cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.14nr4
title: Data from: Using multi-response models to investigate pathogen coinfections across scales: insights from emerging diseases of amphibians

description: 1.Associations among parasites affect many aspects of host-parasite
 dynamics, but a lack of analytical tools has limited investigations of
 parasite correlations in observational data that are often nested across
 spatial and biological scales. 2.Here we illustrate how hierarchical,
 multiresponse modeling can characterize parasite associations by allowing
 for hierarchical structuring, offering estimates of uncertainty, and
 incorporating correlational model structures. After introducing the
 general approach, we apply this framework to investigate coinfections
 among four amphibian parasites (the trematodes Ribeiroia ondatrae and
 Echinostoma spp., the chytrid fungus Batrachochytrium dendrobatidis, and
 ranaviruses) and among &gt;2000 individual hosts, 90 study sites, and
 five amphibian host species. 3.Ninety-two percent of sites and 80% of
 hosts supported two or more pathogen species. Our results revealed strong
 correlations between parasite pairs that varied by scale (from among hosts
 to among sites) and classification (microparasite versus macroparasite),
 but were broadly consistent across taxonomically diverse host species. At
 the host-scale, infection by the trematode R. ondatrae correlated
 positively with the microparasites, B. dendrobatidis and ranavirus, which
 were themselves positively associated. However, infection by a second
 trematode (Echinostoma spp.) correlated negatively with B. dendrobatidis
 and ranavirus, both at the host- and site-level scales, highlighting the
 importance of differential relationships between micro- and
 macroparasites. 4.Given the extensive number of coinfecting symbiont
 combinations inherent to natural systems, particularly across multiple
 host species, multiresponse modeling of cross-sectional field data offers
 a valuable tool to identify a tractable number of hypothesized
 interactions for experimental testing while accounting for uncertainty and
 potential sources of co-exposure. For amphibians specifically, the high
 frequency of co-occurrence and coinfection among these pathogens – each of
 which is known to impair host fitness or survival – highlights the urgency
 of understanding parasite associations for conservation and disease
 management.
description: SupInfoMetaDataCoinfection_dataMetadata for Coinfection scriptcoinfection_dataConifection data setanalysis 2R script for coinfection analysis
DOI: 10.5061/dryad.m2r31
title: Data from: A multilocus phylogenetic analysis of Escallonia (Escalloniaceae): diversification in montane South America

description: The mountains of South America are hotspots of plant diversity. How this
 diversity originated and evolved, and what roles geographic and
 environmental factors may have played in the diversification of lineages
 occurring in these regions is not well understood. Escallonia, a
 morphologically and ecologically diverse group of shrubs and trees widely
 distributed in these mountains, provides an ideal opportunity for studying
 the historical underpinnings that have shaped the extraordinarily
 distinctive, diverse, and endangered flora of these regions, and for
 evaluating the role of abiotic factors in the process of lineage
 divergence. I analyzed neutral DNA sequence data from two nuclear loci and
 one chloroplast locus using maximum parsimony, maximum likelihood, and
 Bayesian phylogenetic approaches. I used a Bayesian approach to analyze
 the geographic structure of gene trees, and a phylogenetically controlled
 decomposition of the variance in bioclimatic variables to analyze the
 eco-climatic structure of gene trees. I found i) that Escallonia is
 monophyletic, ii) a remarkable level of geographical and climatic
 phylogenetic structure, iii) that Escallonia likely originated in the
 tropical Andes, and iv) a widespread absence of species exclusivity.
 Geography played an important role early on the history of Escallonia by
 separating populations that later diversify likely in isolation. Although
 geographic isolation was generally accompanied by changes in climate, it
 is not clear whether environmental gradients along elevation have
 influenced more recent diversification events, or species have evolved
 broader environmental tolerances.
description: cpDNA.fasAlignment of chloroplast data (partial psbA gene, psbA - trnH intergenic spacer, partial trnH gene) for all individuals. Fasta format.MYC_AllIndividuals.fasAlignment of nuclear marker (1st intron of MYC-like gene) for all individuals. Fasta format.NIA_AllIndividualsAlignment of nuclear marker (3rd intron of NIA gene) for all individuals. Fasta format.
DOI: 10.5061/dryad.7994
title: Data from: Discord reigns among nuclear, mitochondrial, and phenotypic estimates of divergence in nine lineages of trans-Beringian birds

