cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d9s00
title: Data from: Natural variation, differentiation and genetic tradeoffs of ecophysiological traits in response to water limitation in Brachypodium distachyon and its descendent allotetraploid B. hybridum (Poaceae)

description: Differences in tolerance to water stress may underlie ecological
 divergence of closely-related ploidy lineages. However, the mechanistic
 basis of physiological variation governing eco-geographical cytotype
 segregation is not well understood. Here, using Brachypodium distachyon
 and its derived allotetraploid B. hybridum as model, we test the
 hypothesis that, for heteroploid annuals, ecological divergence of
 polyploids in drier environments is based on trait differentiation
 enabling drought-escape. We demonstrate that under water limitation
 allotetraploids maintain higher photosynthesis and stomatal conductance
 and show earlier flowering than diploids, concordant with a drought-escape
 strategy to cope with water stress. Increased heterozygosity, greater
 genetic variability and plasticity of polyploids could confer a superior
 adaptive capability. Consistent with these predictions, we document (1)
 greater standing within-population genetic variation in water use
 efficiency and flowering time in allotetraploids, and (2) the existence of
 (non-linear) environmental clines in physiology across allotetraploid
 populations. Increased gas exchange and diminished WUE occurred at the
 driest end of the gradient, consistent with a drought-escape strategy.
 Finally, we found that allotetraploids showed weaker genetic correlations
 than diploids congruous with the expectation of relaxed pleiotropic
 constraints in polyploids. Our results suggest evolutionary divergence of
 ecophysiological traits in each ploidy lineage.
description: DATA MANZANEDA ET AL
 EVOLUTIONGas exchange data (Phot,
 gs) Flw time data, isotope signal 13C/12C
DOI: 10.5061/dryad.7nk99
title: Data from: Experimental assemblage of novel plant-herbivore interactions: ecological host shifts after 40 million years of isolation

description: Geographic isolation is the first step in insect herbivore diet
 specialization. Such specialization is postulated to increase insect
 fitness, but may simultaneously reduce insect ability to colonize novel
 hosts. During the Paleocene-Eocene, plants from the order Zingiberales
 became isolated either in the Paleotropics or in the Neotropics. During
 the Cretaceous, rolled-leaf beetles diversified in the Neotropics
 concurrently with neotropical Zingiberales. Using a community of Costa
 Rican rolled-leaf beetles and their Zingiberales host plants as study
 system, we explored if previous geographic isolation precludes insects to
 expand their diets to exotic hosts. We recorded interactions between
 rolled-leaf beetles and native Zingiberales by combining DNA barcodes and
 field records for 7450 beetles feeding on 3202 host plants. To determine
 phylogenetic patterns of diet expansions, we set 20 field plots including
 five exotic Zingiberales, recording beetles feeding on these exotic hosts.
 In the laboratory, using both native and exotic host plants, we reared a
 subset of insect species that had expanded their diets to the exotic
 plants. The original plant-herbivore community comprised 24 beetle species
 feeding on 35 native hosts, representing 103 plant-herbivore interactions.
 After exotic host plant introduction, 20% of the beetle species expanded
 their diets to exotic Zingiberales. Insects only established on exotic
 hosts that belong to the same plant family as their native hosts.
 Laboratory experiments show that beetles are able to complete development
 on these novel hosts. In conclusion, rolled-leaf beetles are pre-adapted
 to expand their diets to novel host plants even after millions of years of
 geographic isolation.
description: B_Data_for_cluster_analyses_Fig_2Dataset 1. Matrix of quantitative interactions used to generate cluster analysis (Fig. 2)C_Data_time_to_pupation_Fig_4Dataset 2. Data to generate Fig. 4. Time to pupation of rolled-leaf beetles reared on native and novel hosts.D_Data_proportion_emergence_Fig_5Dataset 3. Data to generate Fig. 5. Proportion of emergence of adult rolled-leaf beetles reared on native and novel hosts.
DOI: 10.15468/dl.upvfep
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Portuguese Stick Insects (Phasmatodea)"
 ]
}

