cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pk27h
title: Data from: Beyond surrogacy: A multi-taxon approach to conservation biogeography

description: Biogeographic analysis of species turnover (β diversity) of plants and
 animals among regions often yields conflicting results, with regions of
 high β diversity identified for some taxonomic groups but not others. Such
 discordance calls into question use of surrogate taxa to forge
 conservation plans. This discordance begs for a means of comparing
 multiple taxa across phyla in a manner that is cost-effective, considers
 limitations in computer resources in certain global regions, and is
 understood by policy makers and land managers. As a test case for a method
 taking into account these considerations, we used species lists for ten
 organismal groups (spanning plants, vertebrates, and invertebrates) to
 identify regions of high β diversity using Monmonier’s algorithm, a
 spatially explicit technique that is readily implemented and interpreted.
 Data were for montane (&gt;1000 m elevation) species across the
 Eastern Arc of Tanzania and Kenya and surrounding areas. Our results
 indicate that surrogacy does not make for the most effective expenditure
 of conservation efforts. We also show that to use a multi-taxon approach
 one need not to rely on intensive surveys of areas in order to make
 conservation decisions, including reserve selection. Our approach also
 eliminates the need for complex modeling and comparisons common to many
 GIS-based complementarity techniques. Additionally, a wide variety of
 socioeconomic, political, demographic, geological, climatological, and
 evolutionary factors can be incorporated into the technique to help shape
 conservation biogeography from a local and regional perspective. This
 technique can bridge the gap between conservation biogeography theory and
 application in tropical regions and beyond.
description: Smith-Patten_Patten_dataPresence/absence data for each taxon used in the study.Smith-Patten_Patten_calculator_matricesCalculator used for pairwise Jaccard’s dissimilarity indices; resulting matrices for all taxaSmith-Patten_Patten_BARRIER_outputRaw BARRIER 2.2 output for all taxaSmith-Patten_Patten_C_ProgramC program to create bootstrap matrices
DOI: 10.5061/dryad.2260t
title: Data from: Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites

description: Understanding the genetic architecture of host resistance is key for
 understanding the evolution of host–parasite interactions. Evolutionary
 models often assume simple genetics based on few loci and strong
 epistasis. It is unknown, however, whether these assumptions apply to
 natural populations. Using a quantitative trait loci (QTL) approach, we
 explore the genetic architecture of resistance in the crustacean Daphnia
 magna to two of its natural parasites: the horizontally transmitted
 bacterium Pasteuria ramosa and the horizontally and vertically transmitted
 microsporidium Hamiltosporidium tvaerminnensis. These two systems have
 become models for studies on the evolution of host–parasite interactions.
 In the QTL panel used here, Daphnia’s resistance to P. ramosa is
 controlled by a single major QTL (which explains 50% of the observed
 variation). Resistance to H. tvaerminnensis horizontal infections shows a
 signature of a quantitative trait based in multiple loci with weak
 epistatic interactions (together explaining 38% variation). Resistance to
 H. tvaerminnensis vertical infections, however, shows only one QTL
 (explaining 13.5% variance) that colocalizes with one of the QTLs for
 horizontal infections. QTLs for resistance to Pasteuria and
 Hamiltosporidium do not colocalize. We conclude that the genetics of
 resistance in D. magna are drastically different for these two parasites.
 Furthermore, we infer that based on these and earlier results, the
 mechanisms of coevolution differ strongly for the two host–parasite
 systems. Only the Pasteuria–Daphnia system is expected to follow the
 negative frequency-dependent selection (Red Queen) model. How coevolution
 works in the Hamiltosporidium–Daphnia system remains unclear.
description: SNP array based linkage
 mapGenotypes of F2 panel
 clonesgeno_final.csv
DOI: 10.25574/28124
title: Chandra X-ray Observatory ObsId 28124

description: PHANGS-Chandra: A Legacy Survey for Detailing the First Billion Years of X-ray Evolution in Galaxies
DOI: 10.5061/dryad.gq0pb
title: Data from: ModelOMatic: fast and automated comparison between RY, nucleotide, amino acid, and codon substitution models