description: Proposals for genetic thresholds for species delimitation assume that
 simple genetic datasets (e.g. mitochondrial sequence data) are correlated
 with speciation; i.e. that such datasets accurately reflect organismal
 lineage divergence. We used taxonomically stratified phenotypic levels of
 differentiation (populations, subspecies, and species) among nine avian
 lineages using paired, trans-Beringian samples from three lineages each in
 three orders (Anseriformes, Charadriiformes, and Passeriformes) to test
 this assumption. Using mitochondrial DNA (mtDNA) sequence data and nuclear
 genomic data (AFLPs), we found a lack of concordance between these two
 genomes in their respective estimates of divergence and little or no
 relationship between phenotype (taxonomic relatedness) and genetic
 differentiation between taxon pairs. There are several possible reasons
 for the discord observed (e.g. selection on one of the genomes or perhaps
 lineage sorting), but the implications are that genetic estimates of
 lineage divergence may not be correlated with estimates from other parts
 of the genome, are not well correlated with the speciation process, and
 are thus not reliable indicators of species limits.
description: Nine combined AFLP
 datasets for Humphries and Winker 2010 Molecular EcologySingle text file of nine
 separate AFLP datasets for Humphries and Winker 2010 Molecular
 Ecology.
DOI: 10.5061/dryad.ff71n
title: Data from: Tracing the colonization and diversification of the worldwide seabird ectoparasite Ixodes uriae

description: Historical patterns of dispersal and population isolation are key
 components shaping contemporary genetic diversity across landscapes and
 require explicit consideration when examining the relative role of
 different factors in driving the evolution of host specificity in
 parasitic organisms. In this study, we investigate the worldwide
 colonisation history of a common ectoparasite of seabirds, the tick Ixodes
 uriae. This tick has a circumpolar distribution across both hemispheres,
 but has repeatedly formed host-specific races within different regions. By
 combining mitochondrial and nuclear data, we infer how this species spread
 to its present-day distribution and how the colonisation process has
 affected the geographic and host-associated structure of this tick within
 regions. We demonstrate that I. uriae is highly structured and isolates
 into four genetic groups that correspond to well-defined geographical
 regions. Molecular dating suggests that the diversification of I. uriae
 began in the early Miocene (22 Myr) and that this tick colonised most of
 the Southern hemisphere before moving into northern latitudes via two
 independent routes. However, no relationship between the degree of host
 race divergence and colonisation history was evident, supporting previous
 hypotheses that host specialization evolves relatively rapidly in this
 parasite, but does not typically lead to speciation. We discuss the
 possible historical and contemporary mechanisms of large scale dispersal
 for this ectoparasite and how its biological characteristics may condition
 current patterns of genetic diversity. More generally, our results
 illustrate how combining broad-scale sampling and modern molecular tools
 can help disentangle complex patterns of diversification in widespread
 parasites.
description: Dietrich_Uriae_CO3_alignment_2Dietrich_Uriae_microsatellite_data_2
DOI: 10.5061/dryad.bk469
title: Data from: Inbreeding-related trade-offs in stress-resistance in the ant Formica exsecta

description: Inbred individuals and populations are predicted to suffer from inbreeding
 depression, especially in times of stress. Under natural conditions,
 organisms are exposed to more than one stressor at any one time,
 highlighting the importance of stress resistance traits. We studied how
 inbreeding- and immunity-related traits are correlated under different
 dietary conditions in the ant Formica exsecta. Its natural diet varies in
 the amount and nature of plant secondary compounds and the level of free
 radicals, all of which require detoxification to maintain organismal
 homeostasis. We found that inbreeding decreased general antibacterial
 activity under dietary stress, suggesting inbreeding-related physiological
 trade-offs.
description: ROS_survivalROS_lytic_Day44DayROS_qPCR
DOI: 10.5061/dryad.8638h
title: Data from: Chimpanzees, bonobos and children successfully coordinate in conflict situations

