cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bp6gv
title: Data from: Diversification of the genus Anopheles and a Neotropical clade from the Late Cretaceous

description: The Anopheles genus is a member of the Culicidae family and consists of
 approximately 460 recognized species. The genus is composed of 7 subgenera
 with diverse geographical distributions. Despite its huge medical
 importance, a consensus has not been reached on the phylogenetic
 relationships among Anopheles subgenera. We assembled a comprehensive
 dataset comprising the COI, COII and 5.8S rRNA genes and used maximum
 likelihood and Bayesian inference to estimate the phylogeny and divergence
 times of six out of the seven Anopheles subgenera. Our analysis reveals a
 monophyletic group composed of the three exclusively Neotropical
 subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to
 diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age
 of the last common ancestor of the Anopheles genus was ca. 110 Ma. The
 monophyly of all Anopheles subgenera was supported, although we failed to
 recover a significant level of statistical support for the monophyly of
 the Anopheles genus. The ages of the last common ancestors of the
 Neotropical clade and the Anopheles and Cellia subgenera were inferred to
 be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to
 statistically support the monophyly of the Anopheles genus because of an
 unresolved polytomy between Bironella and A. squamifemur.
description: AlignmentConcatenated alignment in nexus formatconcat.nexDatadata.zip
DOI: 10.5061/dryad.516s0
title: Data from: Temporal and spatial activity-associated energy partitioning in free-swimming sea snakes

description: 1. Partitioning energy between critical basal functions and
 activity-associated behaviours is a primary determinant of animal
 survival. Consequently, habitat selection is likely to be driven by the
 efficiency with which resources can be acquired from a heterogeneous
 energy landscape. 2. Determining how energy partitioning is achieved
 across temporal and spatial scales is particularly challenging in aquatic
 animals due to the logistical limitations in estimating field metabolic
 rates (FMR) while simultaneously examining habitat choice. 3. Here,
 accelerometry telemetry and bimodal respirometry were used to correlate
 vectorial dynamic body acceleration (VeDBA) with oxygen consumption rates
 (V̇o2) of sea snakes (Hydrophis curtus and H. elegans) across an
 ecologically-relevant temperature range. Subsequently, VeDBA of
 free-roaming snakes was used to estimate activity-associated FMR within a
 near-shore environment over diel, seasonal and spatial scales. 4. Diel
 changes in activity explained short-term patterns in FMR, whereas seasonal
 changes in water temperature drove long-term patterns. Spatial analyses
 demonstrated that activity-associated FMR was elevated in productive
 seagrass and mudflat habitats, indicative of a concentration of foraging
 efforts. 5. Our findings illustrate for the first time how sea snakes
 partition activity-associated FMR across time and space, providing an
 approach by which we can monitor the impacts of, and vulnerabilities to,
 natural and anthropogenic disturbances like warming and trawl fisheries.
description: FE-2016-00921
 PackagePackage containing all
 processed data used for all analyses in the paper FE-2016-00921. Data
 package contains a .csv file with data used to construct laboratory
 calibration equations relating bimodal metabolic rates in sea snakes to
 body acceleration. Data package also contains a .csv file with field
 acceleration data and estimated field metabolic rates for all individuals
 in this study.
DOI: 10.5061/dryad.k46k2
title: Data from: Early development of vocal interaction rules in a duetting songbird

