cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8p6m07g
title: Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids

description: The genetic basis of parallel evolution of similar species is of great
 interest in evolutionary biology. In the adaptive radiation of Lake
 Victoria cichlid fishes, sister species with either blue or red-back male
 nuptial coloration have evolved repeatedly, often associated with
 shallower and deeper water, respectively. One such case are blue and
 red-backed Pundamilia species, for which we recently showed that a young
 species pair may have evolved through “hybrid parallel speciation”.
 Coalescent simulations suggested that the older species P. pundamilia
 (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new
 “nyererei-like” and “pundamilia-like” species evolved from the admixed
 population. Here, we use genome scans to study the genomic architecture of
 differentiation, and assess the influence of hybridization on the
 evolution of the younger species pair. For each of the two species pairs,
 we find over 300 genomic regions, widespread across the genome, which are
 highly differentiated. A subset of the most strongly differentiated
 regions of the older pair are also differentiated in the younger pair.
 These shared differentiated regions often show parallel allele frequency
 differences, consistent with the hypothesis that admixture-derived alleles
 were targeted by divergent selection in the hybrid population. However,
 two thirds of the genomic regions that are highly differentiated between
 the younger species are not highly differentiated between the older
 species, suggesting independent evolutionary responses to selection
 pressures. Our analyses reveal how divergent selection on
 admixture-derived genetic variation can facilitate new speciation events.
description: Candidate regions of
 parallel selection on admixture variationThe 41 shared highly
 divergent regions (SHDRs) that group the species by male nuptial
 coloration and are thus candidates of parallel selection. The genes in the
 vicinity of the regions are shown above. The Fst values between the older
 species at Makobe Island and between the younger species at Python Island
 are shown in windows of 15 SNPs. Windows that the HMM approach assigned to
 the high differentiation state are shown with red or orange color. The
 next row shows excess allele sharing (fd) in windows of 20 kb. Windows
 that have a TWISST weight of the color topology &gt;0.66 are indicated in
 black. The next rows show the mean nucleotide diversity, dxy, difference
 in nucleotide diversity, extended haplotype length (EHL) statistics,
 Tajima's D and the recombination rate.parallel_shdr_selInfo_fullListOfGenes.pdfCandidate regions of parallel selection on admixture variationbed file indicating the locations of the candidate regions of parallel selection on admixture variationshdr_parallel_selection_regions.bed
DOI: 10.15468/dl.57g278
title: Occurrence Download

description: A dataset containing 93213 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "Year is greater than or equal to 2010",
 "Continent is Europe",
 "TaxonKey is Trollius europaeus",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 93213 records from 339 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001707-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k6k42cq
title: Data from: White matter lesions: spatial heterogeneity, links to risk factors, cognition, genetics, atrophy

description: Objectives: To investigate spatial heterogeneity of white matter lesions
 or hyperintensities (WMH). Methods: MRI scans of 1836 participants (median
 age 52.2±13.16) encompassing a wide age range (22–84 years) from the
 cross-sectional Study of Health in Pomerania (SHIP, Germany) were included
 as discovery set identifying spatially distinct components of WMH using a
 structural covariance approach. Scans of 307 participants (median age
 73.8±10.2, with 747 observations) from the Baltimore Longitudinal Study of
 Aging (BLSA, USA) were included to examine differences in longitudinal
 progression of these components. The associations of these components with
 vascular risk factors, cortical atrophy, Alzheimer’s disease (AD) genetics
 and cognition were then investigated using linear regression. Results: WMH
 were found to occur non-uniformly, with higher frequency within spatially
 heterogeneous patterns encoded by four components, which were consistent
 with common categorizations of deep and periventricular WMH, while further
 dividing the latter into posterior, frontal and dorsal components.
 Temporal trends of the components differed both cross-sectionally and
 longitudinally. Frontal periventricular WMH were most distinctive as they
 appeared in the 5th decade of life, whereas the other components appeared
 later in life during the 6th decade. Furthermore, frontal WMH were
 associated with systolic blood pressure and with pronounced atrophy
 including AD-related regions. AD polygenic risk score was associated with
 the dorsal periventricular component in elderly. Cognitive decline was
 associated with the dorsal component. Conclusions: These results support
 the hypothesis that the appearance of WMH follows age and
 disease-dependent regional distribution patterns, potentially influenced
 by differential underlying pathophysiological mechanisms, and possibly
 with a differential link to vascular and neurodegenerative changes.
description: Online Supplementary
 MaterialsDryad Online
 Supplementary Materials with supplementary tables: Table.e-1, Table.e-2,
 Table.e-3, Table.e-4, Table.e-5, Table.e-6, Table.e-7, Table.e-8, and
 supplementary figures Figure.e-1, Figure.e-2, Figure.e-3, Figure.e-4 ,
 Figure.e-5, Figure.e-6, Figure.e-7 and supplementary sections Section.e-1,
 Section.e-2, Section.e-3, Section.e-4, Section.e-5, Section.e-6,
 Section.e-7, Section.e-8, Section.e-9, Section.e-10Habes_et_al_2018_NEUROLOGY_Accepted_SuppMat.docx
DOI: 10.5061/dryad.g7v1b
title: Data from: A framework for resolving cryptic species: a case study from the lizards of the Australian Wet Tropics

