cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02vs1
title: Data from: No evidence that genetic compatibility drives extra-pair behavior in female blue-footed boobies

description: The function of female birds' extra-pair (EP) behavior has remained
 an unresolved question in ornithology and behavioral ecology for &gt;
 30 yr. The genetic compatibility hypothesis (GCH) proposes that females
 benefit by acquiring biological sires that yield more heterozygous, and
 therefore fitter, offspring than their social mates. We used ten
 polymorphic microsatellite loci to test GCH predictions and its assumption
 that fitness increases with heterozygosity in blue-footed boobies Sula
 nebouxii, a long-lived tropical seabird. Our predictions were not
 supported. Heterozygosity was uncorrelated with quality indicators
 (fledging probability, fledgling or adult body size or mass, adult
 ornamentation, mean breeding success). Females were no more likely to have
 EP behavior or chicks when their social mates were less heterozygous or
 compatible, nor were EP males more heterozygous or compatible than the
 males they cuckolded. Finally, EP chicks were no more heterozygous than
 within-pair chicks overall or in half-sib comparisons, nor were
 within-pair chicks from all-within-pair nests more heterozygous that those
 with EP nest-mates. There are both methodological and biological
 explanations for these consistently negative results. Inadequate sample
 size is possible but unlikely, since our samples were comparable or larger
 than those of similar studies with significant findings. Lack of identity
 disequilibrium (within-individual heterozygosity correlation) among our
 marker loci could be responsible, and suggests either insufficient marker
 coverage or lack of inbreeding, bottleneck, and/or admixture. An
 independent social pedigree revealed infrequent inbreeding, suggesting
 that pressure on females to select sires that maximize offspring
 heterozygosity may be genuinely lax. Alternatively, it is possible that
 the GCH is only upheld when selection on young is strongest; this would
 not be detected in our sample, which was taken during an extremely
 productive year. Whatever their cause, our results expand the taxonomic
 breadth of avian EP behavior analyses and should be considered in future
 evaluations of the GCH.
description: BFB
 microsat/fitness/EPPBlue-footed booby
 heterozygosity, relatedness, fitness, extra-pair paternity, and pedigree
 data. Tables contained in the dataset and variables are described in the
 first worksheet ("Table and Variable Descriptions"), and each
 dataset in a separate worksheet of the Excel file.HetDryad.xlsx
DOI: 10.5061/dryad.5kh0b362
title: Data from: Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling

description: There is a well-established allometric relationship between brain and body
 mass in mammals. Deviation of relatively increased brain size from this
 pattern appears to coincide with enhanced cognitive abilities. To examine
 whether there is a phylogenetic structure to such episodes of changes in
 encephalization across mammals, we used phylogenetic techniques to analyse
 brain mass, body mass and encephalization quotient (EQ) among 630 extant
 mammalian species. Among all mammals, anthropoid primates and odontocete
 cetaceans have significantly greater variance in EQ, suggesting that
 evolutionary constraints that result in a strict correlation between brain
 and body mass have independently become relaxed. Moreover, ancestral state
 reconstructions of absolute brain mass, body mass and EQ revealed patterns
 of increase and decrease in EQ within anthropoid primates and cetaceans.
 We propose both neutral drift and selective factors may have played a role
 in the evolution of brain–body allometry.
description: Brain and Body
 Measurements of MammalsThis database includes
 individual brain and body measurements collected from literature sources
 and our own collection (Sherwood). The second column "Species Name
 (from original article)" is the name that was used in the published
 article, however, some articles were very old and the names have now been
 updated (see column 1 for the most recent name). In some cases, age class
 or body mass was estimated from Silva & Downing 1995. Please see the
 Notes column for these instances. For the dataset from Mace et al. (1981),
 we corrected for measurement error by subtracting 0.59 g from all rodent
 species from this dataset as proposed by Isler & van Schaik
 (2006).brain_body_database_v2.txt
DOI: 10.5061/dryad.c6344
title: Data from: Communication value of mistakes in dark-eyed junco song

