cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jsxksn06q
title: Data from: Heterospecific mating interactions as an interface between ecology and evolution

description: Reproductive interference (costly interspecific sexual interactions) are
 well-understood to promote divergence in mating-relevant traits (i.e.
 reproductive character displacement: RCD), but it can also reduce
 population growth, eventually leading to local extinction of one of the
 species. The ecological and evolutionary processes driven by reproductive
 interference can interact with each other. These interactions are likely
 to influence whether the outcome is co-existence or extinction, but remain
 little studied. In this paper, we first develop an eco-evolutionary
 perspective on reproductive interference by integrating ecological and
 evolutionary processes in a common framework. We also present a simple
 model to demonstrate the eco-evolutionary dynamics of reproductive
 interference. We then identify a number of factors that are likely to
 influence the relative likelihoods of extinction or RCD. We discuss
 particularly relevant factors by classifying them into four categories:
 the nature of the traits responding to selection, the mechanisms
 determining the expression of these traits, mechanisms of reproductive
 interference, and the ecological background. We highlight previously
 underappreciated ways in which these factors may influence the relative
 likelihoods of RCD and local extinction. By doing so, we also identify
 questions and future directions that will increase our holistic
 understanding of the outcomes of reproductive interference.
description: An R script for individual based simulation models of
 reinforcement. There are two species, which can hybridize with each
 other. All hybrids die soon after fertilization (complete postzytotic
 isolation). A polygenic trait for mate choice (e.g. body size) can evolve.
 Demographic dynamics is also explicitly modelled. Densities of the two
 species are limited by different resources. Organisms are haploids and
 hermaphrodites.
description: Simulation results for the publication was made using a Windows
 10 computer. A single run takes a few minutes.
DOI: 10.15468/dl.4mf445
title: Occurrence Download

description: A dataset containing 2344 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canis lupus baileyi"
 ]
}

 The dataset includes 2344 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002467-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9zw3r22br
title: Data from: Can paternal effects via seminal fluid contribute to the evolution of polyandry?

description: Genetic benefits from mating with multiple males are thought to favor the
 evolution of polyandry. However, recent evidence suggests that nongenetic
 paternal effects via seminal fluid might contribute to the observed
 effects of polyandry on offspring performance. Here we test this
 hypothesis using the field cricket Teleogryllus oceanicus. Using
 interference RNA we first show that at least one seminal fluid protein is
 essential for embryo survival. We then show that polyandrous females mated
 to three different males produced embryos with higher pre-hatching
 viability than did monandrous females mated with the same male three
 times. Pseudo-polyandrous females that obtained sperm and seminal fluid
 from a single male and seminal fluid from two additional males, had
 embryos with viabilities intermediate between monandrous and polyandrous
 females. Our results suggest either that ejaculate mediated paternal
 effects on embryo viability have both genetic and nongenetic components,
 or that seminal fluids transferred by castrated males provide only a
 subset of proteins contained within the normal ejaculate, and are unable
 to exert their full effect on embryo viability.
DOI: 10.5061/dryad.sxksn0315
title: Data from: Along with intraspecific functional trait variation, individual performance is key to resolving community assembly processes

