cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1m0t8
title: Data from: How cuckoos find and choose host nests for parasitism

description: How cuckoos find the nests of their hosts and choose nests with respect to
 egg phenotype for parasitism is a long-standing puzzle that has so far not
 been solved. We recently developed an experimental design to shed light on
 this mystery by studying the egg-laying behavior of common cuckoos
 (Cuculus canorus) in nests of its Oriental reed warbler (Acrocephalus
 orientalis) host. Our results showed that common cuckoos only parasitized
 host nests with host activities but ignored the egg phenotypes in the
 nests. Furthermore, cuckoos distinguished between nest types of
 black-browed reed warbler (Acrocephalus bistrigiceps) and Oriential reed
 warbler and chose to parasitize the latter. This study provides strong
 evidence for host activities being a prime factor affecting cuckoo
 parasitism. Cuckoos must first locate the general site of host nests from
 activities by the host and then target the nests for parasitism. These
 observations reject the optimal egg-laying hypothesis stating that cuckoos
 are capable of choosing to lay eggs in host nests with visually matching
 egg phenotypes. Therefore, our studies challenge the idea that cuckoos
 recognize eggs that match their own.
description: Data_table
 1_group1Data for group 1 in
 Table 1Data_table
 1_group2Data for group 2 in
 Table 1Data_figure
 3Data
 for Figure 3Data_figure
 4Data
 for Figure 4ESM Video
 S1-S4Video recording for
 S1-S4.
DOI: 10.5061/dryad.cq5h4
title: Data from: Genetic mating system and mate selection in smallmouth bass

description: Mating systems are an important factor influencing the variance in
 reproductive success among individuals within natural populations and thus
 have important ecological and evolutionary implications. We used molecular
 pedigree reconstruction techniques with microsatellite DNA data to
 characterize the genetic mating system and mate selection in adult
 smallmouth bass spawning in Lake Opeongo. The genetic mating system of
 smallmouth bass in this system can be characterized as predominantly
 monogamous with a low rate of polygynandry particularly among larger
 individuals. Iteroparous individuals showed a complete absence of
 interannual mate fidelity, presumably due to the low annual return rate of
 spawning adults. Within a season, individuals from both sexes pursued
 additional mating opportunities with males showing greater variance in
 mate number than females. Female mate selection appeared to be largely
 random with little evidence for elevated levels of inbreeding in this
 population. Multiple mating females pursued additional males to whom they
 were less related than the first male with which they spawned within a
 given season, however, this pattern varied among years. The mating pattern
 observed in this population would likely limit the strength of sexual
 selection and thus could account for the lack of sexual dimorphism and the
 absence of alternative reproductive tactics in this species.
description: Nesting
 MalesThe Nesting Males data
 file contains microsatellite genotype data along with sample number, nest
 id, xy coordinates, fork length, external tag numbers, sampling year, and
 code id for each individual.Swim-up
 FryThe swim-up fry data
 file contains microsatellite genotype data along with sample id, nest id,
 xy coordinates, sampling year, and code id for each
 individuals.Reconstructed
 FemalesThe reconstructed female
 data file contains pedigree reconstructed microsatellite genotype data for
 spawning females along with code id, sampling year, xy coordinates, and
 fork length of male spawning partner.
DOI: 10.21227/j3st-1492
title: "Raw impedance spectra during insulation ageing from initial state to breakdown"

description: "This dataset contains raw impedance spectra measured from 100 Hz to 10 MHz during insulation ageing experiments.The data cover the full degradation process from the initial condition until insulation breakdown, defined by insulation resistance dropping below 1 M\u03a9.All shared data correspond directly to measurement outputs without post-processing or feature extraction."
DOI: 10.15468/47t3za
title: Sandakerveien - fremmede arter

description: Observasjonsdata for karplanter i et veiavsnitt av Sandakerveien, Oslo kommune. Hovedsakelig fremmede arter. Data er samlet in i 2024. Multimediefilen inneholder én-til-mange lenker til bilder for hver post i forekomstfilen (når tilgjengelig)
DOI: 10.5061/dryad.3402n
title: Data from: Landscape genomics and pathway analysis to understand genetic adaptation of South African indigenous goat populations