description: Exchange of vocal signals is an important aspect of animal communication.
 Although birdsong is the premier model for understanding vocal
 development, the development of vocal interaction rules in birds and
 possible parallels to humans have been little studied. Many tropical
 songbirds engage in complex engage in vocal interactions in the form of
 duets between mated pairs. In some species duets show precise temporal
 coordination and follow rules (duet codes) governing which song type one
 bird uses to reply to each of the song types of its mate. We determined
 whether these duetting rules are acquired during early development in
 canebrake wrens. Results show that juveniles acquire a duet code by
 singing with a mated pair of adults and that juveniles gradually increase
 their fidelity to the code over time. Additionally, we found that
 juveniles exhibit poorer temporal coordination than adults and improve
 their coordination as time progresses. Human turn-taking, an analogous
 rule to temporal coordination, is learned during early development. We
 report that the ontogeny of vocal interaction rules in songbirds is
 analogous to that of human conversation rules.
description: duet codes juveniles vs
 adultsDuet code adherence of
 juveniles vs adultsduet codes juvs vs adults
 2017.csvData file juvenile duet
 codesDuet code adherence of
 juveniles over timeduet codes juvs only
 2017.csvDuet coordination adults
 vs. juvenilesData file of duet
 coordination adults vs. juvenilesDuet coordination adult vs juvs
 2017.xlsxjuvenile script
 2017R
 script with all analyses performedDuet coordination only
 juvsData file of duet
 coordination in juveniles by date
DOI: 10.5061/dryad.15081
title: Data from: Heritable variation in circulating glucocorticoids and endocrine flexibility in a free-living songbird

description: Phenotypic flexibility is a central way that organisms cope with
 challenging and changing environments. As endocrine signals mediate many
 phenotypic traits, heritable variation in hormone levels, or their
 context-dependent flexibility, could present an important target for
 selection. Several studies have estimated the heritability of circulating
 glucocorticoid levels under acute stress conditions, but little is known
 about the potential for either baseline hormone levels or rapid endocrine
 flexibility to evolve. Here we assessed the potential for selection to
 operate on the elevation (circulating hormone levels) and flexibility of
 glucocorticoid reaction norms to acute restraint stress. Multivariate
 animal models revealed low but significant heritability in baseline
 (h2=0.13-0.14) and stress-induced glucocorticoids (h2=0.18), and moderate
 heritability in glucocorticoid flexibility in response to acute stress
 (h2=0.38) in free-living juvenile tree swallows (Tachycineta bicolor;
 n=408). Baseline glucocorticoids were not genetically correlated with
 either stress-induced glucocorticoids or glucocorticoid flexibility. These
 findings indicate that baseline glucocorticoids and the acute stress
 response are distinct traits that can be independently shaped by
 selection. Microevolutionary changes that influence the expression or
 flexibility of these endocrine mediators of phenotype may be an important
 way that populations adapt to changing environments and novel threats.
description: Pedigree and phenotypic
 dataData on genetic
 parentage, rearing environment, and phenotype of nestling tree
 swallowsStedman et
 al_Heritability.xls
DOI: 10.5061/dryad.b3bn2
title: Data from: Body composition QTLs identified in intercross populations are reproducible in consomic mouse strains

description: Genetic variation contributes to individual differences in obesity, but
 defining the exact relationships between naturally occurring genotypes and
 their effects on fatness remains elusive. As a step toward positional
 cloning of previously identified body composition quantitative trait loci
 (QTLs) from F2 crosses of mice from the C57BL/6ByJ and 129P3/J inbred
 strains, we sought to recapture them on a homogenous genetic background of
 consomic (chromosome substitution) strains. Male and female mice from
 reciprocal consomic strains originating from the C57BL/6ByJ and 129P3/J
 strains were bred and measured for body weight, length, and adiposity.
 Chromosomes 2, 7, and 9 were selected for substitution because previous F2
 intercross studies revealed body composition QTLs on these chromosomes. We
 considered a QTL confirmed if one or both sexes of one or both reciprocal
 consomic strains differed significantly from the host strain in the
 expected direction after correction for multiple testing. Using these
 criteria, we confirmed two of two QTLs for body weight (Bwq5-6), three of
 three QTLs for body length (Bdln3-5), and three of three QTLs for
 adiposity (Adip20, Adip26 and Adip27). Overall, this study shows that
 despite the biological complexity of body size and composition, most QTLs
 for these traits are preserved when transferred to consomic strains; in
 addition, studying reciprocal consomic strains of both sexes is useful in
 assessing the robustness of a particular QTL.
description: Data for Mouse Phenome
 Database_Reed_Bachmanov_June_2015Contains body
 composition data for consomic mice
DOI: 10.5061/dryad.8vm8d
title: Data from: Batch effects in a multi-year sequencing study: false biological trends due to changes in read lengths