description: Species contributing high proportions to community biomass strongly
 influence ecosystem processes within the community. Studies have shown
 that dominant species may serve as nurse plants, helping to ensure biomass
 stability of the subordinate species under stress conditions. The question
 is widely debated as to whether either niche differentiation or neutral
 processes drive the net outcome of plant interactions within a subordinate
 plant community. To answer this question, requires precise estimates of
 individual variation in functional traits and performance. In a five-year
 mesocosm experiment, the functional responses of a subordinate plant
 community to the removal of the dominant species were evaluated across two
 drought-stress scenarios. Small scale (i.e., large pots) wetland
 communities were constructed comprising one dominant species (Carex elata)
 and three subordinate species. Removal of the dominant species allowed
 evaluation of the net effects of drought and interspecific interactions.
 We estimated the functional divergences for three traits (specific leaf
 area, leaf dry matter content and height growth allocation) and compared
 these with performance differences quantified individually. This enabled
 distinctions to be made between deterministic (i.e., niche
 differentiation) and neutral processes driving the drought response of the
 subordinate community. We showed that the dominant species decreased
 relative performance differences within the subordinate plant community
 under conditions of permanent drought stress. These changes were
 associated with the convergence of traits related to resource acquisition
 and growth. The dominant species equalised species performance differences
 by supressing relatively drought-tolerant species with low competitive
 ability and by supporting the less drought-tolerant species with
 relatively high competitive ability. Meanwhile, under conditions of
 interannual drought, the subordinate species likely coexisted due to
 differentiation in resource-use strategies and the interaction with the
 dominant species. Inclusion of individual variation in performance with a
 functional trait approach provides valuable insights into the processes
 structuring plant communities. Ours is the first study to provide evidence
 that subordinate species exposed to drought may coexist via neutral
 processes arising from their interactions with the dominant species,
 leading to functional convergence of traits associated with the trade-off
 between stress tolerance and competitive ability.
DOI: 10.5061/dryad.1vhhmgqqk
title: Neurofilament light chain (NfL) as a biomarker of hereditary transthyretin-mediated amyloidosis

description: To identify changes in the proteome associated with onset and progression
 of ATTRv amyloidosis, we performed an observational, case-controlled study
 which compared proteomes of patients with ATTRv amyloidosis and healthy
 controls. Plasma levels of &gt;1,000 proteins were measured in
 patients with ATTRv amyloidosis with polyneuropathy who received either
 placebo or patisiran in the APOLLO study and in healthy controls. The
 impact of patisiran on the time profile of each protein was determined by
 linear mixed model at 0, 9, and 18 months. Neurofilament light chain (NfL)
 was further assessed using an orthogonal quantitative approach. Levels of
 66 proteins were significantly changed with patisiran vs placebo, with NfL
 change most significant (p &lt; 10−20). Analysis of changes in protein
 levels demonstrated that the proteome of patisiran-treated patients
 trended toward healthy controls at 18 months. Healthy controls' NfL
 levels were 4-fold lower than in patients with ATTRv amyloidosis with
 polyneuropathy (16.3 vs 69.4 pg/mL, effect: −53.1 pg/mL, 95% CI [–60.5 to
 −45.9]). NfL levels at 18 months increased with placebo (99.5 vs 63.2
 pg/mL, 36.3 pg/mL, [16.5–56.1]) and decreased with patisiran treatment
 (48.8 vs 72.1 pg/mL, −23.3 pg/mL, [–33.4 to −13.1]) from baseline. At 18
 months, improvement in modified Neuropathy Impairment Score +7 following
 patisiran significantly correlated with reduced NfL (R = 0.43,
 [0.29–0.55]). Findings suggest NfL may serve as a biomarker of nerve
 damage and polyneuropathy in ATTRv amyloidosis, may enable earlier
 diagnosis of patients with ATTRv amyloidosis, and facilitate monitoring of
 disease progression. This study provides Class III evidence that NfL
 levels may enable earlier diagnosis of polyneuropathy in patients with
 ATTRv amyloidosis and facilitate monitoring of disease progression.
description: This supplementary data comprises: Table
 e-1 A comprehensive list of all proteins that
 significantly changed between placebo- and patisiran-treated hereditary
 transthyretin (ATTRv) amyloidosis patients over time during the APOLLO
 study Table e-2 Comparisons of
 levels of neurofilament light chain (NfL) between healthy controls and
 placebo- or patisiran-treated patients at baseline, 9 months, or 18
 months Table e-3 Comparisons of
 levels of NfL in baseline APOLLO patients at different polyneuropathy
 disability (PND) scores Table e-4
 Comparisons of levels of NfL in baseline APOLLO patients that
 were in the prespecified cardiac subpopulation or not to healthy
 controls Table e-5 Comparisons of
 levels of NfL in healthy controls and placebo- or patisiran-treated
 patients at baseline or 18 months between groups.
DOI: 10.15468/dl.6xdbjs
title: Occurrence Download

