cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.61vk4
title: Data from: The social and ecological costs of an ‘over-extended’ phenotype

description: Extended phenotypes offer a unique opportunity to experimentally
 manipulate and identify sources of selection acting on traits under
 natural conditions. The social cichlid fish Neolamprologus multifasciatus
 builds nests by digging up aquatic snail shells, creating an extended
 sexual phenotype that is highly amenable to experimental manipulation
 through addition of extra shells. Here, we find sources of both positive
 sexual selection and opposing natural selection acting on this trait;
 augmenting shell nests increases access to mates, but also increases
 social aggression and predation risk. Increasing the attractiveness of one
 male also changed social interactions throughout the social network and
 altered the entire community structure. Manipulated males produced and
 received more displays from neighbouring females, who also joined
 augmented male territories at higher rates than unmanipulated groups.
 However, males in more attractive territories received more aggression
 from neighbouring males, potentially as a form of social policing. We also
 detected a significant ecological cost of the ‘over-extended'
 phenotype; heterospecific predators usurped augmented nests at higher
 rates, using them as breeding sites and displacing residents. Using these
 natural experiments, we find that both social and ecological interactions
 generate clear sources of selection mediating the expression of an
 extended phenotype in the wild.
description: ExtendedPhenotypeData for manipulations of individual shell nests of Neolamprologus multifasciatusmultifasc network dataInteraction frequency per five minute observation for each member of five separate communities.
DOI: 10.25625/a2z8t8/qyjnto
title: footprint_Forst_MC_70%.tab

description: :unav
DOI: 10.25625/a2z8t8/vz1mfo
title: footprint_2023_Forst_MC_80%.tab

description: :unav
DOI: 10.25625/a2z8t8/ydwpot
title: footprint_2019_Vechta_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/iqdk90
title: footprint_2019_Mariensee_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/xhsmr6
title: footprint_2021_Wendhausen_MC_80%.tab

description: :unav
DOI: 10.5061/dryad.7dn7m
title: Data from: Taxonomic revision of genus Ablattaria Reitter (Coleoptera, Silphidae) employing geometric morphometrics

description: The genus Ablattaria Reitter, 1884 (Coleoptera: Silphidae: Silphinae) is
 revised. Four taxa are recognized as valid species: Ablattaria arenaria
 (Kraatz, 1876), A. cribrata (Ménétries, 1832), A. laevigata (Fabricius,
 1775) and A. subtriangula Reitter, 1905. Ablattaria laevigata var.
 meridionalis Ganglbauer, 1899 is newly treated as a junior subjective
 synonym of A. laevigata. Lectotypes are designated for Phosphuga arenaria
 Kraatz, 1876, Ablattaria arenaria var. punctigera Reitter, 1884,
 Ablattaria arenaria var. alleoni Portevin, 1926, Silpha cribrata
 Ménétries, 1832, Silpha laevigata Fabricius, 1775, Silpha gibba Brullé,
 1832, Ablattaria gibba var. costulata Portevin, 1926, Ablattaria gibba
 var. distinguenda Portevin, 1926, Ablattaria gibba var. punctata Portevin,
 1926 and Ablattaria subtriangula Reitter, 1905. The distribution of all
 taxa is mapped, based on material examined. Geometric morphometric methods
 were used to evaluate shape variability in Ablattaria. Results indicated
 sexual dimorphism in all species. Shape inconsistency was found between
 the sexes of all taxa when tested independently. The first two relative
 warp axes indicated 65.17% shape variation in males and 65.72% in females.
 Canonical variate analysis separated the taxa studied. There was minimal
 overlap between some groups in both sexes. Differences in body shape
 between populations of A. laevigata from Central Europe, Italy and Greece
 + Turkey were also examined. Relative warps implied 58.01% shape
 variability on both axes in males and 64.78% in females. CVA revealed
 noticeable overlaps between the groups, although the Italian population
 demonstrated a higher separation in both sexes.
description: Ablattaria_DataDistribution data on Ablattaria Reitter (Coleoptera: Silphidae)Ablattaria_DataDistribution data of Ablattaria Reitter (Coleoptera: Silphidae), Excel table
DOI: 10.25625/a2z8t8/7bk7jy
title: footprint_2022_Forst_AF_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/l6zkov
title: footprint_2022_Vechta_MC_80%.tab

description: :unav
DOI: 10.25625/a2z8t8/tim45z
title: Forst_AF_precipitation_1h.tab