description: As we collect range-wide genetic data for morphologically-defined species,
 we increasingly unearth evidence for cryptic diversity. Delimiting this
 cryptic diversity is challenging, both because the divergences span a
 continuum and because the lack of overt morphological differentiation
 suggests divergence has proceeded heterogeneously. Here, we address these
 challenges as we diagnose and describe species in three co-occurring
 species groups of Australian lizards. By integrating genomic and
 morphological data with data on hybridization and introgression from
 contact zones, we explore several approaches – and their relative benefits
 and weaknesses – for testing the validity of cryptic lineages. More
 generally, we advocate that genetic delimitations of cryptic diversity
 must consider whether these lineages are likely to be durable and
 persistent through evolutionary time.
description: Supplementary
 InformationSinghal_etal_CrypticLineagesAWT_SI_v6.pdfAppendix 1: Taxonomic revisions of the species groupsSinghal_etal_CrypticLineagesAWT_appendix_v6.pdfPseudo-Reference Genomes (PRGs)PRG.tar.gz: a tarred, gzipped directory of the pseudo-reference genomes (PRGs) for each lineage included in the study.PRG.tar.gzVariant Calls (VCFs)VCFs.tar.gz: a tarred, gzipped directory of variant calls (VCFs) for each lineage included in the study - VCFs are filtered with respect to coverage & quality as reported in text - VCFs are phased - this includes both variant and invariant sitesVCFs.tar.gz
DOI: 10.5061/dryad.gs340
title: Data from: The skull and endocranium of a Lower Jurassic ichthyosaur based on digital reconstructions

description: Even after 200 years of study, some details of the cranial anatomy of
 ichthyosaurs, one of the most successful groups of marine vertebrates in
 the Mesozoic, are still unclear. New information on the braincase, palate
 and occiput are provided from three-dimensional scans of an exceptionally
 preserved ichthyosaur (‘Hauffiopteryx’ typicus) skull from the Toarcian
 (183–174 Ma, Lower Jurassic) of Strawberry Bank, England. This ichthyosaur
 has unusual, hollow, tubular hyoid bars. The occipital and braincase
 region is fully reconstructed, creating the first digital cranial endocast
 of an ichthyosaur. Enlarged optic lobes and an enlarged cerebellum suggest
 neuroanatomical adaptations that allowed it to be a highly mobile, visual
 predator. The olfactory region also appears to be enlarged, suggesting
 that olfaction was more important for ichthyosaurs than has been assumed.
 Phylogenetic analysis suggests this ichthyosaur is closely related to, but
 distinct from, Hauffiopteryx, and positioned within Thunnosauria, a more
 derived position than previously recovered. These results further our
 knowledge of ichthyosaur cranial anatomy in three dimensions and provide a
 platform in which to study the anatomical adaptations that allowed
 ichthyosaurs to dominate the marine realm during the Mesozoic
description: Phylogenetic
 detailsOverview of methods of
 phylogenetic analysis, character choice, and results of the
 analysis.Mareketal2015-supplement.docx
DOI: 10.5061/dryad.h0v84
title: Data from: Comparing macroecological patterns across continents: evolution of climatic niche breadth in varanid lizards

