cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.484pm
title: Data from: Fast adaptive responses in the oral jaw of Lake Victoria cichlids

description: Rapid morphological changes in response to fluctuating natural
 environments are a common phenomenon in species that undergo adaptive
 radiation. The dramatic ecological changes in Lake Victoria provide a
 unique opportunity to study environmental effects on cichlid morphology.
 This study shows how four haplochromine cichlids adapted their premaxilla
 to a changed diet over the past 30 years. Directly after the diet change
 toward larger and faster prey in the late 1980s, the premaxilla (upper
 jaw) changed in a way that is in agreement with a more food manipulating
 feeding style. During the 2000s, two zooplanktivorous species showed a
 reversal of morphological changes after returning to their original diet,
 whereas two other species showed no reversal of diet and morphology. These
 rapid changes indicate a potential for extremely fast adaptive responses
 to environmental fluctuations, which are likely inflicted by competition
 release and increase, and might have a bearing on the ability of
 haplochromines to cope with environmental changes. These responses could
 be due to rapid genetic change or phenotypic plasticity, for which there
 is ample evidence in cichlid fish structures associated with food capture
 and processing. These versatile adaptive responses are likely to have
 contributed to the fast adaptive radiation of haplochromines.
description: Excel file premaxilla H.
 pyrrhocephalusMorphological
 measurements of the premaxilla of H. pyrrhocephalus from the years
 1978-2011.Premaxilla
 pyr.xlsxExcel file premaxilla H.
 laparogrammaTanden
 lap.xlsExcel file premaxilla H.
 tanaosTanden
 tanaos.xlsExcel file premaxilla P.
 degeniTanden.xls
DOI: 10.5281/zenodo.18283393
title: Human brain and mouse cardiac immunofluorescence images with expert nuclear and cell segmentation annotations
DOI: 10.5281/zenodo.18283392
title: Human brain and mouse cardiac immunofluorescence images with expert nuclear and cell segmentation annotations
DOI: 10.5061/dryad.p1602
title: Data from: Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

description: Understanding the response of permafrost microbial communities to climate
 warming is crucial for evaluating ecosystem feedbacks to global change.
 This study investigated soil bacterial and archaeal communities by
 Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost
 thaw gradient at different depths in Alaska with thaw progression for over
 three decades. Over 4.6 million passing 16S rRNA gene sequences were
 obtained from a total of 97 samples, corresponding to 61 known classes and
 470 genera. Soil depth and the associated soil physical-chemical
 properties had predominant impacts on the diversity and composition of the
 microbial communities. Both richness and evenness of the microbial
 communities decreased with soil depth. Acidobacteria, Verrucomicrobia,
 Alpha- and Gamma-Proteobacteria dominated the microbial communities in the
 upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria
 and Firmicutes increased toward deeper soils. Effects of thaw progression
 were absent in microbial communities in the near-surface organic soil,
 likely due to greater temperature variation. Thaw progression decreased
 the abundances of potential bacterial decomposers of recalcitrant carbon
 (C) (Spartobacteria) in the lower organic soil, but increased the
 abundances of those (Actinomycetales, Chitinophaga, etc.) in the mineral
 soil. Such observations may reflect altered soil C sources in the organic
 and mineral horizons. Specifically, thaw progression could have increased
 labile C in the organic soil horizon through stimulated plant growth, but
 decreased labile C in the mineral soil due to microbial respiration.
description: soil_metadataUclust_representative_sequencesOTU_table_classified_by_RDP.txt
DOI: 10.5061/dryad.k6m50
title: Data from: Evolution of the additive genetic variance–covariance matrix under continuous directional selection on a complex behavioural phenotype

description: Given the pace at which human-induced environmental changes occur, a
 pressing challenge is to determine the speed with which selection can
 drive evolutionary change. A key determinant of adaptive response to
 multivariate phenotypic selection is the additive genetic
 variance–covariance matrix (G). Yet knowledge of G in a population
 experiencing new or altered selection is not sufficient to predict
 selection response because G itself evolves in ways that are poorly
 understood. We experimentally evaluated changes in G when closely related
 behavioural traits experience continuous directional selection. We applied
 the genetic covariance tensor approach to a large dataset (n = 17 328
 individuals) from a replicated, 31-generation artificial selection
 experiment that bred mice for voluntary wheel running on days 5 and 6 of a
 6-day test. Selection on this subset of G induced proportional changes
 across the matrix for all 6 days of running behaviour within the first
 four generations. The changes in G induced by selection resulted in a
 fourfold slower-than-predicted rate of response to selection. Thus,
 selection exacerbated constraints within G and limited future adaptive
 response, a phenomenon that could have profound consequences for
 populations facing rapid environmental change.
description: Careau_et_al_G-matrix_DATA_DRYADCareau_et_al_G-matrix_PEDIGREE_DRYADCareau_et_al_G-matrix_CODE_TENSOR_SIMULATIONTensorExampleMod_pop1aTensorExampleMod_pop1bTensorExampleMod_pop1cTensorExampleMod_pop2aTensorExampleMod_pop1dTensorExampleMod_pop2bTensorExampleMod_pop2cTensorExampleMod_pop2d
DOI: 10.5878/kcc7-jh59
title: The Gothenburg SOM Survey 2023
title: SOM-undersökningen i Göteborg 2023

description: In the autumn of 2023, the eighth edition of the Gothenburg SOM survey was conducted. A total of 9,000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.

