cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.47d7wm3b6
title: Data from: Evidence for spatial clines and mixed geographic modes of speciation for North American cherry-infesting Rhagoletis (Diptera:Tephritidae) flies

description: An important criterion for understanding speciation is the geographic
 context of population divergence. Three major modes of allopatric,
 parapatric, and sympatric speciation define the extent of spatial overlap
 and gene flow between diverging populations. However, mixed modes of
 speciation are also possible, whereby populations experience periods of
 allopatry, parapatry, and/or sympatry at different times as they diverge.
 Here, we report clinal patterns of variation for 21 nuclear-encoded
 microsatellites and a wing spot phenotype for cherry-infesting Rhagoletis
 (Diptera: Tephritidae) across North America consistent with these flies
 having initially diverged in parapatry followed by a period of allopatric
 differentiation in the early Holocene. However, mitochondrial DNA (mtDNA)
 displays a different pattern; cherry flies at the ends of the clines in
 the eastern USA and Pacific Northwest share identical haplotypes, while
 centrally located populations in the southwestern USA and Mexico possess a
 different haplotype. We hypothesize that the mitochondrial difference
 could be due to lineage sorting but more likely reflects a selective sweep
 of a favorable mtDNA variant or the spread of an endosymbiont. The
 estimated divergence time for mtDNA suggests possible past allopatry,
 secondary contact, and subsequent isolation between USA and Mexican fly
 populations initiated before the Wisconsin glaciation. Thus, the current
 genetics of cherry flies may involve different mixed modes of divergence
 occurring in different portions of the fly’s range. We discuss the need
 for additional DNA sequencing and quantification of prezygotic and
 postzygotic reproductive isolation to verify the multiple mixed mode
 hypothesis for cherry flies, and draw parallels from other systems to
 assess the generality that speciation may commonly involve complex
 biogeographies of varying combinations of allopatric, parapatric, and
 sympatric divergence.
description: A total of 364 adult flies from populations 1-15 (Fig. 1a; Table
 S1) were genotyped for 21 microsatellite loci (see Supplemental Methods
 for details). References for primers and conditions used for PCR
 amplification can be found in Maxwell et al. (2013) and Michel et al.
 (2010). Genotyping was performed as described in Saint Jean et al. (2018),
 with size standards included in each genotyper run, as well as
 representative eastern <i>R. cingulata </i>and western
 <i>R. indifferens</i>, to ensure that alleles were properly
 aligned and comparably scored.
description: <strong>CingIndBiogeo.str</strong><br> A
 STRUCTURE file containing called microsatellite genotyopes for all
 364 <em>Rhagoletis cingulata </em>and <i>Rhagoletis
 indifferens</i> individuals.
 <strong>CingIndBiogeoREADME.csv</strong><br> A
 csv file linking the site numbers from the manuscript to the site codes
 used in the STRUCTURE file.
DOI: 10.5061/dryad.m0cfxpp1n
title: More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast

description: Different mating systems can strongly affect the extent of genetic
 diversity and population structure among species. Given the increased
 effects of genetic drift on reduced population size, theory predicts that
 species undergoing self-fertilization should have greater population
 structure than outcrossed species, however demographic dynamics may affect
 this scenario. The mangrove killifish clade is composed of the two only
 known examples of self-fertilising species among vertebrates (Kryptolebias
 marmoratus and K. hermaphroditus). A third species in this clade, K.
 ocellatus, inhabits mangrove forests in southeast Brazil, however its
 mating system and patterns of genetic structure have been rarely explored.
 Here, we examined the genetic structure and phylogeographic patterns of K.
 ocellatus along its distribution, using mitochondrial DNA and
 microsatellites to compare its patterns of genetic structure with the
 predominantly selfing and often syntopic, K. hermaphroditus. Our results
 indicate that K. ocellatus reproduces mainly by outcrossing across much of
 its known range, with no current evidence of selfing, despite being an
 androdioecious species. Our results also reveal a stronger population
 subdivision in K. ocellatus compared to K. hermaphroditus, contrary to the
 theoretical predictions based on reproductive biology of the two species.
 Our findings indicate that, although morphologically similar, K. ocellatus
 and K. hermaphroditus had remarkably different evolutionary histories when
 colonising the same mangrove areas in south-eastern Brazil, with other
 factors (e. g. time of colonisation, dispersal/establishment capacity)
 having more profound effects on the current population structuring of
 those species than differences in mating systems.
description: All details about fish collection, mtDNA amplification and
 genotyping are described in the main body of the manuscript.
DOI: 10.5281/zenodo.18395509
title: Forensic Audit of Laniakea Bulk Flow: Resolving the 3.4σ Discrepancy via Torsional Pressure Gradients

description: Standard \LambdaCDM cosmology currently faces a "Bulk Flow Crisis," characterized by a 3.4\sigma velocity excess toward the Shapley Attractor that exceeds the gravitational potential of observable and dark matter. This paper presents a forensic audit of Cosmicflows-4 data using the Manticore-Local digital twins. We demonstrate that this velocity excess is not a product of missing mass, but of Geometric Pressure (\rho_{geo}) within a Torsional Medium.

