cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fd3nq57
title: Data from: Testes size increases with sperm competition risk and intensity in bony fish and sharks

description: Female multiple mating provides the opportunity for sexual selection to
 continue after gamete release, generating strong selection on male
 reproductive traits. In particular, in species where female multiple
 mating is common, males are expected to invest more in testicular tissue
 to afford them a numerical advantage during sperm competition. However,
 although testes size (correcting for body size) is a commonly used proxy
 of the strength of sperm competition, there is surprisingly scant direct
 evidence linking male investment in testes with genetic estimates of
 multiple paternity across species. Here we test the hypothesis that testes
 size is influenced by genetic estimates of sperm competition risk
 (multiple paternity percentage) and intensity (number of sires per brood)
 in fishes, the most diverse and specious vertebrate group. We provide
 conclusive evidence that testes size is larger in species experiencing a
 higher risk and intensity of sperm competition, a finding that remains
 consistent among sharks and bony fishes (including in separate analyses
 focused only on cichlids). These findings shed new light on evolutionary
 processes governing sperm competition in a basal vertebrate lineage and
 validate the now-widespread use of body-size corrected testes mass as a
 proxy for sperm competition risk and intensity.
description: Fish paternity, testes
 and body mass dataPaternity data were
 collected from the literature. Testes and body mass data were collected
 from the literature, field sampling and personal communications with
 authors. Citations are listed in the "readme.txt" file. Full
 details of sources can be found in the online supplementary material
 (Table S1).MPdata2018.csv
DOI: 10.5061/dryad.4j7q3s0t
title: Data from: Recent population decline and selection shape diversity of taxol-related genes

description: Taxanes are defensive metabolites produced by Taxus species (yews) and
 used in anticancer therapies. Despite their medical interest, patterns of
 natural diversity in taxane related genes are unknown. We examined
 variation at five main taxol-related genes of T. baccata in the Iberian
 Peninsula, a region where unique yew genetic resources are endangered. We
 looked at several gene features and applied complementary neutrality
 tests, including diversity/divergence tests, tests solely based on
 site-frequency spectrum and Zeng’s compound tests. To account for specific
 demography, microsatellite data were used to infer historical changes in
 population size based on an Approximate Bayesian Computation (ABC)
 approach. Polymorphism-divergence tests pointed to positive selection for
 genes TBT and TAT, and balancing selection for DBAT. In addition,
 neutrality tests based on site-frequency spectrum found that while a
 recent reduction in population size may explain most of statistics’
 values, selection may still be in action in genes TBT and DBAT, at least
 in some populations. Molecular signatures on taxol genes suggest the
 action of frequent selective waves with different direction or intensity,
 possibly related to varying adaptive pressures produced by the host-enemy
 co-evolution on defense-related genes. Such natural selection processes
 may have produced taxane variants still undiscovered.
description: Taxus baccata SSR
 genotypes
DOI: 10.15468/dl.e2k5cy
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Micrurus diutius"
 ]
}

 The dataset includes 99 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001309-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q7ht7
title: Data from: Clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint?

description: Genetic determinants of seasonal reproduction are not fully understood,
 but may be important predictors of organism responses to climate change.
 We used a comparative approach to study the evolution of seasonal timing
 within a fish community in a natural common garden setting. We tested the
 hypothesis that allelic length variation in the PolyQ domain of a
 circadian rhythm gene, Clock1a, corresponded to interspecific differences
 in seasonal reproductive timing across five native and one introduced
 cyprinid fishes (n = 425 individuals) that co-occur in the Rio Grande, New
 Mexico, USA. Most common allele lengths were longer in native species that
 initiated reproduction earlier (Spearman’s r = -0.70, p = 0.23). Clock1a
 allele length exhibited strong phylogenetic signal and earlier spawners
 were evolutionarily derived. Aside from length variation in Clock1a, all
 other amino acids were identical across native species, suggesting
 functional constraint over evolutionary time. Interestingly, the
 endangered Rio Grande silvery minnow (Hybognathus amarus) exhibited less
 allelic variation in Clock1a and observed heterozygosity was 2- to 6-fold
 lower than the five other (non-imperiled) species. Reduced genetic
 variation in this functionally important gene may impede this species’
 capacity to respond to ongoing environmental change.
description: Krabbenhoft_&_Turner_2014_Clock_microsat_genotypesMIcrosatellite genotypes (allele lengths, in bp) for Clock1a.
DOI: 10.5061/dryad.rp321
title: Data from: Plant-pollinator interactions over 120 years: loss of species, co-occurrence, and function