 The dataset includes 18 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000620-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d1f44
title: Data from: Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the mussel Mytilus edulis

description: Genome scans of population differentiation identify candidate loci for
 adaptation but provide little information on how selection has influenced
 the genetic structure of these loci. Following a genome scan, we
 investigated the nature of the selection responsible for the outlying
 differentiation observed between populations of the marine mussel Mytilus
 edulis at a leucine/arginine polymorphism (L31R) in the antimicrobial
 peptide MGD2. We analysed DNA sequence polymorphisms, allele frequencies
 and population differentiation of polymorphisms closely linked to L31R,
 and pairwise and third-order linkage disequilibria. An outlying level of
 population differentiation was observed at L31R only, while no departure
 from panmixia was observed at linked loci surrounding L31R, as in most of
 the genome. Selection therefore seems to affect L31R directly. Three
 hypotheses can explain the lack of differentiation in the chromosomal
 region close to L31R: (i) hitchhiking has occurred but migration and
 recombination subsequently erased the signal, (ii) selection was weak
 enough and recombination strong enough to limit the hitchhiking effect to
 a very small chromosomal region or (iii) selection acted on a pre-existing
 polymorphism (i.e. standing variation) at linkage equilibrium with its
 background. Linkage equilibrium was observed between L31R and linked
 polymorphisms in every population analysed, as expected under the three
 hypotheses. However, linkage disequilibrium was observed in some
 populations between pairs of loci located upstream and downstream to L31R,
 generating a complex pattern of third-order linkage disequilibria which is
 best explained by the hypothesis of selection on a pre-existing
 polymorphism. We hypothesise that selection could be either balanced,
 maintaining alleles at different frequencies depending on the pathogen
 community encountered locally by mussels, or intermittent, resulting in
 sporadic fluctuations in allele frequency.
description: MEC-13-0218_AFLP_DataMEC-13-0218_MGD2_SeqDegappedDNA sequence alignmentMGD2_polycodominant nuclear marker dataset
DOI: 10.5061/dryad.32qh8
title: Data from: ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps

description: Partial clonality is commonly used in Eukaryotes and has large
 consequences for their evolution and ecology. Assessing accurately the
 relative importance of clonal versus sexual reproduction matters for
 studying and managing such species. Here, we proposed a Bayesian approach,
 ClonEstiMate, to infer rates of clonality c from populations sampled twice
 over a short time interval, ideally one generation time. The method relies
 on the likelihood of the transitions between genotype frequencies of
 ancestral and descendent populations, using an extended Wright-Fisher
 model explicitly integrating reproductive modes. Our model provides
 posterior probability distribution of inferred c, given the assumed rates
 of mutation, as well as inbreeding and selfing when occurring. Tested
 under various conditions, this model provided accurate inferences of c,
 especially when the amount of information was modest, i.e. low sample
 sizes, few loci, low polymorphism and strong linkage disequilibrium.
 Inferences remained robust when mutation models and rates were
 misinformed. However, the method was sensitive to moderate frequencies of
 null alleles and when the time interval between required samplings
 exceeding two generations. Misinformed rates on mating modes (inbreeding
 and selfing) also resulted in biased inferences. Our method was tested on
 eleven datasets covering five partially clonal species, for which the
 extent of clonality was formerly deciphered. It delivered highly
 consistent results with previous information on the biology of those
 species. ClonEstiMate represents a powerful tool for detecting and
 inferring clonality in finite populations, genotyped with SNPs or
 microsatellites. It is freely available at
 http://https://w"&gt;https://w w w 6.rennes.inra.fr / igepp_eng/
 Productions/ Software.
description: data_Dryad_MolEcolRes_Becheler_etalThis xlxs.file provides 3 sheets supporting the fully detailed results of our MS : sheet "precision interval" -&gt; cross-validation of the methods on divers simulated populations. For each combination of populational, genetic and prior parameters, 100 repetitions were done, allowing estimating the precision interval. Sheet "posterior distribution" -&gt; the posterior probability for each value of c are delivered for divers simulated populations evolving with true c=0.4. Sheet "results CloNcaSe" -&gt; estimation of c by CloNcaSe for simulated populations of 100 individuals,exhaustively sampled, from c=0 to c=1. An equivalent of read me is provided at the end of the tables.data_Dryad_MolEcolRes.xlsx
DOI: 10.5061/dryad.bq3fn37
title: Data from: Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans

description: Organismal fitness is relevant in many contexts in biology. The most
 meaningful experimental measure of fitness is competitive fitness, when
 two or more entities (e.g., genotypes) are allowed to compete directly. In
 theory, competitive fitness is simple to measure: an experimental
 population is initiated with the different types in known proportions and
 allowed to evolve under experimental conditions to a predefined endpoint.
 In practice, there are several obstacles to obtaining robust estimates of
 competitive fitness in multicellular organisms, the most pervasive of
 which is simply the time it takes to count many individuals of different
 types from many replicate populations. Methods by which counting can be
 automated in high throughput are desirable, but for automated methods to
 be useful, the bias and technical variance associated with the method must
 be (a) known, and (b) sufficiently small relative to other sources of bias
 and variance to make the effort worthwhile. The nematode Caenorhabditis
 elegans is an important model organism, and the fitness effects of
 genotype and environmental conditions are often of interest. We report a
 comparison of three experimental methods of quantifying competitive
 fitness, in which wild-type strains are competed against GFP-marked
 competitors under standard laboratory conditions. Population samples were
 split into three replicates and counted (1) "by eye" from a
 saved image, (2) from the same image using CellProfiler image analysis
 software, and (3) with a large particle flow cytometer (a "worm
 sorter"). From 720 replicate samples, neither the frequency of
 wild-type worms nor the among-sample variance differed significantly
 between the three methods. CellProfiler and the worm sorter provide at
 least a tenfold increase in sample handling speed with little (if any)
 bias or increase in variance.
description: Suppl Table
 S2_dataAll count
 data
DOI: 10.5061/dryad.38m4p
title: Data from: Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos

