cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.75n5q
title: Data from: Z chromosome divergence, polymorphism, and relative effective population size in a genus of lekking birds

description: Sex chromosomes contribute disproportionately to species boundaries as
 they diverge faster than autosomes and often have reduced diversity. Their
 hemizygous nature contributes to faster divergence and reduced diversity,
 as do some types of selection. In birds, other factors (mating system and
 bottlenecks) can further decrease the effective population size of
 Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked
 divergence and effective population sizes for two polygynous sage-grouse
 species and compared them to estimates from birds with various mating
 systems. We found lower diversity and higher FST for Z-linked loci than
 for autosomes, as expected. The πZ/πA ratio was 0.38 in Centrocercus
 minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged,
 parapatric population of C. urophasianus, a broad range given the mating
 system among these groups is presumably equivalent. The full data set had
 unequal males and females across groups, so we compared an equally
 balanced reduced set of C. minimus and individuals pooled from both C.
 urophasianus subgroups recovering similar estimates: 0.54 for C.
 urophasianus and 0.38 for C. minimus. We provide further evidence that
 NeZ/NeA in birds is often lower than expected under random mating or
 monogamy. The lower ratio in C. minimus could be a consequence of stronger
 selection or drift acting on Z loci during speciation, as this species
 differs strongly from C. urophasianus in sexually selected characters with
 minimal mitochondrial divergence. As C. minimus also exhibited lower
 genomic diversity, it is possible that a more severe demographic history
 may contribute to its lower ratio.
description: HC.auto.2popsThis file is a text file in Arelquin input format. It could easily be manipulated into other formats. The 2 groups represent autosome data for 2 species C. urophasianus and C. minimus.HC.auto.3popsThis file is a text file in Arelquin input format. It contains autosome SNP genotypes for three groups. Two groups of C. urophasianus (one is GRSG which represents the southern part of the range and the other is BiState which represents the diverged population on the border between California and Nevada). The third group is the Gunnison Sage-grouse data.Z.2pops.4.arlequinThis is a text file that is in Arlequin input format. It contains Z chromosome data for C. urophasianus and C. minimus.Z.3pops.4.arlequinThis is a text file in Arlequin input format and represents Z chromosome data for three groups (2 C. urophasianus - one (GRSG) is the southern part of the range and the other (BiState) is the diverged population on the border between California and Nevada). The third group is Gunnison Sage-grouse.mean FST by chromosomeThis file is a text file that shows the mean FST values between C. urophasianus and C. minimus for each chromosome (1 - 10) as well as the Z chromosome.
DOI: 10.5061/dryad.3n9r2
title: Data from: Interactive effects of disturbance and dispersal on community assembly

description: The traditional debate on alternative community states has been over
 whether or not they exist. Studies of community assembly have examined the
 role of assembly history in driving community divergence, but the context
 in which assembly history becomes important is a continued topic of
 interest. In this study, we created communities of bacterivorous ciliated
 protists in laboratory microcosms and manipulated assembly history,
 disturbance frequency, and the presence of dispersal among local
 communities to investigate the mechanisms behind community divergence.
 Specifically, we sought to understand how the role of assembly history
 changed in response to disturbance, dispersal, and the combination of the
 two. Assembly history influenced the identity of the dominant species
 through priority effects, and dispersal and disturbance showed interactive
 effects on both alpha and beta diversity. Dispersal substantially
 increased alpha diversity, but only in the absence of disturbance, and it
 reduced beta diversity, but not in the presence of low or mixed
 disturbance. These results demonstrate that the role of assembly history
 and the strength of priority effects depend on community context,
 suggesting that understanding the interactions between various factors
 shaping community assembly is important for understanding how ecological
 communities are structured.
description: Ojima and Jiang Raw
 DataIndividual abundance
 data for each species collected in the lab, as well as calculated alpha
 and beta diversities.
DOI: 10.5061/dryad.8326
title: Data from: Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