description: Molecular phylogenetics is a powerful tool for inferring both the process
 and pattern of evolution from genomic sequence data. Statistical
 approaches, such as maximum likelihood and Bayesian inference, are now
 established as the preferred methods of inference. The choice of models
 that a researcher uses for inference is of critical importance, and there
 are established methods for model selection conditioned on a particular
 type of data, such as nucleotides, amino acids, or codons. A major
 limitation of existing model selection approaches is that they can only
 compare models acting upon a single type of data. Here we extend model
 selection to allow comparisons between models describing different types
 of data by introducing the idea of adapter functions, which project
 aggregated models onto the originally observed sequence data. These
 projections are implemented in the program ModelOMatic and used to perform
 model selection on 3,722 families from the PANDIT database, 68 genes from
 an arthropod phylogenomic data set, and 248 genes from a vertebrate
 phylogenomic data set. For the PANDIT and arthropod data, we find that
 amino acid models are selected for the overwhelming majority of
 alignments; with progressively smaller numbers of alignments selecting
 codon and nucleotide models, and no families selecting RY-based models. In
 contrast, nearly all alignments from the vertebrate data set select
 codon-based models. The sequence divergence, the number of sequences, and
 the degree of selection acting upon the protein sequences may contribute
 to explaining this variation in model selection. Our ModelOMatic program
 is fast, with most families from PANDIT taking fewer than 150 seconds to
 complete, and should therefore be easily incorporated into existing
 phylogenetic pipelines.
description: Whelan_ModelOMaticAppendixAppendix for ModelOMatic
DOI: 10.5061/dryad.t9j7g
title: Data from: Ocean circulation model predicts high genetic structure in a long-lived pelagic developer

description: Understanding the movement of genes and individuals across marine
 seascapes is a long-standing challenge in marine ecology, and can inform
 our understanding of local adaptation, the persistence and movement of
 populations, and the spatial scale of effective management. Patterns of
 gene flow in the ocean are often inferred based on population genetic
 analyses coupled with knowledge of species’ dispersive life histories.
 However, genetic structure is the result of time-integrated processes, and
 may not capture present-day connectivity between populations. Here we use
 a high-resolution oceanographic circulation model to predict larval
 dispersal along the complex coastline of western Canada that includes the
 transition between two well-studied zoogeographic provinces. We simulate
 dispersal in a benthic sea star with a 6-10 week pelagic larval phase, and
 test predictions of this model against previously observed genetic
 structure including a strong phylogeographic break within the
 zoogeographical transition zone. We also test predictions with new genetic
 sampling in a site within the phylogeographic break. We find that the
 coupled genetic and circulation model predicts the high degree of genetic
 structure observed in this species, despite its long pelagic duration.
 High genetic structure on this complex coastline can thus be explained
 through ocean circulation patterns which tend to retain passive larvae
 within 20 - 50 km of their parents, suggesting a necessity for close-knit
 design of Marine Protected Area networks.
description: drogue locations days 0,
 40, 70Latitude and longitude
 of simulated particles at day 0 (seed site), 40 (beginning of simulated
 competency period) and 70 (end of simulated competency period). Within
 each of 11 regions (site), particles were released at 40 seed locations
 (seed), at multiple half-hour intervals (starttime).All microsatellite
 genotypesGenotypes for 7
 microsatellites for 6 regions in British Columbia, Southeast Alaska, and
 California, with approximate latitude and longitude of collection site,
 and date of collection.Microsatellite
 genotypes.xlsx
DOI: 10.5061/dryad.6vd4v
title: Data from: The evolutionary history of Afrocanarian blue tits inferred from genome-wide SNPs

