cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.82d4q
title: Data from: Differences in speed and duration of bird migration between spring and autumn

description: It has been suggested that birds migrate faster in spring than in autumn
 because of competition for arrival order at breeding grounds and
 environmental factors such as increased daylight. Investigating spring and
 autumn migration performances is important for understanding ecological
 and evolutionary constraints in the timing and speed of migration. We
 compiled measurements from tracking studies and found a consistent
 predominance of cases showing higher speeds and shorter durations during
 spring compared to autumn, in terms of flight speeds (airspeed, ground
 speed, daily travel speed), stopover duration, and total speed and
 duration of migration. Seasonal differences in flight speeds were
 generally smaller than those in stopover durations and total
 speed/duration of migration, indicating that rates of foraging and fuel
 deposition were more important than flight speed in accounting for
 differences in overall migration performance. Still, the seasonal
 differences in flight speeds provide important support for time selection
 in spring migration.
description: Spring and autumn bird
 migration speed, list of casesList of published cases
 with detailed data about different components of bird migration speed
 during autumn and spring.Seasonbirdmigrationspeed_table(2).csvPrintable overview of bird migration speed cases in spring and autumnPrintable overview of bird migration speed cases in spring and autumn, same data as in .csv file.Printable_overview_birdmigration.pdf
DOI: 10.7910/dvn/tpesiq
title: Replication Data for: "Measurement of Unmet Need for Contraception: A Counterfactual Approach"

description: This replication package reproduces the results for the paper entitled "Measurement of Unmet Need for Contraception: A Counterfactual Approach," which is published in Studies in Family Planning. This package contains the Stata Do-File (.do) that replicates the tables and figures in the main paper. All data that are used for this study are available for free download after registering with the DHS Program at http://dhsprogram.com/data/. The pooled analytic dataset is comprised of Individual Recode (IR) files in Stata format (.dta) for 2,073,523 women from 80 DHS surveys that cover 56 countries from 2010 to 2019. The Stata do file can be modified to run for one or multiple datasets.
DOI: 10.5061/dryad.bh78m
title: Data from: Restricted gene flow between resident Oncorhynchus mykiss and an admixed population of anadromous steelhead

description: The species Oncorhynchus mykiss is characterized by a complex life history
 that presents a significant challenge for population monitoring and
 conservation management. Many factors contribute to genetic variation in
 O. mykiss populations, including sympatry among migratory phenotypes,
 habitat heterogeneity, hatchery introgression, and immigration (stray)
 rates. The relative influences of these and other factors are contingent
 on characteristics of the local environment. The Rock Creek subbasin in
 the middle Columbia River has no history of hatchery supplementation and
 no dams or artificial barriers. Limited intervention and minimal
 management have led to a dearth of information regarding the genetic
 distinctiveness of the extant O. mykiss population in Rock Creek and its
 tributaries. We used 192 SNP markers and collections sampled over a 5-year
 period to evaluate the temporal and spatial genetic structures of O.
 mykiss between upper and lower watersheds of the Rock Creek subbasin. We
 investigated potential limits to gene flow within the lower watershed
 where the stream is fragmented by seasonally dry stretches of streambed,
 and between upper and lower watershed regions. We found minor genetic
 differentiation within the lower watershed occupied by anadromous
 steelhead (FST = 0.004), and evidence that immigrant influences were
 prevalent and ubiquitous. Populations in the upper watershed above partial
 natural barriers were highly distinct (FST = 0.093) and minimally impacted
 by apparent introgression. Genetic structure between watersheds paralleled
 differences in local demographics (e.g., variation in size), migratory
 restrictions, and habitat discontinuity. The evidence of restricted gene
 flow between putative remnant resident populations in the upper watershed
 and the admixed anadromous population in the lower watershed has
 implications for local steelhead productivity and regional conservation.
description: Matala et
 al_7-20-17DRYAD_Matala et
 al_7-20-17.xlsx
DOI: 10.5061/dryad.fv8jv
title: Data from: Stay tuned: active amplification tunes tree-cricket ears to track temperature-dependent song frequency

description: Tree cricket males produce tonal songs, used for mate attraction and
 male–male interactions. Active mechanics tunes hearing to conspecific song
 frequency. However, tree cricket song frequency increases with
 temperature, presenting a problem for tuned listeners. We show that the
 actively amplified frequency increases with temperature, thus shifting
 mechanical and neuronal auditory tuning to maintain a match with
 conspecific song frequency. Active auditory processes are known from
 several taxa, but their adaptive function has rarely been demonstrated. We
 show that tree crickets harness active processes to ensure that auditory
 tuning remains matched to conspecific song frequency, despite changing
 environmental conditions and signal characteristics. Adaptive tuning
 allows tree crickets to selectively detect potential mates or rivals over
 large distances and is likely to bestow a strong selective advantage by
 reducing mate-finding effort and facilitating intermale interactions.
description: An .zip archive of
 article raw dataData are organised in
 self-explanatory nested folders. Vibrometry and neurophysiology data are
 in separate folders.Mhatre_et_al_Stay_tuned.zip
DOI: 10.6084/m9.figshare.29314439
title: Data from: Global patterns and gaps in research on salinity tolerance of inland fishes