description: Extensively raised livestock populations in most smallholder farming
 communities are exposed to harsh and heterogeneous climates and disease
 pathogen that they adapt to in order to survive. Majority of these
 livestock species including goats are of non-descript breeds and their
 response to natural selection presented by heterogeneous environments is
 still unresolved. This study investigated genetic diversity and its
 association with environmental and geographic conditions in 194 South
 African indigenous goats from different geographic using Illumina goat
 SNP50K genotypes. The Tankwa goats formed a homogeneous genetic cluster
 restricted to the Northern Cape province. Overall, the Boer, Kalahari Red,
 and Savanna showed a wide geographic spread of shared genetic components
 whereas the village ecotypes revealed a longitudinal distribution. The
 relative importance of environmental factors on genetic variation of goat
 populations was assessed using Redundancy Analysis (RDA). Variance
 partitioning using Model I with both climatic and geographic variables
 explained 22% of the total variation while model II with climatic
 variables accounted for 17%. Model III, which accounted for geographic
 variables, explained 1% of the total variation. The first axis (Model I)
 of the RDA analysis, revealed 329 outlier SNPs. Landscape genomic
 approaches of Spatial Analysis Method identified a total of 843 (1.75%)
 SNPs, while Latent Factor Mixed Models identified 714 (1.48%) SNPs
 significantly associated with environmental variables. Significant markers
 were within genes involved in biological functions potentially important
 for environmental adaptation. Overall, the study suggested environmental
 factors to have some effect in shaping the genetic variation of South
 African indigenous goat populations.
description: SA_Goatpopulation_2017South African indigenous goat population genotyping data.R-Codes_Mdladlaet alR codes used for RDA and geographic plot of ADMIXTURE
DOI: 10.6084/m9.figshare.31157696
title: Supplementary Material from DNA methylation reflects tissue and caste identity but not parasitism-induced changes in a social insect

description: Supplementary_Files.zip
DOI: 10.6084/m9.figshare.31157696.v1
title: Supplementary Material from DNA methylation reflects tissue and caste identity but not parasitism-induced changes in a social insect

description: Supplementary_Files.zip
DOI: 10.5061/dryad.1b5t7
title: Data from: Trait variation in response to varying winter temperatures, diversity patterns and signatures of selection along the latitudinal distribution of the widespread grassland plant Arrhenatherum elatius

description: Across Europe, genetic diversity can be expected to decline toward the
 North because of stochastic and selective effects which may imply
 diminished phenotypic variation and less potential for future genetic
 adaptations to environmental change. Understanding such latitudinal
 patterns can aid provenance selection for breeding or assisted migration
 approaches. In an experiment simulating different winter temperatures, we
 assessed quantitative trait variation, genetic diversity, and
 differentiation for natural populations of the grass Arrhenatherum elatius
 originating from a large latitudinal gradient. In general, populations
 from the North grew smaller and had a lower flowering probability. Toward
 the North, the absolute plastic response to the different winter
 conditions as well as heritability for biomass production significantly
 declined. Genetic differentiation in plant height and probability of
 flowering were very strong and significantly higher than under neutral
 expectations derived from SNP data, suggesting adaptive differentiation.
 Differentiation in biomass production did not exceed but mirrored patterns
 for neutral genetic differentiation, suggesting that migration-related
 processes caused the observed clinal trait variation. Our results
 demonstrate that genetic diversity and trait differentiation patterns for
 A. elatius along a latitudinal gradient are likely shaped by both local
 selection and genetic drift.
description: Arrhenaterum_quantitative_dataQuantitative responses (biomass, height, flowering) of Arrhenatherum elatius in response to different winter temperature scenarios.Arrhenatherum_elatius_GBS_5026loci_for_spagediSNP data (5026 loci, SPAGeDI format) for the eight populations of Arrhenatherum elatius included in the experiment.
DOI: 10.5061/dryad.b277d
title: Data from: FiSSE: A simple non-parametric test for the effects of a binary character on lineage diversification rates