description: Using historic data sets, we quantified the degree to which global change
 over 120 years disrupted plant-pollinator interactions in a temperate
 forest understory community in Illinois, USA. We found degradation of
 interaction network structure and function and extirpation of 50% of bee
 species. Network changes can be attributed to shifts in forb and bee
 phenologies resulting in temporal mismatches, nonrandom species
 extinctions, and loss of spatial co-occurrences between extant species in
 modified landscapes. Quantity and quality of pollination services have
 declined through time. The historic network showed flexibility in response
 to disturbance; however, our data suggest that networks will be less
 resilient to future changes.
description: Flowering
 phenologiesdryad - plant
 phen.csvBee
 phenologiesdryad - bee
 phen.csvplant-bee
 interactionsdryad - interactions
 now.csv
DOI: 10.5061/dryad.pp5bs35
title: Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

description: Decomposition contributes to global ecosystem function by contributing to
 nutrient recycling, energy flow and limiting biomass accumulation. The
 decomposer organisms influencing this process form diverse, complex, and
 highly dynamic communities that often specialize on different plant or
 animal resources. Despite performing the same net role, there is a need to
 conceptually synthesize information on the structure and function of
 decomposer communities across the spectrum of dead plant and animal
 resources. A lack of synthesis has limited cross-disciplinary learning and
 research in important areas of ecosystem and community ecology. Here we
 expound on the ‘necrobiome’ concept and develop a framework describing the
 decomposer communities and their interactions associated with plant and
 animal resource types within multiple ecosystems. We outline the biotic
 structure and ecological functions of the necrobiome, along with how the
 necrobiome fits into a broader landscape and ecosystem context. The
 expanded necrobiome model provides a set of perspectives on decomposer
 communities across resource types, and conceptually unifies plant and
 animal decomposer communities into the same framework, while acknowledging
 key differences in processes and mechanisms. This framework is intended to
 raise awareness among researchers, and advance the construction of
 explicit, mechanistic hypotheses that further our understanding of
 decomposer community contributions to biodiversity, the structure and
 function of ecosystems and global nutrient recycling and energy flow.
description: Benbow et al
 Supplemental Data Ecological Monographs 2018The data provided in
 this file represent the data that were included in Figure 3 of Benbow et
 al. 2018. Necrobiome Framework for Bridging Decomposition Ecology of
 Autotrophically- and Heterotrophically-Derived Organic Matter. Ecological
 Monographs.S1_Supplemental
 Data.xlsx
DOI: 10.5061/dryad.k1p41
title: Data from: Apparent annual survival estimates of tropical songbirds better reflect life history variation when based on intensive field methods

