cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0b707
title: Data from: Co-evolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection

description: Microbes that protect their hosts from pathogenic infection are widespread
 components of the microbiota of both plants and animals. It has been found
 that interactions between ‘defensive’ microbes and pathogens can be
 genotype-specific and even underlie the variation in host resistance to
 pathogenic infection. These observations suggest a dynamic co-evolutionary
 association between pathogens and defensive microbes, but direct evidence
 of co-evolution is lacking. We tested the hypothesis that defensive
 microbes and pathogens could co-evolve within host populations by
 co-passaging a microbe with host-defensive properties (Enterococcus
 faecalis) and a pathogen (Staphylococcus aureus) within Caenorhabditis
 elegans nematodes. Using both phenotypic and genomic analyses across
 evolutionary time, we found patterns of pathogen local adaptation and
 defensive microbe–pathogen co-evolution via fluctuating selection
 dynamics. Moreover, co-evolution with defensive microbes resulted in more
 rapid and divergent pathogen evolution compared to pathogens evolved
 independently in host populations. Taken together, our results indicate
 the potential for defensive microbes and pathogens to co-evolve, driving
 interaction specificity and pathogen evolutionary divergence in the
 absence of host evolution.
description: All data
 filesAll data files (CSV
 files) for each figure in paper along with supporting
 files.Ford
 et al. all files.zip
DOI: 10.5061/dryad.6528d
title: Data from: Plant performance was greater in the soils of more distantly related plants for an herbaceous understory species

description: Growing evidence suggests that plant–soil interactions have important
 implications for plant community composition. However, the role of
 phylogenetic relatedness in governing interactions between plants and soil
 biota is unclear, and more case studies are needed to help build a general
 picture of whether and how phylogeny might influence plant–soil
 interactions. We performed a glasshouse experiment to test whether degree
 of phylogenetic relatedness between Aquilegia canadensis and six
 co-occurring heterospecifics affects A. canadensis biomass through soil
 legacy effects. We also compared performance of A. canadensis in soils
 conditioned by invasive Alliaria petiolata versus native heterospecifics,
 hypothesizing that conditioning by A. petiolata would suppress the
 performance of the focal native plant. A. canadensis performed
 significantly better in distant relatives’ soils than in close relatives’
 soils, and this effect disappeared with soil sterilization, consistent
 with close relatives sharing similar pathogens. Contrary to our
 expectations, soils conditioned by the invasive species A. petiolata
 versus by native species had similar effects on A. canadensis. The greater
 performance of A. canadensis in soils of more versus less distant
 relatives is consistent with a hypothesis of phylogenetically constrained
 pathogen escape, a phenomenon expected to promote coexistence of
 phylogenetically distant species. However, pairwise plant–soil feedback
 experiments are needed to create a stronger coexistence prediction.
description: Sweet_Burns_2017
DOI: 10.5061/dryad.7kb06
title: Data from: Spatial storage effect promotes biodiversity during adaptive radiation

description: Many ecological communities are enormously diverse. Variation in
 environmental conditions over time and space provides opportunities for
 temporal and spatial storage effects to operate, potentially promoting
 species coexistence and biodiversity. While several studies have provided
 empirical evidence supporting the significance of the temporal storage
 effect for coexistence, empirical tests of the role of the spatial storage
 effect are rare. In particular, we know little about how the spatial
 storage effect contributes to biodiversity over evolutionary timescales.
 Here, we report the first experimental study on the role of the spatial
 storage effect in the maintenance of biodiversity in evolving
 metacommunities, using the bacterium Pseudomonas fluorescens SBW25 as a
 laboratory model of adaptive radiation. We found that intercommunity
 spatial heterogeneity promoted phenotypic diversity of P. fluorescens in
 the presence of dispersal among local communities, by allowing the spatial
 storage effect to operate. Mechanistically, greater niche differences
 among P. fluorescens phenotypes arose in metacommunities with
 intercommunity spatial heterogeneity, facilitating negative
 frequency-dependent selection, and thus, the coexistence among P.
 fluorescens phenotypes. These results highlight the importance of the
 spatial storage effect for biodiversity over evolutionary timescales.
description: Spatial storage
 W3Data are density (CFU
 per ml).
DOI: 10.5061/dryad.6vr5888
title: Data from: Common bottlenose dolphin (Tursiops truncatus) behavior in an active narrow seaport