description: BACKGROUND: Tunicates represent a key metazoan group as the sister-group
 of vertebrates within chordates. The six complete mitochondrial genomes
 available so far for tunicates have revealed distinctive features.
 Extensive gene rearrangements and particularly high evolutionary rates
 have been evidenced with regard to other chordates. This peculiar
 evolutionary dynamics has hampered the reconstruction of tunicate
 phylogenetic relationships within chordates based on mitogenomic data.
 RESULTS: In order to further understand the atypical evolutionary dynamics
 of the mitochondrial genome of tunicates, we determined the complete
 sequence of the solitary ascidian Herdmania momus. This genome from a
 stolidobranch ascidian presents the typical tunicate gene content with 13
 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the
 same strand. However, it also presents a novel gene arrangement,
 highlighting the extreme plasticity of gene order observed in tunicate
 mitochondrial genomes. Probabilistic phylogenetic inferences were
 conducted on the concatenation of the 13 mitochondrial protein-coding
 genes from representatives of major metazoan phyla. We show that whereas
 standard homogeneous amino acid models support an artefactual sister
 position of tunicates relative to all other bilaterians, the CAT and
 CAT+BP site- and time-heterogeneous mixture models place tunicates as the
 sister-group of vertebrates within monophyletic chordates. Moreover, the
 reference phylogeny indicates that tunicate mitochondrial genomes have
 experienced a drastic acceleration in their evolutionary rate that equally
 affects protein-coding and ribosomal-RNA genes. CONCLUSION: This is the
 first mitogenomic study supporting the new chordate phylogeny revealed by
 recent phylogenomic analyses. It illustrates the beneficial effects of an
 increased taxon sampling coupled with the use of more realistic amino acid
 substitution models for the reconstruction of animal phylogeny.
description: Singh-BMCGenomics2009_AA_13proteinsAmino acid concatenation of 13 mitochondrial genes for 54 metazoansSingh-BMCGenomics2009_NT_13proteinsNucleotide concatenation of 13 mitochondrial protein-coding genes for 54 metazoansSingh-BMCGenomics2009_AA_13proteins_CATBPBayesian consensus tree obtained under the CAT-BP mixture model using PhyloBayes
DOI: 10.5061/dryad.sp20s
title: Data from: Rapid nectar-meal effects on a predator’s capacity to kill mosquitoes

description: Using Evarcha culicivora, an East African jumping spider (Salticidae), we
 investigate how nectar meals function in concert with predation
 specifically at the juvenile stage between emerging from the egg sac and
 the first encounter with prey. Using plants and using artificial nectar
 consisting of sugar alone or sugar plus amino acids, we show that the
 plant species (Lantana camara, Ricinus communis, Parthenium
 hysterophorus), the particular sugars in the artificial nectar (sucrose,
 fructose, glucose, maltose), the concentration of sugar (20%, 5%, 1%) and
 the duration of pre-feeding fasts (3 days, 6 days) influence the
 spider's prey-capture proficiency on the next day after the nectar
 meal. However, there were no significant effects of amino acids. Our
 findings suggest that benefits from nectar feeding are derived primarily
 from access to particular sugars, with fructose and sucrose being the most
 beneficial, glucose being intermediate and maltose being no better than a
 water-only control.
description: Supplementary Data File
 - spider & nectarData from 'Rapid
 nectar-meal effects on a predator’s capacity to kill
 mosquitoes'Supplementary Data
 File.doc
DOI: 10.5061/dryad.nf5dr6c
title: Data from: A resource-rational theory of set size effects in human visual working memory

description: Encoding precision in visual working memory decreases with the number of
 encoded items. Here, we propose a normative theory for such set size
 effects: the brain minimizes a weighted sum of an error-based behavioral
 cost and a neural encoding cost. We construct a model from this theory and
 find that it predicts set size effects. Notably, these effects are
 mediated by probing probability, which aligns with previous empirical
 findings. The model accounts well for effects of both set size and probing
 probability on encoding precision in nine delayed-estimation experiments.
 Moreover, we find support for the prediction that the total amount of
 invested resource can vary non-monotonically with set size. Finally, we
 show that it is sometimes optimal to encode only a subset or even none of
 the relevant items in a task. Our findings raise the possibility that
 cognitive “limitations” arise from rational cost minimization rather than
 from constraints.
description: Experimental data and
 Matlab codeThis zip file contains
 the data of experiments E1-E7 and Matlab code to fit the resource-rational
 model to a dataset and to create figures 2D, 2E, 3A, and 6 from the
 paper.VandenBerg_Ma_2018_data_and_code.zip
DOI: 10.15468/dl.vnn8bc
title: Occurrence Download

description: A dataset containing 54546 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "GadmGid is CAN.9.50.1_1",
 "Geometry POLYGON((-177.62063 30.26598,-11.37937 30.26598,-11.37937 90.00000,-177.62063 90.00000,-177.62063 30.26598))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2025-2026"
 ]
}