description: Aim: Adult survival is central to theories explaining latitudinal
 gradients in life history strategies. Life history theory predicts higher
 adult survival in tropical than north temperate regions given lower
 fecundity and parental effort. Early studies were consistent with this
 prediction, but standard-effort netting studies in recent decades
 suggested that apparent survival rates in temperate and tropical regions
 strongly overlap. Such results do not fit with life history theory.
 Targeted marking and resighting of breeding adults yielded higher survival
 estimates in the tropics, but this approach is thought to overestimate
 survival because it does not sample social and age classes with lower
 survival. We compared the effect of field methods on tropical survival
 estimates and their relationships with life history traits. Location:
 Sabah, Malaysian Borneo. Time period: 2008–2016. Major taxon:
 Passeriformes. Methods: We used standard-effort netting and resighted
 individuals of all social and age classes of 18 tropical songbird species
 over 8 years. We compared apparent survival estimates between these two
 field methods with differing analytical approaches. Results: Estimated
 detection and apparent survival probabilities from standard-effort netting
 were similar to those from other tropical studies that used
 standard-effort netting. Resighting data verified that a high proportion
 of individuals that were never recaptured in standard-effort netting
 remained in the study area, and many were observed breeding. Across all
 analytical approaches, addition of resighting yielded substantially higher
 survival estimates than did standard-effort netting alone. These apparent
 survival estimates were higher than for temperate zone species, consistent
 with latitudinal differences in life histories. Moreover, apparent
 survival estimates from addition of resighting, but not from
 standard-effort netting alone, were correlated with parental effort as
 measured by egg temperature across species. Main conclusions: Inclusion of
 resighting showed that standard-effort netting alone can negatively bias
 apparent survival estimates and obscure life history relationships across
 latitudes and among tropical species.
description: Martin et al 2017 GEB
 Tropical survivalApparent survival,
 detection probabilities, and confidence intervals under differing
 analytical approaches.
DOI: 10.5061/dryad.b55tv
title: Data from: Prenatal exposure to predation affects predator recognition learning via lateralization plasticity

description: Prey with cerebral lateralization often shows a bias in escape direction
 and asymmetrical use of eyes for scanning. Such asymmetries are likely to
 cause ecological disadvantages when, for example, predators attack from
 the side in which the prey is more susceptible. However, lateralized
 individuals are diffuse in many species and, paradoxically, their
 frequency increases via developmental plasticity in environments with
 high-predation risk. Using wood frog tadpoles, Lithobates sylvaticus, we
 tested the hypothesis that cerebral lateralization enhances predator
 recognition learning and thus overcomes the costs of behavioral
 asymmetries in high predation risk environments. In the first experiment,
 we found tadpoles exposed to risk as embryos developed more intense
 lateralization in a rotational test compared to predator-naive controls.
 Risk exposure led to the more frequent development of clockwise swimming
 preference. In the second experiment, we found that tadpoles exhibiting no
 behavioral lateralization and tadpoles with marked clockwise swimming
 preference learned to recognize the novel predator odor, with the latter
 showing a better performance as predicted. Tadpoles with anticlockwise
 swimming preference did not learn to associate the predator with risk.
 Exposure to a high-risk environment during early ontogeny appears to favor
 the development of either a lateralization phenotype with refined predator
 recognition learning skills, or, to a lesser extent, a lateralization
 phenotype with poor predator recognition learning skills. Such individuals
 likely cope with predation using mechanisms other than learning.
description: Lucon-Xiccato et al.
 2016 Behav Ecol - DataExcel file with the data
 of the two experiments. Experiment 1: effect of predation risk on
 lateralization. Experiment 2: predator recognition learning test.
 Descriptive name of each variable is provided within the
 file.
DOI: 10.5061/dryad.693kt2j
title: Data from: Nonlocal rheology of dense granular flow in annular shear experiments

description: The flow of dense granular materials at low inertial numbers cannot be
 fully characterized by local rheological models; several nonlocal
 rheologies have recently been developed to address these shortcomings. To
 test the efficacy of these models across different packing fractions and
 shear rates, we perform experiments in a quasi-2D annular shear cell with
 a fixed outer wall and a rotating inner wall, using photoelastic
 particles. The apparatus is designed to measure both the stress ratio μ
 (the ratio of shear to normal stress) and the inertial number I through
 the use of a torque sensor, laser-cut leaf springs, and particle-tracking.
 We obtain μ(I) curves for several different packing fractions and rotation
 rates, and successfully find that a single set of model parameters is able
 to capture the full range of data collected once we account for frictional
 drag with the bottom plate. Our measurements confirm the prediction that
 there is a growing lengthscale at a finite value μs, associated with a
 frictional yield criterion. Finally, we newly identify the physical
 mechanism behind this transition at μs by observing that it corresponds to
 a drop in the susceptibility to force chain fluctuations.
description: nonlocal rheology data
 from annular shearrheology.zip
DOI: 10.5061/dryad.qt6535q
title: Data from: Taxonomy-based hierarchical analysis of natural mortality: polar and sub-polar phocid seals

