cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j2g8t411
title: Data from: Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils

description: Understanding how communities assemble is a central goal of ecology. This
 is particularly relevant for communities of arbuscular mycorrhizal fungi
 (AMF), because the community composition of these beneficial plant
 symbionts influences important ecosystem processes. Moreover, AMF may be
 used as sensitive indicators of ecological soil quality if they respond to
 environmental variation in a predictable way. Here we use a molecular
 profiling technique (T-RFLP of 25S rRNA gene fragments) to test which
 factors determine AM fungal community composition in 40 agricultural soils
 in the Netherlands. In particular, we test whether species richness,
 dominance structure and community nestedness are influenced by management
 type (in pairs of organically and conventionally farmed fields), and we
 examine the contribution of crop species (maize versus potato), soil type
 (sand versus clay textured soils), and habitat (plant root versus bulk
 soil) on AMF community characteristics. AMF richness varied from 1 to 11
 taxa per field. Communities from species poor fields were found to be
 subsets of those in richer fields, indicating nestedness and a progressive
 “loss” from the species pool. AMF taxa richness and occurrence in soil and
 plant roots were highly correlated, and richness was related to management
 intensity (phosphate availability and grass cropping history together
 explained 34% and 50% of richness in roots and soils). Soil type together
 with soil chemical parameters explained only 17% of variance in AMF
 community structure. We synthesize these results by discussing the
 potential contribution of a “bottle-neck effect” on AMF communities
 through increased stochastic effects under environmental stress.
description: T-RFsRelative abundance (in
 percentage) of consecutive fragments recovered from each field by
 T-RFLP.
DOI: 10.5061/dryad.4vr063d
title: Data from: Agonistic character displacement of genetically based male colour patterns across darters

description: Agonistic character displacement (ACD) occurs when selection to avoid
 maladaptive interspecific aggression leads to the evolution of agonistic
 signals and/or associated behavioural biases in sympatry. Here we test for
 a pattern consistent with ACD in male colour pattern in darters (Percidae:
 Etheostoma). Male colour pattern has been shown to function in male-male
 competition rather than female mating preferences in several darter
 species. Additionally, males bias their aggression towards conspecific
 over heterospecific males in sympatry but not in allopatry, consistent
 with divergent ACD in male behavioural biases. We use a common garden
 approach to show that differences in male colour pattern among four
 closely related darter species are genetically based. Additionally, we
 demonstrate that some aspects of male colour pattern exhibit enhanced
 differences in sympatric compared to allopatric populations of two darter
 species, consistent with ACD. However, other male colour traits are more
 similar between species in sympatry compared to allopatry, indicating that
 not all signal components are under strong divergent selection in
 sympatry. This study provides evidence that interspecific male-male
 aggressive interactions alone can promote elaborate male signal evolution
 both between and within species. We discuss the implications this has for
 male-driven ACD and cascade ACD.
description: color_dataRaw color measurements for common garden (CG) study and agonistic character displacement (ACD) study. S = sympatric, A = allopatric, ot = orangethroat darter (E. spectabile), rb = rainbow darter (E. caeruleum), R = red coloration, B = blue coloration, r = R value, g = G value, b =B value, Prop = proportion, DF = dorsal fin, AF = anal fin, CF = caudal fin.
DOI: 10.5061/dryad.q7v72
title: Data from: Contact and contagion: bighorn sheep demographic states vary in probability of transmission given contact