description: Social animals need to coordinate with others to reap the benefits of
 group-living even when individuals' interests are misaligned. We
 compare how chimpanzees, bonobos and children coordinate their actions
 with a conspecific in a Snowdrift game, which provides a model for
 understanding how organisms coordinate and make decisions under conflict.
 In study 1, we presented pairs of chimpanzees, bonobos and children with
 an unequal reward distribution. In the critical condition, the preferred
 reward could only be obtained by waiting for the partner to act, with the
 risk that if no one acted, both would lose the rewards. Apes and children
 successfully coordinated to obtain the rewards. Children used a
 ‘both-partner-pull’ strategy and communicated during the task, while some
 apes relied on an ‘only-one-partner-pulls' strategy to solve the
 task, although there were also signs of strategic behaviour as they waited
 for their partner to pull when that strategy led to the preferred reward.
 In study 2, we presented pairs of chimpanzees and bonobos with the same
 set-up as in study 1 with the addition of a non-social option that
 provided them with a secure reward. In this situation, apes had to
 actively decide between the unequal distribution and the alternative. In
 this set-up, apes maximized their rewards by taking their partners'
 potential actions into account. In conclusion, children and apes showed
 clear instances of strategic decision-making to maximize their own rewards
 while maintaining successful coordination.
description: Dataset_Study1aData Study 1aDataset_Study 1bData Study 1bDataset_Study 2Data Study 2
DOI: 10.5061/dryad.46h6j
title: Data from: When genes move farther than offspring: gene flow by male gamete dispersal in the highly philopatric bat species Thyroptera tricolor

description: For species characterized by philopatry of both sexes, mate selection
 represents an important behavior for inbreeding avoidance, yet the
 implications for gene flow are rarely quantified. Here we present evidence
 of male gamete mediated gene flow resulting from extra-group mating in
 Spix’s disk-winged bat, Thyroptera tricolor, a species which demonstrates
 all-offspring philopatry. We used microsatellite and capture-recapture
 data to characterize social group structure and the distribution of mated
 pairs at two sites in southwestern Costa Rica over four breeding seasons.
 Relatedness and genetic spatial autocorrelation analyses indicated strong
 kinship within groups and over short distances (&lt;50 m), resulting
 from matrilineal group structure and small roosting home ranges (~ 0.2
 ha). Despite high relatedness among group members, observed inbreeding
 coefficients were low (FIS = 0.010 and 0.037). Parentage analysis
 indicated mothers and offspring belonged to the same social group, while
 fathers belonged to different groups, separated by large distances (~ 500
 m) when compared to roosting home ranges. Simulated random mating
 indicated mate choice was not based on intermediate levels of relatedness,
 and mated pairs were less related than adults within social groups on
 average. Isolation-by-distance (IBD) models of genetic neighborhood area
 based on father-offspring distances provided direct estimates of mean
 gamete dispersal distances (ˆr ) greater than 10 roosting home range
 equivalents. Indirect estimates based on genetic distance provided even
 larger estimates of ˆr , suggesting direct estimates were biased low.
 These results suggest extra-group mating reduces the incidence of
 inbreeding in T. tricolor, and male gamete dispersal facilitates gene flow
 in lieu of natal dispersal of young.
description: DemogDatabase_Km23Capture records and demographic data for site Km23DemogDatabase_SirenaCapture and demographic data for site SirenaKm23_Genotype_DataMicrosatellite genotype data for site Km23Sirena_Genotype_DataGenotype data file for the site SirenaRCode_GroupRelatednessScript for calculating the relatedness of each individual to all other individuals within a social group. Uses output from the program ML Relate (i.e. relatedness values in table format)
DOI: 10.5061/dryad.8512
title: Data from: Arrival and diversification of caviomorph rodents and platyrrhine primates in South America.

