quality; NatalTQ = Natal territory qualityDryad_AFR_RLS.xlsx
DOI: 10.5061/dryad.46320g1
title: Data from: Acid-sensing ion channels emerged over 600 MYA and are conserved throughout the deuterostomes

description: Acid-sensing ion channels (ASICs) are proton-gated ion channels broadly
 expressed in the vertebrate nervous system, converting decreased
 extracellular pH into excitatory sodium current. ASICs were previously
 thought to be a vertebrate-specific branch of the DEG/ENaC family, a
 broadly conserved but functionally diverse family of channels. Here, we
 provide phylogenetic and experimental evidence that ASICs are conserved
 throughout deuterostome animals, showing that ASICs evolved over 600
 million years ago. We also provide evidence of ASIC expression in the
 central nervous system of the tunicate, Oikopleura dioica. Furthermore, by
 comparing broadly related ASICs, we identify key molecular determinants of
 proton sensitivity and establish that proton sensitivity of the ASIC4
 isoform was lost in the mammalian lineage. Taken together, these results
 suggest that contributions of ASICs to neuronal function may also be
 conserved broadly in numerous animal phyla.
description: Fig_1A_deuterostome_ASIC_cDNA_sequencesThese cDNAs were inserted into the pSP64 polyA vector before cRNA tanscription and expression in oocytes.Fig_3_Alignment_Vertebrate_ASIC4MAFFT alignment used for ASIC4 phylogeny in Figure 3.Fig_3_vertebrate_ASIC4_cDNA_sequencescDNA sequences for novel ASIC4s from Figure 3. cDNAs were inserted into pSP64 polyA vector before cRNA transciprtion and expression in oocytes.Fig_4_ASIC4_ASIC1a_chimera_cDNA_sequencescDNA sequences of chimeras tested in Figure 4. All cDNAs were inserted into pSP64 vector before cRNA transcription and expression in oocytes.Fig_S1_Alignment_Deuterostome_DEGENaCMAFFT alignment of DEG ENaC sequences from various deuterostomes contributing to phylogeny in Fig S1A.Fig_S1A_Oikopleura_dioica_cDNA_sequencescDNA sequences of DEG ENaC subunits from Oikopleura dioica, shown with asterisks in Figure S1A. cDNAs were inserted into pSP64 poly A vector before cRNA transcription and expression in oocytes.
DOI: 10.15468/dl.s6t3zr
title: Occurrence Download

description: A dataset containing 873 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Pituophis catenifer",
 "Year 1960-2026"
 ]
}

 The dataset includes 873 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000837-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.38c5g
title: Data from: Fight or flight? - Flight increases immune gene expression but does not help to fight an infection

description: Flight represents a key trait in most insects, being energetically
 extremely demanding, yet often necessary for foraging and reproduction.
 Additionally, dispersal via flight is especially important for species
 living in fragmented landscapes. Even though, based on life-history
 theory, a negative relationship may be expected between flight and
 immunity, a number of previous studies have indicated flight to induce an
 increased immune response. In this study, we assessed whether induced
 immunity (i.e. immune gene expression) in response to 15min forced flight
 treatment impacts individual survival of bacterial infection in the
 Glanville fritillary butterfly (Melitaea cinxia). We were able to confirm
 previous findings of flight induced immune gene expression, but still
 observed substantially stronger effects on both gene expression levels and
 lifespan due to bacterial infection compared to flight treatment. Even
 though gene expression levels of some immunity-related genes were elevated
 due to flight, these individuals did not show increased survival of
 bacterial infection, indicating that flight induced immune activation does
 not protect them from the negative effects of bacterial infection.
 Finally, an interaction between flight and immune treatment indicated a
 potential trade-off: flight treatment increased immune gene expression in
 naïve individuals only, whereas in infected individuals no increase in
 immune gene expression was induced by flight. Our results suggest that the
 up-regulation of immune genes upon flight is based on a general stress
 response rather than reflects an adaptive response to cope with potential
 infections during flight or in new habitats.
description: Raw Ct values
 qPCRContains information on
 raw Ct values for all used genes used in this study. Additionally the file
 contains information on the individuals used to obtain these Ct values in
 the study.Dryad_Raw Ct
 values.xlsxPhenotypic
 dataContains information on
 phenotypic traits for all individuals used in this
 study.
DOI: 10.5061/dryad.2cf46
title: Data from: The role of transcriptomes linked with responses to light environment on seedling mortality in a subtropical forest, China

description: Differences in seedling survival in trees have a lasting imprint on
 seedling, juvenile and adult community structure. Identifying the drivers
 of these differences, therefore, is a critical research objective that
 ultimately requires knowledge regarding how organismal function interacts
 with the local environment to influence survival rates. In tree
 communities, differences in light use strategies are frequently invoked to
 explain differences in seedling demographic performance through growth and
 survival trade-offs. For example, shade-tolerant species grow slowly and
 have higher survival rates, whereas shade-intolerant species grow quickly
 but have lower survival rates. Thus, functional traits related to
 photosynthesis should be strong predictors of demographic rates, but
 results in the literature are mixed indicating that additional or
 alternative information regarding organismal function should be
 considered. Here, we provide a community-wide inventory of transcriptomes
 in a subtropical tree community. This information is utilized to determine
 the degree to which species share homologous genes related to gene
 ontologies for light use and harvesting. These species similarities are
 used in neighbourhood generalized linear mixed-effects models of seedling
 survival that evaluated seedling survival as a function of the
 transcriptomic, functional trait and phylogenetic composition of the local
 neighbourhood. The results show neighbourhood similarity in three of the
 15 gene ontologies evaluated are significantly related to survival rates
 based on neighbourhood composition. For two of these ontologies, survival
 rates increase when neighbours are similar in their gene tree composition
 indicating the importance of abiotic filtering and performance
 hierarchies. Synthesis. The present work takes a novel approach by
 sequencing the transcriptomes of naturally co-occurring tree species in a
 subtropical forest in China. The results show that the transcriptomic
 similarity of species is a significant predictor of differential survival.
 The study demonstrates that exploring the functional genomic similarity of
 non-model species in nature has the potential to increase the breadth and
 depth of our understanding of how gene function influences species
 co-occurrence and population dynamics in communities.
description: Hanetal.2017.JEcol