The dataset has changed somewhat in relation to the codebook, in order to reduce the risk of re-identification. The following changes have been made:
Variables removed: mtidn1, gbgprob_txt, anparti, trygg_txt, ansex_txt, anspraak, angrupp, f51, f64, ssyk, ssyk96, mellanomr20, mellanomr, sdn 
Variables added: samhällsgrupp
Variables aggregated: f58, f55c
description: Hösten 2023 genomfördes för åttonde gången en SOM-undersökning i Göteborgs stad, där totalt 9000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.

Datasetet har förändrats något i förhållande till kodboken, för att minska risken för bakvägsidentifiering. Följande förändringar har gjorts: 
Borttagna variabler: mtidn1, gbgprob_txt, anparti, trygg_txt, ansex_txt, anspraak, angrupp, f51, f64, ssyk, ssyk96, mellanomr20, mellanomr, sdn 
Tillagda variabler: samhällsgrupp
Aggregerade variabler: f58, f55c
DOI: 10.82294/dvnh4puno
title: COPUS. Territorio: Caquetá. Sector: Educación. Año: 2024
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2024 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Educación (educación formal) en el departamento de Caquetá.
DOI: 10.5061/dryad.3hh83
title: Data from: Faster-X Effects in two Drosophila lineages

description: Under certain circumstances, X-linked loci are expected to experience more
 adaptive substitutions than similar autosomal loci. To look for evidence
 of faster-X evolution, we analyzed the evolutionary rates of coding
 sequences in two sets of Drosophila species, the melanogaster and
 pseudoobscura clades, using whole-genome sequences. One of these, the
 pseudoobscura clade, contains a centric 15 fusion between the ancestral X
 chromosome and the autosomal arm homologous to 3L in D.melanogaster. This
 offers an opportunity to study the same loci in both an X-linked and an
 autosomal context, and to compare these loci with those that are only
 X-linked or only autosomal. We therefore investigated these clades for
 evidence of faster-X evolution with respect to nonsynonymous
 substitutions, finding mixed results. Overall, there was consistent
 evidence for a faster-X effect in the melanogaster clade, but not in the
 pseudoobscura clade, except for the comparison between D. pseudoobscura
 and its close relative, Drosophila persimilis. Ananalysis of 20
 polymorphism data on a set of genes from D. pseudoobscura that evolve
 rapidly with respect to their protein sequences revealed no evidence for a
 faster-X effect with respect to adaptive protein sequence evolution; their
 rapid evolution is instead largely attributable to lower selective
 constraints. Faster-X evolution in the melanogaster clade was not related
 to male-biased gene expression; surprisingly, however, female-biased genes
 showed evidence for faster-X effects.
description: Sequence
 alignmentsPairwise alignments for
 the analysed speciesAlignments.zip
DOI: 10.5878/1arr-2e08
title: The Gothenburg SOM Survey 2023
title: SOM-undersökningen i Göteborg 2023

description: In the autumn of 2023, the eighth edition of the Gothenburg SOM survey was conducted. A total of 9,000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.

The dataset has changed somewhat in relation to the codebook, in order to reduce the risk of re-identification. The following changes have been made:
Variables removed: mtidn1, gbgprob_txt, anparti, trygg_txt, ansex_txt, anspraak, angrupp, f51, f64, ssyk, ssyk96, mellanomr20, mellanomr, sdn 
Variables added: samhällsgrupp
Variables aggregated: f58, f55c
description: Hösten 2023 genomfördes för åttonde gången en SOM-undersökning i Göteborgs stad, där totalt 9000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.