description: Macroecological analyses often test hypotheses at the global scale, or
 among more closely related species in a single region (e.g. continent).
 Here, we test several hypotheses about climatic niche widths among
 relatively closely related species that occur across multiple continents,
 and compare patterns within and across continents to see if they differ.
 We focus on the lizard genus Varanus (monitor lizards), which occurs in
 diverse environments in Africa, Asia, and Australia. We address three main
 questions. (1) How do climatic niche breadths of species on a given niche
 axis change based on the position of species along that niche axis? (e.g.
 are species that occur in more extreme environments more narrowly
 specialized for those conditions?) (2) Are there trade-offs in niche
 breadths on temperature and precipitation axes among species, or are niche
 widths on different axes positively related? (3) Is variation in niche
 breadths among species explained primarily by within-locality seasonal
 variation, or by differences in climatic conditions among localities
 across the species range? We generate a new time-calibrated phylogeny for
 Varanus and test these hypotheses within and between continents using
 climatic data and phylogenetic methods. Our results show that patterns on
 each continent often parallel each other and global patterns. However, in
 many other cases, the strength of relationships can change dramatically
 among closely related species on different continents. Overall, we found
 that: (1) species in warmer environments have narrower temperature niche
 breadths, but there is no relationship between precipitation niche breadth
 and niche position; (2) temperature and precipitation niche breadths tend
 to be positively related among species, rather than showing trade-offs;
 (3) within-locality seasonal variation explains most variation in climatic
 niche breadths. Some of these results are concordant with previous studies
 (in amphibians and North American lizards), and might represent general
 macroecological patterns.
description: Ecography
 data
DOI: 10.15468/fm2v67
title: University of North Carolina Asheville

description: The UNCA Fungarium was started in 2022 by Dr. Jonathan Horton and his undergraduate research student, Ari Puentes. The collection focuses on fleshy fungi of the southern Appalachians, particularly western North Carolina. As the Fungarium grows it will include voucher specimens from Dr. Horton and his students' research, as well as contributed specimens from students in his Mycology course and members of the Asheville Mushroom Club.  The goal is to have DNA bar codes for specimens, especially ectomycorrhizal species.
DOI: 10.5061/dryad.q39k3
title: Data from: Multi-speed genome diploidization and diversification after an ancient allopolyploidization

description: Hybridization and genome doubling (allopolyploidy) have led to
 evolutionary novelties as well as to the origin of new clades and species.
 Despite the importance of allopolyploidization, the dynamics of
 post-polyploid diploidization (PPD) at the genome level has been only
 sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17
 genera and c. 56 species endemic to Australia and New Zealand. Our
 phylogenetic and cytogenomic analyses revealed that MICR originated via an
 inter-tribal hybridization between ancestors of Crucihimalayeae (n = 8;
 maternal genome) and Smelowskieae (n = 7; paternal genome), both native to
 the Northern Hemisphere. The reconstructed ancestral allopolyploid genome
 (n = 15) originated probably in north-eastern Asia or western North
 America during the Late Miocene (c. 10.6 - 7 million years ago) and
 reached the Australian mainland via long-distance dispersal. In Australia,
 the allotetraploid genome diverged into at least three main subclades
 exhibiting different levels of PPD and diversity: 1.25-fold descending
 dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial
 Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial
 Pachycladon (11 spp.), and 2.1 to 3.75-fold DD of n = 15 → n = 7 - 4 in
 the largely annual crown group genera (42 spp. in 15 genera). These
 results are among the first to demonstrate multi-speed genome evolution in
 taxa descending from a common allopolyploid ancestor. It is suggested that
 clade-specific PPD can operate at different rates and efficacies, and can
 be tentatively linked to life histories and the extent of taxonomic
 diversity.
description: CHS_alignmentMultiple alignment of CHS gene.ndhF_alignmentMultiple alignment of ndhF gene.PHYA_alignmentMultiple alignment of PHYA gene.
DOI: 10.5061/dryad.t9r3g
title: Data from: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