 The dataset includes 54546 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000521-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fyjkrt
title: Occurrence Download

description: A dataset containing 205 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '3189883', TRUE)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 205 records were derived from 382 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000502-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.984r37k
title: Data from: Plant community responses to long-term fertilization: changes in functional group abundance drive changes in species richness

description: Declines in species richness due to fertilization are typically rapid and
 associated with increases in aboveground production. However, in a
 long-term experiment examining the impacts of fertilization in an early
 successional community, we found it took 14 years for plant species
 richness to significantly decline in fertilized plots, despite
 fertilization causing a rapid increase in aboveground production. To
 determine what accounted for this lag in the species richness response, we
 examined several potential mechanisms. We found evidence suggesting the
 abundance of one functional group—tall species with long-distance (runner)
 clonality—drove changes in species richness, and we found little support
 for other mechanisms. Tall runner species initially increased in abundance
 due to fertilization, then declined dramatically and were not abundant
 again until later in the experiment, when species richness and the
 combined biomass of all other functional groups (non-tall runner)
 declined. Over 86 % of the species found throughout the course of our
 study are non-tall runner, and there is a strong negative relationship
 between non-tall runner and tall runner biomass. We therefore suggest that
 declines in species richness in the fertilized treatment are due to high
 tall runner abundance that decreases the abundance and richness of
 non-tall runner species. By identifying the functional group that drives
 declines in richness due to fertilization, our results help to elucidate
 how fertilization decreases plant richness and also suggest that declines
 in richness due to fertilization can be lessened by controlling the
 abundance of species with a tall runner growth form.
description: dataset_dickson_gross_oecologiaThis data file contains the species composition, biomass, diversity, and functional grouping of plants in the unfertilized and fertilized subplots of the Early Successional treatment of the Main Croppling System Experiment. Also includes soil nitrogen concentrations, relationship between burning and plant diversity, and field operations log.
DOI: 10.5061/dryad.134c4
title: Data from: Diversity in morphology and locomotory behavior is associated with niche expansion in the semi-aquatic bugs

description: Acquisition of new ecological opportunities is a major driver of
 adaptation and species diversification [ 1–4 ]. However, how groups of
 organisms expand their habitat range is often unclear [ 3 ]. We study the
 Gerromorpha, a monophyletic group of heteropteran insects that occupy a
 large variety of water surface-associated niches, from small puddles to
 open oceans [ 5, 6 ]. Due to constraints related to fluid dynamics [ 7–9 ]
 and exposure to predation [ 5, 10 ], we hypothesize that selection will
 favor high speed of locomotion in the Gerromorpha that occupy water-air
 interface niches relative to the ancestral terrestrial life style. Through
 biomechanical assays and phylogenetic reconstruction, we show that only
 species that occupy water surface niches can generate high maximum speeds.
 Basally branching lineages with ancestral mode of locomotion, consisting
 of tripod gait, achieved increased speed on the water through increasing
 midleg length, stroke amplitude, and stroke frequency. Derived lineages
 evolved rowing as a novel mode of locomotion through simultaneous sculling
 motion almost exclusively of the midlegs. We demonstrate that this change
 in locomotory behavior significantly reduced the requirement for high
 stroke frequency and energy expenditure. Furthermore, we show how the
 evolution of rowing, by reducing stroke frequency, may have eliminated the
 constraint on body size, which may explain the evolution of larger
 Gerromorpha. This correlation between the diversity in locomotion
 behaviors and niche specialization suggests that changes in morphology and
 behavior may facilitate the invasion and diversification in novel
 environments.
description: Concatenated sequence
 alignmentsThis file contains
 concatenated sequence alignments of 14 genetic markers used to construct
 the phylogeny of our samples.Concatenated
 alignments.fastaGenbank accession
 numbersThis table contains the
 Genbank accession numbers for the genetic sequences used to construct the
 phylogeny.Newick_TreeThis file is the reconstructed phylogenetic tree of our sample in Newick format.R ScriptThis file is the R script used to analyse our data.Table of biomechanical variablesThis table contains the quantitative biomechanical variable measured and analysed in our study.Table.xlsxREADMEThis file is the README file link to this submission. It contains descriptions and details for all files linked to this study.
DOI: 10.5061/dryad.mr72b
title: Data from: How fish eggs are preadapted for the evolution of matrotrophy