description: The Galveston Ship Channel (GSC) is a narrow, congested waterway that
 supports large-scale shipping, commercial fishing, dolphin tourism, and
 recreation. Human activity and common bottlenose dolphins (Tursiops
 truncatus) converge in the GSC with potentially negative consequences on
 the dolphins. Elevated land-based tracking and behavioral observation of
 dolphins and vessels were conducted along the GSC in June-August 2013
 using a digital theodolite. Positional information was used to calculate
 dolphin movement patterns and proximity to vessels. Log-likelihood ratio
 and Chi-square contingency tests were used to assess behavioral states,
 and generalized additive models were used to analyze movement patterns
 (i.e., swimming speed, reorientation rate, and linearity) relative to
 endogenous and exogenous factors and vessel presence. Dolphins regularly
 use the GSC to forage (57% of observed behavioral states) and socialize
 (27%), and it is not a travel corridor for accessing other favorable sites
 (traveling=5%). Dolphin behavior varied significantly based on time of
 day, group size, calf presence, and general boat presence. When boats were
 present, the proportion of time dolphins spent socializing and foraging
 was significantly less than expected by chance. Swimming speeds increased
 significantly in the presence of small recreational boats,
 dolphin-watching tour boats, shrimp trawlers, and when tour boats and
 shrimp trawlers were both present. Reorientation rate increased
 significantly in the presence of tour boats and trawlers. Dolphin
 behavioral responses to vessel presence may result in decreased energy
 consumption due to disrupted foraging activity. Without proper management,
 the observed behavioral changes may be detrimental to individuals within
 this population in the short term, with potential long-term consequences
 to health and survivorship.
description: Datadata csv for
 GAM
DOI: 10.5061/dryad.g89s5
title: Data from: Pouch brooding marsupial frogs transfer nutrients to developing embryos

description: Marsupial frogs have a unique reproductive mode in which females carry
 eggs enclosed in a sealed dorsal brood pouch. While most anurans are
 considered to be oviparous with lecithotrophic eggs, the extensively
 vascularized membrane of the brood pouch in marsupial frogs suggests
 potential opportunities for nutrient transfer. We tested for matrotrophy
 in the live-bearing Gastrotheca excubitor (Hemiphractidae), through
 feeding insects labelled with a 13C-fatty acid and a 15N-amino acid to
 brooding marsupial frogs. We observed significant increases of δ13C and
 δ15N in both maternal pouch tissues and embryos, suggesting nutrient
 transfer. Embryo dry mass also increased with developmental stage,
 providing further direct evidence for matrotrophy. These results suggest
 that in addition to gas exchange, the vascularized brood pouch membrane of
 G. excubitor also enables maternal nutrient transfer. This finding
 revealed a suspected but untested trait in the evolution of parental care
 in marsupial frogs, in contrast to previous work on Gastrotheca species
 that release tadpoles, and suggests greater complexity in reproductive and
 provisioning modes than previously thought.
description: Warne-Catenazzi 2016
 Biology Letters DataThis excel file contains
 3 worksheets detailing the reproductive data, and isotope data for the
 frogs, their embryos, and their insect diet.
DOI: 10.5061/dryad.jq470
title: Data from: Validation of a rodent model of source memory