description: Sexual signals contain information on individual quality or motivation,
 and most explanations for their reliability are based on signal costs. A
 recent suggestion is that signaling mistakes, defined as deviations from
 typical signal design, provide cues on individual quality, contributing to
 reliable communication even when signal design is not costly. We describe
 several atypical song traits in dark-eyed juncos (Junco hyemalis) that may
 be mistakes during song production or development and occur in up to 6% of
 songs. These putative mistakes were more frequent in an urban versus a
 wildland population, and individuals differed in their frequency of
 mistakes. Some atypical signals were more frequent in younger males or
 were negatively related to paternity success, supporting the hypothesis
 that fewer mistakes indicate individual quality. We also discuss
 unexpected results, such as some atypical signals being more frequent in
 more ornamented males and in songs with lower performance demands. Song
 consistency (similarity across syllable renditions) was positively related
 to male age and paternity success; nonetheless, relations with paternity
 were stronger when looking at the most deviant syllable renditions,
 suggesting that the perceptual salience of large mistakes may mediate
 receiver responses to song consistency. Results indicate that signaling
 mistakes reveal relevant information to play a role in communication.
description: DatasetFerreira et al 2016 Am Nat Dryad.xls
DOI: 10.5061/dryad.256kh
title: Data from: Global invasion history of the Tropical Fire Ant: a stowaway on the first global trade routes

description: Biological invasions are largely thought to be contemporary, having
 recently increased sharply in the wake of globalization. However, human
 commerce had already become global by the mid-16th century when the
 Spanish connected the New World with Europe and Asia via their Manila
 galleon and West Indies trade routes. We use genetic data to trace the
 global invasion of one of the world's most widespread and invasive
 pest ants, the Tropical Fire Ant, Solenopsis geminata. Our results reveal
 a pattern of introduction of Old World populations that is highly
 consistent with historic trading routes suggesting that Spanish trade
 introduced the Tropical Fire Ant to Asia in the 16th century. We identify
 southwestern Mexico as the most likely source for the invasive
 populations, which is consistent with the use of Acapulco as the major
 Spanish port on the Pacific Ocean. From there, the Spanish galleons
 brought silver to Manila, which served as a hub for trade with China. The
 genetic data document a corresponding spread of S. geminata from Mexico
 via Manila to Taiwan and from there, throughout the Old World. Our
 descriptions of the worldwide spread of S. geminata represent a rare
 documented case of a biological invasion of a highly invasive and globally
 distributed pest species due to the earliest stages of global commerce.
description: Read
 MeContents of files
 submitted to DataDryadREAD
 MEgeminata_msats_datasetmicrosatellite data in Genepop formatgeminata_mtDNA_datasetmitochondrial COI data in NEXUS formatBEAST1.7.5BEAST XML file for Bayesian analysis of COI dataStructurama2.0_inputStructurama2 msat input file for Bayesian clusteringDAPC R codeR commands for DAPC analyses in the adegenet1.3-8 package.msat_20regionsRegional assignments for DAPC analyses.msat_coordinatesCollection coordinates for DAPC analyses.ABC_AnalysisA_headerHeader file for DIY ABC analysis A.ABC_AnalysisB_headerHeader file for DIY ABC analysis B.ABC_AnalysisC_headerHeader file for DIY ABC analysis C.ABC_AnalysisD_headerHeader file for DIY ABC analysis D.
DOI: 10.5061/dryad.8sn65
title: Data from: Identification of North Sea molluscs with DNA barcoding

description: Sequence-based specimen identification, known as DNA barcoding, is a
 common method complementing traditional morphology-based taxonomic
 assignments. The fundamental resource in DNA barcoding is the availability
 of a taxonomically reliable sequence database to use as a reference for
 sequence comparisons. Here, we provide a reference library including 579
 sequences of the mitochondrial cytochrome c oxidase subunit I for 113
 North Sea mollusc species. We tested the efficacy of this library by
 simulating a sequence-based specimen identification scenario using Best
 Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with
 three different threshold values. Each identification result was compared
 with our prior morphology-based taxonomic assignments. Our simulation
 resulted in 87.7% congruent identifications (93.8% when excluding
 singletons). The highest number of congruent identifications was obtained
 with BCM and ASB and a 0.05 threshold. We also compared identifications
 with genetic clustering (Barcode Index Numbers, BINs) computed by the
 Barcode of Life Datasystem (BOLD). About 68% of our morphological
 identifications were congruent with BINs created by BOLD. Forty-nine
 sequences were clustered in 16 discordant BINs, and these were divided in
 two classes: sequences from different species clustered in a single BIN
 and conspecific sequences divided in more BINs. Whereas former
 incongruences were probably caused by BOLD entries in need of a taxonomic
 update, the latter incongruences regarded taxa requiring further
 investigations. These include species with amphi-Atlantic distribution,
 whose genetic structure should be evaluated over their entire range to
 produce a reliable sequence-based identification system.
description: COI
 alignmentAlignment of 579 COI
 sequences used for the analyses.North_Sea_molluscs_COI.fasFigure F1Neighbor-Joining tree based on K2P distances of 579 COI sequences from North Sea molluscs.North_Sea_molluscs_COI.nwk
DOI: 10.5061/dryad.1m2v66g
title: Data from: Asymmetric evolutionary responses to sex-specific selection in a hermaphrodite