description: Platyrrhine primates and caviomorph rodents are clades of mammals that
 colonized South America during its period of isolation from the other
 continents, between 100 and 3 million years ago (Mya). Until now, no
 molecular study investigated the timing of the South American colonization
 by these two lineages with the same molecular data set. Using sequences
 from three nuclear genes (ADRA2B, vWF, and IRBP, both separate and
 combined) from 60 species, and eight fossil calibration constraints, we
 estimated the times of origin and diversification of platyrrhines and
 caviomorphs via a Bayesian relaxed molecular clock approach. To account
 for the possible effect of an accelerated rate of evolution of the IRBP
 gene along the branch leading to the anthropoids, we performed the datings
 with and without IRBP (3768 sites and 2469 sites, respectively). The time
 window for the colonization of South America by primates and by rodents is
 demarcated by the dates of origin (upper bound) and radiation (lower
 bound) of platyrrhines and caviomorphs. According to this approach,
 platyrrhine primates colonized South America between 37.0 +/- 3.0 Mya (or
 38.9 +/- 4.0 Mya without IRBP) and 16.8 +/- 2.3 (or 20.1 +/- 3.3) Mya, and
 caviomorph rodents between 45.4 +/- 4.1 (or 43.7 +/- 4.8) Mya and 36.7 +/-
 3.7 (or 35.8 +/- 4.3) Mya. Considering both the fossil record and these
 molecular datings, the favored scenarios are a trans-Atlantic migration of
 primates from Africa at the end of the Eocene or beginning of the
 Oligocene, and a colonization of South America by rodents during the
 Middle or Late Eocene. Based on our nuclear DNA data, we cannot rule out
 the possibility of a concomitant arrival of primates and rodents in South
 America. The caviomorphs radiated soon after their arrival, before the
 Oligocene glaciations, and these early caviomorph lineages persisted until
 the present. By contrast, few platyrrhine fossils are known in the
 Oligocene, and the present-day taxa are the result of a quite recent,
 Early Miocene diversification.
description: Poux_SystBiol_2006Nucleotide concatenation alignment of 3 nuclear genes for 62 taxa.Poux_SystBiol_2006_ChronogramChronogram inferred from the 3 nuclear gene concatenation.
DOI: 10.5061/dryad.5fc56
title: Data from: MHC genotype predicts mate choice in the ring-necked pheasant Phasianus colchicus

description: Females of several vertebrate species selectively mate with males on the
 basis of the major histocompatibility complex (MHC) genes. As
 androgen-mediated maternal effects have long-lasting consequences for the
 adult phenotype, both mating and reproductive success may depend on the
 combined effect of MHC genotype and exposure to androgens during early
 ontogeny. We studied how MHC-based mate choice in ring-necked pheasants
 (Phasianus colchicus) was influenced by an experimental in ovo
 testosterone (T) increase. There was no conclusive evidence of in ovo T
 treatment differentially affecting mate choice in relation to MHC
 genotype. However, females avoided mating with males with a wholly
 different MHC genotype compared with males sharing at least one MHC
 allele. Females also tended to avoid mating with MHC-identical males,
 though not significantly so. These findings suggest that female pheasants
 preferred males with intermediate MHC dissimilarity. Male MHC
 heterozygosity or diversity did not predict the expression of ornaments or
 male dominance rank. Thus, MHC-based mating preferences in the ring-necked
 pheasant do not seem to be mediated by ornaments’ expression and may have
 evolved mainly to reduce the costs of high heterozygosity at MHC loci for
 the progeny, such as increased risk of autoimmune diseases or disruption
 of coadapted gene pools.
description: Phenotypic
 traitsThis file contains data
 of phenotypic traits and MHC genotype of ring-necked pheasant males
 included in the studyBaratti_et_al_morphology.txtBehaviourThis file contains the number of copulations of each male-female pair, alongside with different metrics of MHC genotype (distances or similarity between mating partners, different categorizations of MHC genotype)Baratti_et_al_behaviour.txt
DOI: 10.5061/dryad.cq032
title: Data from: The dual nature of hemocyanin in the establishment and persistence of the squid-vibrio symbiosis