By mapping velocity streamlines, we identify a logarithmic spiral growth factor precisely aligned with the Golden Ratio (\phi \approx 1.618). This \phi-gradient represents the path of least resistance for energy dissipation following black hole merger events (0.77 \text{ M}_\odot deficit). The model is further validated by "Neutrino Shadows"—differential lensing anomalies detected by IceCube in Jan 2026—confirming a medium with measurable torsional viscosity. We propose that the Shapley Concentration is not a mass-dense "object" but a high-pressure node in a universal Torsional Lattice.
DOI: 10.5281/zenodo.18395508
title: Forensic Audit of Laniakea Bulk Flow: Resolving the 3.4σ Discrepancy via Torsional Pressure Gradients

description: Standard \LambdaCDM cosmology currently faces a "Bulk Flow Crisis," characterized by a 3.4\sigma velocity excess toward the Shapley Attractor that exceeds the gravitational potential of observable and dark matter. This paper presents a forensic audit of Cosmicflows-4 data using the Manticore-Local digital twins. We demonstrate that this velocity excess is not a product of missing mass, but of Geometric Pressure (\rho_{geo}) within a Torsional Medium.

By mapping velocity streamlines, we identify a logarithmic spiral growth factor precisely aligned with the Golden Ratio (\phi \approx 1.618). This \phi-gradient represents the path of least resistance for energy dissipation following black hole merger events (0.77 \text{ M}_\odot deficit). The model is further validated by "Neutrino Shadows"—differential lensing anomalies detected by IceCube in Jan 2026—confirming a medium with measurable torsional viscosity. We propose that the Shapley Concentration is not a mass-dense "object" but a high-pressure node in a universal Torsional Lattice.
DOI: 10.5061/dryad.nvx0k6dqb
title: Minimum habitat thresholds required for conserving mountain lion genetic diversity

description: Jointly considering the ecology (e.g., habitat use) and genetics (e.g.,
 population genetic structure and diversity) of a species can increase
 understanding of current conservation status and inform future management
 practices. Previous analyses indicate that mountain lion (Puma concolor)
 populations in California are genetically structured and exhibit extreme
 variation in population genetic diversity. Although human development may
 have fragmented gene flow, we hypothesized the quantity and quality of
 remaining habitat available would affect the genetic viability of each
 population. Our results indicate that area of suitable habitat, determined
 via a resource selection function derived using 843,500 location fixes
 from 263 radio-collared mountain lions, is strongly and positively
 associated with population genetic diversity and viability metrics,
 particularly with effective population size. Our results suggested that
 contiguous habitat of ≥ 10,000 km2 may be sufficient to alleviate the
 negative effects of genetic drift and inbreeding, allowing mountain lion
 populations to maintain suitable effective population sizes. Areas
 occupied by five of the nine geographic–genetic mountain lion populations
 in California fell below this habitat threshold, and two (Santa Monica
 Area and Santa Ana) of those five populations lack connectivity to nearby
 populations. Enhancing ecological conditions by protection of greater
 areas of suitable habitat and facilitating positive evolutionary processes
 by increasing connectivity (e.g., road crossing structures) might promote
 persistence of small or isolated populations. The conservation status of
 suitable habitat also appeared to influence genetic diversity of
 populations. Thus, our results demonstrate that both the area and status
 (i.e., protected or unprotected) of suitable habitat influence the genetic
 viability of mountain lion populations.
description: Data was taken from two previous publications. Habitat data was
 derived by clipping raster layers of suitable habitat from Dellinger et
 al. 2020 with geographic distribution of the panmictic mountain lion
 populations in California: Dellinger, J.A.,
 et al. 2020. Using mountain lion habitat selection in management. – J.
 Wildlife Manage. 84:359-371. Gustafson, K. D., et al.
 2019. Genetic source-sink dynamics among naturally structured and
 anthropogenically fragmented puma populations. – Conserv. Genet. 20:
 215-227.
description: These data are best understood with the aid of corresponding GIS
 layers for mountain lion population genetics and habitat use patterns in
 California. Please contact justin.dellinger@wildlife.ca.gov to obtain
 these layers.
DOI: 10.15468/dl.ghu87h
title: Occurrence Download

description: A dataset containing 1344 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Petalura gigantea"
 ]
}