description: A dataset containing 65266 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((4 7,3 7,3 6,4 6,4 7))",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 65266 records from 139 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002430-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2jm63xsmg
title: Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection

description: Studies of controlled lab animals and natural populations represent two
 insightful extremes of microbiota research. We bridged these two
 approaches by transferring lab-bred female C57BL/6 mice from a
 conventional mouse facility to an acclimation room and then to an outdoor
 enclosure, to investigate how the gut microbiota changes with environment.
 Mice residing under constant conditions served as controls. Using
 16S rRNA sequencing of fecal samples, we found that the shift in
 temperature and humidity, as well as exposure to a natural environment,
 increased microbiota diversity and altered community composition.
 Community composition in mice exposed to high temperatures and humidity
 diverged as much from the microbiota of mice housed outdoors as from the
 microbiota of control mice. Additionally, infection with the nematode
 Trichuris muris modulated how the microbiota responded to environmental
 transitions: The dynamics of several families were buffered by
 the nematodes, while invasion rates of two taxa acquired outdoors were
 magnified. These findings suggest that gut bacterial communities respond
 dynamically and simultaneously to changes within the host’s body (e.g.,
 the presence of nematodes) and to changes in the wider environment of the
 host.
description: IgG and worm counts File:
 IgG_WormCount.csv. This file contains the <em>Trichuris
 muris</em>-specific IgG optical density values and the final worm
 counts of individual mice at the experimental endpoint (i.e., 28 days
 post-infection). Mice are distinguished by their ID number.
 Metadata and sequencing information File:
 Metadata_Sequencing.csv. This file contains information on the
 environment, infection groups, deworming treatment, mass, and cage and
 outdoor wedge distributions of individual mice throughout the experiment.
 Up to six timepoints of data were collected for each mouse. Individual
 mice are distinguished by their ID number. The sample_ID names match the
 ID names in the 16S rRNA sequence files available from the NCBI Sequence
 Read Archive database. The number and proportion of sequencing reads
 (Forward: R1; Reverse: R2) and information on the yields and the quality
 of reads for each fecal sample that was sequenced are also
 presented.
DOI: 10.5061/dryad.6t1g1jwws
title: Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)

description: Evidence from natural systems suggests that hybridization between animal
 species is more common than traditionally thought, but the overall
 contribution of introgression to standing genetic variation within species
 remains unclear for most animal systems. Here, we use targeted
 exon-capture to sequence thousands of nuclear loci and complete
 mitochondrial genomes from closely related chipmunk species in the Tamias
 quadrivittatus group that are distributed across the Great Basin and the
 central and southern Rocky Mountains of North America. This recent
 radiation includes six overlapping, ecologically distinct species (T.
 canipes, T. cinereicollis, T. dorsalis, T. quadrivittatus, T. rufus, and
 T. umbrinus) that show evidence for widespread mitochondrial introgression
 across species boundaries. Such evidence has historically derived from a
 handful of markers, typically focused on mitochondrial loci, to describe
 patterns of introgression; consequently, the extent of introgression of
 nuclear genes is less well characterized. We conducted a series of
 phylogenomic and species-tree analyses to resolve the phylogeny of six
 species in this group. In addition, we performed several population
 genomic analyses to characterize nuclear genomes and infer coancestry
 among individuals. Furthermore, we used emerging quartets-based approaches
 to simultaneously infer the species tree (SVDquartets) and identify
 introgression (HyDe). We found that, in spite of rampant introgression of
 mitochondrial genomes between some species pairs (and sometimes involving
 up to three species), there appears to be little to no evidence for
 nuclear introgression. These findings mirror other genomic results where
 complete mitochondrial capture has occurred between chipmunk species in
 the absence of appreciable nuclear gene flow. The underlying causes of
 recurrent massive cytonuclear discordance remain unresolved in this group
 but mitochondrial DNA appears highly misleading of population histories as
 a whole. Collectively, it appears that chipmunk species boundaries are
 largely impermeable to nuclear gene flow and that hybridization, while
 pervasive with respect to mtDNA, has likely played a relatively minor role
 in the evolutionary history of this group.
description: The data set was generated by targeted sequencing using a set of
 capture probes designged by JMG for chipmunks. Reads were assembled usig
 ARC, an assember designed by  BAJS, SHS and MLS.
description: We have provided two simple nexus files. The first contains of
 all the contigs for the nuclear data contatenated, but with contig
 bourndaries delimited. The second nexus file contains the mtDNA data that
 were published previously (Sarver et al. 2017. GB&E, 9:7-19. doi.org/10.1093/gbe/evx034).
DOI: 10.5061/dryad.fxpnvx0pp
title: E. coli aminoglycoside treatment