description: It is widely assumed that phenotypic traits can influence rates of
 speciation and extinction, and several statistical approaches have been
 used to test for correlations between character states and lineage
 diversification. Recent work suggests that model-based tests of
 state-dependent speciation and extinction are sensitive to model
 inadequacy and phylogenetic pseudoreplication. We describe a simple
 non-parametric statistical test ("FiSSE") to assess the effects
 of a binary character on lineage diversification rates. The method
 involves computing a test statistic that compares the distributions of
 branch lengths for lineages with and without a character state of
 interest. The value of the test statistic is compared to a null
 distribution generated by simulating character histories on the observed
 phylogeny. Our tests show that FiSSE can reliably infer trait-dependent
 speciation on phylogenies of several hundred tips. The method has low
 power to detect trait-dependent extinction but can infer state-dependent
 differences in speciation even when net diversification rates are
 constant. We assemble a range of macroevolutionary scenarios that are
 problematic for likelihood-based methods, and we find that FiSSE does not
 show similarly elevated false positive rates. We suggest that
 non-parametric statistical approaches, such as FiSSE, provide an important
 complement to formal process-based models for trait-dependent
 diversification.
description: evolution_16-0770FiSSE analysis code, examples, testing datasets, analysis results, and batch processing scripts to accompany Rabosky & Goldberg (2017)Evolution_16-0770.zip
DOI: 10.5061/dryad.44c0r
title: Data from: Population genomics reveals a candidate gene involved in bumble bee pigmentation

description: Variation in bumble bee color patterns is well-documented within and
 between species. Identifying the genetic mechanisms underlying such
 variation may be useful in revealing evolutionary forces shaping rapid
 phenotypic diversification. The widespread North American species Bombus
 bifarius exhibits regional variation in abdominal color forms, ranging
 from red-banded to black-banded phenotypes and including geographically
 and phenotypically intermediate forms. Identifying genomic regions linked
 to this variation has been complicated by strong, near species level,
 genome-wide differentiation between red- and black-banded forms. Here, we
 instead focus on the closely related black-banded and intermediate forms
 that both belong to the subspecies B. bifarius nearcticus. We analyze an
 RNA sequencing (RNAseq) data set and identify a cluster of single
 nucleotide polymorphisms (SNPs) within one gene, Xanthine
 dehydrogenase/oxidase-like, that exhibit highly unusual differentiation
 compared to the rest of the sequenced genome. Homologs of this gene
 contribute to pigmentation in other insects, and results thus represent a
 strong candidate for investigating the genetic basis of pigment variation
 in B. bifarius and other bumble bee mimicry complexes.
description: Data from Pimsler,
 Jackson, and Lozier. 2017. Population genomics reveals a candidate gene
 involved in bumble bee pigmentation. Ecology and
 Evolution.ZIP file containing
 folders of input and output files for SNP data, outlier analyses, and
 confirmation re-sequencing alignments.Pimsler_etal_2017_E&E_DRYAD.zip
DOI: 10.5061/dryad.5gm12
title: Data from: Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds: a case study of the Norwegian Lundehund