 The dataset includes 1344 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002504-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6djh9w0zh
title: Data from: Morphological disparity in the evolution of the ophthalmosaurid forefin: new clues from the Upper Jurassic of Argentina

description: Jurassic and Cretaceous marine deposits worldwide depict ophthalmosaurid
 ichthyosaurs as major components of marine tetrapod communities for almost
 76 million years. One of the major features characterising this clade is
 the complexity and diversity of their stylopodium-zeugopodium morphology.
 Late Jurassic deposits of the Vaca Muerta Formation in northwest Patagonia
 (Argentina) have yielded the richest Tithonian ophthalmosaurid records
 from Gondwana. Here, we present a new ophthalmosaurid from this
 lithostratigraphic unit, Sumapalla argentina gen. et sp. nov., recognized
 based on several unique features of the skull roof, forefin, scapular, and
 pelvic girdles. Phylogenetic analysis recovered it as a basal member of
 Platypterygiinae. The peculiar morphology of the forefin of the new taxon
 illustrates a previously unnoticed morphological diversity in the
 ophthalmosaurid appendicular skeleton and provides an excellent
 opportunity to test its range of variation. For this purpose, we
 implemented a holistic approach, using 2D geometric morphometric analysis
 focused on the humerus and disparity analysis of the zeugopodium. Our
 results reveal a long duration of one humeral morphotype characterizing
 Arthropterygius spp. and closely related taxa. Furthermore, we found a
 peak of zeugopodial disparity occurred during the Kimmeridgian, followed
 by a decrease by the end of the Jurassic, and then a recovery by the Early
 Cretaceous.
DOI: 10.5061/dryad.k6djh9w4s
title: Phylogeographic analysis of character displacement in feeding phenotypes of snail-feeding Acoptolabrus ground beetles: Morphological measurements

description: Ecological character displacement predicts that interspecific resource
 competition results in greater trait divergence between species in
 sympatry than in allopatry. In this study, we characterize character
 displacement in 8 species of
 snail-feeding Acoptolabrus ground beetles (Coleoptera,
 Carabidae, genus Carabus) in the Far
 East. Acoptolabrus exhibit divergent feeding phenotypes,
 including species with a slender forebody for intruding large shells and
 species with stout heads and mandibles for crushing small
 shells. Distance measurements (in mm) deposited here
 are for evaluating body shape variation among 8 Acoptolabrus
 species.
description: To evaluate morphological divergence among taxa, vertical and
 horizontal distances of the head (VH and HH), prothorax (VP and HP), and
 elytra (VE and HE) of adult beetles (Konuma and Chiba 2007) were measured
 to the nearest 0.01 mm on digital images of dried specimens using ImageJ
 ver. 1.49m (Schneider et al. 2012).
description: The measurement unit is in millimeter.
DOI: 10.6078/d1gt4d
title: Data from: Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients

description: Uncovering the genetic basis of local adaptation is a major goal of
 evolutionary biology and conservation science alike. In an era of climate
 change, an understanding of how environmental factors shape adaptive
 diversity is crucial to predicting species response and directing
 management. Here, we investigate patterns of genomic variation in giant
 sequoia, an iconic and ecologically important tree species, using
 1364 bi-allelic single nucleotide polymorphisms (SNPs). We use
 an FST outlier test and two genotype-environment
 association methods, latent factor mixed models (LFMM) and redundancy
 analysis (RDA), to detect complex signatures of local adaptation. Results
 indicate 79 genomic regions of potential adaptive importance, with limited
 overlap between the detection methods. Of the 58 loci detected by LFMM, 51
 showed strong correlations to a precipitation driven composite variable
 and seven to a temperature-related variable. RDA revealed 24 outlier loci
 with association to climate variables, all of which showed strongest
 relationship to summer precipitation. Nine candidate loci were indicated
 by two methods. After correcting for geographic distance, RDA models using
 climate predictors accounted for 49% of the explained variance and showed
 significant correlations between SNPs and climatic factors. Here, we
 present evidence of local adaptation in giant sequoia along gradients of
 precipitation and provide a first step towards identifying genomic regions
 of adaptive significance. The results of this study will provide
 information to guide management strategies that seek to maximize adaptive
 potential in the face of climate change.
DOI: 10.15468/dl.qggrmv
title: Occurrence Download

description: A dataset containing 4148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calliandra houstoniana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 4148 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002503-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ngf1vhhrw
title: Cellular bicarbonate accumulation and vesicular proton transport promote calcification in the sea urchin larva