description: :unav
DOI: 10.25625/a2z8t8/8f6ohx
title: footprint_2020_Wendhausen_AF_80%.tab

description: :unav
DOI: 10.25625/a2z8t8/tzbcuk
title: footprint_Wendhausen_AF_80%.tab

description: :unav
DOI: 10.5061/dryad.06640
title: Data from: Concatenated alignments and the case of the disappearing tree

description: BackgroundAnalyzed individually, gene trees for a given taxon set tend to
 harbour incongruent or conflicting signals. One popular approach to deal
 with this circumstance is to use concatenated data. But especially in
 prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of
 generating genetic diversity, there are open questions as to whether
 concatenation amplifies or averages phylogenetic signals residing in
 individual genes. Here we investigate concatenations of prokaryotic and
 eukaryotic datasets to investigate possible sources of incongruence in
 phylogenetic trees and to examine the level of overlap between individual
 and concatenated alignments.ResultsWe analyzed prokaryotic datasets
 comprising 248 invidual gene trees from 315 genomes at three taxonomic
 depths spanning gammaproteobacteria, proteobacteria, and prokaryotes
 (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual
 gene trees from 85 genomes at two taxonomic depths: across
 plants-animals-fungi and within fungi. Consistent with previous findings,
 the branches in trees made from concatenated alignments are, in general,
 not supported by any of their underlying individual gene trees, even
 though the concatenation trees tend to possess high bootstrap proportions
 values. For the prokaryote data, this observation is independent of
 phylogenetic depth and sequence conservation. The eukaryotic data show
 much better agreement between concatenation and single gene trees. LGT
 frequencies in trees were estimated using established methods. Sequence
 length in individual alignments, but not sequence divergence, was found to
 correlate with the generation of branches that correspond to the
 concatenated tree.ConclusionsThe weak correspondence of concatenation
 trees with single gene trees gives rise to the question where the
 phylogenetic signal in concatenated trees is coming from. The eukaryote
 data reveals a better correspondence between individual and concatenation
 trees than the prokaryote data. The question of whether the lack of
 correspondence between individual genes and the concatenation tree in the
 prokaryotic data is due to LGT or phylogenetic artefacts is remains
 unanswered. If LGT is the cause of incongruence between concatenation and
 individual trees, we would have expected to see greater degrees of
 incongruence for more divergent prokaryotic data sets, which was not
 observed, although estimated rates of LGT suggest that LGT is responsible
 for at least some of the observed incongruence.
description: resourcesThe Zip-file include 8 Folders. Each containing phylogenetic trees and alignments for one dataset.
DOI: 10.25625/a2z8t8/bbwjg8
title: footprint_2022_Forst_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/u9tbr5
title: footprint_Wendhausen_AF_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/wyzl6o
title: Wendhausen_MC_meteo_30min.tab

description: :unav
DOI: 10.5061/dryad.qc6nv
title: Data from: Avian top predator and the landscape of fear: responses of mammalian mesopredators to risk imposed by the golden eagle

