cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29207582.v1
title: Analysis_Calls_Past.txtData for: Reinforcement and cline evolution over half a century in the Upland chorus frog (Pseudacris feriarum)

description: <strong>Analysis_Calls_Past.txt</strong> : Acoustic signaling data for male calls from past populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present_Other.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, temperature-corrected pulse rate, pulse number, dominant frequency, call duration, and call rate.
<strong>Analysis_Geno_Admix.txt</strong> : Admixture data estimated using DAPC in the present population used as input for the genetic cline analysis. Data includes the locality, distance from allopatry, number of samples, and admixture proportion.
<strong>Analysis_Geno_SNPs.vcf</strong> : SNP data (acquired using RADseq) for the present population.
<strong>Analysis_Geno.lfmm</strong> : SNP data formatted in the .lfmm format for the present population.
<strong>Analysis_Locs_Past.txt</strong> : Locality information for the past populations cline analysis, including distance from allopatry.
<strong>Analysis_Locs_Present.txt</strong> : Locality information for the present populations cline analysis, including distance from allopatry.
<strong>Analysis_Present_Coords.txt</strong> : Locality information for the present populations, including coordinates.
DOI: 10.6084/m9.figshare.29207585
title: Analysis_Geno_SNPs.vcf

description: <strong>Analysis_Calls_Past.txt</strong> : Acoustic signaling data for male calls from past populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present_Other.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, temperature-corrected pulse rate, pulse number, dominant frequency, call duration, and call rate.
<strong>Analysis_Geno_Admix.txt</strong> : Admixture data estimated using DAPC in the present population used as input for the genetic cline analysis. Data includes the locality, distance from allopatry, number of samples, and admixture proportion.
<strong>Analysis_Geno_SNPs.vcf</strong> : SNP data (acquired using RADseq) for the present population.
<strong>Analysis_Geno.lfmm</strong> : SNP data formatted in the .lfmm format for the present population.
<strong>Analysis_Locs_Past.txt</strong> : Locality information for the past populations cline analysis, including distance from allopatry.
<strong>Analysis_Locs_Present.txt</strong> : Locality information for the present populations cline analysis, including distance from allopatry.
<strong>Analysis_Present_Coords.txt</strong> : Locality information for the present populations, including coordinates.
DOI: 10.6084/m9.figshare.29207585.v2
title: Analysis_Geno_SNPs.vcf

description: <strong>Analysis_Calls_Past.txt</strong> : Acoustic signaling data for male calls from past populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present_Other.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, temperature-corrected pulse rate, pulse number, dominant frequency, call duration, and call rate.
<strong>Analysis_Geno_Admix.txt</strong> : Admixture data estimated using DAPC in the present population used as input for the genetic cline analysis. Data includes the locality, distance from allopatry, number of samples, and admixture proportion.
<strong>Analysis_Geno_SNPs.vcf</strong> : SNP data (acquired using RADseq) for the present population.
<strong>Analysis_Geno.lfmm</strong> : SNP data formatted in the .lfmm format for the present population.
<strong>Analysis_Locs_Past.txt</strong> : Locality information for the past populations cline analysis, including distance from allopatry.
<strong>Analysis_Locs_Present.txt</strong> : Locality information for the present populations cline analysis, including distance from allopatry.
<strong>Analysis_Present_Coords.txt</strong> : Locality information for the present populations, including coordinates.
DOI: 10.6084/m9.figshare.29207585.v1
title: Analysis_Geno_SNPs.vcfData for: Reinforcement and cline evolution over half a century in the Upland chorus frog (Pseudacris feriarum)

description: <strong>Analysis_Calls_Past.txt</strong> : Acoustic signaling data for male calls from past populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, and temperature-corrected pulse rate.
<strong>Analysis_Calls_Present_Other.txt</strong> : Acoustic signaling data for male calls from present populations. Data includes the locality information, individual ID, temperature-corrected pulse rate, pulse number, dominant frequency, call duration, and call rate.
<strong>Analysis_Geno_Admix.txt</strong> : Admixture data estimated using DAPC in the present population used as input for the genetic cline analysis. Data includes the locality, distance from allopatry, number of samples, and admixture proportion.
<strong>Analysis_Geno_SNPs.vcf</strong> : SNP data (acquired using RADseq) for the present population.
<strong>Analysis_Geno.lfmm</strong> : SNP data formatted in the .lfmm format for the present population.
<strong>Analysis_Locs_Past.txt</strong> : Locality information for the past populations cline analysis, including distance from allopatry.
<strong>Analysis_Locs_Present.txt</strong> : Locality information for the present populations cline analysis, including distance from allopatry.
<strong>Analysis_Present_Coords.txt</strong> : Locality information for the present populations, including coordinates.
DOI: 10.15468/dl.7n6nnh
title: Occurrence Download