description: A common challenge in phylogenetic reconstruction is to find enough
 suitable genomic markers to reliably trace splitting events with short
 internodes. Here we present phylogenetic analyses based on genome-wide
 single-nucleotide polymorphisms (SNPs) of an enigmatic avian radiation,
 the subspecies complex of Afrocanarian blue tits (Cyanistes teneriffae).
 The two sister species, the Eurasian blue tit (Cyanistes caeruleus) and
 the azure tit (Cyanistes cyanus), constituted the outgroup. We generated a
 large data set of SNPs for analysis of population structure and phylogeny.
 We also adapted our protocol to utilize degraded DNA from old museum skins
 from Libya. We found strong population structuring that largely confirmed
 subspecies monophyly, and constructed a coalescent-based phylogeny with
 full support at all major nodes. The results are consistent with a recent
 hypothesis that La Palma and Libya are relic populations of an ancient
 Afrocanarian blue tit, although a small data set for Libya could not
 resolve its position relative to La Palma. The birds on the eastern
 islands of Fuerteventura and Lanzarote are similar to those in Morocco.
 Together they constitute the sister group to the clade containing the
 other Canary Islands (except La Palma), in which El Hierro is sister to
 the three central islands. Hence, extant Canary Islands populations seem
 to originate from multiple independent colonisation events. We also found
 population divergences in a key reproductive trait, viz. sperm length,
 which may constitute reproductive barriers between certain populations. We
 recommend a taxonomic revision of this polytypic species, where several
 subspecies should qualify for species rank.
description: SNPs and sperm length
 dataDryad.xlsxCOI sequencesCOI.fasSNAPP 2000SNPs input fileSNAPP_2000SNPs.xmlSNAPP Libya input fileSNAPP_Libya.xmlStructure 7500 SNPs input fileStructure input data.txtStructure input data (Libyan set)
DOI: 10.5061/dryad.qk22t
title: Data from: Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift

description: The evolution of diversity in the marine ecosystem is poorly understood,
 given the relatively high potential for connectivity, especially for
 highly mobile species such as whales and dolphins. The killer whale
 (Orcinus orca) has a worldwide distribution, and individual social groups
 travel over a wide geographic range. Even so, regional populations have
 been shown to be genetically differentiated, including among different
 foraging specialists (ecotypes) in sympatry. Given the strong matrifocal
 social structure of this species together with strong resource
 specialisations, understanding the process of differentiation will require
 an understanding of the relative importance of both genetic drift and
 local adaptation. Here we provide a high resolution analysis based on
 nuclear SNP markers and inference about differentiation at both neutral
 loci and those potentially under selection. We find that all population
 comparisons, within or among foraging ecotypes, show significant
 differentiation, including populations in parapatry and sympatry. Loci
 putatively under selection show a different pattern of structure compared
 to neutral loci, and are associated with gene ontology terms reflecting
 physiologically relevant functions (e.g. related to digestion). The
 pattern of differentiation for one ecotype in the North Pacific suggests
 local adaptation and shows some fixed differences among sympatric
 ecotypes. We suggest that differential habitat use and resource
 specialisations have promoted sufficient isolation to allow differential
 evolution at neutral and functional loci, but that the process is recent
 and dependent on both selection and drift.
description: RT_Oorc11-VariantFinal.2.4.2-DryadGATK Unified genotyper results from multisample genotype calling of RAD sequencing of killer whales worldwide
DOI: 10.5061/dryad.qj007
title: Data from: Plant defense phenotypes determine the consequences of volatile emission for individuals and neighbors

description: Plants are at the trophic base of terrestrial ecosystems, and the
 diversity of plant species in an ecosystem is a principle determinant of
 community structure. This may arise from diverse functional traits among
 species. In fact, genetic diversity within species can have similarly
 large effects. However, studies of intraspecific genetic diversity have
 used genotypes varying in several complex traits, obscuring the specific
 phenotypic variation responsible for community-level effects. Using lines
 of the wild tobacco Nicotiana attenuata genetically altered in specific
 well-characterized defense traits and planted into experimental
 populations in their native habitat, we investigated community-level
 effects of trait diversity in populations of otherwise isogenic plants. We
 conclude that the frequency of defense traits in a population can
 determine the outcomes of these traits for individuals. Furthermore, our
 results suggest that some ecosystem-level services afforded by genetically
 diverse plant populations could be recaptured in intensive monocultures
 engineered to be functionally diverse.
description: Appendix1_Fig1_091208
 SouthernFull original Southern
 blot image (includes lines not used in this
 publication).AppendixFig1_phytohormones_data_screeningDC5Data for Appendix Figure 1AppendixFig2_TPS10_crosses_transcriptsData for Appendix Figure 2Fig1_AppendixFig3_glasshouse_field_dataData for Figure 1 and Appendix Figure 3Fig4_Manduca_sexta_glasshouse_assayData for Figure 4Figs5_6_7_8_10_field_season2_screensData for figures 6-8, 10Figs5_7_8_field_season1_screen_finalData for figures 5, 7, 8Figs7_8_9_field_season2_finalData for figures 7-9
DOI: 10.5878/2yry-se63
title: The Gothenburg SOM Survey 2018
title: SOM-undersökningen i Göteborg 2018