description: High-throughput sequencing is a powerful tool, but suffers biases and
 errors that must be accounted for to prevent false biological conclusions.
 Such errors include batch effects, technical errors only present in
 subsets of data due to procedural changes within a study. If overlooked
 and multiple batches of data are combined, spurious biological signals can
 arise, particularly if batches of data are correlated with biological
 variables. Batch effects can be minimized through randomisation of sample
 groups across batches. However, in long-term or multi-year studies where
 data are added incrementally, full randomisation is impossible and batch
 effects may be a common feature. Here we present a case study where false
 signals of selection were detected due to a batch effect in a multi-year
 study of Alpine ibex (Capra ibex). The batch effect arose because
 sequencing read length changed over the course of the project and
 populations were added incrementally to the study, resulting in non-random
 distributions of populations across read lengths. The differences in read
 length caused small misalignments in a subset of the data, leading to
 false variant alleles and thus false SNPs. Pronounced allele frequency
 differences between populations arose at these SNPs because of the
 correlation between read length and population. This created highly
 statistically significant, but biologically spurious, signals of selection
 and false associations between allele frequencies and the environment. We
 highlight the risk of batch effects and discuss strategies to reduce the
 impacts of batch effects in multi-year high-throughput sequencing studies.
description: False SNPs caused by
 batch effectThis file is a vcf file
 containing the SNP calls at the eight SNPs identified as outliers. Seven
 of these SNPs were false variants caused by differences in read
 length.outlier.snps.C.ibex.batch.effects.recode.vcfdemultiplexing.file.Alpine.ibex.Capra.ibexThe demultiplexing file. Includes the sample name, population, sex, the barcodes used, sequencing length and data generator.VCF_filterPolym.Lischer.H.E.LScript to remove SNPs only polymorphic relative to the genome. This was used to remove SNPs when aligning Capra ibex RADseq to the Capra domestica genome.
DOI: 10.5061/dryad.jr747k3
title: Data from: Convergent evolution of locomotor morphology but not performance in gymnotiform swimmers

description: Convergent evolution of a novel locomotor strategy implies that a fitness
 benefit may be associated with the new gait. Opportunities to study this
 phenomenon are often constrained by a lack of transitional taxa, but
 teleost fishes offer examples of extant species across such evolutionary
 shifts in gait. For instance, one species from Osteoglossiformes and the
 entire order of Gymnotiformes independently evolved a novel gait,
 gymnotiform locomotion, where thrust is produced by the undulation of an
 elongate anal fin. Here, we investigate whether this convergence in gait
 is also associated with similarities in shape, burst swimming abilities,
 and/or steady‐swimming energetics. Specifically, we measured body and fin
 morphology of fish within Gymnotiformes and Osteoglossiformes, along with
 closely related Siluriformes and Cypriniformes, to examine the link
 between gymnotiform locomotion and morphology in a phylogenetic context.
 Second, we tested the burst swimming capabilities and oxygen consumption
 during endurance swimming of a subset of the same gymnotiform,
 osteoglossiform, and cypriniform species, including “transitional”
 Osteoglossiformes that exhibit intermediate gaits, to determine if the
 evolution of this specialized gait is associated with a change in either
 of these performance metrics. Our results suggest that convergence on the
 gymnotiform gait is associated with morphological convergence, but does
 not constrain a fish's maximum sprinting speeds or their energetic
 demands during steady swimming.
description: Linear morphological
 measurements of 89 speciesSpecies averages of
 linear morphological measurements collected on 89 species. These data were
 used to run the principle components analysis shown in Figure 1.
 Abbreviations are given in Table S2.WhitlowSantiniOufiero2018_MuseumSpecimenMorphology.csvCost of transport data (Uopt and MinCOT)Contains swimming mode, minimum cost of transport (minCOT), and speed at minCOT (Uopt), along with individual fish ID, temperature, and morphological PCA values for each individual of seven species tested. These data were used to create Figure 3.WhitlowSantiniOufiero2018_CostOfTransportData.csvPhylogenetic treePhylogenetic tree used to generate the phylomorphospace depicted in Figure 1 and to correct swimming performance metrics for phylogenetic relatedness using the PGLMM method described in the paper. GenBank accession numbers are provided in Table S1 and sequence alignments are available upon request.WhitlowSantiniOufiero2018_Phylogeny.treeMaximum sprint speed dataContains the highest speed achieved during all sprinting trials, swimming mode, individual ID, temperature, and morphological PCA values for each fish tested for performance. These data were used to create Figure 2.WhitlowSantiniOufiero2018_MaxSprintData.csv
DOI: 10.5061/dryad.hf823
title: Data from: Implicit racial attitudes influence perceived emotional intensity on other-race faces

