cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7921
title: Data from: Post-Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow

description: Range expansions and gene flow as micro-evolutionary processes played a
 leading role in the population demographic history of marine organisms.
 Herein, we sequenced partial mtDNA Cox1 gene from 26 assigned geographic
 populations in order to understand how Irish moss (Chondrus crispus)
 responded to severe climatic oscillations during the Pleistocene
 glaciations and contemporary forces such as gene flow. Phylogeographic
 patterns indicated that haplotype frequency distributions were strongly
 skewed, with nearly half found only in single samples and thus restricted
 to a single population. Analysis of molecular variance revealed that most
 of the variation was within populations with no significant genetic
 structuring on either side of the Atlantic. Demographic analyses indicated
 that ISI (Irish Sea and Ireland) and NS (the North Sea) areas experienced
 a slight trend of increase in population size over time, whereas EC (the
 English Channel) area experienced expansion beginning approximately
 170,000-360,000 BP. The observed complex genetic pattern of C. crispus is
 consistent with a scenario of multiple unrelated founding events by
 survival of this species in at least three putative Pleistocene refugia
 along the European coastline, and subsequent trans-Atlantic dispersal
 combined with contiguous northward population expansion predating the LGM
 and geographically gene flow.
description: Original dataset
 (Cox1)This is an archive zip
 file, which contains all the original mtDNA Cox1 sequence data on both
 region and population levels. For each population, the abbreviation is the
 same as that given in Table 1 in this manuscript accepted by Journal of
 Evolutionary Biology. Likewise, general sequences were aligned and defined
 with Clustal X and DNAsp softwares, and primary analyses like AMOVA with
 Arlequin were also included.
DOI: 10.7927/2mvt-f503
title: IPCC AR6 Synthesis Report SPM.5 (a): Net global greenhouse gas (GHG) emissions

description: Development of greenhouse gas (GHG) emissions pathways consistent with implemented policies and mitigation strategies. The figure shows pathways with colored ranges denoting the 5th to 95th percentiles across models. The red range represents emissions pathways assuming policies that were implemented by the end of 2020, as well as the Nationally Determined Contributions (NDCs). The green range shows pathways limiting global warming to 2°C (&gt;67%), while the blue range shows pathways limiting warming to 1.5°C (&gt;50%) with no or limited overshoot. The black line depicts past emissions (2000–2015). The error bar in 2015 indicates the 5th to 95th percentile uncertainty range of non-harmonized emissions across pathways. The figure also includes a "net zero" line indicating the long-term goal for methane emissions reduction.
DOI: 10.5061/dryad.1ds88
title: Data from: Low evolutionary potential for egg-to-adult viability in Drosophila melanogaster at high temperatures

description: To cope with the increasing and less predictable temperature forecasts
 under climate change, many terrestrial ectotherms will have to migrate or
 rely on adaptation through plastic or evolutionary means. Studies suggest
 that some ectotherms have a limited potential to change their upper
 thermal limits via evolutionary shifts, but research has mostly focused on
 adult life stages under laboratory conditions. Here we use replicate
 populations of Drosophila melanogaster and a nested half sib/full sib
 quantitative genetic design to estimate heritabilities and genetic
 variance components for egg-to-adult viability under both laboratory and
 semi-natural field conditions, encompassing cold, benign and hot
 temperatures in two separate populations. The results demonstrated
 temperature-specific heritabilities and additive genetic variances for
 egg-to-adult viability. Heritabilities and genetic variances were higher
 under cold and benign compared to hot temperatures when tested under
 controlled laboratory conditions. Tendencies towards lower evolutionary
 potential at higher temperatures were also observed under semi-natural
 conditions although the results were less clear in the field setting.
 Overall the results suggest that ectotherms that already experience
 temperatures close to their upper thermal tolerance limits have a
 restricted capacity to adapt to higher temperatures by evolutionary means.
description: Data from the nested
 half sib full sib quantitative genetic designData from the nested
 half sib full sib quantitative genetic design used to estimate
 heritabilities and genetic variance components for egg-to-adult viability
 under laboratory (lab) and semi-natural field (field) conditions,
 encompassing cold (1), benign (2), and hot (3) temperatures in populations
 from Innisfail (1) and Melbourne (2), Australia. Each egg (id), sire
 (sire), dam (dam), and replicate vial (rep) is assigned a unique
 identification code. Data used for estimating genetic correlations are
 presented in spreadsheets 'Lab_cor_inn' and Lab_cor_melb'.
 In the remaining spreadsheets data from each individual test environment
 and population are presented.Data_kristensen_et
 al..xls
DOI: 10.5061/dryad.fc7mn
title: Data from: Solar radiation during rewarming from torpor in elephant shrews: supplementation or substitution of endogenous heat production?