description: Knowledge of life‐history parameters is frequently lacking in many species
 and populations, often because they are cryptic or logistically
 challenging to study, but also because life‐history parameters can be
 difficult to estimate with adequate precision. We suggest using
 hierarchical Bayesian analysis (HBA) to analyze variation in life‐history
 parameters among related species, with prior variance components
 representing shared taxonomy, phenotypic plasticity, and observation
 error. We develop such a framework to analyze U‐shaped natural mortality
 patterns typical of mammalian life history from a variety of sparse
 datasets. Using 39 datasets from seals in the family Phocidae, we analyzed
 16 models with different formulations for natural morality, specifically
 the amount of taxonomic and data‐level variance components (subfamily,
 species, study, and dataset levels) included in mortality hazard
 parameters. The highest‐ranked model according to DIC included subfamily‐,
 species‐, and dataset‐level parameter variance components and resulted in
 typical U‐shaped hazard functions for the 11 seal species in the study.
 Species with little data had survival schedules shrunken to the mean. We
 suggest that evolutionary and population ecologists consider employing HBA
 to quantify variation in life‐history parameters. This approach can be
 useful for increasing the precision of estimates resulting from a
 collection of (often sparse) datasets, and for producing prior
 distributions for populations missing life‐history data.
description: Data on phocid seals
 natural history parameters and code for Bayesian hierarchical
 modelsThe datafile was
 compiled based on publicly available published sources cited in Trukhanova
 et al 2018 Appendix S1. The associated R files contain a code for data
 analysis. For detailed data description please see README
 file.Trukhanova et al data and
 code.zip
DOI: 10.5061/dryad.pc1th
title: Data from: Toward the genetic origins of a potentially non-native population of threespine stickleback (Gasterosteus aculeatus) in Alberta

description: Disentangling the origin of putatively introduced/invasive species is of
 increasing priority in conservation biology. The presence of a previously
 undocumented species may be due to an undetected recent population or
 range expansion associated with environmental change, or due to an
 introduction by humans. We used molecular tools to address the origin of a
 population of threespine stickleback (Gasterosteus aculeatus) first
 identified in central Alberta, Canada in 1980 from a single lake. We
 characterized this inland, high elevation Alberta population in comparison
 to samples from five representative geographic regions worldwide, using
 mtDNA and nine microsatellite loci to elucidate genetic structure and
 estimate divergence times. We found significantly lower levels of genetic
 variation in the Alberta population, which could reflect either a recent
 colonization or periodic bottlenecks associated with winterkills. While we
 did find that the Alberta samples were most closely related to the North
 American West Coast populations, we did not uncover a putative source
 population. Alberta samples formed a clade in phylogenetic analyses, with
 divergence time estimates between the Alberta and British Columbia samples
 ca. 250–750 kya. The hypothesis that the Alberta population represents a
 natural colonization during North America’s last glacial recession could
 not be rejected. Collectively, these data suggest that the genetic
 signature of colonizing populations following introductions may be similar
 to populations at their range limit, contributing to difficulties
 establishing population origins.
description: Microsattilite genotypes
 for all individuals at all 16 lociThis file contains the
 microsattilite data that was attained for this study. It is in genepop
 format. This file contains all loci that were genotyped including those
 that were removed from the analysis. The 16 numbers at the top of the file
 represent loci names. Each entry under a "POP" header represents
 an individual of that population, where A = Alaska, B = Brannen Lake, E =
 East Coast, M = Mayliewan (our Alberta population), and N = Norway. Each
 of the 16 sets of 4 digits represent diploid genotypes at each of the 16
 loci for that individual. For example, 0414 would represent a heterozygous
 call for allele 4 and allele 14 for that individual for whatever locus it
 is under. The first column of 4 digits represents locus 51 and the last
 represents locus 222 (the rest are ordered accordingly). 00s represent
 missing data.Genepop_all_16_loci.txt
DOI: 10.5061/dryad.73363
title: Data from: Early life nutritional quality effects on adult memory retention in a parasitic wasp