description: Source memory represents the origin (source) of information. Recently, we
 proposed that rats (Rattus norvegicus) remember the source of information.
 However, an alternative to source memory is the possibility that rats
 selectively encoded some, but not all, information rather than retrieving
 an episodic memory. We directly tested this "encoding-failure"
 hypothesis. Here, we show that rats remember the source of information,
 under conditions that cannot be attributed to encoding failure. Moreover,
 source memory lasted at least 7 days but was no longer present 14 days
 after studying. Our findings suggest that long-lasting source memory may
 be modeled in nonhumans. Our model should facilitate attempts to elucidate
 the biological underpinnings of source-memory impairments in human memory
 disorders such as Alzheimer's disease.
description: DRYAD data
 archiveRaw data for encoding
 failure experiment and retention interval experiment.
DOI: 10.15468/dl.9f69fh
title: Occurrence Download

description: A dataset containing 8527 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Global Register of Introduced and Invasive Species - United States (Contiguous) (ver.2.0, 2022)"
 ]
}

 The dataset includes 8527 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001379-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9n36s
title: Data from: Evidence for specificity in symbiont-conferred protection against parasitoids

description: Many insects harbour facultative symbiotic bacteria, some of which have
 been shown to provide resistance against natural enemies. One of the
 best-known protective symbionts is Hamiltonella defensa, which in pea
 aphid (Acyrthosiphon pisum) confers resistance against attack by
 parasitoid wasps in the genus Aphidius (Braconidae). We asked (i) whether
 this symbiont also confers protection against a phylogenetically distant
 group of parasitoids (Aphelinidae) and (ii) whether there are consistent
 differences in the effects of bacteria found in pea aphid biotypes adapted
 to different host plants. We found that some H. defensa strains do provide
 protection against an aphelinid parasitoid Aphelinus abdominalis.
 Hamiltonella defensa from the Lotus biotype provided high resistance to A.
 abdominalis and moderate to low resistance to Aphidius ervi, while the
 reverse was seen from Medicago biotype isolates. Aphids from Ononis showed
 no evidence of symbiont-mediated protection against either wasp species
 and were relatively vulnerable to both. Our results may reflect the
 different selection pressures exerted by the parasitoid community on
 aphids feeding on different host plants, and could help explain the
 maintenance of genetic diversity in bacterial symbionts.
description: Parasitism data for A.
 pisumData collected in the
 laboratory on the effects of facultative symbiont Hamiltonella defensa in
 pea aphids (Acyrthosiphon pisum) on parasitism by two parasitoid species
 (Aphidius ervi and Aphelinus abdominalis). ‘Block’ is the temporal block
 in which the experiment was carried out; ‘Clone’ is the aphid clone code;
 ‘Hamiltonella’ refers to the presence of the symbiont Hamiltonella defensa
 (‘Yes’ = present, ‘No’=cured); ‘Wasp’ gives the genus of the parasitoid;
 ‘Plant’ is the biotype of the aphid.Parasitoid complete data
 Proceedings B for Dryad.txt
DOI: 10.5061/dryad.6nr62
title: Data from: Telomere dynamics in parasitic great spotted cuckoos and their magpie hosts

description: Although little is known on the impact of environment on telomere length
 dynamics, it has been suggested to be affected by stress, lifestyle and/or
 life-history strategies of animals. We here compared telomere dynamics in
 erythrocytes of hatchlings and fledglings of the brood parasite great
 spotted cuckoos (Clamator glandarius) and of magpies (Pica pica), their
 main host in Europe. In magpie chicks, telomere length decreased from
 hatching to fledging while no significant change in telomere length of
 great spotted cuckoo chicks was found. Moreover, we found interspecific
 differences in the association between laying date and telomere
 shortening. Interspecific differences in telomere shortening were
 interpreted as a consequence of differences in lifestyle and life-history
 characteristics of magpies and great spotted cuckoos. In comparison with
 magpies, cuckoos experience reduced sibling competition and higher access
 to resources, and, consequently, lower stressful environmental conditions
 during the nestling phase. These characteristics also explain the
 associations between telomere attrition and environmental conditions (i.e.
 laying date) for magpies and the absence of association for great spotted
 cuckoos. These results therefore fit expectations on telomere dynamics
 derived from interspecific differences in lifestyle and life-history of
 brood parasites and their bird hosts.
description: Telomere length of
 magpie and great spotted cuckoo nestlingsTelomere length of
 magpie and great spotted cuckoo nestlings soon after hatching and before
 fledging. We also show telomere attrition values and laying-date of each
 studied nest. Values are means estimates per study
 nest.data.xlsx
DOI: 10.5061/dryad.s25d3
title: Data from: Habitat traits and species interactions differentially affect abundance and body size in pond-breeding amphibians