description: Many small mammals bask in the sun during rewarming from heterothermy, but
 the implications of this behaviour for their energy balance remain little
 understood. Specifically, it remains unclear whether solar radiation
 supplements endogenous metabolic thermogenesis (i.e., rewarming occurs
 through the additive effects of internally-produced and external heat), or
 whether solar radiation reduces the energy required to rewarm by
 substituting (i.e, replacing) metabolic heat production. To address this
 question, we examined patterns of torpor and rewarming rates in eastern
 rock elephant shrews (Elephantulus myurus) housed in outdoor cages with
 access to either natural levels of solar radiation or levels that were
 experimentally reduced by means of shade cloth. We also tested whether
 acclimation to solar radiation availability was manifested via phenotypic
 flexibility in basal metabolic rate (BMR), non-shivering thermogenesis
 (NST) capacity and/or summit metabolism (Msum). Rewarming rates varied
 significantly among treatments, with elephant shrews experiencing natural
 solar radiation levels rewarming faster than conspecifics experiencing
 solar radiation levels equivalent to approximately 20% or 40% of natural
 levels. BMR differed significantly between individuals experiencing
 natural levels of solar radiation and conspecifics experiencing
 approximately 20% of natural levels, but no between-treatment difference
 was evident for NST capacity or Msum. The positive relationship between
 solar radiation availability and rewarming rate, together with the absence
 of acclimation in maximum non-shivering and total heat production
 capacities, suggests that under the conditions of this study solar
 radiation supplemented rather than substituted metabolic thermogenesis as
 a source of heat during rewarming from heterothermy.
description: Body temperature and
 weather dataBody temperature (page
 1) and weather (page 2) data.Respirometry
 dataBasal metabolic rate,
 non-shivering thermogenesis and summit metabolism data
DOI: 10.5061/dryad.16qc5
title: Data from: Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals

description: Convergent evolution occurs when the same trait arises independently in
 multiple lineages. In most cases of phenotypic convergence such
 transitions are adaptive, so finding the underlying molecular causes of
 convergence can provide insight into the process of adaptation. Convergent
 evolution at the genomic level also lends itself to study by comparative
 methods, though molecular convergence can also occur by chance, adding
 noise to this process. Parker et al. (2013) studied convergence across the
 genomes of several mammals, including echolocating bats and dolphins.
 Based on a null distribution of site-specific likelihood support (SSLS)
 generated using simulated topologies, they concluded that there was
 evidence for genome-wide adaptive convergence between echolocating taxa.
 Here we demonstrate that methods based on SSLS do not adequately measure
 convergence, and reiterate the use of an empirical null model that
 directly compares convergent substitutions between all pairs of species.
 We find that when the proper comparisons are made there is no surprising
 excess of convergence between echolocating mammals, even in sensory genes.
description: Data from echolocation
 convergence studyThe data in this folder
 accompany the publication: Thomas GWC and Hahn MW. 2015 Determining the
 null model for detecting adaptive convergence from genomic data: a case
 study using echolocating mammals. Molecular Biology and Evolution. The
 files in this repository are: 1. alignments: The 6,400 amino acid
 alignments (in fasta format) of the 9 mammals used in this study along
 with the ancestral states as inferred by PAML. 2. species_tree.nwk The
 newick formatted species tree inferred from the original alignments with
 RAxML and average consensus. Internal nodes have been labeled to
 correspond with the labels of the ancestral state sequences from the
 alignments.echolocation_data.zip
DOI: 10.60507/fk2/kerg69/sctntq
title: Krater_5806_images.zip
DOI: 10.60507/fk2/kerg69/rr39qv
title: GÜNZEL_Krater_5806_readme.txt
DOI: 10.60507/fk2/kerg69/z5tqym
title: Krater_5806_model.zip
DOI: 10.60507/fk2/kerg69
title: Attic Red-Figure Krater in the Museum Alte Kulturen Tübingen (Inv. 5806)