description: 1. Understanding both contact and probability of transmission given
 contact are key to managing wildlife disease. However, wildlife disease
 research tends to focus on contact heterogeneity, in part because
 probability of transmission given contact is notoriously difficult to
 measure. Here we present a first step toward empirically investigating
 probability of transmission given contact in free-ranging wildlife. 2. We
 used measured contact networks to test whether bighorn sheep demographic
 states vary systematically in infectiousness or susceptibility to
 Mycoplasma ovipneumoniae, an agent responsible for bighorn sheep
 pneumonia. 3. We built covariates using contact network metrics,
 demographic information, and infection status, and used logistic
 regression to relate those covariates to lamb survival. The covariate set
 contained degree, a classic network metric describing node centrality, but
 we also built covariates that broke the network metrics into particular
 categories that differentiated between contacts with yearlings, ewes with
 lambs, and ewes without lambs, and animals with and without active
 infections. 4. Yearlings, ewes with lambs, and ewes without lambs showed
 similar group membership patterns, but direct interactions involving touch
 occurred at a rate two orders of magnitude higher between lambs and
 reproductive ewes than between any classes of adults or yearlings, and one
 order of magnitude higher than direct interactions between lambs. 5.
 Although yearlings and non-reproductive bighorn ewes regularly carried
 Mycoplasma ovipneumoniae, our models suggest that a contact with an
 infected reproductive ewe had approximately five times the odds of
 producing a lamb mortality event of an identical contact with an infected
 dry ewe or yearling. Consequently, management actions targeting infected
 animals might lead to unnecessary removal of young animals who carry
 pathogens but rarely transmit. 6. This analysis demonstrates a simple
 logistic regression approach for testing a priori hypotheses about
 variation in odds of transmission given contact for free-ranging hosts,
 and may be broadly applicable for investigations in wildlife disease
 ecology.
description: Lamb survival data with
 network-derived covariates..csv file with 56 rows.
 Rows contain lamb survival data and covariate information for 56 lambs
 monitored in three bighorn sheep herds during three different
 summers.LambSurvDataset_ForPublication_Final.csv
DOI: 10.15468/dl.cgffdd
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Croton tiglium"
 ]
}

 The dataset includes 48 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001188-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.st6tn
title: Data from: A quantitative framework to estimate the relative importance of environment, spatial variation and patch connectivity in driving community composition

description: Perhaps the most widely used quantitative approach in metacommunity
 ecology is the estimation of the importance of local environment vs.
 spatial structuring using the variation partitioning framework. Contrary
 to metapopulation models, however, current empirical studies of
 metacommunity structure using variation partitioning assume a
 space-for-dispersal substitution due to the lack of analytical frameworks
 that incorporate patch connectivity predictors of dispersal dynamics.
 Here, a method is presented that allows estimating the relative importance
 of environment, spatial variation and patch connectivity in driving
 community composition variation within metacommunities. The proposed
 approach is illustrated by a study designed to understand the factors
 driving the structure of a soft-bottom marine polychaete metacommunity.
 Using a standard variation partitioning scheme (i.e. where only
 environmental and spatial predictors are used), only about 13% of the
 variation in metacommunity structure was explained. With the connectivity
 set of predictors, the total amount of explained variation increased up to
 51% of the variation. These results highlight the importance of
 considering predictors of patch connectivity rather than just spatial
 predictors. Given that information on connectivity can be estimated by
 commonly available data on species distributions for a number of taxa, the
 framework presented here can be readily applied to past studies as well,
 facilitating a more robust evaluation of the factors contributing to
 metacommunity structure.
description: Polychaeta_MMarch sampling (2013)Polychaeta_SSeptember sampling (2013)
DOI: 10.5061/dryad.q3r06g1
title: Data from: Longevity and life history coevolve with oxidative stress in birds