description: Genetic rescue, outcrossing with individuals from a related population, is
 used to augment genetic diversity in populations threatened by severe
 inbreeding and extinction. The endangered Norwegian Lundehund dog
 (henceforth Lundehund) underwent at least two severe bottlenecks in the
 1940s and 1960s that each left only five inbred dogs, and the
 approximately 1500 dogs remaining world-wide today appear to descend from
 only two individuals. The Lundehund has a high prevalence of a
 gastrointestinal disease, to which all remaining dogs may be predisposed.
 Outcrossing is currently performed with three Nordic Spitz breeds:
 Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of
 single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48
 dogs from the four breeds revealed substantially lower genetic diversity
 for the Lundehund (HE 0.035) than for other breeds (HE 0.209-0.284).
 Analyses of genetic structure with 16K linkage disequilibrium-pruned SNPs
 showed four distinct genetic clusters. Pairwise FST values between
 Lundehund and the candidate breeds were highest for Icelandic Sheepdog,
 followed by Buhund and Norrbottenspets. We assessed the presence of
 outlier loci among candidate breeds and examined flanking genome regions
 (1 megabase) for genes under possible selection to identify potential
 adaptive differences among breeds; outliers were observed in flanking
 regions of genes associated with key functions including the immune
 system, metabolism, cognition and physical development. We suggest
 crossbreeding with multiple breeds as the best strategy to increase
 genetic diversity for the Lundehund and reduce the incidence of health
 problems. For this project, the three candidate breeds were first selected
 based on phenotypes and then subject to genetic investigation. Because
 phenotypes are often paramount for domestic breed owners, such a strategy
 could provide a helpful approach for genetic rescue and restoration of
 other domestic populations at risk, by ensuring the involvement of owners,
 breeders and managers at the start of the project.
description: NordicDogs_IDExcel file with list of individuals and dog breeds: NordicDogs_ID.xlsxNordicDogs_4mars2014PED file with individual data: NordicDogs_4mars2014.pedNordicDogs_4mars2014MAP file with data on genetic markers: NordicDogs_4mars2014.map
DOI: 10.5061/dryad.rs714
title: Data from: Non-random patterns of invasion and extinction reduce phylogenetic diversity in island bird assemblages

description: Anthropogenically driven changes in bird communities on oceanic islands
 exemplify the biotic upheaval experienced by island floras and faunas.
 While the influence of invasions and extinctions on species richness and
 beta-diversity of island bird assemblages have been explored, little is
 known about the impact of these invasions and extinctions on phylogenetic
 diversity. Here we quantify phylogenetic diversity of island bird
 assemblages resulting from extinctions alone, invasions alone, and the
 combination of extinctions and invasions in the historic time period (1500
 CE to the current), and compare it to the expected phylogenetic diversity
 that would result if these processes involved randomly selected island
 bird species. We assessed phylogenetic diversity and structure at the
 scale of the island (n =152), the archipelago containing the islands
 (n=22), and the four oceans containing the archipelagos using three
 measures. We found that extinction, invasion, and the combination of
 invasion and extinction generally resulted in lower phylogenetic diversity
 than expected, regardless of the spatial scale examined. We conclude that
 extinction and invasion of birds on islands are non-random with respect to
 phylogeny and that these processes generally leave bird assemblages with
 lower phylogenetic diversity than we would expect under random invasion or
 extinction.
description: Island bird
 phylogeniesIsland bird phylogenies,
 list of species added, fossil calibrations. See ReadMe file for full
 descriptionBaiser_etal_2017_Ecography.zip
DOI: 10.5061/dryad.8kk06
title: Data from: Genome-wide association analysis in dogs implicates 99 loci as risk variants for anterior cruciate ligament rupture

description: Anterior cruciate ligament (ACL) rupture is common condition that can be
 devastating and life changing, particularly in young adults. A non-contact
 mechanism is typical. Second ACL ruptures through rupture of the
 contralateral ACL or rupture of a graft repair is also common. Risk of
 rupture is increased in females. ACL rupture is also common in dogs.
 Disease prevalence exceeds 5% in several dog breeds, ~100 fold higher than
 human beings. We provide insight into the genetic etiology of ACL rupture
 by genome-wide association study (GWAS) in a high-risk breed using 98 case
 and 139 control Labrador Retrievers. We identified 129 single nucleotide
 polymorphisms (SNPs) within 99 risk loci. Associated loci
 (P&lt;5.0E-04) explained approximately half of phenotypic variance in
 the ACL rupture trait. Two of these loci were located in uncharacterized
 or non-coding regions of the genome. A chromosome 24 locus containing nine
 genes with diverse functions met genome-wide significance (P=3.63E-0.6).
 GWAS pathways were enriched for c-type lectins, a gene set that includes
 aggrecan, and a gene set encoding membrane transport proteins with a
 variety of physiological functions. Genotypic risk estimated for each dog
 based on the risk contributed by each GWAS locus showed clear separation
 of ACL rupture cases and controls. Power analysis of the GWAS data set
 estimated that ~172 loci explain the genetic contribution to ACL rupture
 in the Labrador Retriever. Heritability was estimated at 0.48. We conclude
 ACL rupture is a moderately heritable highly polygenic complex trait. Our
 results implicate c-type lectin pathways in ACL homeostasis.
description: cr237_dryad.famPlink binary format fam file for 237 Labrador retrievers phenotyped for ACL rupture. 1= unaffected, 2 = affectedcr237_dryad.bedPlink binary format .bed file for 237 labrador retrievers phenotyped for ACL rupturecr237_dryad.bimPlink binary format .bim file for 237 Labrador retrievers phenotyped for ACL rupture
DOI: 10.5061/dryad.4tv3q
title: Data from: Aquatic microfauna alter larval food resources and affect development and biomass of West Nile and Saint Louis encephalitis vector Culex nigripalpus (Diptera: Culicidae)