description: Attic Red-Figure Krater in the Museum Alte Kulturen (University of Tübingen, Inv. 5806) showing Menelaos pursuing Helen, with Eros and fleeing women on side A and women fleeing to an altar on side B. Possibly attributable to early mannerists, close to Leningrad painter. Date: around 460 BC.
description: Agisoft Metashape/Reality Capture, 2.2.0
description: Blender, 4.0
description: ZBrush, 2023.2
description: SubstanceDesigner, 15.0.3
description: SubstancePainter, 11.1.0
DOI: 10.5061/dryad.97vt8
title: Data from: Limits on information transduction through amplitude and frequency regulation of transcription factor activity

description: Signaling pathways often transmit multiple signals through a single shared
 transcription factor (TF) and encode signal information by differentially
 regulating TF dynamics. However, signal information will be lost unless it
 can be reliably decoded by downstream genes. To understand the limits on
 dynamic information transduction, we apply information theory to quantify
 how much gene expression information the yeast TF Msn2 can transduce to
 target genes in the amplitude or frequency of its activation dynamics. We
 find that although the amount of information transmitted by Msn2 to single
 target genes is limited, information transduction can be increased by
 modulating promoter cis-elements or by integrating information from
 multiple genes. By correcting for extrinsic noise, we estimate an upper
 bound on information transduction. Overall, we find that information
 transduction through amplitude and frequency regulation of Msn2 is limited
 to error-free transduction of signal identity, but not signal intensity
 information.
description: Supplementary_Source_Data
DOI: 10.5061/dryad.7930
title: Data from: A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat

description: One of the most widely distributed bats in the New World, the big brown
 bat (Eptesicus fuscus) exhibits well-documented geographic variation in
 morphology and life history traits, suggesting the potential for
 significant phylogeographic structure as well as adaptive differentiation
 among populations. In a pattern broadly consistent with morphologically
 defined subspecies, we found deeply divergent mitochondrial lineages
 restricted to different geographic regions. In contrast, sequence data
 from two nuclear loci suggest a general lack of regional genetic structure
 except for peripheral populations in the Caribbean and Mexico/South
 America. Coalescent analyses suggest that the striking difference in
 population structure between genomes cannot be attributed solely to
 different rates of lineage sorting, but is likely due to male-mediated
 gene flow homogenizing nuclear genetic diversity across most of the
 continental range. Despite this ongoing gene flow, selection has
 apparently been effective in producing and maintaining adaptive
 differentiation among populations, while strong female site fidelity,
 maintained over the course of millions of years, has produced remarkably
 deep divergence among geographically isolated matrilines. Our results
 highlight the importance of evaluating multiple genetic markers for a more
 complete understanding of population structure and history.
description: Combined mtDNA NEXUS
 file for Eptesicus fuscusNEXUS file with recoded
 mtDNA control region data (excluding "extra" repeats and
 recoding multiple base indels as single nucleotides). Used for BEAST
 analysis on which Figure 2 is based.EPFU.CRND2recoded.nexarchive of IMa2filesArchive contains 16 IMa2 input files. Eight files for analysis of eastern versus western populations and eight files for analysis of three populations (east v. NW v. SW). In each set, the files include the nCR locus and one of eight portions of the Enol locus. Indels are recoded as nucleotides.IMa2files.tar
DOI: 10.5281/zenodo.18385617
title: VSL_BRAND1_1F_1_23C_0k_EDLC_Single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5281/zenodo.18046664
title: VSL_BRAND1_1F_1_23C_0k_EDLC_Single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5061/dryad.j5h92
title: Data from: Habitat fragmentation in coastal southern California disrupts genetic connectivity in the Cactus Wren (Campylorhynchus brunneicapillus)