description: A dataset containing 373055 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Robinia pseudoacacia L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 373055 records from 2877 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014368-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.58132/cek2q1
title: Induced Droplet Ovalisation (IDO): Image-based microfluidic method for high-throughput and label-free characterization of microbial proteolytic strains from wastewater sludge

description: High-speed camera recordings for image analysis of bacterial colonies encapsulated in gelatine droplets (Dataset for https://www.sciencedirect.com/science/article/pii/S0925400525013309).Detailed description can be found in the attached readme.txt.Aims: To develop a label-free, high-throughput microfluidic method for screening proteolytic bacteria from environmental samples, overcoming the limits of traditional cultivation.Methods: Single cells were encapsulated in gelatine droplets, deformed in a custom microfluidic device, and analyzed via high-speed imaging and AI-based classification.Conclusions: The IDO method distinguished proteolytic from non-proteolytic strains with higher sensitivity, throughput, and recovery than plate assays, offering a cost-efficient and scalable tool for microbial and hydrogel studies.
DOI: 10.5061/dryad.43c323g
title: Data from: Grass invasion and drought interact to alter the diversity and structure of native plant communities

description: Understanding the interactive effects of species invasions and climate
 change is essential for predicting future shifts in biodiversity. Because
 multiple stressors can interact in synergistic or antagonistic ways, it is
 notoriously difficult to anticipate their combined effects on species
 assemblages. However, some hypotheses predict that plant invasions will
 become increasingly problematic as climate change improves conditions for
 invaders or lowers the biotic resistance of native communities. In a
 four-year field experiment, we quantified the individual and interactive
 effects of invasion by a globally problematic C4 grass, Imperata
 cylindrica, and chronic simulated drought imposed by rainout shelters on
 the whole plant communities of regenerating longleaf pine forest. Invasion
 both inhibited plant colonization and enhanced plot-level extinctions,
 resulting in a severe (60%) loss of plant diversity across all functional
 groups, including perennial grasses and forbs, annual forbs, and woody
 species and dramatic shifts in community composition. Experimental drought
 reduced diversity by 20%, and caused a shift in the dominant functional
 groups, but had no significant effect on cover of the invader. The invader
 partially ameliorated water stress in the drought treatment such that
 invaded plots had higher soil moisture than uninvaded plots. Consequently,
 the combined effects of invasion and drought were lower than expected from
 an additive model of multiple stressors. These findings, which may have
 broader implications for how other C4 grass invaders will interact with
 drought to shift native community dynamics, challenge the perception that
 climate change will exacerbate invasions. In revealing that invasive
 species pose a major threat to the diversity and structure of native
 communities despite their moderating effects on abiotic stress, this work
 also highlights that management of aggressive invaders may be critical to
 preserving biodiversity regardless of future climate.
description: species.listList of plant species identified in the experiment.percent.cover.alldatesPercent cover of plant species greater than 5% for all time points in the experiment.percent.cover.summersPercent cover of all plant species identified for summer dates in the experiment.plot.treatment.identifierList of treatments applied to plots.soil.moistureSoil volumetric water content measured in four locations in each plot.READMEThis file provides an explanation of the datasets in this folder.
DOI: 10.5061/dryad.10668
title: Data from: Detecting macroevolutionary self-destruction from phylogenies