Datasetet har förändrats något i förhållande till kodboken, för att minska risken för bakvägsidentifiering. Följande förändringar har gjorts: 
Borttagna variabler: mtidn1, gbgprob_txt, anparti, trygg_txt, ansex_txt, anspraak, angrupp, f51, f64, ssyk, ssyk96, mellanomr20, mellanomr, sdn 
Tillagda variabler: samhällsgrupp
Aggregerade variabler: f58, f55c
DOI: 10.5061/dryad.mr72n
title: Data from: Some don't like it hot: microhabitat-dependent thermal and water stresses in a trailing edge population

description: 1. The distributional limits of species in response to environmental
 change are usually studied at large temporal and/or geographical scales.
 However, organismal scale habitat variation can be overlooked when
 investigating large-scale averages of key factors such as temperature. We
 examine how microhabitat thermal conditions relate to physiological
 limits, which may contribute to recent range shifts in an intertidal alga.
 2. We defined the onset and maximum temperatures of the heat-shock
 response (HSR) for a southern edge population of Fucus vesiculosus, which
 has subsequently become extinct. The physiological threshold for
 resilience (assayed using chlorophyll fluorescence) coincided with
 declining HSR, determined from the temperature-dependent induction of
 seven heat-shock protein transcripts. 3. In intertidal habitats,
 temperature affects physiology directly by controlling body temperature
 and indirectly through evaporative water loss. We investigated the
 relationship between the thermal environment and in situ molecular HSR at
 microhabitat scales. Over cm to m scales, four distinct microhabitats were
 defined in algal patches (canopy surface, patch edge, subcanopy, submerged
 channels), revealing distinct thermal and water stress environments during
 low-tide emersion. 4. The in situ HSR agreed with estimated tissue
 temperatures in all but one microhabitat. Remarkably, in the most
 thermally extreme microhabitat (canopy surface), the HSR was essentially
 absent in desiccated tissue, providing a potential escape from the
 cellular metabolic costs of thermal stress. 5. Meteorological records,
 microenvironmental thermal profiles and HSR data indicate that the maximum
 HSR is approached or exceeded in hydrated tissue during daytime low tides
 for much of the year. Furthermore, present-day summer seawater
 temperatures are sufficient to induce HSR during high-tide immersion,
 preventing recovery and resulting in continuous HSR during daytime
 low-tide cycles over the entire summer. 6. HSR in the field matched
 microhabitat temperatures more closely than local seawater or atmospheric
 data, suggesting that the impacts of climatic change are best understood
 at the microhabitat scale, particularly in intertidal areas.
description: FE-2014-00335_Gene
 Expression DataGene expression data for
 the field and laboratory experiments. Cycle threshold (Ct) values and
 normalized relative expression values of seven Hsp
 transcripts.FE-2014-00335_FvFm
 DataFv/Fm of Fucus
 vesiculosus following 24 h recovery at 15 ºC from 3 h heat-shock at 24,
 28, 32 and 36 ºC and controls.FE-2014-00335_temperature dataTemperature data used in Figures 2, 5, S2 and S3. Microhabitat temperatures for Ria Formosa on sampling days. Air temperatures in Faro for 2008 and 2012. Water temperatures in the Ria Formosa in 2012. Daily temperatures and monthly averages for 1973 – 2011.
DOI: 10.5061/dryad.hc445
title: Data from: Penalized Multi-Marker versus Single-Marker Regression methods for genome-wide association studies of quantitative traits

description: The data from genome-wide association studies (GWAS) in humans are still
 predominantly analyzed using single marker association methods. As an
 alternative to Single Marker Analysis (SMA), all or subsets of markers can
 be tested simultaneously. This approach requires a form of Penalized
 Regression (PR) as the number of SNPs is much larger than the sample size.
 Here we review PR methods in the context of GWAS, extend them to perform
 penalty parameter and SNP selection by False Discovery Rate (FDR) control,
 and assess their performance in comparison with SMA. PR methods were
 compared with SMA using realistically simulated GWAS data with a
 continuous phenotype and real data. Based on these comparisons our
 analytic FDR criterion may currently be the best approach to SNP selection
 using PR for GWAS. We found that PR with FDR control provides
 substantially more power than SMA with genome-wide type-I error control
 but somewhat less power than SMA with Benjamini-Hochberg FDR control
 (SMA-BH). PR with FDR based penalty parameter selection controlled the FDR
 somewhat conservatively while SMA-BH may not achieve FDR control in all
 situations. Differences among PR methods seem quite small when the focus
 is on SNP selection with FDR control. Incorporating linkage disequilibrium
 into the penalization by adapting penalties developed for covariates
 measured on graphs can improve power but also generate more false
 positives or wider regions for follow-up. We recommend the Elastic Net
 with a mixing weight for the Lasso penalty near 0.5 as the best method.
description: GenotypeDataReplicate18Chrom21R rda file containing the genotype matrix for 201 individuals and 21204 SNPs on chromosome 2118.RdaPhenotypeReplicate18Phenotype for 201 individuals for data replicate 18 corresponding to the genotype matrix for chromosome 21 and the 8-QTL scenarioY18.Rda
DOI: 10.5061/dryad.7215m
title: Data from: Genetic control of contagious asexuality in the pea aphid

