cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r87k3
title: Data from: Sky island diversification meets the multispecies coalescent – divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

description: Microhexura montivaga is a miniature tarantula-like spider endemic to the
 highest peaks of the southern Appalachian mountains and is known only from
 six allopatric, highly disjunct montane populations. Because of severe
 declines in spruce-fir forest in the late 20th century, M. montivaga was
 formally listed as a US federally endangered species in 1995. Using DNA
 sequence data from one mitochondrial and seven nuclear genes, patterns of
 multigenic genetic divergence were assessed for six montane populations.
 Independent mitochondrial and nuclear discovery analyses reveal obvious
 genetic fragmentation both within and among montane populations, with five
 to seven primary genetic lineages recovered. Multispecies coalescent
 validation analyses [guide tree and unguided Bayesian Phylogenetics and
 Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear-only
 data congruently recover six or seven distinct lineages; BFD analyses
 using combined nuclear plus mitochondrial data favour seven or eight
 lineages. In stark contrast to this clear genetic fragmentation, a survey
 of secondary sexual features for available males indicates morphological
 conservatism across montane populations. While it is certainly possible
 that morphologically cryptic speciation has occurred in this taxon, this
 system may alternatively represent a case where extreme population genetic
 structuring (but not speciation) leads to an oversplitting of lineage
 diversity by multispecies coalescent methods. Our results have clear
 conservation implications for this federally endangered taxon and
 illustrate a methodological issue expected to become more common as
 genomic-scale data sets are gathered for taxa found in naturally
 fragmented habitats.
description: Microhex_Standard_POFADdistancesmultigenic genetic distance file generated by POFAD 1.01Microhex_noc5c6_StandardPOFADdistances.txtMicrohexura_nonStandardized_POFADdistancesmultigenic genetic distance file generated by POFAD 1.01Microhex_noc5c6_nonStandardPOFADdistances.txtPhasedMatrices_ArchivePhased phylogenetic matrices, Nexus formatMorphology_Plates_ArchiveMorphology images, JPG formatSTRUCTURE_input_outputSTRUCTURE input and out filesRAxML_COI_bipartitionsCOI RAxML .tre fileRAxML_nuclear_tre_filesnuclear RAxML .tre filesMicrohexura_AssembliesTrinity assemblies from two Microhexura population transcriptomes
DOI: 10.5061/dryad.6nt0d
title: Data from: Understanding the mechanisms of anti-tropical divergence in the seabird White-faced Storm-petrel (Procellariiformes: Pelagodroma marina) using a multi-locus approach

description: Analytical methods that apply coalescent theory to multilocus data have
 improved inferences of demographic parameters that are critical to
 understanding population divergence and speciation. In particular, at the
 early stages of speciation, it is important to implement models that
 accommodate conflicting gene trees, and benefit from the presence of
 shared polymorphisms. Here, we employ eleven nuclear loci and the
 mitochondrial control region to investigate the phylogeography and
 historical demography of the pelagic seabird White-faced Storm-petrel
 (Pelagodroma marina) by sampling subspecies across its antitropical
 distribution. Groups are all highly differentiated: global mitochondrial
 ΦST = 0.89 (P &lt; 0.01) and global nuclear ΦST varies between 0.22
 and 0.83 (all P &lt; 0.01). The complete lineage sorting of the
 mitochondrial locus between hemispheres is corroborated by approximately
 half of the nuclear genealogies, suggesting a long-term antitropical
 divergence in isolation. Coalescent-based estimates of demographic
 parameters suggest that hemispheric divergence of P. marina occurred
 approximately 840 000 ya (95% HPD 582 000–1 170 000), in the absence of
 gene flow, and divergence within the Southern Hemisphere occurred 190 000
 ya (95% HPD 96 000–600 000), both probably associated with the profound
 palaeo-oceanographic changes of the Pleistocene. A fledgling sampled in St
 Helena (tropical South Atlantic) suggests recent colonization from the
 Northern Hemisphere. Despite the great potential for long-distance
 dispersal, P. marina antitropical groups have been evolving as
 independent, allopatric lineages, and divergence is probably maintained by
 philopatry coupled with asynchronous reproductive phenology and local
 adaptation.
description: individual_accessionsindividual accession numbers for all the dataset sequencesPmarina_STRUCTURE_inputInput file for structure (nuclear loci only)Pmarina_IMa2_inputInput datafile for IMa2 analysis (includes both the mitochondrial and nuclear loci)Pmarina_NJtree_newickNJ tree resulting from the POFAD analysis, in newick formatPmarinaCRaligned fasta file with all control region sequences.Pema1fasta file for anonymous nuclear locus Pema1Pema3fasta file for anonymous nuclear locus Pema3Pema5fasta file for anonymous locus Pema5Pema6fasta file for anonymous nuclear locus Pema6Pema7fasta file for anonymous nuclear locus Pema7Pema8fasta file for anonymous nuclear locus Pema8Pema9fasta file for anonymous nuclear locus Pema9Pema11fasta file for anonymous nuclear locus Pema11Pema12fasta file for anonymous nuclear locus Pema12Pema13fasta file for anonymous nuclear locus Pema13Pema14fasta file for anonymous nuclear locus Pema14
DOI: 10.5061/dryad.r4q8j
title: Data from: The evolutionary legacy of size-selective harvesting extends from genes to populations