description: 1. In recent studies, habitat traits have emerged as stronger predictors
 of species occupancy, abundance, richness and diversity than competition.
 However, in many cases, it remains unclear whether habitat also mediates
 processes more subtle than competitive exclusion, such as growth, or
 whether intra- and interspecific interactions among individuals of
 different species may be better predictors of size. 2. To test whether
 habitat traits are a stronger predictor of abundance and body size than
 intra- and interspecific interactions, we measured the density and body
 size of three species of larval salamanders in 192 ponds across a
 landscape. 3. We found that the density of larvae was best predicted by
 models that included habitat features, while models incorporating
 interactions among individuals of different species best explained the
 body size of larvae. Additionally, we found a positive relationship
 between focal species density and congener density, while focal species
 body size was negatively related to congener density. 4. We posit that
 salamander larvae may not experience competitive exclusion and thus
 reduced densities, but instead compensate for increased competition
 behaviourally (e.g. reduced foraging), resulting in decreased growth. The
 discrepancy between larval density and body size, a strong predictor of
 fitness in this system, also highlights a potential shortcoming in using
 density or abundance as a metric of habitat quality or population health.
description: Larval Density and Mean
 SizeDataFileFinal.txt
DOI: 10.5061/dryad.254s7
title: Data from: Evolution of fitness trade-offs in locally adapted populations of Pseudomonas fluorescens

description: Local adaptation seems to be common in natural systems, but the genetic
 causes of its evolution remain poorly understood. Here we characterize the
 genetic causes of trade-offs generating local adaptation in populations of
 Pseudomonas fluorescens that had previously been evolved for
 specialization on three different carbon resources. We measured the
 fitness effects of mutations that arose during selection in that
 environment and in alternative environments to quantify the degree of
 specialization. We find that all mutations are beneficial in the
 environment of selection and that those arising later during adaptation
 are associated with increasingly antagonistic effects in alternative
 environments compared with those arising earlier, consistent with a
 multioptima version of Fisher’s geometric model of adaptation. We also
 find that fitness of pairs of beneficial mutations are consistently less
 than additive in selection environments, producing a pattern of
 diminishing returns, but are more variable in alternative environments,
 being either positive or negative. Finally, we find that mutations in
 genes associated with loss of motility are beneficial across all
 environments, whereas mutations involving other functions, such as gene
 regulation, had more variable effects, being more environment specific.
 Taken together, these results provide a detailed account of the genetics
 of specialization and suggest that the evolution of trade-offs associated
 with local adaptation may often result from the antagonistic effects of
 beneficial mutations substituted later in adaptation.
description: Competitive fitness
 dataThis data file contains
 estimates of fitness and standard error from competition experiments.
 Mutations carried by each genotype can be found in the manuscript (Table
 A2). The protocol for the competition experiments is described in the
 manuscript. The column titled "assay_env" contains the
 environment that particular competition was carried out in (G = glucose, M
 = mannose, X = Xylose, A = MIX).mean_log_fitness_full_set.csv
DOI: 10.5061/dryad.f1j38k7
title: Data from: Across a migratory divide: divergent migration directions and non-breeding grounds of Eurasian reed warblers revealed by geolocators and stable isotopes