description: Achieving long-term persistence of species in urbanized landscapes
 requires characterizing population genetic structure to understand and
 manage the effects of anthropogenic disturbance on connectivity.
 Urbanization over the past century in coastal southern California has
 caused both precipitous loss of coastal sage scrub habitat and declines in
 populations of the cactus wren (Campylorhynchus brunneicapillus). Using 22
 microsatellite loci, we found that remnant cactus wren aggregations in
 coastal southern California comprised 20 populations based on strict exact
 tests for population differentiation, and 12 genetic clusters with
 hierarchical Bayesian clustering analyses. Genetic structure patterns
 largely mirrored underlying habitat availability, with cluster and
 population boundaries coinciding with fragmentation caused primarily by
 urbanization. Using a habitat model we developed, we detected stronger
 associations between habitat-based distances and genetic distances than
 Euclidean geographic distance. Within populations, we detected a positive
 association between available local habitat and allelic richness and a
 negative association with relatedness. Isolation-by-distance patterns
 varied over the study area, which we attribute to temporal differences in
 anthropogenic landscape development. We also found that genetic bottleneck
 signals were associated with wildfire frequency. These results indicate
 that habitat fragmentation and alterations have reduced genetic
 connectivity and diversity of cactus wren populations in coastal southern
 California. Management efforts focused on improving connectivity among
 remaining populations may help to ensure population persistence.
description: Cactus Wren Clusters and
 Geographic Coordinates-GENALEXThis is a GENALEX format
 file with the data split into groups as detected in clustering analyses.
 Geographic coordinates are indicated on the second
 sheet.cacws_genalex_clusters.xlsxCactus Wren Populations and Geographic Coordinates-GENALEXThis is genetic data from cactus wrens divided into populations as determined following Waples & Gaggiotti (2006) and is in GENALEX format. Geographic data can be obtained in the associated "clusters" data file.cacws_genalex_pops.xlsxcacws_genalex_clustersThis file contains microsatellite data and geographic coordinates for all of the individuals analyzed in the study. The format is GENALEX and samples are arranged according to clustering results.IBD_FinalDatasets_DryadData used for IBD and landscape analyses.Dispersal_Habitat_ModelGeoreferenced dispersal habitat model output in .img format with associated metadata
DOI: 10.5061/dryad.cq4fd
title: Data from: Topography as a driver of diversification in the Cape Floristic Region of South Africa

description: The rugged topography of the Cape Floristic Region (CFR), South Africa, is
 frequently invoked to explain the spectacular radiation of the Cape flora,
 but the mechanisms involved remain unclear. Where recent authors emphasize
 the importance of elevation gradients as stimuli for ecological
 speciation, earlier workers stressed the role of topography as an
 isolating mechanism, particularly in montane lineages. Using six Cape
 plant lineages, we tested whether elevation niches are phylogenetically
 conserved. We then assessed whether high-elevation species are more
 consistently range-restricted than low-elevation species, and whether
 high-elevation sisters show stronger range exclusivity (allopatry) and
 weaker ecological and phenotypic differentiation, suggestive of
 nonecological speciation. Elevation niches tend to be phylogenetically
 conserved. Also, high-elevation species are more consistently
 range-restricted than low-elevation species, potentially explaining the
 generally stronger range exclusivity of high-elevation sisters. While the
 high-elevation zone is less homogeneous ecologically, more data are
 required to demonstrate that high-elevation sister species show generally
 weaker ecological and phenotypic differentiation. Topographic complexity
 promotes geographical isolation at high elevations, thereby providing
 opportunities for nonecological, vicariant speciation. While recognizing
 the need for additional data, we suggest that the upland and lowland
 floras of the CFR may differ with regard to predominant speciation mode.
description: Georeferenced locality
 data for six Cape lineagesThis data file contains
 geographical coordinate data for herbarium specimens representing six
 lineages of Cape plants. The precision of geo-referencing is indicated via
 a precision score. Specimens used were mostly from BOL, NBG and/or PRE.
 For each record, we indicate the source herbarium, collector and
 collection details (including a verbal description) and the coordinate
 data.Verboom&al_georef_data.xlsx
DOI: 10.5061/dryad.gd5qb
title: Data from: No evidence for MHC class I based disassortative mating in a wild population of great tits