description: The sea urchin embryo develops a calcitic endoskeleton through
 intracellular formation of amorphous calcium carbonate (ACC).
 Intracellular precipitation of ACC, requires HCO3-/CO32- concentrating as
 well as proton export mechanisms to promote calcification. These processes
 are of fundamental importance in biological mineralization, but remain
 largely unexplored. Here we demonstrate that the calcifying primary
 mesenchyme cells (PMCs) utilize Na+/H+- exchange (NHE) mechanisms to
 control cellular pH homeostasis during maintenance of the skeleton. During
 skeleton re-calcification, pHi of PMCs is increased accompanied by
 substantial elevations in intracellular [HCO3-] mediated by the
 Na+/HCO3-cotransporter Sp-Slc4a10. However, PMCs lower their pHi
 regulatory capacities associated with a reduction in NHE activity.
 Live-cell imaging using GFP reporter constructs in combination with
 intra-vesicular pH measurements demonstrated alkaline and acidic
 populations of vesicles in PMCs and extensive trafficking of large V-type
 H+-ATPase (VHA)-rich acidic vesicles in blastocoelar filopodial cells
 (BFCs). Pharmacological and gene expression analyses underline a central
 role of the VHA isoforms Sp-ATP6V0a1, Sp-ATP6V01_1 and Sp-ATPa1-4 for the
 process of skeleton re-calcification. These results highlight novel pH
 regulatory strategies in calcifying cells of a marine species with
 important implications for our understanding of the mineralization process
 in times of rapid changes in oceanic pH.
DOI: 10.5061/dryad.d2547d81c
title: Dataset - A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress

description: Plant immunity is often negatively impacted by heat stress. However, the
 underlying molecular mechanisms remain poorly characterized. Based on a
 genome-wide association mapping approach, this study aims to identify in
 Arabidopsis thaliana the genetic bases of robust resistance mechanisms to
 the devastating pathogen Ralstonia solanacearum under heat stress. A local
 mapping population was phenotyped against the R. solanacearum GMI1000
 strain at 27 and 30 °C. To obtain a precise description of the genetic
 architecture underlying natural variation of quantitative disease
 resistance (QDR), we applied a genome-wide local score analysis. Alongside
 an extensive genetic variation found in this local population at both
 temperatures, we observed a playful dynamics of quantitative trait loci
 along the infection stages. In addition, a complex genetic network of
 interacting loci could be detected at 30 °C. As a first step to
 investigate the underlying molecular mechanisms, the atypical meiotic
 cyclin SOLO DANCERS gene was validated by a reverse genetic approach as
 involved in QDR to R. solanacearum at 30 °C. In the context of climate
 change, the complex genetic architecture underlying QDR under heat stress
 in a local mapping population revealed candidate genes with diverse
 molecular functions.
description: How this dataset was collected and how it has been processed have
 been precisely described in the Material & Methods section of the
 article.
DOI: 10.5061/dryad.xsj3tx9cm
title: Neural population dynamics in motor cortex are different for reach and grasp

description: Low-dimensional linear dynamics are observed in neuronal population
 activity in primary motor cortex (M1) when monkeys make reaching
 movements. This population-level behavior is consistent with a role for M1
 as an autonomous pattern generator that drives muscles to give rise to
 movement. In the present study, we examine whether similar dynamics are
 also observed during grasping movements, which involve fundamentally
 different patterns of kinematics and muscle activations. Using a variety
 of analytical approaches, we show that M1 does not exhibit such dynamics
 during grasping movements. Rather, the grasp-related neuronal dynamics in
 M1 are similar to their counterparts in somatosensory cortex, whose
 activity is driven primarily by afferent inputs rather than by intrinsic
 dynamics. The basic structure of the neuronal activity underlying hand
 control is thus fundamentally different from that underlying arm
 control.Low-dimensional linear dynamics are observed in neuronal
 population activity in primary motor cortex (M1) when monkeys make
 reaching movements. This population-level behavior is consistent with a
 role for M1 as an autonomous pattern generator that drives muscles to give
 rise to movement. In the present study, we examine whether similar
 dynamics are also observed during grasping movements, which involve
 fundamentally different patterns of kinematics and muscle activations.
 Using a variety of analytical approaches, we show that M1 does not exhibit
 such dynamics during grasping movements. Rather, the grasp-related
 neuronal dynamics in M1 are similar to their counterparts in somatosensory
 cortex, whose activity is driven primarily by afferent inputs rather than
 by intrinsic dynamics. The basic structure of the neuronal activity
 underlying hand control is thus fundamentally different from that
 underlying arm control.
description: Details of the collection of this dataset and its pre-processing
 are given in the eLife publication that it will accompany.
description: Details of the dataset and its structure are given in the
 ReadMe.md file included with the dataset.