description: Freshwater salinization is an emerging threat impacting one-third of the world's freshwater bodies. However, the salinity tolerance of many inland fishes remains understudied, despite being a crucial factor in determining species distributions and fitness. We analyzed a global database of experimental salinity tolerance of inland fishes, compiled from 128 sources, to investigate geographical and taxonomic biases. Additionally, we examined how salinity tolerance relates to fish traits and how experimental data align with field-reported salinity levels..Experimental data on salinity tolerance was available for less than 1% of the world’s inland fishes, with data severely lacking from diverse tropical regions and orders such as Siluriformes. Most studies focused on relatively large and widely distributed species from North America, Europe and Oceania. Our results showed that fish salinity tolerance was strongly associated with fish habitat type, taxonomy, aspects of morphology, migratory behaviour and the experimental approach used (direct vs. gradual). Our results also showed significant, though sometimes weak relationships between field-reported salinity levels and experimental estimates. Overall, maximum salinities reported for habitats occupied by inland fishes were lower than experimentally-estimated tolerances.Improved understanding of fish salinity tolerance will be essential for assessing impacts of freshwater salinization and forecasting the invasion potential of non-native species.<br>
DOI: 10.6084/m9.figshare.29314439.v1
title: Data from: Global patterns and gaps in research on salinity tolerance of inland fishes

description: Freshwater salinization is an emerging threat impacting one-third of the world's freshwater bodies. However, the salinity tolerance of many inland fishes remains understudied, despite being a crucial factor in determining species distributions and fitness. We analyzed a global database of experimental salinity tolerance of inland fishes, compiled from 128 sources, to investigate geographical and taxonomic biases. Additionally, we examined how salinity tolerance relates to fish traits and how experimental data align with field-reported salinity levels..Experimental data on salinity tolerance was available for less than 1% of the world’s inland fishes, with data severely lacking from diverse tropical regions and orders such as Siluriformes. Most studies focused on relatively large and widely distributed species from North America, Europe and Oceania. Our results showed that fish salinity tolerance was strongly associated with fish habitat type, taxonomy, aspects of morphology, migratory behaviour and the experimental approach used (direct vs. gradual). Our results also showed significant, though sometimes weak relationships between field-reported salinity levels and experimental estimates. Overall, maximum salinities reported for habitats occupied by inland fishes were lower than experimentally-estimated tolerances.Improved understanding of fish salinity tolerance will be essential for assessing impacts of freshwater salinization and forecasting the invasion potential of non-native species.<br>
DOI: 10.5061/dryad.q0d23
title: Data from: The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time

description: Insight to the spatial and temporal scales of coevolution is key to
 predicting the outcome of host–parasite interactions and spread of
 disease. For bacteria infecting long-lived hosts, selection to overcome
 host defences is just one factor shaping the course of evolution;
 populations will also be competing with other microbial species and will
 themselves be facing infection by bacteriophage viruses. Here, we examine
 the temporal and spatial patterns of bacterial adaptation against natural
 phage populations from within leaves of horse chestnut trees. Using a
 time-shift experiment with both sympatric and allopatric phages from
 either contemporary or earlier points in the season, we demonstrate that
 bacterial resistance is higher against phages from the past, regardless of
 spatial sympatry or how much earlier in the season phages were collected.
 Similarly, we show that future bacterial hosts are more resistant to both
 sympatric and allopatric phages than contemporary bacterial hosts.
 Together, our results suggest the evolution of relatively general
 bacterial resistance against phages in nature and are contrasting to
 previously observed patterns of phage adaptation to bacteria from the same
 tree hosts over the same time frame, indicating a potential asymmetry in
 coevolutionary dynamics.
description: Time-shift
 dataResults of
 cross-inoculation between bacteria from either July or September and
 phages from June, July, August, or September and across eight horse
 chestnut trees (either sympatric combinations or allopatric
 combinations).Data for
 dryad.xlsx
DOI: 10.15468/dl.fw5mmv
title: Occurrence Download

description: A dataset containing 863 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "Country is one of (Mexico)",
 "EventDate 2020-01-01-2026-01-26"
 ]
 }
 ]
}