description: In the autumn of 2018, the third edition of the Gothenburg SOM survey was conducted. A total of 5000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.
description: Hösten 2018 genomfördes för tredje gången en SOM-undersökning i Göteborgs stad, där totalt 5000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär, och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.
DOI: 10.5878/mpjn-xs62
title: The Gothenburg SOM Survey 2018
title: SOM-undersökningen i Göteborg 2018

description: In the autumn of 2018, the third edition of the Gothenburg SOM survey was conducted. A total of 5000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.
description: Hösten 2018 genomfördes för tredje gången en SOM-undersökning i Göteborgs stad, där totalt 5000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär, och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.
DOI: 10.5061/dryad.1546n
title: Data from: Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response

description: Organisms across the tree of life use a variety of mechanisms to respond
 to stress-inducing fluctuations in osmotic conditions. Cellular response
 mechanisms and phenotypes associated with osmoadaptation also play
 important roles in bacterial virulence, human health, agricultural
 production and many other biological systems. To improve understanding of
 osmoadaptive strategies, we have generated 59 high-quality draft genomes
 for the haloarchaea (a euryarchaeal clade whose members thrive in
 hypersaline environments and routinely experience drastic changes in
 environmental salinity) and analyzed these new genomes in combination with
 those from 21 previously sequenced haloarchaeal isolates. We propose a
 generalized model for haloarchaeal management of cytoplasmic osmolarity in
 response to osmotic shifts, where potassium accumulation and sodium
 expulsion during osmotic upshock are accomplished via secondary transport
 using the proton gradient as an energy source, and potassium loss during
 downshock is via a combination of secondary transport and non-specific ion
 loss through mechanosensitive channels. We also propose new mechanisms for
 magnesium and chloride accumulation. We describe the expansion and
 differentiation of haloarchaeal general transcription factor families,
 including two novel expansions of the TATA-binding protein family, and
 discuss their potential for enabling rapid adaptation to environmental
 fluxes. We challenge a recent high-profile proposal regarding the
 evolutionary origins of the haloarchaea by showing that inclusion of
 additional genomes significantly reduces support for a proposed
 large-scale horizontal gene transfer into the ancestral haloarchaeon from
 the bacterial domain. The combination of broad (17 genera) and deep (≥5
 species in four genera) sampling of a phenotypically unified clade has
 enabled us to uncover both highly conserved and specialized features of
 osmoadaptation. Finally, we demonstrate the broad utility of such
 datasets, for metagenomics, improvements to automated gene annotation and
 investigations of evolutionary processes.
description: GeneraSpecificMolecularMarkersThe Haloarcula, Halorubrum and Haloferax genera contain seven, fourteen, and fifteen sequenced members respectively. Genes that are unique, universal to the genus, and single-copy in these genera may serve as good molecular markers for metagenomic analyses. We include a list of the homology clusters as well as the protein translations, multiple alignments and a hidden Markov model for each proposed molecular marker.Supplementary_Code_1_MySQL_database_miningScripts for accessing haloarchaeal genomic data in a navigable SQL database. A copy of the database file is available upon request.Supplementary_Dataset_5_All_pI_histogramsSupplementary_Dataset_6_Abnormal_GC_regionsSupplementary_Dataset_6_All_GC_plotsSupplementary_Dataset_7_All_GC_changepoint_plots
DOI: 10.5061/dryad.d334b
title: Data from: The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