description: Size-selective harvesting is assumed to alter life histories of exploited
 fish populations, thereby negatively affecting population productivity,
 recovery, and yield. However, demonstrating that fisheries-induced
 phenotypic changes in the wild are at least partly genetically determined
 has proved notoriously difficult. Moreover, the population-level
 consequences of fisheries-induced evolution are still being
 controversially discussed. Using an experimental approach, we found that
 five generations of size-selective harvesting altered the life histories
 and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio
 rerio). Fish adapted to high positively size selective fishing pressure
 invested more in reproduction, reached a smaller adult body size, and were
 less explorative and bold. Phenotypic changes seemed subtle but were
 accompanied by genetic changes in functional loci. Thus, our results
 provided unambiguous evidence for rapid, harvest-induced phenotypic and
 evolutionary change when harvesting is intensive and size selective.
 According to a life-history model, the observed life-history changes
 elevated population growth rate in harvested conditions, but slowed
 population recovery under a simulated moratorium. Hence, the evolutionary
 legacy of size-selective harvesting includes populations that are
 productive under exploited conditions, but selectively disadvantaged to
 cope with natural selection pressures that often favor large body size.
description: Growth
 dataGrowth
 dataReproductive
 dataReproductive
 dataMetabolic rate
 dataMetabolic
 ratemetabolic rate
 data.xlsxBehavioral
 dataBehavioral
 dataSNP
 dataSNP
 data
DOI: 10.5061/dryad.71gt8
title: Data from: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

description: Evaluating the genetic and demographic independence of populations of
 threatened species is important for determining appropriate conservation
 measures, but different technologies can yield different conclusions.
 Despite multiple studies, the taxonomic status and extent of gene flow
 between the main breeding populations of Black-footed Albatross
 (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still
 controversial. Here, we employ double digest RADseq to quantify the extent
 of genomewide divergence and gene flow in this species. Our genomewide
 data set of 9760 loci containing 3455 single nucleotide polymorphisms
 yielded estimates of genetic diversity and gene flow that were generally
 robust across seven different filtering and sampling protocols and suggest
 a low level of genomic variation (θ per site = ~0.00002–0.00028), with
 estimates of effective population size (Ne = ~500–15 881) falling far
 below current census size. Genetic differentiation was small but
 detectable between Japan and Hawaii (FST ≈ 0.038–0.049), with no FST
 outliers. Additionally, using museum specimens, we found that effect sizes
 of morphological differences by sex or population rarely exceeded 4%.
 These patterns suggest that the Hawaiian and Japanese populations exhibit
 small but significant differences and should be considered separate
 management units, although the evolutionary and adaptive consequences of
 this differentiation remain to be identified.
description: VCF Files of 7 Datasets
 used for AnalysisVCF files for all 7
 datasets used for analysis, along with a csv file of individual ID #s and
 a csv file with a description of each dataset (see Table 1 in publication
 for more information).Datasets.zip
DOI: 10.6084/m9.figshare.31158652
title: <b>Goldstonian Concordance Bible (GCB) — Canonical Index + Machine-Readable Masterfile (v2026-01-26)</b>