description: Phylogenetic analyses have lent support to the concept of lineage
 selection: that biological lineages can have heritable traits that
 influence their capacity to persist and diversify, and thereby affect
 their representation in biodiversity. While many discussions have focused
 on “positive” lineage selection, where stably heritable properties of
 lineages enhance their diversification rate, there are also intriguing
 examples that seem to represent “negative” lineage selection, where traits
 reduce the likelihood that a lineage will persist or speciate. In this
 article, we test whether a particular pattern of negative lineage
 selection is detectable from the distributions of the trait on a
 phylogeny. “Self-destructive” traits are those that arise often but then
 disappear again because they confer either a raised extinction rate or
 they are prone to a high rate of trait loss. For such a trait, the
 reconstructed origins will tend to be dispersed across the tips of the
 phylogeny, rather than defining large clades of related lineages that all
 share the trait. We examine the utility of four possible measures of
 “tippiness” as potential indicators of macroevolutionary self-destruction,
 applying them to phylogenies on which trait evolution has been simulated
 under different combinations of parameters for speciation, extinction,
 trait gain, and trait loss. We use an efficient simulation approach that
 starts with the required number of tips with and without the trait and
 uses a model to work “backwards” to construct different possible trees
 that result in that set of tips. We then apply these methods to a number
 of case studies: salt tolerance in grasses, color polymorphism in birds of
 prey, and selfing in nightshades. We find that the relative age of
 species, measured from tip length, can indicate a reduced speciation rate
 but does not identify traits that increase the extinction rate or the
 trait loss rate. We show that it is possible to detect cases of
 macroevolutionary self-destruction by considering the number of tips with
 the trait that arise from each inferred origin, and the degree to which
 the trait is scattered across the phylogeny. These metrics, and the
 methods we present, may be useful for testing macroevolutionary hypotheses
 from phylogenetic patterns.
description: Supplementary
 information for: Detecting Macroevolutionary Self-Destruction from
 PhylogeniesTable S1: Additional
 high-lability parameter combinations used in the simulations. Figure S1:
 Additional simulation results on TARS values of the evolutionary models
 described in Table S1. Figure S2: Additional simulation results on NoTO
 values of the evolutionary models described in Table S1. Figure S3:
 Additional simulation results on SSCD values of the evolutionary models
 described in Table S1. Figure S4: Additional simulation results on FPD
 values of the evolutionary models described in Table S1. Figure S5:
 Distributions of FPD values of the six evolutionary models described in
 Table 1Bromham.SuppInfo.pdf
DOI: 10.5061/dryad.693j8
title: Data from: A modular framework characterizes micro- and macroevolution of Old World monkey dentitions

description: The study of modularity can provide a foundation for integrating
 development into studies of phenotypic evolution. The dentition is an
 ideal phenotype for this as it is developmentally relatively simple,
 adaptively highly significant, and evolutionarily tractable through the
 fossil record. Here, we use phenotypic variation in the dentition to test
 a hypothesis about genetic modularity. Quantitative genetic analysis of
 size variation in the baboon dentition indicates a genetic modular
 framework corresponding to tooth type categories. We analyzed covariation
 within the dentitions of six species of Old World monkeys (OWMs) to assess
 the macroevolutionary extent of this framework: first by estimating
 variance–covariance matrices of linear tooth size, and second by
 performing a geometric morphometric (GM) analysis of tooth row shape. For
 both size and shape, we observe across OWMs a framework of anterior and
 postcanine modules, as well as submodularity between the molars and
 premolars. Our results of modularity by tooth type suggest that adult
 variation in the OWM dentition is influenced by early developmental
 processes such as odontogenesis and jaw patterning. This study presents a
 comparison of genotypic modules to phenotypic modules, which can be used
 to better understand their action across evolutionary time scales.
description: all_linear_dataThis file accompanies the data that were used in the manuscript: Grieco TM, Rizk OT, and Hlusko LJ. A modular framework characterizes micro- and macroevolution of Old World monkey dentitions. Evolution manuscript 12-0224.R1. We have uploaded seven text files in addition to a README file. The first file (all_linear_data.txt) contains 23 columns. The first is an abbreviation of the genus and species for each individual. The second, third, and fourth columns indicate the holding museum, that museum's specimen identification number and the sex of the individual. The remaining columns are the linear tooth measurements of the maxillary left teeth. Abbreviations follow the convention described in our manuscript. The other six data files contain the landmark data for the six Old World Monkey species. The name of the file indicates the species. These files are text versions of the .tps files associated with the software used in our data collection protocol (see manuscript for details). Below each set of landmarks is a file path that indicates the museum abbreviation and specimen number, as noted for the linear data. We are aware that we misspelled "melalophos" in the landmark data files. Please accept our apologies. Please contact Leslea Hlusko at hlusko@berkeley.edu for more information or if you need a different version of the data files.Cercopithecus_mitisColobus_guerezaMacaca_fascicularisPapio_hamadryasPresbytis_melalophosPresbytis_rubicunda
DOI: 10.5061/dryad.4c8f8
title: Data from: Do ecological communities disperse across biogeographic barriers as a unit?