description: Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic
 studies owing in part to their ubiquity throughout the genome and ease of
 collection. Restriction site associated DNA sequencing (RADseq) methods
 are becoming increasingly popular for SNP data collection, but an
 assessment of the best practises for using these data in phylogenetics is
 lacking. We use computer simulations, and new double digest RADseq
 (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the
 accuracy of RAD loci for phylogenetic inference. We compare the two
 primary ways RAD loci are used during phylogenetic analysis, including the
 analysis of full sequences (i.e., SNPs together with invariant sites), or
 the analysis of SNPs on their own after excluding invariant sites. We find
 that using full sequences rather than just SNPs is preferable from the
 perspectives of branch length and topological accuracy, but not of
 computational time. We introduce two new acquisition bias corrections for
 dealing with alignments composed exclusively of SNPs, a conditional
 likelihood method and a reconstituted DNA approach. The conditional
 likelihood method conditions on the presence of variable characters only
 (the number of invariant sites that are unsampled but known to exist is
 not considered), while the reconstituted DNA approach requires the user to
 specify the exact number of unsampled invariant sites prior to the
 analysis. Under simulation, branch length biases increase with the amount
 of missing data for both acquisition bias correction methods, but branch
 length accuracy is much improved in the reconstituted DNA approach
 compared to the conditional likelihood approach. Phylogenetic analyses of
 the empirical data using concatenation or a coalescent-based species tree
 approach provide strong support for many of the accepted relationships
 among phrynosomatid lizards, suggesting that RAD loci contain useful
 phylogenetic signal across a range of divergence times despite the
 presence of missing data. Phylogenetic analysis of RAD loci requires
 careful attention to model assumptions, especially if downstream analyses
 depend on branch lengths.
description: SupplementMaterialsSupplemental model description, tables, and figures.Concatenated RAD loci for phrynosomatid lizardsConcatenated RAD loci for phrynosomatid lizards in phylip format for analyses in RAxML. Includes the full data, SNPs only, partition information files, and output from RAxML analyses.data_1.zip
DOI: 10.5061/dryad.j42m7
title: Data from: Global effects of soil and climate on leaf photosynthetic traits and rates

description: Aim: The influence of soil properties on photosynthetic traits in higher
 plants is poorly quantified in comparison with that of climate. We address
 this situation by quantifying the unique and joint contributions to global
 leaf-trait variation from soils and climate. Location: Terrestrial
 ecosystems world-wide. Methods: Using a trait dataset comprising 1509
 species from 288 sites, with climate and soil data derived from global
 datasets, we quantified the effects of 20 soil and 26 climate variables on
 light-saturated photosynthetic rate (Aarea), stomatal conductance (gs),
 leaf nitrogen and phosphorus (Narea and Parea) and specific leaf area
 (SLA) using mixed regression models and multivariate analyses. Results:
 Soil variables were stronger predictors of leaf traits than climatic
 variables, except for SLA. On average, Narea, Parea and Aarea increased
 and SLA decreased with increasing soil pH and with increasing site
 aridity. gs declined and Parea increased with soil available P (Pavail).
 Narea was unrelated to total soil N. Joint effects of soil and climate
 dominated over their unique effects on Narea and Parea, while unique
 effects of soils dominated for Aarea and gs. Path analysis indicated that
 variation in Aarea reflected the combined independent influences of Narea
 and gs, the former promoted by high pH and aridity and the latter by low
 Pavail. Main conclusions: Three environmental variables were key for
 explaining variation in leaf traits: soil pH and Pavail, and the climatic
 moisture index (the ratio of precipitation to potential
 evapotranspiration). Although the reliability of global soil datasets lags
 behind that of climate datasets, our results nonetheless provide
 compelling evidence that both can be jointly used in broad-scale analyses,
 and that effects uniquely attributable to soil properties are important
 determinants of leaf photosynthetic traits and rates. A significant future
 challenge is to better disentangle the covarying physiological, ecological
 and evolutionary mechanisms that underpin trait–environment relationships.
description: photosynthesis_trait_worldwideThe file includes: A legend sheet with all variables and their description. A data sheet including trait data (SLA, Nmass, Pmass, Amass, Narea, Parea, Aarea, gs) associated with soil and climate variables which derived (except for annual precipitation and temperature) from worldwide soil and climate datasets Trait data were collated from sources listed in 'references' sheet and in Wright et al 2004 Nature.globamax_data_160609 (for GEB ms).xlsx
DOI: 10.5285/48d0bf43-0598-ceb2-e063-7086abc062f1
title: Atlantic meridional overturning circulation observed by the RAPID-MOCHA-WBTS (RAPID-Meridional Overturning Circulation and Heatflux Array-Western Boundary Time Series) array at 26N from 2004 to 2024 (v2024.1a).