description: Genes of the major histocompatibility complex (MHC) are regarded as a
 potentially important target of mate choice due to the fitness benefits
 that may be conferred to the offspring. According to the complementary
 genes hypothesis, females mate with MHC dissimilar males to enhance the
 immunocompetence of their offspring or to avoid inbreeding depression.
 Here, we investigate whether selection favours a preference for maximally
 dissimilar or optimally dissimilar MHC class I types, based on MHC
 genotypes, average amino acid distances and the functional properties of
 the antigen-binding sites (MHC supertypes); and whether MHC type
 dissimilarity predicts relatedness between mates in a wild great tit
 population. In particular, we explore the role that MHC class I plays in
 female mate choice decisions while controlling for relatedness and spatial
 population structure, and examine the reproductive fitness consequences of
 MHC compatibility between mates. We find no evidence for the hypotheses
 that females select mates on the basis of either maximal or optimal MHC
 class I dissimilarity. A weak correlation between MHC allele sharing and
 relatedness, and between MHC supertype sharing and relatedness suggests
 that MHC dissimilarity at functional variants may not provide an effective
 index of relatedness. Moreover the reproductive success of pairs did not
 vary with MHC dissimilarity. Our results provide no support for the
 suggestion that selection favours, or that mate choice realises, a
 preference for complimentary MHC types.
description: Great tit social pairs -
 relatedness/allele/supertype/reproduction dataMHC allele sharing, MHC
 supertype sharing, relatedness and reproductive output data of the great
 tit social pairs used in the studypairs
 relatedness:allele:supertype:reproduction
 data.xlsindividual allele &
 supertype dataGreat tit MHC allele and
 MHC supertype dataMHC allele aminoacid
 distancesThe amino acid distance
 estimates and standard errors between each great tit MHC
 allele
DOI: 10.5061/dryad.hh63d
title: Data from: A structured population model suggests that long life and post-reproductive lifespan promote the evolution of cooperation

description: Social organization correlates with longevity across animal taxa. This
 correlation has been explained by selection for longevity by social
 evolution. The reverse causality is also conceivable but has not been
 sufficiently considered. We constructed a simple, spatially structured
 population model of asexually reproducing individuals to study the effect
 of temporal life history structuring on the evolution of cooperation.
 Individuals employed fixed strategies of cooperation or defection towards
 all neighbours in a basic Prisoner׳s Dilemma paradigm. Individuals aged
 and transitioned through different life history stages asynchronously
 without migration. An individual׳s death triggered a reproductive event by
 one immediate neighbour. The specific neighbour was chosen
 probabilistically according to the cumulative payoff from all local
 interactions. Varying the duration of pre-reproductive, reproductive, and
 post-reproductive life history stages, long-term simulations allowed a
 systematic evaluation of the influence of the duration of these specific
 life history stages. Our results revealed complex interactions among the
 effects of the three basic life history stages and the benefit to defect.
 Overall, a long post-reproductive stage promoted the evolution of
 cooperation, while a prolonged pre-reproductive stage has a negative
 effect. In general, the total length of life also increased the
 probability of the evolution of cooperation. Thus, our specific model
 suggests that the timing of life history transitions and total duration of
 life history stages may affect the evolution of cooperative behaviour. We
 conclude that the causation of the empirically observed association of
 life expectancy and sociality may be more complex than previously
 realized.
description: Raw Data for Simulation
 OutcomesThis file contains a
 table in which we list all outcomes for the different simulations that we
 performed to study the effect of life history structuring on the evolution
 of cooperation.RossYJTBI8048_DryadDataFile.xlsx