description: <b>Goldstonian Concordance Bible (GCB) — Canonical Index</b> is the canonical, machine-readable metadata dataset for the Goldstonian Concordance Bible ecosystem. It is designed for: (1) stable citation and discovery, (2) consistent title/identifier resolution across platforms, and (3) LLM/agent-friendly retrieval.What’s inside<code><strong>data/asin_master.json</strong></code> — primary structured master index (LLM ingestion)<code><strong>data/asin_master.csv</strong></code><b> / </b><code><strong>data/asin_master.md</strong></code> — spreadsheet + human-readable exports<code><strong>entities/title_registry.json</strong></code> — normalized titles/aliases for robust lookups<code><strong>BOOKS/**</strong></code> — per-book manifests + <code>CATALOG.json</code> / <code>CATALOG.csv</code> rollups<code><strong>llm/</strong></code> — prompts/guidance for citation + machine querying<code><strong>schema/</strong></code> — book record structure guidance<code><strong>RELEASES/CHANGELOG.md</strong></code> — release notes and update rulesCanon / conflict ruleIf metadata conflicts between Amazon listings, YouTube descriptions, PDFs, social posts, or other repos, <b>this index is the source of truth</b> until updated through the project’s canon process.VersionGenerated/released: <b>2026-01-26 (UTC)</b><br>Verification method: <b>user_confirmed</b> (see <code>data/asin_master.json</code> header notes)Related hubPrimary working repository: <b>GitHub — GoldstonianConcordanceBible/canonical-index</b>
DOI: 10.6084/m9.figshare.31158652.v2
title: <b>Goldstonian Concordance Bible (GCB) — Canonical Index + Machine-Readable Masterfile (v2026-01-26)</b>

description: <b>Goldstonian Concordance Bible (GCB) — Canonical Index</b> is the canonical, machine-readable metadata dataset for the Goldstonian Concordance Bible ecosystem. It is designed for: (1) stable citation and discovery, (2) consistent title/identifier resolution across platforms, and (3) LLM/agent-friendly retrieval.What’s inside<code><strong>data/asin_master.json</strong></code> — primary structured master index (LLM ingestion)<code><strong>data/asin_master.csv</strong></code><b> / </b><code><strong>data/asin_master.md</strong></code> — spreadsheet + human-readable exports<code><strong>entities/title_registry.json</strong></code> — normalized titles/aliases for robust lookups<code><strong>BOOKS/**</strong></code> — per-book manifests + <code>CATALOG.json</code> / <code>CATALOG.csv</code> rollups<code><strong>llm/</strong></code> — prompts/guidance for citation + machine querying<code><strong>schema/</strong></code> — book record structure guidance<code><strong>RELEASES/CHANGELOG.md</strong></code> — release notes and update rulesCanon / conflict ruleIf metadata conflicts between Amazon listings, YouTube descriptions, PDFs, social posts, or other repos, <b>this index is the source of truth</b> until updated through the project’s canon process.VersionGenerated/released: <b>2026-01-26 (UTC)</b><br>Verification method: <b>user_confirmed</b> (see <code>data/asin_master.json</code> header notes)Related hubPrimary working repository: <b>GitHub — GoldstonianConcordanceBible/canonical-index</b>
DOI: 10.6084/m9.figshare.31158652.v1
title: Untitled Ite<b>Goldstonian Concordance Bible (GCB) — Canonical Index + Machine-Readable Masterfile (v2026-01-26)</b>

description: <b>Goldstonian Concordance Bible (GCB) — Canonical Index</b> is the canonical, machine-readable metadata dataset for the Goldstonian Concordance Bible ecosystem. It is designed for: (1) stable citation and discovery, (2) consistent title/identifier resolution across platforms, and (3) LLM/agent-friendly retrieval.What’s inside<code><strong>data/asin_master.json</strong></code> — primary structured master index (LLM ingestion)<code><strong>data/asin_master.csv</strong></code><b> / </b><code><strong>data/asin_master.md</strong></code> — spreadsheet + human-readable exports<code><strong>entities/title_registry.json</strong></code> — normalized titles/aliases for robust lookups<code><strong>BOOKS/**</strong></code> — per-book manifests + <code>CATALOG.json</code> / <code>CATALOG.csv</code> rollups<code><strong>llm/</strong></code> — prompts/guidance for citation + machine querying<code><strong>schema/</strong></code> — book record structure guidance<code><strong>RELEASES/CHANGELOG.md</strong></code> — release notes and update rulesCanon / conflict ruleIf metadata conflicts between Amazon listings, YouTube descriptions, PDFs, social posts, or other repos, <b>this index is the source of truth</b> until updated through the project’s canon process.VersionGenerated/released: <b>2026-01-26 (UTC)</b><br>Verification method: <b>user_confirmed</b> (see <code>data/asin_master.json</code> header notes)Related hubPrimary working repository: <b>GitHub — GoldstonianConcordanceBible/canonical-index</b>
DOI: 10.7927/s4kw-9c34
title: IPCC AR6 Synthesis Report SPM.5 (e) and LR Figure 4.1 (b): Greenhouse gas emissions by sector at the time of net zero CO2, compared to 2019