description: The RAPID-MOCHA-WBTS (RAPID-Meridional Overturning Circulation and Heatflux Array-Western Boundary Time Series) programme has produced a continuous time series of the Atlantic Meridional Overturning Circulation (AMOC) at 26N that started in April 2004. This release of the time series covers the period from April 2004 to March 2024. The 26N AMOC time series is derived from measurements of temperature, salinity, pressure and water velocity from an array of moored instruments that extend from the east coast of the Bahamas to the continental shelf off Africa east of the Canary Islands. The AMOC calculation also uses estimates of the transport in the Florida Strait derived from sub-sea cable measurements calibrated by regular hydrographic cruises. The component of the AMOC associated with the wind driven Ekman layer is derived from ERA5 reanalysis. This release of the data includes a document with a brief description of the calculation of the AMOC time series and references to more detailed description in published papers. The 26N AMOC time series and the data from the moored array are curated by the British Oceanographic Data Centre (BODC). The RAPID-MOCHA-WBTS programme is a joint effort between NERC in the UK (Principle Investigator Ben Moat since 2021, Eleanor Frajka-Williams from 2020 to 2021, David Smeed from 2012 to 2020, and Stuart Cunningham from 2004 to 2012), NOAA (PIs Ryan Smith and Denis Volkov) and NSF (PIs Prof. Bill Johns and Prof. Shane Elipot, Uni. Miami) in the USA.
DOI: 10.5067/asdc/firexaq_analysis_data_1
title: FIREX-AQ Analysis and Supplementary Data
DOI: 10.5067/asdc/firexaq_aerosol_aircraftinsitu_dc8_data_1
title: FIREX-AQ DC-8 In-Situ Aerosol Data
DOI: 10.5061/dryad.gs7j4
title: Data from: Unlinked Mendelian inheritance of red and black pigmentation in snakes: implications for Batesian mimicry

description: Identifying the genetic basis of mimetic signals is critical to
 understanding both the origin and dynamics of mimicry over time. For
 species not amenable to large laboratory breeding studies, widespread
 color polymorphism across natural populations offers a powerful way to
 assess the relative likelihood of different genetic systems given observed
 phenotypic frequencies. We classified color phenotype for 2,175 ground
 snakes (Sonora semiannulata) across the continental United States to
 analyze morph ratios and test among competing hypotheses about the genetic
 architecture underlying red and black coloration in coral snake mimics. We
 found strong support for a two-locus model under simple Mendelian
 inheritance, with red and black pigmentation being controlled by separate
 loci. We found no evidence of either linkage disequilibrium between loci
 or sex linkage. In contrast to Batesian mimicry systems like butterflies
 in which all color signal components are linked into a single “supergene,”
 our results suggest that the mimetic signal in colubrid snakes can be
 disrupted through simple recombination and that color evolution is likely
 to involve discrete gains and losses of each signal component. Both
 outcomes are likely to contribute to the exponential increase in rates of
 color evolution seen in snake mimicry systems over insect systems.
description: Compiled museum data for
 all Sonora sp. sampledPhenotypic data
 (including color morph) for all Sonora sp. sampled from the 12 collections
 featured in this manuscriptfull_output.csvData input file for likelihood modelData input file for running the model.R script fileindata_final.csvScript file for likelihood modelScript file for generating likelihood analysis of color morph geneticsmodel.R
DOI: 10.5067/asdc/firexaq_aerosolcloud_aircraftremotesensing_er2_cpl_data_1
title: FIREX-AQ ER-2 Cloud Physics Lidar Remotely Sensed Data
DOI: 10.5067/asdc/firexaq_cloud_aircraftinsitu_dc8_data_1
title: FIREX-AQ DC-8 In-Situ Cloud Data
DOI: 10.5067/asdc/firexaq_ground_insitu_data_1
title: FIREX-AQ In-Situ Ground Data
DOI: 10.5067/asdc/firexaq_hsrl_aircraftremotesensing_dc8_data_1
title: FIREX-AQ DC-8 High-Spectral Resolution Lidar (HSRL) Remotely Sensed Data
DOI: 10.5067/asdc/firexaq_jvalue_aircraftinsitu_dc8_data_1
title: FIREX-AQ DC-8 In-Situ J Value Data