description: Aminoglycosides are broad-spectrum antibiotics whose mechanism of action
 is under debate. It is widely accepted that membrane voltage potentiates
 aminoglycoside activity, which is ascribed to voltage-dependent drug
 uptake. In this paper, we measured the response of Escherichia coli
 treated with aminoglycosides and discovered that the bactericidal action
 arises not from the downstream effects of voltage dependent drug uptake,
 but rather directly from dysregulated membrane potential. In the absence
 of voltage, aminoglycosides are taken into cells and exert bacteriostatic
 effects by inhibiting translation. However, cell killing was immediate
 upon re-polarization. The hyperpolarization arose from altered ATP flux,
 which induced a reversal of the F1Fo-ATPase to hydrolyze ATP and generated
 the deleterious voltage. Heterologous expression of an ATPase inhibitor
 completely eliminated bactericidal activity, while loss of the F-ATPase
 reduced the electrophysiological response to aminoglycosides. Our data
 support a model of voltage induced death, and separates aminoglycoside
 bacteriostasis and bactericide in E. coli.
description: Data was collected on an inverted fluorescence microscope using a
 488 nm and 561 nm excitation.  Raw data was pre-processed by correcting
 uneven illumination, registering frames in time, and subtracting an
 estimated background.  Each cell has a time trace that is provided here,
 and each cell is part of a population that represents 1 biological
 replicate.  Each biological replicate comes from an indepenently grown and
 imaged population of bacteria.
description: Data was analyzed with Matlab (R2018a).  Extraction files and
 subfiles are included.
DOI: 10.15468/dl.nwjds4
title: Occurrence Download

description: A dataset containing 1356 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senegalia nigrescens"
 ]
}

 The dataset includes 1356 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002469-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hdr7sqvfp
title: Data from: Immune checkpoint protein VSIG4 as a biomarker of aging in Murine adipose tissue

description: Adipose tissue is recognized as a major source of systemic inflammation
 with age, driving age-related tissue dysfunction and pathogenesis.
 Macrophages (Mϕ) are central to these changes yet adipose tissue Mφ (ATMs)
 from aged mice remain poorly characterized. To identify biomarkers
 underlying changes in aged adipose tissue, we performed an unbiased
 RNA-seq analysis of ATMs from young (10-week old) and healthy aged
 (80-week old) mice. One of the genes identified, V-set
 immunoglobulin-domain-containing 4 (VSIG4/CRIg), encodes a Mφassociated
 complement receptor and B7 family-related immune checkpoint protein. Here,
 we demonstrate that Vsig4 expression is highly upregulated with age in
 perigonadal white adipose tissue (gWAT) in two mouse strains (inbred
 C57BL/6J and outbred NIH Swiss) independent of gender. The accumulation of
 VSIG4 was mainly associated with a 4-fold increase in the proportion of
 VSIG4+ ATMs (13% to 52%). In a longitudinal study, VSIG4 expression in
 gWAT showed a strong correlation with age within a cohort of male and
 female mice and correlated strongly with physiological frailty index (PFI,
 a multi-parameter assessment of health) in male mice. Our results indicate
 that VSIG4 is a novel biomarker of aged murine ATMs. VSIG4 expression was
 also found to be elevated in other aging tissues (e.g., thymus), and was
 strongly induced in tumor-adjacent stroma in cases of spontaneous and
 xenograft lung cancer models. VSIG4 expression was recently associated
 with cancer and several inflammatory diseases with diagnostic and
 prognostic potential in both mice and humans. Further investigation is
 required to determine whether VSIG4-positive Mϕ contribute to
 immunosenescence and/or systemic age-related deficits.
DOI: 10.5061/dryad.931zcrjhj
title: Data from: Thermal tolerance and the importance of microhabitats for Andean frogs in the context of land-use and climate change