description: Teleost fishes evolved livebearing via egg retention 14 times. Matrotrophy
 has evolved within 12 of those lineages. By contrast, squamate reptiles
 evolved livebearing over 115 times, but only two to four of those lineages
 are known to have evolved matrotrophy. Is the discrepancy between these
 organisms in the probability of this transition caused by differences in
 their eggs? We show that the eggs of oviparous species in the superorder
 Atherinomorpha can acquire small organic molecules from their surrounding
 environment against a concentration gradient via mechanisms of active
 transport. Uptake rates were inhibited by competing radiolabelled amino
 acids against unlabelled versions of themselves. Transport was
 non-specific as uptake rates were similar for l-leucine and its
 biologically uncommon enantiomer d-leucine. Eggs are also capable of
 transporting larger microspheres across the membrane, but transport is
 inhibited at temperatures below 4°C, suggesting active transport occurs
 via pinocytosis. Conflict theory predicts that the ability of the egg to
 acquire maternal resources will facilitate the embryo–parent arms race
 that leads to the evolution of matrotrophy following the transition to
 livebearing. The shelled eggs of amniotes lack such access to maternal
 resources when retained in the evolution of viviparity.
description: Egg
 MasterRadioactivity data for
 all experiments performed for the study.Supplemental
 ImagesSupplemental Microsphere
 Images Stored as pdfSupplemental
 Photos.pdf
DOI: 10.5061/dryad.bk2690n
title: Data from: Mizutama: a quick, easy, and accurate method for counting erythrocytes

description: Hematological profiles are routinely used to assess the health status of
 animals. Several methods have been developed for blood-cell counting, but
 typically they are expensive and/or time-consuming. Here, we present a
 free image-processing software, Mizutama, developed for counting cells in
 photographs of blood smears. Mizutama uses the thresholding method to
 transform original photographs into grayscale trinary images. Following a
 number of parameters, Mizutama searches in the image for cells of a given
 size, with a nucleus size relative to cytoplasm surface area. The software
 is not only easy, versatile, and intuitive to handle, but is also fast
 when counting cells in photographs. Moreover, we show that it is highly
 accurate, failing to detect only c. 1.4% of avian red cells in ordinary
 microscopic photographs. The Mizutama application may greatly facilitate
 the counting of erythrocytes and other blood cells in physiological
 studies, saving time and money.
description: MizutamaThe rar file includes the software Mizutama (designed to count cells in blood smears), as well as the user manual.mizutama.rarTable_S1Raw data showing for each photograph the actual counting of erythrocytes, the count performed by Mizutama, and the parameters considered in the software.
DOI: 10.5061/dryad.t00nn
title: Data from: Long-term changes in the seasonal timing of landbird migration on the Pacific Flyway

description: The seasonal phenology of latitudinal movements is one of the key
 life-history traits of migratory birds. We used quantile regression to
 examine long-term changes in the timing of spring and autumn migration in
 5 species of migratory passerine birds captured at a banding station in
 northern California, USA, over a 22 yr period from 1987 to 2008. Our 5
 study species included 3 short-distance migrants, Pacific-slope Flycatcher
 (Empidonax difficilis), Orange-crowned Warbler (Oreothlypis celata), and
 Wilson's Warbler (Cardellina pusilla); and 2 long-distance migrants,
 Swainson's Thrush (Catharus ustulatus) and Yellow Warbler (Setophaga
 petechia). Median timing of migration advanced in spring for 2 of the 5
 species (−2.5 days decade−1) but was delayed during autumn migration for 3
 of the species (+2.9 days decade−1). The duration of the migration period
 also became compressed in some species but more protracted in others. We
 tested whether annual variation in migration timing was related to 3
 indices of regional climatic conditions: the Pacific–North American index,
 multivariate El Niño–Southern Oscillation index, and North Atlantic
 Oscillation index. Climate indices explained relatively little of the
 variation in migration timing (r2 &lt; 0.35), but advances in spring
 migration and delays in autumn migration were associated with warm, wet
 conditions during positive phases of the climate indices. The strongest
 effects of climatic conditions on migration timing were found among
 short-distance migrants, with the largest changes in timing due to
 variation in the El Niño–Southern Oscillation and Pacific–North American
 indices. Linkages between the timing of movements and climatic conditions
 indicate that passerine birds on the Pacific coast exhibit phenotypic
 plasticity in their migration timing, but future studies based on
 experimental methods are needed to test alternative ecological mechanisms.
description: Capture
 DataA
 comma-delimited file with the capture data for 5 species of songbirds at
 the Coyote Creek banding station, San Jose, Santa Clara Co., California,
 1987 to 2008.CaptureData.csvWeather DataA comma-delimited file with monthly or bimonthly averages for three climatic indexes, 1980 to 2009. The three indices include: MEI = Multivariate El Nino/Southern Oscillation Index, NAO = North Atlantic Oscillation index, PNA = Pacific/North American indexWeatherData.csvSpring MigrationAn R script for spring migration, quantile regression and modeling median arrival vs. climatic indicesSpringMigration.RAutumn MigrationAn R script for autumn migration, quantile regression and modeling median arrival vs. climatic indicesAutumnMigration.RWeather AnalysisAn R script for analysis of climate variablesWeatherAnalysis.RREAD MEMetadata for data files and R scripts