description: Top predators may induce extensive cascading effects on lower trophic
 levels, for example, through intraguild predation (IGP). The impacts of
 both mammalian and avian top predators on species of the same class have
 been extensively studied, but the effects of the latter upon mammalian
 mesopredators are not yet as well known. We examined the impact of the
 predation risk imposed by a large avian predator, the golden eagle (Aquila
 chrysaetos, L.), on its potential mammalian mesopredator prey, the red fox
 (Vulpes vulpes, L.), and the pine marten (Martes martes, L.). The study
 combined 23 years of countrywide data from nesting records of eagles and
 wildlife track counts of mesopredators in Finland, northern Europe. The
 predation risk of the golden eagle was modeled as a function of territory
 density, density of fledglings produced, and distance to nearest active
 eagle territory, with the expectation that a high predation risk would
 reduce the abundances of smaller sized pine martens in particular. Red
 foxes appeared not to suffer from eagle predation, being in fact most
 numerous close to eagle nests and in areas with more eagle territories.
 This is likely due to similar prey preferences of the two predators and
 the larger size of foxes enabling them to escape eagle predation risk.
 Somewhat contrary to our prediction, the abundance of pine martens
 increased from low to intermediate territory density and at close
 proximity to eagle nests, possibly because of similar habitat preferences
 of martens and eagles. We found a slightly decreasing trend of marten
 abundance at high territory density, which could indicate that the
 response in marten populations is dependent on eagle density. However,
 more research is needed to better establish whether mesopredators are
 intimidated or predated by golden eagles, and whether such effects could
 in turn cascade to lower trophic levels, benefitting herbivorous species.
description: Observed game abundances
 and estimated eagle densities in Finland, 1989-2011File contains data from
 Finnish wildlife triangle census (winters 1989-2011) and the yearly
 estimated eagle densities at these census triangle locations. triangleID=
 the identifier of an individual triangle. mhare= observed tracks of
 mountain hare. rfox= observed tracks of red fox. pmarten= observed tracks
 of pine marten. grouse= sightings of grouse (sum of capercaillie, black
 grouse, willow grouse and hazel grouse). accday= accumulation of snow
 tracks in days. dnn= distance to nearest active eagle nest. forest=
 percentage of forest in landscape within 5 km radius (CORILIS). farm=
 percentage of farmland in landscape within 5 km radius (CORILIS).
 terrdens= estimated density of active golden eagle territories (number
 refers to sigma used in the smoothing). fledgedens= estimated density of
 golden eagle fledglings in the previous year (number refers to sigma used
 in the smoothing).Data_GEgame.txt
DOI: 10.25625/a2z8t8/cp2t4l
title: footprint_2020_Mariensee_AF_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/m3nja3
title: footprint_2021_Dornburg_AF_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/g61cq7
title: Dornburg_AF_meteo_30min.tab

description: :unav
DOI: 10.25625/a2z8t8/7hbmoh
title: Wendhausen_MC_fluxes_30min.tab

description: :unav
DOI: 10.25625/a2z8t8/jfqukk
title: Vechta_AF_fluxes_30min.tab

description: :unav
DOI: 10.5061/dryad.dp4qg
title: Data from: Alternative reproductive tactics arising from a continuous behavioral trait: callers vs. satellites in field crickets

description: Alternative reproductive tactics may arise when natural enemies use sexual
 signals to locate the signaler. In field crickets, elevated costs to male
 calling due to acoustically orienting parasitoid flies create opportunity
 for an alternative tactic, satellite behavior, where noncalling males
 intercept females attracted to callers. Although the caller-satellite
 system in crickets that risk detection by parasitoids resembles distinct
 behavioral phenotypes, a male’s propensity to behave as caller or
 satellite can be a continuously variable trait over several temporal
 scales, and an individual may pursue alternate tactics at different times.
 We modeled a caller-satellite-parasitoid system as a spatially explicit
 interaction among male and female crickets using individual-based
 simulation. Males varied in their propensity to call versus behave as a
 satellite from one night to the next. We varied mortality, density, sex
 ratio, and female mating behavior, and recorded lifetime number of mates
 as a function of a male’s probability of calling (vs. acting as a
 satellite) along a gradient in parasitism risk. Frequently, the optimal
 behavior switched abruptly from being pure caller (call every night) to
 pure satellite (never call) as parasitism rate increased. However, mixed
 strategies prevailed even with high parasitism risk under conditions of
 higher background mortality rate, decreasing density, increasing
 female-biased sex ratio, and increasing female choosiness. In natural
 populations, high parasitoid pressure alone would be unlikely to yield
 fixation of pure satellite behavior.
description: Average life-time
 reproductive success of simulated male cricketsAverage life-time
 reproductive success of simulated male crickets as a function of tendency
 for satellite behavior across variation in risk of parasitism if calling,
 under variation in population density, sex ratio, mortality rate, female
 phonotaxis, and female propensity to mate.Archived Data -
 Data.txt
DOI: 10.82294/dvnrpjacr
title: COPUS. Territorio: Cali. 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 la ciudad de Cali.
DOI: 10.25625/a2z8t8/ivlrhx
title: Mariensee_MC_precipitation_1h.tab

description: :unav
DOI: 10.25625/a2z8t8/za1nfq
title: footprint_2019_Wendhausen_AF_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/exgxwv
title: footprint_2021_Vechta_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/ebrnwv
title: footprint_2024_Wendhausen_AF_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/rdldlz
title: footprint_2022_Dornburg_AF_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/xkh85c
title: variables_name_unit_eddycov.tab

description: :unav
DOI: 10.25625/a2z8t8/lcl3id
title: Dornburg_MC_fluxes_30min.tab

description: :unav
DOI: 10.25625/a2z8t8/mlb3ce
title: footprint_2022_Forst_AF_70%.tab