 The dataset includes 863 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000455-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1j1f3
title: Data from: Sexual dimorphism and retinal mosaic diversification following the evolution of a violet receptor in butterflies

description: Numerous animal lineages have expanded and diversified the opsin-based
 photoreceptors in their eyes underlying color vision behavior. However,
 the selective pressures giving rise to new photoreceptors and their
 spectral tuning remain mostly obscure. Previously, we identified a violet
 receptor (UV2) that is the result of a UV opsin gene duplication specific
 to Heliconius butterflies. At the same time the violet receptor evolved,
 Heliconius evolved UV-yellow coloration on their wings, due to the pigment
 3-hydroxykynurenine (3-OHK) and the nanostructure architecture of the
 scale cells. In order to better understand the selective pressures giving
 rise to the violet receptor, we characterized opsin expression patterns
 using immunostaining (14 species) and RNA-Seq (18 species), and
 reconstructed evolutionary histories of visual traits in five major
 lineages within Heliconius and one species from the genus Eueides. Opsin
 expression patterns are hyperdiverse within Heliconius. We identified six
 unique retinal mosaics and three distinct forms of sexual dimorphism based
 on ommatidial types within the genus Heliconius. Additionally,
 phylogenetic analysis revealed independent losses of opsin expression,
 pseudogenization events, and relaxation of selection on UVRh2 in one
 lineage. Despite this diversity, the newly evolved violet receptor is
 retained across most species and sexes surveyed. Discriminability modeling
 of behaviorally preferred 3-OHK yellow wing coloration suggests that the
 violet receptor may facilitate Heliconius color vision in the context of
 conspecific recognition. Our observations give insights into the selective
 pressures underlying the origins of new visual receptors.
description: Sequence alignment fasta
 files of 634 loci from 5 Heliconius speciesThis is a compressed
 directory of 634 anonymous loci obtained from RNA-Seq data and aligned for
 phylogenetic analysis. The data come from 5 Heliconius species: Heliconius
 melpomene, Heliconius erato, Heliconius sara, Heliconius doris, and
 Heliconius charithonia. Briefly, we performed Illumina RNA sequencing
 followed by de novo transcriptome assembly. BLAST was used to determine
 orthology across species and the selected loci were aligned using Clustal
 W. This file contains the final 634 loci used to reconstruct the
 Heliconius phylogeny. The file is a zipped directory containing each locus
 as a separate aligned fasta file. File names include the original
 (arbitrary) locus number and the length of the locus, but loci themselves
 are anonymous (i.e., are not annotated/named). Each file contains 5
 sequences labelled as so: char (Heliconius charithonia), dori (Heliconius
 doris), erat (Heliconius erato), melp (Heliconius melpomene), sara
 (Heliconius sara). See publication Methods section for a more detailed
 description of methodology.Dryad_submission_of_634_aligned_RNAseq_loci_Heliconius.zip
DOI: 10.5061/dryad.4jp82
title: Data from: Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants

description: Signaling pathways regulated by heterotrimeric G-proteins exist in all
 eukaryotes. The regulator of G-protein signaling (RGS) proteins are key
 interactors and critical modulators of the Gα protein of the heterotrimer.
 However, while G-proteins are widespread in plants, RGS proteins have been
 reported to be missing from the entire monocot lineage, with two
 exceptions. A single amino acid substitution-based adaptive coevolution of
 the Gα:RGS proteins was proposed to enable the loss of RGS in monocots. We
 used a combination of evolutionary and biochemical analyses and homology
 modeling of the Gα and RGS proteins to address their expansion and its
 potential effects on the G-protein cycle in plants. Our results show that
 RGS proteins are widely distributed in the monocot lineage, despite their
 frequent loss. There is no support for the adaptive coevolution of the
 Gα:RGS protein pair based on single amino acid substitutions. RGS proteins
 interact with, and affect the activity of, Gα proteins from species with
 or without endogenous RGS. This cross-functional compatibility expands
 between the metazoan and plant kingdoms, illustrating striking
 conservation of their interaction interface. We propose that additional
 proteins or alternative mechanisms may exist which compensate for the loss
 of RGS in certain plant species.
description: Hackenberg_etal_2016_Gα_RGS_protein_pairsSee README file.
DOI: 10.5061/dryad.8qc7ft62
title: Data from: Quantitative genetics of a carotenoid-based color: heritability and persistent natal environmental effects in the great tit