description: 1. The mechanisms that underpin the evolution of ageing and life histories
 remain elusive. Oxidative stress, which results in accumulated cellular
 damages, is one of the mechanisms suggested to play a role. 2. In this
 paper we set out to test the ‘oxidative stress theory of ageing’ and the
 ‘oxidative stress hypothesis of life histories’ using a comprehensive
 phylogenetic comparison based on an unprecedented dataset of oxidative
 physiology in 88 free-living bird species. 3. We show for the first time
 that bird species with longer lifespan have higher non-enzymatic
 antioxidant capacity and suffer less oxidative damage to their lipids. We
 also found that bird species featuring a faster pace-of-life either
 feature lower non-enzymatic antioxidant capacity or are exposed to higher
 levels of oxidative damage, while adult annual mortality does not relate
 to oxidative state. 4. These results reinforce the role of oxidative
 stress in the evolution of lifespan and also corroborate the role of
 oxidative state in the evolution of life histories among free-living
 birds.
description: Data from: Longevity and
 life history coevolve with oxidative stress in birdsThe data file contains
 all the physiological and life history variables we used in this study.
 The legend column explains each variable.Vagasi_etal_2018_FunctEcol_data_Dryad.xlsx
DOI: 10.5061/dryad.q31407k
title: Data from: The spatial genetic structure of the White‐banded Tanager (Aves, Passeriformes) in fragmented Neotropical savannas suggests two evolutionarily significant units

description: Understanding the genetic structure of a species is crucial for
 evolutionary biology research and species conservation. The objectives of
 this study were to investigate the genetic structure of Neothraupis
 fasciata in Brazilian savannas and to assess genetic differentiation of
 its disjunct population in the Amazonian savannas of the state of Amapá.
 Population genetic structure was assessed in relation to isolation by
 distance and landscape variables connected with habitat heterogeneity. The
 influences of factors, such as habitat fragmentation and core-periphery
 distribution, on genetic diversity were also examined. Data were derived
 from a set of microsatellite loci of adult individuals from nine
 localities: eight distributed across the Cerrado and one in the disjunct
 Amazonian savanna of Amapá. Analysis revealed moderate genetic diversity
 and moderate population genetic structure, with at least two genetic
 clusters, one of which is represented exclusively by the disjunct Amapá
 population. The genetic structure found is not the result of significant
 influences by geographical distance, habitat heterogeneity or the
 core-periphery effect, nor by intense biome fragmentation due to anthropic
 action. The disjunct Amapá population exhibited a moderate level of
 genetic differentiation compared to the Cerrado population, suggesting
 that both can be considered distinct evolutionarily significant units for
 conservation purposes.
description: Genotypes of Neothraupis
 fasciata individuals.Genotypes of Neothraupis
 fasciata individuals from Environmental Protection Area Gama and Cabeça de
 Veado (AGCV), Águas Emendadas Ecological Station (EEAE), Cerrado
 Experiment Field of the Embrapa Amapá (MACA), Ponte Alta do Tocantins
 (PATO), Chapada dos Guimarães National Park (PNCG), Emas National Park
 (PNEM), Grande Sertão Veredas National Park (PGSV), Serra da Canastra
 National Park (PNSC), and Uruçuí (URUC). Missing genotype data is
 indicated by -9.Lima-Rezende et al. - Genotypes
 Neotraupis fasciata.odt
DOI: 10.15468/dl.4r6wv5
title: Occurrence Download

description: A dataset listing the 1837 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((26.87825 -29.47166,27.60918 -29.47166,27.60918 -29.08646,26.87825 -29.08646,26.87825 -29.47166))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 1837 records were derived from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001176-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qn8d9
title: Data from: Carnivore carcasses are avoided by carnivores