description: :unav
DOI: 10.25625/a2z8t8/siqpnh
title: footprint_2023_Forst_MC_70%.tab

description: :unav
DOI: 10.5061/dryad.4903q
title: Data from: Limited influence of local and landscape factors on finescale gene flow in two pond-breeding amphibians

description: Dispersal and gene flow within animal populations are influenced by the
 composition and configuration of the landscape. In this study, we
 evaluated hypotheses about the impact of natural and anthropogenic factors
 on genetic differentiation in two amphibian species, the spotted
 salamander (Ambystoma maculatum) and the wood frog (Lithobates sylvaticus)
 in a commercial forest in central Maine. We conducted this analysis at two
 scales: a local level, focused on factors measured at each breeding pond
 and a landscape level, focused on factors measured between ponds. We
 investigated the effects of a number of environmental factors in 6
 categories including Productivity, Physical, Land Composition, Land
 Configuration, Isolation, and Location. We also investigated the
 relationship of landscape composition and configuration on gene flow.
 Embryos were sampled from 56 spotted salamander breeding ponds and 39 wood
 frog breeding ponds. We used a hierarchical Bayesian approach in the
 program GESTE at each breeding pond and a random forest algorithm in
 conjunction with a network analysis between the ponds. We found overall
 high genetic connectivity across distances up to 17 km for both species
 and a limited effect of natural and anthropogenic factors on gene flow. We
 found the null models best explained patterns of genetic differentiation
 at a local level, and found several factors at the landscape level that
 weakly influenced gene flow. This research indicates multi-scale
 investigations that incorporate local and landscape factors are valuable
 for understanding patterns of gene flow. Our findings suggest that
 dispersal rates in this system are high enough to minimize genetic
 structuring, and that current forestry practices do not significantly
 impede dispersal.
description: WoodFrogGenotypesThis file includes individual microsatellite genotypes (7 loci) for wood frogs (N=888) collected from embryonic samples (one sample per eggmass) at breeding ponds (N=39) near Milford, ME. Genotypes were scored manually in PeakScanner and 0 indicates no alleles were identified at that locus. Pond locations (latitude, longitude) are included. See metadata in file for more information.SpottedSalamanderGenotypesThis file includes individual microsatellite genotypes (8 loci) for spotted salamanders (N=1292) collected from embryonic samples (one sample per eggmass) at breeding ponds (N=56) near Milford, ME. Genotypes were scored manually in PeakScanner and 0 indicates no alleles were identified at that locus. Pond locations (latitude, longitude) are included. See metadata in file for more information.LandscapeDataThis file includes information related to all factors in the landscape-level network analysis for wood frogs and spotted salamanders at each link width (see metadata in file).LocalDataThis file includes information related to all factors in the local-level analysis for wood frogs and spotted salamanders at each buffer width (see metadata in file).
DOI: 10.25625/a2z8t8/hwqbzb
title: footprint_2019_Forst_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/krp8if
title: footprint_Dornburg_MC_70%.tab

description: :unav
DOI: 10.25625/a2z8t8/wtkuyq
title: Dornburg_AF_fluxes_30min.tab

description: :unav
DOI: 10.25625/a2z8t8/wnvmls
title: footprint_2022_Dornburg_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/xfn3us
title: footprint_2024_Forst_AF_80%.tab

description: :unav
DOI: 10.5061/dryad.6s718
title: Data from: A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology

description: The Mexican tetra, Astyanax mexicanus, is a unique model system consisting
 of cave-adapted and surface-dwelling morphotypes which diverged
 &gt;1My ago. This remarkable natural experiment has enabled powerful
 genetic analyses of cave adaptation. Here, we describe the application of
 next-generation sequencing technology to the creation of a high-density
 linkage map. Our map comprises over 2200 markers populating 25 linkage
 groups constructed from genotypic data generated from a single
 genotyping-by-sequencing project. We leveraged emergent genomic and
 transcriptomic resources to anchor hundreds of anonymous Astyanax markers
 to the genome of the zebrafish (Danio rerio), the most closely related
 model organism to our study species. This facilitated the identification
 of 784 distinct connections between our linkage map and the Danio rerio
 genome, highlighting several regions of conserved genomic architecture
 between the two species despite ~150My of divergence. Using a Mendelian
 cave-associated trait as a proof-of-principle, we successfully recovered
 the genomic position of the albinism locus near the gene Oca2. Further,
 our map successfully informed the positions of unplaced Astyanax genomic
 scaffolds within particular linkage groups. This ability to identify the
 relative location, orientation and linear order of unaligned genomic
 scaffolds will facilitate ongoing efforts to improve upon the current
 early draft and assemble future versions of the Astyanax physical genome.
 Moreover, this improved linkage map will enable higher resolution genetic
 analyses and catalyze the discovery of the genetic basis for
 cave-associated phenotypes.
description: Carlson_et_al_2015_GBS_Marker_SequencesGenotyping-By-Sequencing Marker set sequences published in Carlson et al. 2015.Carlson_et_al_2015_GBS_Marker_GenotypesGenotyping-By-Sequencing Marker genotypes published in Carlson et al. 2015.
DOI: 10.25625/a2z8t8/mtvskt
title: footprint_2021_Dornburg_AF_80%.tab