description: We identified and sequenced from the squid Euprymna scolopes two isoforms
 of haemocyanin that share the common structural/physiological
 characteristics of haemocyanin from a closely related cephalopod, Sepia
 officinalis, including a pronounced Bohr effect. We examined the potential
 roles for haemocyanin in the animal's symbiosis with the luminous
 bacterium Vibrio fischeri. Our data demonstrate that, as in other
 cephalopods, the haemocyanin is primarily synthesized in the gills. It
 transits through the general circulation into other tissues and is
 exported into crypt spaces that support the bacterial partner, which
 requires oxygen for its bioluminescence. We showed that the gradient of pH
 between the circulating haemolymph and the matrix of the crypt spaces in
 adult squid favours offloading of oxygen from the haemocyanin to the
 symbionts. Haemocyanin is also localized to the apical surfaces and
 associated mucus of a juvenile-specific epithelium on which the symbionts
 gather, and where their specificity is determined during the recruitment
 into the association. The haemocyanin has an antimicrobial activity, which
 may be involved in this enrichment of V. fischeri during symbiont
 initiation. Taken together, these data provide evidence that the
 haemocyanin plays a role in shaping two stages of the squid–vibrio
 partnership.
description: Phylogeny of hemocyanin
 proteinsHemocyanin-Full_lengthPhylogeny of hemocyanin functional units in Euprymna scolopes and Sepia officinalisHemocyanin-FU
DOI: 10.5061/dryad.60cq733
title: Data from: Is there a disease-free halo at species range limits? The co-distribution of anther-smut disease and its host species

description: 1. While disease is widely recognized as affecting host population size,
 it has rarely been considered to play a role in determining host range
 limits. Many diseases may not be able to persist near the range limit if
 host population density falls below the critical threshold level for
 pathogen invasion. However, in vector- and sexually-transmitted diseases,
 pathogen transmission may be largely independent of host density and
 theory demonstrates that diseases with frequency-dependent transmission
 may persist in small populations near the range limit. 2. Empirical
 studies of disease at species range limits have lagged behind the theory,
 and to date, no previous study has tested the hypothesis that vector or
 sexually transmitted diseases can be maintained at host range limits. 3.
 We studied the distribution of anther-smut disease, a sterilizing
 pollinator-transmitted disease, on four alpine plant species to determine
 whether disease was present at the host range limits. 4. We found that
 host abundance declined towards the elevational range limits, and disease
 extended to the most extreme elevational range limits in three of the four
 host species. Maximum likelihood estimation of the magnitude of the
 disease-free halo showed that it was small or non-existent for all host
 species. Moreover, disease prevalence within populations was often higher
 nearer the host’s range limit than in the range center and was independent
 of host density. 5. Synthesis: Our results show that diseases where
 transmission is frequency-dependent have the potential to affect host
 distributions not just in theory, but also in real world populations.
description: disease-range-limits-main-datasetFull data set including: GPS coordinates, elevation, host density, and disease prevalence for all surveyed host species. The second sheet in the excel file is a readme.Silene vulgaris incidenceLists the order of populations for Silene vulgaris. Only populations with a '1' for order should be used for incidence analyses.Sv.order.lowland.txtDianthus furcatus incidenceLists the order of populations for Dianthus furcatus. Only populations with a '1' for order should be used for incidence analyses.Df.order.txtSilene latifolia incidenceLists the order of populations for Silene latifolia. Only populations with a '1' for order should be used for incidence analyses.Sl.order.lowland.txtDianthus pavonius incidenceLists the order of populations for Dianthus pavonius. Only populations with a '1' for order should be used for incidence analyses.Dp2.order.txt