description: 1. Ecologists have traditionally focused on herbivore carcasses as study
 models in scavenging research. However, some observations of scavengers
 avoiding feeding on carnivore carrion suggest that different types of
 carrion may lead to differential pressures. Untested assumptions about
 carrion produced at different trophic levels could therefore lead
 ecologists to overlook important evolutionary processes and their
 ecological consequences. 2. Our general goal was to investigate the use of
 mammalian carnivore carrion by vertebrate scavengers. In particular, we
 aimed to test the hypothesis that carnivore carcasses are avoided by other
 carnivores, especially at the intra-specific level, most likely to reduce
 exposure to parasitism. 3. We take a three-pronged approach to study this
 principle by: i) providing data from field experiments, ii) carrying out
 evolutionary simulations of carnivore scavenging strategies under risks of
 parasitic infection, and iii) conducting a literature-review to test two
 hypotheses regarding parasite life-history strategies. 4. First, our field
 experiments showed that the mean number of species observed feeding at
 carcasses and the percentage of consumed carrion biomass were
 substantially higher at herbivore carcasses than at carnivore carcasses.
 This occurred even though the number of scavenger species visiting
 carcasses and the time needed by scavengers to detect carcasses were
 similar between both types of carcasses. In addition, we did not observe
 cannibalism. Second, our evolutionary simulations demonstrated that a risk
 of parasite transmission leads to the evolution of scavengers with
 generally low cannibalistic tendencies, and that the emergence of
 cannibalism-avoidance behavior depends strongly on assumptions about
 parasite-based mortality rates. Third, our literature review indicated
 that parasite species potentially able to follow a carnivore–carnivore
 indirect cycle, as well as those transmitted via meat consumption, are
 rare in our study system. 5. Our findings support the existence of a novel
 coevolutionary relation between carnivores and their parasites, and
 suggest that carnivore and herbivore carcasses play very different roles
 in food webs and ecosystems.
description: Moleon et al 2017 JAE
 (carnivore carcasses are avoided by carnivores)
DOI: 10.5061/dryad.10rk4
title: Data from: Antagonistic coevolution accelerates the evolution of reproductive isolation in Tribolium castaneum

description: The evolution of reproductive isolation among populations is often the
 result of selective forces. Among those, parasites exert strong selection
 on host populations and can thus also potentially drive reproductive
 isolation. This hypothesis has yet to be explicitly tested and, here, we
 set up a multigenerational coevolution experiment to explore this
 possibility. Five lines of Tribolium castaneum were allowed to coevolve
 with their natural parasite, Nosema whitei; five paired lines of identical
 origin were maintained in the absence of parasites. After 17 generations,
 we measured resistance within and reproductive isolation between all
 lines. Host lines from the coevolution treatment had considerable higher
 levels of resistance against N. whitei than their paired host lines which
 were maintained in the absence of parasites. Reproductive isolation was
 greater in the coevolved selection regime and correlated with phenotypic
 differentiation in parasite resistance between coevolved host lines. This
 suggests the presence of a selection-driven genetic correlation between
 offspring number and resistance. Our results show that parasites can be a
 driving force in the evolution of reproductive isolation, and thus
 potentially speciation.
description: data main experiment
 Antagonistic coevolution accelerates the evolution of reproductive
 isolation in Tribolium castaneumdata amnat
 RI.txtdata crossinfection
 experiment Antagonistic coevolution accelerates the evolution of
 reproductive isolation in Tribolium castaneumdata amnat crossinfection
 exp.txt
DOI: 10.5061/dryad.41mk8
title: Data from: Quantifying the human impacts on Papua New Guinea reef fish communities across space and time

description: Describing the drivers of species loss and of community change are
 important goals in both conservation and ecology. However, it is difficult
 to determine whether exploited species decline due to direct effects of
 harvesting or due to other environmental perturbations brought about by
 proximity to human populations. Here we quantify differences in species
 richness of coral reef fish communities along a human population gradient
 in Papua New Guinea to understand the relative impacts of fishing and
 environmental perturbation. Using data from published species lists we
 categorize the reef fishes as either fished or non-fished based on their
 body size and reports from the published literature. Species diversity for
 both fished and non-fished groups decreases as the size of the local human
 population increases, and this relationship is stronger in species that
 are fished. Additionally, comparison of modern and museum collections show
 that modern reef communities have proportionally fewer fished species
 relative to 19th century ones. Together these findings show that the reef
 fish communities of Papua New Guinea experience multiple anthropogenic
 stressors and that even at low human population levels targeted species
 experience population declines across both time and space.
description: Species of coral reef
 fish considered in analysis470 species of highly
 visible fishes identified across five sites in Papua New Guinea (Kimbe,
 Bootless Bay, Mline, Madang, Bismarck) during the early 21st century, as
 well as those from holdings of the Museum of Victoria which were made in
 Bootless Bay from 1881-1889Supplemental
 1.csv
DOI: 10.5061/dryad.9f8j2
title: Data from: Genetic evidence for a Janzen-Connell recruitment pattern in reproductive offspring of Pinus halepensis trees.