description: Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the
 most elusive mammals. Due to their subterranean and nocturnal lifestyle,
 their basic biology and evolutionary history remain virtually unknown. Two
 distinct species with allopatric distributions are recognized:
 Chlamyphorus truncatus is restricted to central Argentina, while
 Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay,
 and Bolivia. To test their monophyly and resolve their phylogenetic
 affinities within armadillos, we obtained sequence data from modern and
 museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH
 dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early
 onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]).
 Phylogenetic analyses provided a reference phylogeny and timescale for
 living xenarthran genera. Our results reveal monophyletic pichiciegos as
 members of a major armadillo subfamily (Chlamyphorinae). Their strictly
 fossorial lifestyle probably evolved as a response to the Oligocene
 aridification that occurred in South America after their divergence from
 Tolypeutinae around 32 million years ago (Mya). The ancient divergence
 date (∼17 Mya) for separation between the two species supports their
 taxonomic classification into distinct genera. The synchronicity with
 Middle Miocene marine incursions along the Paraná river basin suggests a
 vicariant origin for pichiciegos by the disruption of their ancestral
 range. Their phylogenetic distinctiveness and rarity in the wild argue in
 favor of high conservation priority.
description: mam60_4genesConcatenation of two mitochondrial (MT-RNR1 and MT-ND1) and two nuclear (BRCA1 and VWF) genes for 60 mammalian taxa. Ambiguously aligned sites have been excluded using Gblocks on each individual gene dataset prior to concatenation.mam60_all_gb_paup_gtrg8_midrootMaximum likelihood phylogram for 60 mammalian taxa obtained from the concatenation of the four genes under the GTR+G8 model using PAUP with TBR branch-swapping on a NJ starting tree.
DOI: 10.25919/xz12-nh93
title: Long-term project observations for project P1361 semester 2025OCTS_05

description: PSR J1227-6208 is a recycled pulsar in a binary with a massive white dwarf companion. A recent timing measurement from combined MeerKAT and Parkes observations shows the companion mass to be between 1.2 and 1.5 solar masses, very close to the Chandrasekhar limit, resulting in potentially profound physical implications. However, the timing precision is limited by the DM timing noise. We propose regular monitoring of this pulsar with the Parkes UWL receiver in conjunction with MeerKAT observations during the following four years. The joint monitoring will significantly improve the constraints on the Post-Keplerian parameters, with Parkes observations contributing to constrain the DM noise due to its large frequency bandwidth. These observations will be added to the already existing 11-year-long timing baseline, of which the later 5 years already include high-precision MeerKAT data and Parkes UWL data. After four years of further timing with the inclusion of UWL observations, we predict an uncertainty on the masses smaller than 0.01 solar masses based on simulations. If UWL is not included, the mass uncertainties may not improve beyond their current values.
DOI: 10.5061/dryad.6pk5d
title: Data from: Microgeographic patterns of genetic divergence and adaptation across environmental gradients in Boechera stricta (Brassicaceae)

description: Abiotic and biotic conditions often vary continuously across the
 landscape, imposing divergent selection on local populations. We used a
 provenance trial approach to examine microgeographic variation in local
 adaptation in Boechera stricta (Brassicaceae), a perennial forb native to
 the Rocky Mountains. In montane ecosystems, environmental conditions
 change considerably over short spatial scales, such that neighboring
 populations can be subject to different selective pressures. Using
 accessions from southern (Colorado) and northern (Idaho) populations, we
 characterized spatial variation in genetic similarity via microsatellite
 markers. We then transplanted genotypes from multiple local populations
 into common gardens in both regions. Continuous variation in local
 adaptation emerged for several components of fitness. In Idaho, genotypes
 from warmer environments (low elevation or south facing sites) were poorly
 adapted to the north-facing garden. In high and low elevation Colorado
 gardens, susceptibility to insect herbivory increased with source
 elevation. In the high elevation Colorado garden, germination success
 peaked for genotypes that evolved at similar elevations as the garden, and
 declined for genotypes from higher and lower elevations. We also found
 evidence for local maladaptation in survival and fecundity components of
 fitness in the low elevation Colorado garden. This approach is a necessary
 first step in predicting how global change could affect evolutionary
 dynamics.
description: Microsatellite
 dataMicrosatellite data from
 population genetics study.microsat.txtIdaho_family_fitnessFamily level data from Idaho gardenColorado_family_fitnessFamily level data from Colorado gardensSeed germination data from Colorado gardensSeed germination data from Colorado gardensgermination.txtIndividual level data from 2011 cohort Idaho gardenIndividual level data from Idaho garden 2011 cohortMV11ind.txtIndividual level data from 2012 cohort Idaho gardenIndividual level data from 2012 cohort Idaho gardenMV12ind.txtIndividual level data from low elevation Colorado garden 2011 cohortIndividual level data from low elevation Colorado garden 2011 cohortCO2011cohort.txtIndividual level data from low elevation Colorado garden 2012 cohortIndividual level data from low elevation Colorado garden 2012 cohortCO2012low.txtIndividual level data from high elevation Colorado garden 2012 cohortIndividual level data from high elevation Colorado garden 2012 cohortSco2012ind.txt
DOI: 10.5061/dryad.ts56p
title: Data from: Trait specific consequences of inbreeding on adaptive phenotypic plasticity