description: Background: Increased disease resistance is a key target of cereal
 breeding programs, with disease outbreaks continuing to threaten global
 food production, particularly in Africa. Of the disease resistance gene
 families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR)
 family is the most prevalent and ancient and is also one of the largest
 gene families known in plants. The sequence diversity in NBS-encoding
 genes was explored in sorghum, a critical food staple in Africa, with
 comparisons to rice and maize and with comparisons to fungal pathogen
 resistance QTL. Results: In sorghum, NBS-encoding genes had significantly
 higher diversity in comparison to non NBS-encoding genes and were
 significantly enriched in regions of the genome under purifying and
 balancing selection, both through domestication and improvement. Ancestral
 genes, pre-dating species divergence, were more abundant in regions with
 signatures of selection than in regions not under selection. Sorghum
 NBS-encoding genes were also significantly enriched in the regions of the
 genome containing fungal pathogen disease resistance QTL; with the
 diversity of the NBS-encoding genes influenced by the type of co-locating
 biotic stress resistance QTL. Conclusions: NBS-encoding genes are under
 strong selection pressure in sorghum, through the contrasting evolutionary
 processes of purifying and balancing selection. Such contrasting
 evolutionary processes have impacted ancestral genes more than
 species-specific genes. Fungal disease resistance hot-spots in the genome,
 with resistance against multiple pathogens, provides further insight into
 the mechanisms that cereals use in the “arms race” with rapidly evolving
 pathogens in addition to providing plant breeders with selection targets
 for fast-tracking the development of high performing varieties with more
 durable pathogen resistance.
description: Protein sequences of NBS
 genes in diverse sorghum genotypesProtein sequences of
 NBS-genes in sorghum for 47 sorghum genotypesone_gene_47samples_protein_masked_20130909.tarMultiple sequence alignments of sorghum NBS genesMultiple sequence alignments of NBS genes identified in the sorghum genomesb.aa.domain.PF00931.alnPhylogenetic tree of NBS genes in sorghumPhylogenetic tree constructed using TreeBest based on the PFAM00931 domain of the NBS genes in the sorghum genomesb..aa.domain.PF00931.fasta.tree.treAlignments of NBS genes across sorghum, maize and riceMultiple sequence alignment of PFAM00931 domains of NBS genes identified in sorghum, maize and rice genomessb.zm.os.aa.domain.PF00931.alnPhylogenetic tree of NBS genes across sorghum, maize and ricePhylogenetic tree, constructed using TreeBest, based on the PFAM00931 domain of NBS genes identified in sorghum, maize and ricesb.zm.os.aa.domain.PF00931.fasta.tree.tre
DOI: 10.5061/dryad.2br40
title: Data from: Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

description: Mapping hybrid defects in contact zones between incipient species can
 identify genomic regions contributing to reproductive isolation and reveal
 genetic mechanisms of speciation. The house mouse features a rare
 combination of sophisticated genetic tools and natural hybrid zones
 between subspecies. Male hybrids often show reduced fertility, a common
 reproductive barrier between incipient species. Laboratory crosses have
 identified sterility loci, but each encompasses hundreds of genes. We map
 genetic determinants of testis weight and testis gene expression using
 offspring of mice captured in a hybrid zone between M. musculus musculus
 and M. m. domesticus. Many generations of admixture enables
 high-resolution mapping of loci contributing to these sterility-related
 phenotypes. We identify complex interactions among sterility loci,
 suggesting multiple, non-independent genetic incompatibilities contribute
 to barriers to gene flow in the hybrid zone.
description: FAM_file.fam file, generated by PLINK, used for genome wide association mapping in GEMMAsample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned.famBIM_file.bim file, generated by PLINK, used for genome wide association mapping in GEMMAsample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned.bimBED_file.bed file, generated by PLINK, used for genome wide association mapping in GEMMAsample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned.bedkinship_matrixKinship matrix, calculated in GEMMA, used for genome wide association mapping in GEMMAsample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned_wtX_KIN.cXX.txt