description: Biogeographic barriers have long been implicated as drivers of biological
 diversification, but how these barriers influence co-occurring taxa can
 vary depending on factors intrinsic to the organism and in their
 relationships with other species. Due to the interdependence among taxa,
 ecological communities present a compelling opportunity to explore how
 interactions among species may lead to a shared response to historical
 events. Here we collect single nucleotide polymorphism (SNP) data from
 five commensal arthropods associated with the Sarracenia alata carnivorous
 pitcher plant, and test for co-diversification across the Mississippi
 River, a major biogeographic barrier in the southeastern United States.
 Population genetic structure in three of the ecologically dependent
 arthropods mirrors that of the host pitcher plant, with divergence time
 estimates suggesting two of the species (the pitcher plant moth Exyra
 semicrocea and a flesh fly Sarcophaga sarraceniae) dispersed synchronously
 across this barrier along with the pitcher plant. Patterns in population
 size and genetic diversity suggest the plant and ecologically dependent
 arthropods dispersed from east to west across the Mississippi River. In
 contrast, species less dependent on the plant ecologically show discordant
 phylogeographic patterns. This study demonstrates that ecological
 relationships may be an important predictor of co-diversification, and
 supports recent suggestions that organismal trait data should be
 prominently featured in comparative phylogeographic investigations.
description: Satler&Carstens2017_dataData sets used in Satler and Carstens (2017). Included are allele and SNP files, as well as general information from pyrad analyses.Satler&Carstens2017_scriptsScripts used to analyze data in Satler and Carstens (2017).
DOI: 10.5061/dryad.8d6fg
title: Data from: Superinfection and the coevolution of parasite virulence and host recovery

description: Parasite strategies of host exploitation may be affected by host defence
 strategies and multiple infections. In particular, within-host competition
 between multiple parasite strains has been shown to select for higher
 virulence. However, little is known on how multiple infections could
 affect the coevolution between host recovery and parasite virulence. Here,
 we extend a coevolutionary model introduced by van Baalen (1998) to
 account for superinfection. When the susceptibility to superinfection is
 low, we recover van Baalen's results and show that there are two
 potential evolutionary endpoints: one with avirulent parasites and poorly
 defended hosts, and another one with high virulence and high recovery.
 However, when the susceptibility to superinfection is above a threshold,
 the only possible evolutionary outcome is one with high virulence and high
 investment into defence. We also show that within-host competition may
 select for lower host recovery, as a consequence of selection for more
 virulent strains. We discuss how different parasite and host strategies
 (superinfection facilitation, competitive exclusion) as well as
 demographic and environmental parameters, such as host fecundity or
 various costs of defence, may affect the interplay between multiple
 infections and host-parasite coevolution. Our model shows the interplay
 between coevolutionary dynamics and multiple infections may be affected by
 crucial mechanistic or ecological details.
description: KadaLion_2015_JEB_scriptsMathematica and R script to run the simulations and re-draw figures from the manuscript "Superinfection and the coevolution of parasite virulence and host recovery''.Dryad data-supercoev2015.zip
DOI: 10.5061/dryad.2s8rr
title: Data from: Diet preferences as the cause of individual differences rather than the consequence

description: Behavioural variation within a species is usually explained as the
 consequence of individual variation in physiology. However, new evidence
 suggests that the arrow of causality may well be in the reverse direction:
 behaviours such as diet preferences cause the differences in physiological
 and morphological traits. Recently, diet preferences were proposed to
 underlie consistent differences in digestive organ mass and movement
 patterns (patch residence times) in red knots (Calidris canutus
 islandica). Red knots are molluscivorous and migrant shorebirds for which
 the size of the muscular stomach (gizzard) is critical for the food
 processing rate. In this study, red knots (C. c. canutus, n = 46) were
 caught at Banc d'Arguin, an intertidal flat ecosystem in Mauritania,
 and released with radio-tags after the measurement of gizzard mass. Using
 a novel tracking system (time-of-arrival), patch residence times were
 measured over a period of three weeks. Whether or not gizzard mass
 determined patch residence times was tested experimentally by offering 12
 of the 46 tagged red knots soft diets prior to release; this reduced an
 individual's gizzard mass by 20-60%. To validate whether the observed
 range of patch residence times would be expected from individual diet
 preferences, we simulated patch residence times as a function of diet
 preferences via a simple departure rule. Consistent with previous
 empirical studies, patch residence times in the field were positively
 correlated with gizzard mass. The slope of this correlation, as well as
 the observed range of patch residence times, was in accordance with the
 simulated values. The 12 birds with reduced gizzard masses did not
 decrease patch residence times in response to the reduction in gizzard
 mass. These findings suggest that diet preferences can indeed cause the
 observed among-individual variation in gizzard mass and patch residence
 times. We discuss how early diet experiences can have cascading effects on
 the individual expression of both behavioural and physiomorphic traits.
 This emphasizes that to understand the ecological consequences of
 individual differences, knowledge of the environment during development is
 required.
description: patchesTable of residence time patches: foraging locations visited by red knots, deployed with radiotransmitters, during the low tide. A description of each column can be found in a separate sheet. Further information is found in the methods section of the publication.benthosTable containing sampled prey items for the red knot, consisting of molluscs of ingestable sizes in the top 4 cm of the sediment. The file contains a separate sheet with column discriptions. More information can be found in the methods section of the publication.