description: Sex allocation theory predicts that simultaneous hermaphrodites evolve to
 an evolutionary stable resource allocation, whereby any increase in
 investment to male reproduction leads to a disproportionate cost on female
 reproduction and vice-versa. However, empirical evidence for sexual
 trade-offs in hermaphroditic animals is still limited. Here, we tested how
 male and female reproductive traits evolved under conditions of reduced
 selection on either male or female reproduction for 40 generations in a
 hermaphroditic snail. This selection favors a reinvestment of resources
 from the sex function under relaxed selection towards the other function.
 We found no such evolutionary response. Instead, juvenile survival and
 male reproductive success significantly decreased in lines where selection
 on the male function (i. e., sexual selection) was relaxed, while relaxing
 selection on the female function had no effect. Our results suggest that
 most polymorphisms under selection in these lines were not
 sex-antagonistic. Rather, they were deleterious mutations affecting
 juvenile survival (thus reducing both male and female fitness) with strong
 pleiotropic effects on male success in a sexual selection context. These
 mutations accumulated when sexual selection was relaxed, which supports
 the idea that sexual selection in hermaphrodites contributes to purge the
 mutation load from the genome as in separate-sex organisms.
description: Behavioral dataset for
 the G20 assayG20.behavior.traits.csvDataset for the G20 assay - female reproductive traisG20.female.rep.function.csvDataset for the G20 assay - Male reproductive traitsG20.male.rep.function.csvDataset for the G35 assay - Male and female behavioral traitsG35.behavior.traits.csvDataset for the G35 assay - Weight and male and female reproductive traitsG35.reproductive.traits.csvDataset for the G38 assay - male and female behavioral traitsG38.behavior.traits.csvDataset for the G38 assay - weight and male and female reproductive traitsG38.reproductive.traits.csv
DOI: 10.5061/dryad.cb850
title: Data from: Coevolutionary patterns and diversification of ant-fungus associations in the asexual fungus-farming ant Mycocepurus smithii in Panama

description: Partner fidelity through vertical symbiont transmission is thought to be
 the primary mechanism stabilizing cooperation in the mutualism between
 fungus-farming (attine) ants and their cultivated fungal symbionts. An
 alternate or additional mechanism could be adaptive partner or symbiont
 choice mediating horizontal cultivar transmission or de novo domestication
 of free-living fungi. Using microsatellite-genotyping for the attine ant
 Mycocepurus smithii and ITS rDNA-sequencing for fungal cultivars, we
 provide the first detailed population-genetic analysis of local ant-fungus
 associations to test for the relative importance of vertical versus
 horizontal transmission in a single attine species. M. smithii is the only
 known asexual attine ant, and it is furthermore exceptional because it
 cultivates a far greater cultivar diversity than any other attine ant.
 Cultivar switching could permit the ants to re-acquire cultivars after
 garden loss, to purge inferior cultivars that are locally mal-adapted or
 that accumulated deleterious mutations under long-term asexuality.
 Compared to other attine ants, symbiont choice and local adaptation of
 ant-fungus combinations may play a more important role than partner
 fidelity feedback in the co-evolutionary process of M. smithii and its
 fungal symbionts.
description: Msmithii microsatellite
 genotype dataThis is a word document
 which contains information about microsatellite genotypic data of the ant
 M. smithii in Panama. See README file for further
 explanation.Msmithii_Microsatellite_Genotype_DATA.doc
DOI: 10.5061/dryad.65286
title: Data from: The strength of negative plant-soil feedback increases from the intraspecific to the interspecific and the functional group level