description: Environmental changes may stress organisms and stimulate an adaptive
 phenotypic response. Effects of inbreeding often interact with the
 environment and can decrease fitness of inbred individuals exposed to
 stress more so than that of outbred individuals. Such an interaction may
 stem from a reduced ability of inbred individuals to respond plastically
 to environmental stress; however, this hypothesis has rarely been tested.
 In this study, we mimicked the genetic constitution of natural inbred
 populations by rearing replicate Drosophila melanogaster populations for
 25 generations at a reduced population size (10 individuals). The
 replicate inbred populations, as well as control populations reared at a
 population size of 500, were exposed to a benign developmental temperature
 and two developmental temperatures at the lower and upper margins of their
 viable range. Flies developed at the three temperatures were assessed for
 traits known to vary across temperatures, namely abdominal pigmentation,
 wing size, and wing shape. We found no significant difference in
 phenotypic plasticity in pigmentation or in wing size between inbred and
 control populations, but a significantly higher plasticity in wing shape
 across temperatures in inbred compared to control populations. Given that
 the norms of reaction for the noninbred control populations are adaptive,
 we conclude that a reduced ability to induce an adaptive phenotypic
 response to temperature changes is not a general consequence of inbreeding
 and thus not a general explanation of inbreeding–environment interaction
 effects on fitness components.
description: Raw Wing
 DataThis file contains the
 coordinates of each landmark from the wing. See Supplementary
 information/appendix in paper for the position of landmarks on the
 wing.WingData.csvPigmentation DataContains the score between 0 and 10 given for each tergite.PigmentationData.csv
DOI: 10.5061/dryad.8837q
title: Data from: Morphological clines and weak drift along an urbanization gradient in the butterfly, Pieris rapae

description: Urban areas are increasing globally, providing opportunities for
 biodiversity researchers to study the process in which species become
 established in novel, highly disturbed habitats. This ecological process
 can be understood through analyses of morphological and genetic variation,
 which can shed light on patterns of neutral and adaptive evolution.
 Previous studies have shown that urban populations often diverge
 genetically from non-urban source populations. This could occur due to
 neutral genetic drift, but an alternative is that selection could lead to
 allele frequency changes in urban populations. The development of genome
 scan methods provides an opportunity to investigate these outcomes from
 samples of genetic variation taken along an urbanization gradient. Here we
 examine morphological variation in wing size and diversity at neutral
 amplified fragment length polymorphisms in the butterfly Pieris rapae L.
 (Lepidoptera, Pieridae) sampled from the center to the periphery of
 Marseille. We utilize established and novel environmental correlation
 approaches to scan genetic variation for evidence of selection. We find
 significant morphological differences in urban populations, as well as
 weak genetic structure and decreased genetic diversity in urban versus
 non-urban sites. However, environmental correlation tests provide little
 support for selection in our dataset. Our comparison of different methods
 and allele frequency clines suggests that loci identified as significant
 are false positives. Although there is some indication that selection may
 be acting on wing size in urban butterflies, genetic analyses suggest P.
 rapae are undergoing neutral drift.
description: Sampling and Ecological
 DataThis file includes data
 on geographical sampling and measured environmental
 variables.Sample&EcologicalData.xlsxGenetic DataThis file contains the genotypic data at all AFLP markers, for each individual Pieris rapae.GeneticData.xlsxMorphological DataThis file contains the morphological wing measurements for Pieris rapae.MorphologicalData.xlsx
DOI: 10.15468/dl.8hhbx3
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Blattodea 01"
 ]
}

 The dataset includes 38 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000621-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.