description: Ciliate protists and rotifers are ubiquitous in aquatic habitats and can
 comprise a significant portion of the microbial food resources available
 to larval mosquitoes, often showing substantial declines in abundance in
 the presence of mosquito larvae. This top-down regulation of protists is
 reported to be strong for mosquitoes inhabiting small aquatic containers
 such as pitcher plants or tree holes, but the nature of these interactions
 with larval mosquitoes developing in other aquatic habitats is poorly
 understood. We examined the effects of these two microbial groups on lower
 trophic level microbial food resources, such as bacteria, small
 flagellates, and organic particles, in the water column, and on Culex
 larval development and adult production. In three independent laboratory
 experiments using two microeukaryote species (one ciliate protist and one
 rotifer) acquired from field larval mosquito habitats and cultured in the
 laboratory, we determined the effects of Culex nigripalpus larval grazing
 on water column microbial dynamics, while simultaneously monitoring larval
 growth and development. The results revealed previously unknown
 interactions that were different from the top-down regulation of microbial
 groups by mosquito larvae in other systems. Both ciliates and rotifers,
 singly or in combination, altered other microbial populations and
 inhibited mosquito growth. It is likely that these microeukaryotes,
 instead of serving as food resources, competed with early instar mosquito
 larvae for microbes such as small flagellates and bacteria in a
 density-dependent manner. These findings help our understanding of the
 basic larval biology of Culex mosquitoes, variation in mosquito production
 among various larval habitats, and may have implications for existing
 vector control strategies and for developing novel microbial-based control
 methods.
description: Mosquito-microeukaryote
 interaction studyThe data include
 measurements of mosquito parameters, population dynamics of
 microeukaryotes, lower trophic microbial (bacteria, small flagellate, etc.
 ) resources, and organic particle dynamics used to test
 mosquito-micoreukaryote interaction hypotheses in three microcosm
 experiments.Mosquito-Microeukaryote
 interaction study data_ Ecol and
 Evol._1.xlsx
DOI: 10.5061/dryad.77v30
title: Data from: A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau

description: Indigenous populations of the Tibetan plateau have attracted much
 attention for their good performance at extreme high altitude. Most
 genetic studies of Tibetan adaptations have used genetic variation data at
 the genome scale, while genetic inferences about their demography and
 population structure are largely based on uniparental markers. To provide
 genome-wide information on population structure, we analyzed new and
 published data of 338 individuals from indigenous populations across the
 plateau in conjunction with worldwide genetic variation data. We found a
 clear signal of genetic stratification across the east-west axis within
 Tibetan samples. Samples from more eastern locations tend to have higher
 genetic affinity with lowland East Asians, which can be explained by more
 gene flow from lowland East Asia onto the plateau. Our findings
 corroborate a previous report of admixture signals in Tibetans, which were
 based on a subset of the samples analyzed here, but add evidence for
 isolation by distance in a broader geospatial context.
description: PLINK formatted genotype
 data for 53 Nepali TibetansCompressed tarball
 archive containing PLINK formatted files (bim, bed, fam) with genotype
 data for 53 Tibetans from highland Nepal (69,427 SNPs).NepaliTibetan.tar.gz