description: Migratory divides represent narrow zones of overlap between parapatric
 populations with distinct migration directions and, consequently, expected
 divergent non-breeding distributions. The composition of the mixed
 population at a migratory divide and the corresponding non-breeding ranges
 remain, however, unknown for many Palaearctic-African migrants. Here, we
 used light-level geolocation to track migration direction and non-breeding
 grounds of Eurasian reed warblers (Acrocephalus scirpaceus) from three
 breeding populations across the species’ migratory divide. Moreover, by
 using feathers grown at non-breeding grounds, we quantified stable isotope
 composition for individuals with known southwestern (SW) and southeastern
 (SE) migration directions. On a larger sample per population, we then
 assessed the proportions of SW- and SE-migrating phenotypes in each of the
 three populations. All tracked reed warblers from Germany and two thirds
 of the birds tagged from the Czech population headed initially SW.
 Nevertheless, about one third of the birds from the Czech site migrated
 towards SE. No tracking data have been obtained for the Bulgarian
 population. The initial migration direction determined by geolocators was
 a strong predictor of the non-breeding region, with SW migrants staying in
 West Africa and SE migrants in Central Africa. Feather δ34S and δ15N
 values confirmed the predominance of SW migrants in the German population,
 the co-occurrence of SW and SE migrants in the Czech population, and
 indicated a high (72%) proportion of SE migrants in the Bulgarian
 population. Thus, the combined approach of geolocator tracking and stable
 isotopic assignments provided clear evidence for the existence of a
 migratory divide in the southeast of Central Europe and predicted
 non-breeding range in Central and Central-Eastern Africa for the eastern
 population.
description: Feather stable isotope
 dataStable isotope (δ13C,
 δ15N, δ34S) data from primary feathers of Eurasian reed warblers sampled
 during breeding in Germany, Czech Republic and Bulgaria (country: DE, CZ,
 BG). The column 'direction' indicates one of the two migratory
 directions as shown by light-level geolocation (SW or SE);
 'nonbreed_position' indicates whether non-breeding site
 positioning data were available.As_Dryad.csv
DOI: 10.5061/dryad.6fb8d37
title: Data from: Gene expression shifts in yellow-bellied marmots prior to natal dispersal

description: The causes and consequences of vertebrate natal dispersal have been
 studied extensively, yet little is known about the molecular mechanisms
 involved. We used RNA-seq to quantify transcriptomic gene expression in
 blood of wild yellow-bellied marmots (Marmota flaviventer) prior to
 dispersing from or remaining philopatric to their natal colony. We tested
 three predictions. First, we hypothesized dispersers and residents will
 differentially express genes and gene networks since dispersal is
 physiologically demanding. Second, we expected differentially expressed
 genes to be involved in metabolism, circadian processes, and immune
 function. Finally, in dispersing individuals, we predicted differentially
 expressed genes would change as a function of sampling date relative to
 dispersal date. We detected 150 differentially expressed genes, including
 genes that have critical roles in lipid metabolism and antigen defense.
 Gene network analysis revealed a module of 126 co-expressed genes
 associated with dispersal that was enriched for extra-cellular immune
 function. Of the dispersal-associated genes, 22 altered expression as a
 function of days until dispersal, suggesting that dispersal-associated
 genes do not initiate transcription on the same time scale. Our results
 provide novel insights into the fundamental molecular changes required for
 dispersal and suggest evolutionary conservation of functional pathways
 during this behavioral process.
description: Trait data for the 43
 individuals/RNA samplesThis data file contains
 trait information concerning the 43 individual marmots, or their blood
 samples (one per individual), analyzed in this study. Much of the data was
 collected in the field (e.g., sex, dispersal status), whereas other data
 were collected in the lab (e.g., RIN score, cell counts).
 "jdate" signifies Julien date.Armenta_dispersal_sample_traits.csvRelatedness matrixThis data file contains a matrix of genetic kinship for the 43 individual marmots analyzed in this study. Kinship was calculated as pair-wise relatedness between individuals based on genotypes taken from 12 microsatellite loci (detailed genotyping methods described in Blumstein et al. 2010 doi:10.1111/j.1420-9101.2010.01967.x).Armenta_relatedness_matrix.csv