description: This panel shows the sectoral contributions of CO2 and non-CO2 emissions sources and sinks at the time when net zero CO2 emissions are reached in illustrative mitigation pathways (IMPs) consistent with limiting warming to 1.5°C with a high reliance on net negative emissions (IMP-Neg) (“high overshoot”), high resource efficiency (IMP-LD), a focus on sustainable development (IMP-SP), renewables (IMP-Ren) and limiting warming to 2°C with less rapid mitigation initially followed by a gradual strengthening (IMP-GS). Positive and negative emissions for different IMPs are compared to GHG emissions from the year 2019. Energy supply (including electricity) includes bioenergy with carbon dioxide capture and storage and direct air carbon dioxide capture and storage. CO2 emissions from land-use change and forestry can only be shown as a net number as many models do not report emissions and sinks of this category separately.
DOI: 10.5061/dryad.23hs1
title: Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

description: Harnessing the power of genomic scans, we test the debated ‘species pump’
 hypothesis that implicates repeated cycles of island connectivity and
 isolation as drivers of divergence. This question has gone understudied
 given the limited resolution of past molecular markers for studying such
 dynamic phenomena. With an average of 32000 SNPs from the genome of 136
 individuals from ten populations of a Caribbean flightless ground cricket
 species (Amphiacusta sanctaecrucis) and a complementary set of statistical
 approaches, we infer a stepping-stone colonization model and high levels
 of genetic differentiation across the Virgin Islands, which have been
 periodically inter-connected until 8 ka. Estimates of divergence times
 from models based on the site frequency spectrum coincide with a period of
 repeated connection and fragmentation of the islands at 75–130 ka. These
 results are consistent with a role of island connectivity cycles in
 promoting genomic divergence and indicate that the genetic distinctiveness
 of island populations has persisted despite subsequent and extended
 interisland connections identified from bathymetric data. We discuss these
 findings in the broader context of Caribbean biogeography, and more
 specifically why high levels of genomic divergence across the Virgin
 Islands associated with repeated connectivity cycles do not actually
 translate into species diversification.
description: Amphiacusta_5558SNPs_StructureFile.txtA structure format file containing 5,558 single bi-allelic SNPs that were used for assessing population structure and genetic differentiation (for STRUCTURE, PCA and procrustes analyses, IBD and estimation of genetic diversity statistics).Amphiacusta10pops5558SNPsStructure.txtAmphiacusta_82443SNPs_ForQuartets.txtA phylip file containing 82,443 single bi-allelic SNPs that were used for the quartet analysis (in SVDquartets).Amphiacusta82443SNPsForQuartets.txtsampleDownMSFS.pyPython script that downsamples the population sizes and calculates the joint folded Site Frequency Spectrum (for the minor allele frequency) of two populations based on a vcf file. Includes an example vcf input file and population map.sampleDownMSFSWithExampleInputFiles.zipInputFilesForFastsimcoal.zipA set of folders containing the input files for analyses with fastsimcoal2, including the calculated joint Site Frequency Spectrum for each of the focal population pairs. Folder and file names follow the population codes used consistently throughout the manuscript.
DOI: 10.5061/dryad.857
title: Data from: A porous convection model for small-scale grass patterns