description: 1. One of the processes that may play a key role in plant species
 coexistence and ecosystem functioning is plant-soil feedback, the effect
 of plants on associated soil communities and the resulting feedback on
 plant performance. Plant-soil feedback at the interspecific level
 (comparing growth on own soil with growth on soil from different species)
 has been studied extensively, while plant-soil feedback at the
 intraspecific level (comparing growth on own soil with growth on soil from
 different accessions within a species) has only recently gained attention.
 Very few studies have investigated the direction and strength of feedback
 among different taxonomic levels, and initial results have been
 inconclusive, discussing phylogeny and morphology as possible
 determinants. 2. To test our hypotheses that the strength of negative
 feedback on plant performance increases with increasing taxonomic level
 and that this relationship is explained by morphological similarities, we
 conducted a greenhouse experiment using species assigned to three
 taxonomic levels (intraspecific, interspecific and functional group
 level). We measured certain fitness-related aboveground traits and used
 them along literature-derived traits to determine the influence of
 morphological similarities on the strength and direction of the feedback.
 3. We found that the average strength of negative feedback increased from
 the intraspecific over the interspecific to the functional group level.
 However, individual accessions and species differed in the direction and
 strength of the feedback. None of our results could be explained by
 morphological dissimilarities or individual traits. 4. Synthesis. Our
 results indicate that negative plant-soil feedback is stronger if the
 involved plants belong to more distantly related species. We conclude that
 the taxonomic level is an important factor in the maintenance of plant
 coexistence with plant-soil feedback as a potential stabilizing mechanism
 and should be addressed explicitly in coexistence research, while the
 traits considered here seem to play a minor role.
description: Bukowski_DataRaw data (traits, biomass) and calculated feedback for biomass.
DOI: 10.5061/dryad.545tv
title: Data from: High Rates of Asymptomatic, Sub-microscopic Plasmodium vivax Infection and Disappearing Plasmodium falciparum Malaria in an Area of Low Transmission in Solomon Islands

description: Introduction: Solomon Islands is intensifying national efforts to achieve
 malaria elimination. A long history of indoor spraying with residual
 insecticides, combined recently with distribution of long lasting
 insecticidal nets and artemether-lumefantrine therapy, has been
 implemented in Solomon Islands. The impact of these interventions on local
 endemicity of Plasmodium spp. is unknown. Methods: In 2012, a
 cross-sectional survey of 3501 residents of all ages was conducted in
 Ngella, Central Islands Province, Solomon Islands. Prevalence of
 Plasmodium falciparum, P. vivax, P. ovale and P. malariae was assessed by
 quantitative PCR (qPCR) and light microscopy (LM). Presence of gametocytes
 was determined by reverse transcription quantitative PCR (RT-qPCR).
 Results: By qPCR, 468 Plasmodium spp. infections were detected
 (prevalence=13.4%; 463 P. vivax, five mixed P. falciparum/P. vivax, no P.
 ovale or P. malariae) versus 130 by LM (prevalence=3.7%; 126 P. vivax,
 three P. falciparum and one P. falciparum/P. vivax). The prevalence of P.
 vivax infection varied significantly among villages (range 3.0-38.5%,
 p&lt;0.001) and across age groups (5.3-25.9%, p&lt;0.001). Of 468
 P. vivax infections, 72.9% were sub-microscopic, 84.5% afebrile and 60.0%
 were both sub-microscopic and afebrile. Local residency, low education
 level of the household head and living in a household with at least one
 other P. vivax infected individual increased the risk of P. vivax
 infection. Overall, 23.5% of P. vivax infections had concurrent
 gametocytaemia. Of all P. vivax positive samples, 29.2% were polyclonal by
 MS16 and msp1F3 genotyping. All five P. falciparum infections were
 detected in residents of the same village, carried the same msp2 allele
 and four were positive for P. falciparum gametocytes. Conclusion: P. vivax
 infection remains endemic in Ngella, with the majority of cases afebrile
 and below the detection limit of LM. P. falciparum has nearly disappeared,
 but the risk of re-introductions and outbreaks due to travel to nearby
 islands with higher malaria endemicity remains.
description: Solomon
 Islands_Ngella_cross-sectional study 2012The file contains the
 epidemiological data used for the analysis and results presented in the
 associated manuscript.SI_Ngella_2012DRYAD.csv
DOI: 10.5061/dryad.pc303
title: Data from: Metaproteomics reveals metabolic transitions between healthy and diseased stony coral Mussismilia braziliensis