description: 1. Global warming is having impacts across the Tree of Life. Understanding
 species’ physiological sensitivity to temperature change and how they
 relate to local temperature variation in their habitats is crucial to
 determining vulnerability to global warming. 2. We ask how species’
 vulnerability varies across habitats and elevations, and how
 climatically-buffered microhabitats can contribute to reduce their
 vulnerability. 3. We measured thermal sensitivity (critical thermal
 maximum – CTmax) of 14 species of Pristimantis frogs inhabiting young and
 old secondary, and primary forests in the Colombian Andes. Exposure to
 temperature stress was measured by recording temperature in the understory
 and across five microhabitats. We determined the frogs’ current
 vulnerability across habitats, elevations and microhabitats accounting for
 phylogeny and then ask how vulnerability varies under four warming
 scenarios: +1.5⁰C, +2⁰C, +3⁰C and +5⁰C. 4. We found that CTmax was
 constant across species regardless of habitat and elevation. However,
 species in young secondary forests are expected to become more vulnerable
 because of increased exposure to higher temperatures. Microhabitat
 variation could enable species to persist within their thermal temperature
 range as long as regional temperatures do not surpass +2°C. The
 effectiveness of microhabitat buffering decreases with a 2-3°C increase,
 and is almost null under a 5°C temperature increase. 5. Microhabitats will
 provide thermal protection to Andean frog communities from climate change
 by enabling tracking of suitable climates through short distance movement.
 Conservation strategies, such as managing landscapes by preserving primary
 forests and allowing regrowth and re-connection of secondary forest would
 offer thermally buffered microhabitats and aid in the survival of this
 group.
description: These data was collected on the western cordillera of the
 Colombian Andes, in the Reserva Mesenia-Paramillo cloud forest, Antioquia
 (-75.8895 lon, 5.4950 lat) between July and August 2014.
 Critical thermal maximum methodology is fully described in
 original paper. Experimental protocols received ANLA (National Agency for
 Environmental Licences) approval (#1579).
description: A tab called "Notes" is available in the file to
 understand how to use this database.
DOI: 10.5061/dryad.tx95x69vq
title: Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects

description: The structure of a genome can be described at its simplest by the number
 of chromosomes and the sex chromosome system it contains. Despite over a
 century of study, the evolution of genome structure on this scale remains
 recalcitrant to broad generalisations that can be applied across clades.
 To address this issue, we have assembled a dataset of 823 karyotypes from
 the insect group Polyneoptera. This group contains orders with a range of
 variations in chromosome number, and offer the opportunity to explore the
 possible causes of these differences. We have analysed this data using
 both phylogenetic and taxonomic approaches. Our analysis allows us to
 assess the importance of rates of evolution, phylogenetic history, sex
 chromosome systems, parthenogenesis, and genome size on variation in
 chromosome number within clades. We find that fusions play a key role in
 the origin of new sex chromosomes and that orders exhibit striking
 differences in rates of fusions, fissions, and polyploidy. Our results
 suggest that the difficulty in finding consistent rules that govern
 evolution at this scale may be due to the presence of many interacting
 forces that can lead to variation among groups.