description: Spatial ecological patterns are usually ascribed to Turing‐type
 reaction‐diffusion or scale‐dependent feedback processes, but
 morphologically indistinguishable patterns can be produced by
 instabilities in fluid flow. We present a new hypothesis that suggests
 that fluid convection and chill damage to plants could form vegetation
 patterns with wavelengths ≈1–2 times the plant height. Previous hypotheses
 for small‐scale vegetation pattern formation relied on a Turing process
 driven by competition for water, which is thought to occur in large
 vegetation patterns. Predictions of the new hypothesis were consistent
 with properties of natural grass patterns in North Carolina, contradicting
 the Turing hypothesis. These results indicate that similarities in pattern
 morphology should not be interpreted as implying similarities in the
 pattern‐forming processes, that small‐wavelength vegetation patterns may
 arise from mechanisms that are distinct from those generating
 long‐wavelength vegetation patterns, and that fluid instabilities should
 be recognized as a cause of ecological patterns.
description: Grass_Photos.zipThese are a set of original images of grass lawn patterns observed at Duke University, North Carolina, November 2008, approximately 2 days after a frost. Four of these images show transects and patches of the lawn where soil moisture measurements were taken. These measurements are described in the excel file. This excel file also includes the appropriate scaling conversions (from pixels to cm) that can be used to make quantitative measurements on the images.
DOI: 10.5061/dryad.r36n0
title: Data from: Climate mediates the effects of disturbance on ant assemblage structure

description: Many studies have focused on the impacts of climate change on biological
 assemblages, yet little is known about how climate interacts with other
 major anthropogenic influences on biodiversity, such as habitat
 disturbance. Using a unique global database of 1128 local ant assemblages,
 we examined whether climate mediates the effects of habitat disturbance on
 assemblage structure at a global scale. Species richness and evenness were
 associated positively with temperature, and negatively with disturbance.
 However, the interaction among temperature, precipitation and disturbance
 shaped species richness and evenness. The effect was manifested through a
 failure of species richness to increase substantially with temperature in
 transformed habitats at low precipitation. At low precipitation levels,
 evenness increased with temperature in undisturbed sites, peaked at medium
 temperatures in disturbed sites and remained low in transformed sites. In
 warmer climates with lower rainfall, the effects of increasing disturbance
 on species richness and evenness were akin to decreases in temperature of
 up to 9°C. Anthropogenic disturbance and ongoing climate change may
 interact in complicated ways to shape the structure of assemblages, with
 hot, arid environments likely to be at greatest risk.
description: Ant assemblage species
 richness and PIEThis data file includes
 details of species richness and PIE from pitfall-trapped ant assemblages
 across the globe. The data includes the following information for 1128
 assemblages: Locality_ID - A unique code for each locality; Source -
 Details of reference source for each dataset; Cluster - Geographic cluster
 used as a random factor in analyses; Latitude - Latitude provided by
 authors; Longitude - Longitude provided by authors; Mean annual
 temperature - Derived from WorldClim; Total annual precipitation - Derived
 from WorldClim; Temperature range - Derived from WorldClim; Disturbance -
 Disturbance described by authors; Hemisphere - Derived from Latitude;
 Continent - Continent provided by authors; Pitfall days - Number of
 pitfalls multiplied by trapping days; Transect length - Distance from
 first to last trap in transect; Species richness - Total number of species
 collected; PIE - Probability of Interspecific Encounter, a measure of
 species evenness. Further details are provided in the
 paper.Data
 appendix.xlsx
DOI: 10.5061/dryad.8dg19
title: Data from: The fitness effect of mutations across environments: Fisher’s geometrical model with multiple optima

description: When are mutations beneficial in one environment and deleterious in
 another? More generally, what is the relationship between mutation effects
 across environments? These questions are crucial to predict adaptation in
 heterogeneous conditions in a broad sense. Empirical evidence documents
 various patterns of fitness effects across environments but we still lack
 a framework to analyse these multivariate data. In this paper, we extend
 Fisher’s geometrical model to multiple environments determining distinct
 peaks. We derive the fitness distribution, in one environment, among
 mutants with a given fitness in another and the bivariate distribution of
 random mutants’ fitnesses across two or more environments. The geometry of
 the phenotype-fitness landscape is naturally interpreted in terms of
 fitness trade-offs between environments. These results may be used to
 fit/predict empirical distributions or to predict the pattern of
 adaptation across heterogeneous conditions. As an example, we derive the
 genomic rate of substitution and of adaptation in a metapopulation divided
 into two distinct habitats in a high migration regime and show that they
 depend critically on the geometry of the phenotype-fitness landscape. --
description: Analytical derivations
 FINALWolfram Mathematica
 notebook containing all analytical derivations from the article: mostly
 moment generating functions of the ditributions and their stochastic
 representations and moments.Simulation
 ChecksThis is a mathematica
 notebook containing the code for the simulation check of all results in
 the article, and generating figures disclosed in the
 article.Simulation_checks.nb