description: :unav
DOI: 10.25625/a2z8t8/aiqq2j
title: footprint_2024_Dornburg_AF_70%.tab

description: :unav
DOI: 10.25625/a2z8t8/g4zkal
title: footprint_2024_Dornburg_MC_70%.tab

description: :unav
DOI: 10.25625/a2z8t8/kotrr8
title: footprint_Wendhausen_MC_80%.tab

description: :unav
DOI: 10.5061/dryad.pq482
title: Data from: Recurrent evolution of melanism in South American felids

description: Morphological variation in natural populations is a genomic test bed for
 studying the interface between molecular evolution and population
 genetics, but some of the most interesting questions involve non-model
 organisms that lack well annotated reference genomes. Many felid species
 exhibit polymorphism for melanism but the relative roles played by genetic
 drift, natural selection, and interspecies hybridization remain uncertain.
 We identify mutations of Agouti signaling protein (ASIP) or the
 Melanocortin 1 receptor (MC1R) as independent causes of melanism in three
 closely related South American species: the pampas cat (Leopardus
 colocolo), the kodkod (Leopardus guigna), and Geoffroy’s cat (Leopardus
 geoffroyi). To assess population level variation in the regions
 surrounding the causative mutations we apply genomic resources from the
 domestic cat to carry out clone-based capture and targeted resequencing of
 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from
 54 individuals (13–21 per species), achieving enrichment of ~500–2500-fold
 and ~150x coverage. Our analysis points to unique evolutionary histories
 for each of the three species, with a strong selective sweep in the pampas
 cat, a distinctive but short melanism-specific haplotype in the Geoffroy’s
 cat, and reduced nucleotide diversity for both ancestral and
 melanism-bearing chromosomes in the kodkod. These results reveal an
 important role for natural selection in a trait of longstanding interest
 to ecologists, geneticists, and the lay community, and provide a platform
 for comparative studies of morphological variation in other natural
 populations.
description: Genomic sequence
 dataThe sequence data file
 is provided as a ZIP archive containing 3 subfolders, one for each of the
 three analyzed species (i.e. Lco - Leopardus colocolo; Lge - Leopardus
 geoffroyi ; Lgu - Leopardus guigna). For each of these species the
 following sequence files are provided in the fasta format: - unmasked
 genomic consensus sequence computed for each and all the Asip and Mc1r
 loci fragments (i.e. for Leopardus colocolo the unmasked consensus
 sequence file is labeled Lco.fa); - genomic consensus sequence computed
 for each and all of the Asip and Mc1r loci fragments and masked for
 repeats and low complexity sequence using RepeatMasker (i.e. for Leopardus
 colocolo the masked consensus sequence file is labeled Lco_rm.fa); -
 haplotype sequence data for each of the genomic fragments and each of the
 analyzed samples, one file per fragment (i.e. Lco_AsipA for AsipA
 fragment) containing two haplotypic sequences per sample. These sequences
 are labeled by indicating the genomic fragment, the species, the
 individual and finally the haplotype (i.e. AsipA_Lco-030_h1
 [organism=Leopardus colocolo] ASIP locus segment A). The samples are
 labeled using the same identifiers as those provided in the manuscript
 (see Table S1 for details).datadryad.zip
DOI: 10.25625/a2z8t8/3sm8qz
title: footprint_Forst_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/rvi2ko
title: footprint_2023_Vechta_MC_90%.tab

description: :unav
DOI: 10.25625/a2z8t8/xphdsd
title: footprint_2021_Dornburg_MC_90%.tab

description: :unav