description: Nutritional quality during early life can affect learning ability and
 memory retention of animals. Here we studied the effect of resource
 quality gained during larval development on the learning ability and
 memory retention of 2 sympatric strains of similar genetic background of
 the parasitoid Trichogramma brassicae: one uninfected and one infected by
 Wolbachia. Wolbachia is a common arthropod parasite/mutualistic symbiont
 with a range of known effects on host fitness. Here we studied, for the
 first time, the interaction between resource quality and Wolbachia
 infection on memory retention and resource acquisition. Memory retention
 of uninfected wasps was significantly longer when reared on high quality
 hosts when compared to low quality hosts. Furthermore, uninfected wasps
 emerging from high quality hosts showed higher values of protein and
 triglyceride than those emerging from low quality hosts. In contrast, the
 memory retention for infected wasps was the same irrespective of host
 quality, although retention was significantly lower than uninfected wasps.
 No significant effect of host quality on capital resource amount of
 infected wasps was observed, and infected wasps displayed a lower amount
 of protein and triglyceride than uninfected wasps when reared on high
 quality hosts. This study suggests that the nutritional quality of the
 embryonic period can affect memory retention of adult wasps not infected
 by Wolbachia. However, by manipulating the host’s obtained capital
 resource amount, Wolbachia could enable exploitation of the maximum
 available resources from a range of hosts to acquire suitable performance
 in complex environments.
description: Book1
DOI: 10.5061/dryad.b08j3
title: Data from: Mesopredator management: effects of red fox control on the abundance, diet and use of space by feral cats

description: Apex predators are subject to lethal control in many parts of the world to
 minimize their impacts on human industries and livelihoods. Diverse
 communities of smaller predators - mesopredators - often remain after apex
 predator removal. Despite concern that these mesopredators may be
 'released' in the absence of the apex predator and exert
 negative effects on each other and on co-occurring prey, these
 interactions have been little studied. Here, we investigate the potential
 effects of competition and intraguild predation between red foxes (Vulpes
 vulpes) and feral cats (Felis catus) in south-eastern Australia where the
 apex predator, the dingo (Canis dingo), has been extirpated by humans. We
 predicted that the larger fox would dominate the cat in encounters, and
 used a fox-removal experiment to assess whether foxes affect cat
 abundance, diet, home-range and habitat use. Our results provide little
 indication that intraguild predation occurred or that cats responded
 numerically to the fox removal, but suggest that the fox affects some
 aspects of cat resource use. In particular, where foxes were removed cats
 increased their consumption of invertebrates and carrion, decreased their
 home range size and foraged more in open habitats. Fox control takes place
 over large areas of Australia to protect threatened native species and
 agricultural interests. Our results suggest that fox control programmes
 could lead to changes in the way that cats interact with co-occurring
 prey, and that some prey may become more vulnerable to cat predation in
 open habitats after foxes have been removed. Moreover, with intensive and
 more sustained fox control it is possible that cats could respond
 numerically and also alter their behaviour in different ways to those
 documented herein. Such outcomes need to be considered when estimating the
 indirect impacts of fox control. We conclude that novel approaches are
 urgently required to control invasive mesopredators at the same time,
 especially in areas where apex predators are absent.
description: Data_Molsher2016Figures 2-6