description: An ability to accurately perceive and evaluate out-group members'
 emotions plays a critical role in intergroup interactions. Here we showed
 that Chinese participants' implicit attitudes toward White people
 bias their perception and judgment of emotional intensity of White
 people's facial expressions such as anger, fear and sadness. We found
 that Chinese participants held pro-Chinese/anti-White implicit biases that
 were assessed in an evaluative implicit association test (IAT). Moreover,
 their implicit biases positively predicted the perceived intensity of
 White people's angry, fearful and sad facial expressions but not for
 happy expressions. This study demonstrates that implicit racial attitudes
 can influence perception and judgment of a range of emotional expressions.
 Implications for intergroup interactions were discussed.
description: Implicit racial
 attitudes, emotional intensity, other-race faces, Chinese
 participantsData.rar
DOI: 10.5061/dryad.ps326
title: Data from: Effects of perceived predation risk and social environment on the development of three-spined stickleback (Gasterosteus aculeatus) morphology

description: Phenotypically plastic changes in response to variation in perceived
 predation risk are widespread, but little is known about if and how social
 environment modulates induced responses to predation risk. We investigated
 the influence of perceived predation risk (i.e. chemical cues from a
 predator) and social environment (i.e. one, two or 20 individuals reared
 together) on three-spined stickleback (Gasterosteus aculeatus) morphology
 in a factorial common garden experiment. We found that exposure to
 chemical cues from potential predators did not influence growth or body
 condition or induce more robust morphological defences (i.e. lateral plate
 numbers and dorsal spine lengths). However, sticklebacks exposed to
 predator cues developed longer caudal peduncles and larger eyes as
 compared with fish from the control treatment. As these responses may
 improve sticklebacks’ ability to avoid piscine predation, they might be
 adaptive. Social environment/density also influenced expression of some
 traits, but these effects were independent of predation-risk treatment
 effects. In general, these results suggest that apart from the classic
 morphological defence structures, which appear mostly constitutive,
 three-spined sticklebacks are capable of expressing potentially adaptive
 morphological responses to chemical cues from potential predators.
description: Three-spine stickleback
 morphologyThis file contains the
 primary data underlying the analyses described in the published article.
 The first tab of the file includes explanation of the variables (columns)
 in the second tab which contains the data.BJLS_data.xlsx
DOI: 10.5061/dryad.6q1q6
title: Data from: Nuclear DNA based species delineations of Coccus scale insects in symbiosis with plants and ants, and the role of plant epicuticular wax in structuring associations