description: Effective seed dispersal, combining both dispersal and post-dispersal
 (establishment) processes, determines population dynamics and colonization
 ability in plants. According to the Janzen-Connell (JC) model, high
 mortality near the mother plant shifts the offspring establishment
 distribution farther away from the mother plant relative to the seed
 dispersal distribution. Yet, extending this prediction to the distribution
 of mature (reproductive) offspring remains a challenge for long-living
 plants. To address this challenge we selected an isolated natural Aleppo
 pine (Pinus halepensis) population in Mt. Pithulim (Israel), expanded from
 five ancestor trees in the beginning of the 20th century into ~2000 trees
 today. Using nine microsatellite markers, we assigned parents to trees
 established during the early stages of population expansion. To elucidate
 the effect of the distance from mother plant on post-dispersal survival,
 we compared the effective seed dispersal kernel, constructed based on the
 distribution of mother-offspring distances, to the seed dispersal kernel,
 computed based on simulations of a mechanistic wind dispersal model. We
 found that the mode of the effective dispersal kernel is shifted farther
 away than the mode of the seed dispersal kernel, reflecting increased
 survival with increasing distance from the mother plant. The parentage
 analysis demonstrated a highly skewed reproductive success and a strong
 directionality in effective dispersal corresponding to the wind regime. We
 thus provide the first evidence that JC effects act also on offspring that
 become reproductive and persisted as adults for many decades, a key
 requirement in assessing the role of post-dispersal processes in shaping
 population and community dynamics.
description: Sample locations and
 microsatellite data of Aleppo pine in Mt. Pithulim study
 siteDataForDRYAD.txt
DOI: 10.5061/dryad.v1c28
title: Data from: Invasive earthworms erode soil biodiversity: a meta-analysis

description: 1. Biological invasions pose a serious threat to biodiversity and
 ecosystem functioning across ecosystems. Invasions by ecosystem engineers,
 in particular, have been shown to have dramatic effects in recipient
 ecosystems. For instance, invasion by earthworms, a belowground
 invertebrate ecosystem engineer, in previously earthworm-free ecosystems
 dramatically alters the physico-chemical characteristics of the soil.
 Studies have shown that such alterations in the soil can have far-reaching
 impacts on soil organisms, which form a major portion of terrestrial
 biodiversity. 2. Here, we present the first quantitative synthesis of
 earthworm invasion effects on soil microorganisms and soil invertebrates
 based on 430 observations from 30 independent studies. 3. Our
 meta-analysis shows a significant decline of the diversity and density of
 soil invertebrates in response to earthworm invasion with anecic and
 endogeic earthworms causing the strongest effects. Earthworm invasion
 effects on soil microorganisms were context-dependent, such as depending
 on functional group richness of invasive earthworms and soil depth.
 Microbial biomass and diversity increased in mineral soil layers, with a
 weak negative effect in organic soil layers, indicating that the mixing of
 soil layers by earthworms (bioturbation) may homogenize microbial
 communities across soil layers. 4. Our meta-analysis provides a compelling
 evidence for negative effects of a common invasive belowground ecosystem
 engineer on belowground biodiversity of recipient ecosystems, which could
 potentially alter the ecosystem functions and services linked to soil
 biota.
description: Ferlian et al. 2017-Soil
 fauna density dataThis data file contains
 the data on soil invertebrate density response to invasive earthworms.
 Data in this file are extracted from the literature.