description: The information content of signals, such as animal coloration, depends on
 the extent to which variation reflects underlying biological processes.
 Although animal coloration has received considerable attention, little
 work has addressed the quantitative genetics of colour variation in
 natural populations. We investigated the quantitative genetics of a
 carotenoid-based colour patch - the ventral plumage of mature great tits
 (Parus major) - in a wild population. Carotenoid-based colours are often
 suggested to reflect environmental variation in carotenoid availability,
 but numerous mechanisms could also lead to genetic variation in
 coloration. Analyses of individuals of known origin showed that while
 plumage chromaticity ('colour') was moderately heritable, there
 was no significant heritability to achromaticity ('brightness').
 We detected multiple long-lasting effects of natal environment, with
 hatching date and brood size both negatively related to plumage
 chromaticity at maturity. Our reflectance measures contrasted in their
 spatiotemporal sensitivity, with plumage chromaticity exhibiting
 significant spatial variation while achromatic variation exhibited marked
 annual variation. Hence, colour variation in this species reflects both
 genetic and environmental influences on different scales. Our analyses
 demonstrate the context-dependence of components of colour variation and
 suggest that colour patches may convey multiple aspects of individual
 state.
description: DatasetArchived dataset.xlsPedigreePedigree for use in quantitative genetic analyses (based on behavioral data: i.e., a social pedigree not a genetic pedigree)
DOI: 10.5061/dryad.6rh86
title: Data from: Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti

description: In many species, alternative developmental pathways lead to the production
 of two distinct phenotypes, promoting the evolution of morphological
 novelty and diversification. Offspring type in marine invertebrates
 influences transport time by ocean currents, which dictate dispersal
 potential and gene flow, and thus has sweeping evolutionary effects on the
 potential for local adaptation and on rates of speciation, extinction, and
 molecular evolution. Here we use the polychaete Streblospio benedicti to
 investigate the effects of dimorphic offspring type on gene flow and
 genetic structure in coastal populations. We use 84 single nucleotide
 polymorphism (SNP) markers for this species to assay populations on the
 East and West Coasts of the United States. Using these markers we found
 that in their native East Coast distribution, populations of S. benedicti
 have high population genetic structure, but this structure is associated
 primarily with geographic separation rather than developmental
 differences. Interestingly, very little genetic differentiation is
 recovered between individuals of different development types when they
 occur in the same or nearby populations, further supporting that this is a
 true case of poecilogony. In addition, we were able to demonstrate that
 the recently introduced West Coast populations (~100ya) likely originated
 from a lecithotrophic population near Delaware.
description: Sequences for SNPs used
 with Illumina's Golden Gate AssayThis is a list of the 84
 SNPs and their flanking regions that were developed for use with
 Illumina's Golden Gate assay. For information on SNP selection,
 criteria and validation please see Zakas et al. (2012) Transcriptome
 analysis and SNP development can resolve population differentiation of
 Streblospio benedicti, a developmentally dimorphic marine annelid. PLoS
 ONE 7, E31613.SNP_list_DRYAD.xlsxStreblospio SNP ListThese are the genotype calls for all of the individuals used in the study for each of the 84 SNPs. It includes the population for each individual and larval type, if known.SNP_list_streblospio.xlsx
DOI: 10.5061/dryad.rf8th
title: Data from: Cool echidnas survive the fire

description: Fires have occurred throughout history, including those associated with
 the meteoroid impact at the Cretaceous-Palaeogene (K-Pg) boundary that
 eliminated many vertebrate species. To evaluate the recent hypothesis that
 the survival of the K-Pg fires by ancestral mammals was dependent on their
 ability to use energy-conserving torpor, we studied body temperature
 fluctuations and activity of an egg-laying mammal, the echidna
 (Tachyglossus aculeatus), often considered to be a ‘living fossil’,
 before, during and after a prescribed burn. All but one study animal
 survived the fire in the prescribed burn area and echidnas remained
 inactive during the day(s) following the fire and substantially reduced
 body temperature during bouts of torpor. For weeks after the fire, all
 individuals remained in their original territories and compensated for
 changes in their habitat with a decrease in mean body temperature and
 activity. Our data suggest that heterothermy enables mammals to outlast
 the conditions during and after a fire by reducing energy expenditure,
 permitting periods of extended inactivity. Therefore, torpor facilitates
 survival in a fire-scorched landscape and consequently may have been of
 functional significance for mammalian survival at the K-Pg boundary.
description: Mean Data_Cool echidnas
 survive the fireIndividual mean
 dataMean
 Data.pdfData figure 2_Cool
 echidnas survive the fireBody temperature traces
 of the same echidna a) 7 days before and b) 7 days after the fire on the
 21th of April.Data figure
 2.pdfData figure 3_Cool
 echidnas survive the fireMean body temperatures
 before and after the burn for a) the control echidnas (n=5) and b) fire
 animals (n=5; individual that died in the fire not shown) in relation to
 c) ambient conditions (maximum ambient temperature; minimum ambient
 temperature; precipitation).Data figure
 3.pdfData figure 4_Cool
 echidnas survive the fireComparison of home
 ranges for individuals of the fire group before (unfilled polygon) and
 after the fire (grey polygon). Home ranges were calculated as MCPs;
 overlap areas are indicated as dashed areas.Data figure
 4.pdf