description: We undertook phylogenetic analysis of nuclear DNA to elucidate species
 boundaries in the symbiotic Coccus scale insects associated with
 mutualistic Crematogaster ants and Macaranga plants occurring in the
 ever-wet forests of Southeast Asia. The coccid specimens clustered into
 ten lineages, each corresponding to a morphospecies assignment. The
 lineage identified as C. secretus was separated from the Main Clade by an
 outgroup. We also examined all pairwise associations among the three
 symbiont guilds to understand how patterns of association were structured.
 The analyses revealed that each ant, plant or coccid operational
 (taxonomic) unit often associated with multiple O(T)Us of each of the
 other two guilds. However, where testing was feasible, a ‘preference’ for
 one or sometimes two partner O(T)Us of each guild was often detected.
 Mutual ‘preferences’ or ‘avoidances’ were relatively common among the
 symbionts, and no conflicts of interest were apparent. The network of
 preferred partners among all three guilds showed compartmentalization
 structured by the presence/absence of plant epicuticular wax, suggesting
 that this feature plays a fundamental role in how the symbionts select
 partners that best serve their needs. To a lesser degree, the network was
 also structured by whether the host plant stems were ant-excavated or
 hollowed naturally.
description: Ant
 ListAn Excel spreadsheet
 listing ant specimens used in the publication, with accompanying
 information on their mtDNA lineages, locality, host plant, and coccid
 associate (where present).Coccus list Table
 S1An
 Excel spreadsheet listing all Coccus specimens used for the publication,
 their morphospecies assignments and nuclear DNA clade, and including
 information on their host plants, host ants, and
 location.Ant Plant Coccus counts
 for binomial testsAn Excel spreadsheet
 showing how counts for the binomial tests were tallied, relying on
 information in the other two accompanying files in this data package (Ant
 list.xlsx & Coccus list Table S1.xlsx). Each of the six sets of tests
 has its own sheet.
DOI: 10.5061/dryad.2j5r8v6v
title: Data from: Propagule pressure and colony social organization are associated with the successful invasion and rapid range expansion of fire ants in China

description: We characterized patterns of genetic variation in populations of the fire
 ant Solenopsis invicta in China using mitochondrial DNA sequences and
 nuclear microsatellite loci to test predictions as to how propagule
 pressure and subsequent dispersal following establishment jointly shape
 the invasion success of this ant in this recently invaded area. Fire ants
 in Wuchuan (Guangdong province) are genetically differentiated from those
 found in other large infested areas of China. The immediate source of ants
 in Wuchuan appears to be somewhere near Texas, which ranks first among
 states in the southern USA infested states in the exportation of goods to
 China. Most colonies from spatially distant, outlying areas in China are
 genetically similar to one another and appear to share a common source
 (Wuchuan, Guangdong province), suggesting that long-distance jump
 dispersal has been a prevalent means of recent spread of fire ants in
 China. Furthermore, most colonies at outlier sites are of the polygyne
 social form (featuring multiple egg-laying queens per nest), reinforcing
 the important role of this social form in the successful invasion of new
 areas and subsequent range expansion following invasion. Several analyses
 consistently revealed characteristic signatures of genetic bottlenecks for
 S. invicta populations in China. The results of this study highlight the
 invasive potential of this pest ant, suggest that the magnitude of
 international trade may serve as a predictor of propagule pressure and
 indicate that rates and patterns of subsequent range expansion are partly
 determined by the interplay between species traits and the trade and
 transportation networks.
description: Yang_et_al_msat_genotypesThis file was created in Excel and includes the multilocus microsatellite genotypes for all individuals used in this study.
DOI: 10.5061/dryad.9037
title: Data from: A fuzzy-set-theory-based approach to analyze species membership in DNA barcoding

description: Reliable assignation of an unknown query sequence to its correct species
 remains a methodological problem for the growing field of DNA barcoding.
 While great advances have been achieved recently, species identification
 from barcodes can still be unreliable if the relevant biodiversity has
 been insufficiently sampled. We here propose a new notion of species
 membership for DNA barcoding - fuzzy membership, based on fuzzy set theory
 - and illustrate its successful application to four real datasets (bats,
 fishes, butterflies and flies) with more than 5000 random simulations. Two
 of the datasets comprise especially dense species/population level
 samples. In comparison with current DNA barcoding methods, the newly
 proposed minimum distance (MD) plus fuzzy set approach, and another
 computationally simple method, “best close match”, outperform two
 computationally sophisticated Bayesian and BootstrapNJ methods. The new
 method proposed here has great power in reducing false positive species
 identification compared with other methods when conspecifics of the query
 are absent from the reference database.
description: datasetsFour real datasets used in this study are included here (Bat.fas, Fish.fas, Butterfly.fas and Fly.fas).