description: Infectious diseases such as white plague syndrome (WPS) and black band
 disease (BBD) have caused massive coral loss worldwide. We performed a
 metaproteomic study on the Abrolhos coral Mussismilia braziliensis to
 define the types of proteins expressed in healthy corals compared to WPS-
 and BBD-affected corals. A total of 6363 MS/MS spectra were identified as
 361 different proteins. Healthy corals had a set of proteins that may be
 considered markers of holobiont homoeostasis, including tubulin, histone,
 Rab family, ribosomal, peridinin–chlorophyll a-binding protein, F0F1-type
 ATP synthase, alpha-iG protein, calmodulin and ADP-ribosylation factor.
 Cnidaria proteins found in healthy M. braziliensis were associated with
 Cnidaria–Symbiodinium endosymbiosis and included chaperones (hsp70, hsp90
 and calreticulin), structural and membrane modelling proteins (actin) and
 proteins with functions related to intracellular vesicular traffic (Rab7
 and ADP-ribosylation factor 1) and signal transduction (14-3-3 protein and
 calmodulin). WPS resulted in a clear shift in the predominance of
 proteins, from those related to aerobic nitrogen-fixing bacteria (i.e.
 Rhizobiales, Sphingomonadales and Actinomycetales) in healthy corals to
 those produced by facultative/anaerobic sulphate-reducing bacteria (i.e.
 Enterobacteriales, Alteromonadales, Clostridiales and Bacteroidetes) in
 WPS corals. BBD corals developed a diverse community dominated by
 cyanobacteria and sulphur cycle bacteria. Hsp60, hsp90 and
 adenosylhomocysteinase proteins were produced mainly by cyanobacteria in
 BBD corals, which is consistent with elevated oxidative stress in hydrogen
 sulphide- and cyanotoxin-rich environments. This study demonstrates the
 usefulness of metaproteomics for gaining better comprehension of coral
 metabolic status in health and disease, especially in reef systems such as
 the Abrolhos that are suffering from the increase in global and local
 threatening events.
description: GenInfo
 Identifiers_Garcia et al., 2016_MolEcolThe excel file keeps
 GenInfo Identifiers (gi) numbers of all proteins identified in Mussismilia
 braziliensis healthy and affected by Whit-plague Syndrome and Black Band
 Diseased from Abrolhos Bank area, in Brazil.
DOI: 10.5061/dryad.83qh4
title: Data from: The effect of hybrid transgression on environmental tolerance in experimental yeast crosses

description: Evidence is rapidly accumulating that hybridization generates adaptive
 variation. Transgressive segregation in hybrids could promote the
 colonization of new environments. Here, we use an assay to select hybrid
 genotypes that can proliferate in environmental conditions beyond the
 conditions tolerated by their parents, and we directly compete them
 against parental genotypes in habitats across environmental clines. We
 made 45 different hybrid swarms by crossing yeast strains (both
 Saccharomyces cerevisiae and S. paradoxus) with different genetic and
 phenotypic divergence. We compared the ability of hybrids and parents to
 colonize seven types of increasingly extreme environmental clines,
 representing both natural and novel challenges (mimicking pollution
 events). We found that a significant majority of hybrids had greater
 environmental ranges compared to the average of both their parents’ ranges
 (mid-parent transgression), but only a minority of hybrids had ranges
 exceeding their best parent (best-parent transgression). Transgression was
 affected by the specific strains involved in the cross and by the test
 environment. Genetic and phenotypic crossing distance predicted the extent
 of transgression in only two of the seven environments. We isolated a set
 of potentially transgressive hybrids selected at the extreme ends of the
 clines and found that many could directly outcompete their parents across
 whole clines and were between 1.5- and 3-fold fitter on average.
 Saccharomyces yeast is a good model for quantitative and replicable
 experimental speciation studies, which may be useful in a world where
 hybridization is becoming increasingly common due to the relocation of
 plants and animals by humans.
description: environmental range raw
 dataRaw data file (.xls)
 containing environmental ranges of all parental strains, F1 hybrids and F2
 hybrid swarms.relative fitness
 dataRaw data file (.xls)
 containing all data from relative fitness assays.transgression per
 genetic distance classRaw data file (.xls)
 containing data on genetic crossing distance, distance category, F1
 transgression, and F2 transgression per environment.