description: Although evolutionary transitions from sexual to asexual reproduction are
 frequent in eukaryotes, the genetic bases of such shifts toward asexuality
 remain largely unknown. We addressed this issue in an aphid species where
 both sexual and obligate asexual lineages coexist in natural populations.
 These sexual and asexual lineages may occasionally interbreed because some
 asexual lineages maintain a residual production of males potentially able
 to mate with the females produced by sexual lineages. Hence, this species
 is an ideal model to study the genetic basis of the loss of sexual
 reproduction with quantitative genetic and population genomic approaches.
 Our analysis of the co-segregation of ~300 molecular markers and
 reproductive phenotype in experimental crosses pinpointed an X-linked
 region controlling obligate asexuality, this state of character being
 recessive. A population genetic analysis (&gt;400-marker genome scan)
 on wild sexual and asexual genotypes from geographically distant
 populations under divergent selection for reproductive strategies detected
 a strong signature of divergent selection in the genomic region identified
 by the experimental crosses. These population genetic data confirm the
 implication of the candidate region in the control of reproductive mode in
 wild populations originating from 700 km apart. Patterns of genetic
 differentiation along chromosomes suggest bidirectional gene flow between
 populations with distinct reproductive modes, supporting contagious
 asexuality as a prevailing route to permanent parthenogenesis in pea
 aphids. This genetic system provides new insights into the mechanisms of
 coexistence of sexual and asexual aphid lineages.
description: Genotype data used for
 genome scans and construction of genetic mapsThe Excel sheet entitled
 "Genotype_genome_scan" contains the genotypes of 109 individuals
 at 436 microsatelitte markers used for genome scan analyses. The Excel
 sheet entitled "Genotype_genetic_map" contains genotype data at
 343 polymorphic microsatelitte markers on a 3-generation pedigree that
 have been used to construct genetic maps.genotype_data.xlsx
DOI: 10.5061/dryad.39gc6
title: Data from: Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers

description: Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool
 for population genomic studies of nonmodel species. However, to utilize
 the potential of the method fully, many parameters affecting library
 quality and single nucleotide polymorphism (SNP) discovery require
 optimization, especially for conifer genomes with a high repetitive DNA
 content. In this study, we explored strategies for effective GBS analysis
 in pine species. We constructed GBS libraries using HpaII, PstI and
 EcoRI-MseI digestions with different multiplexing levels and examined the
 effect of restriction enzymes on library complexity and the impact of
 sequencing depth and size selection of restriction fragments on sequence
 coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for
 the GBS data, and then developed a reference-free SNP calling strategy for
 haploid pine genomes. Our GBS procedure proved to be effective in SNP
 discovery, producing 7000–11 000 and 14 751 SNPs within and among three
 pine species, respectively, from a PstI library. This investigation
 provides guidance for the design and analysis of GBS experiments,
 particularly for organisms for which genomic information is lacking.
description: 3pines_snps3pines-referenceGBS Data Processing Flowfileter_snp_in _contigs_2filter_contigsfilter-specific-GATKfilter-specific-stacksreference_generated_M1snp_filtersnp_filter_1transform-for-stacksunified_common_SNPs9pd_snp.vcfreference_pd9pt_snp9pt-reference9py_snp9py-reference
DOI: 10.5061/dryad.td03f
title: Data from: A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success

description: In summer 2012, we initiated a large-scale field experiment in southern
 Ontario, Canada, to determine whether exposure to clothianidin
 seed-treated canola (oil seed rape) has any adverse impacts on honey bees.
 Colonies were placed in clothianidin seed-treated or control canola fields
 during bloom, and thereafter were moved to an apiary with no surrounding
 crops grown from seeds treated with neonicotinoids. Colony weight gain,
 honey production, pest incidence, bee mortality, number of adults, and
 amount of sealed brood were assessed in each colony throughout summer and
 autumn. Samples of honey, beeswax, pollen, and nectar were regularly
 collected, and samples were analyzed for clothianidin residues. Several of
 these endpoints were also measured in spring 2013. Overall, colonies were
 vigorous during and after the exposure period, and we found no effects of
 exposure to clothianidin seed-treated canola on any endpoint measures.
 Bees foraged heavily on the test fields during peak bloom and residue
 analysis indicated that honey bees were exposed to low levels (0.5–2 ppb)
 of clothianidin in pollen. Low levels of clothianidin were detected in a
 few pollen samples collected toward the end of the bloom from control
 hives, illustrating the difficulty of conducting a perfectly controlled
 field study with free-ranging honey bees in agricultural landscapes.
 Overwintering success did not differ significantly between treatment and
 control hives, and was similar to overwintering colony loss rates reported
 for the winter of 2012–2013 for beekeepers in Ontario and Canada. Our
 results suggest that exposure to canola grown from seed treated with
 clothianidin poses low risk to honey bees.
description: PeerJ
 RawData