cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.00fs2
title: Data from: Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)

description: Crassulacean acid metabolism (CAM) is a modified form of photosynthesis
 that has arisen independently at least 35 times in flowering plants. The
 occurrence of CAM is often correlated with shifts to arid, semiarid, or
 epiphytic habits, as well as transitions in leaf morphology (e.g.
 increased leaf thickness) and anatomy (e.g. increased cell size and
 packing). We assess shifts between C3 and CAM photosynthesis in the
 subfamily Agavoideae (Asparagaceae) through phylogenetic analysis of
 targeted loci captured from the nuclear and chloroplast genomes of over 60
 species. Carbon isotope data was used as a proxy for mode of
 photosynthesis in extant species and ancestral states were estimated on
 the phylogeny. Ancestral character state mapping suggests three
 independent origins of CAM in the Agavoideae. CAM species differ from C3
 species in climate space and are found to have thicker leaves with densely
 packed cells. C3 ancestors of CAM species show a predisposition toward
 CAM-like morphology. Leaf characteristics in the ancestral C3 species may
 have enabled the repeated evolution of CAM in the Agavoideae subfamily.
 Anatomical changes, including a tendency toward 3D venation, may have
 initially arisen in C3 ancestors in response to aridity as a way to
 increase leaf succulence for water storage.
description: CrossSectionMeasurementsCross section data generated from leaf cross sections, imaged using a Zeiss microscope and analyzed in ImageJ.Gene treesGene trees produced from 272 single copy genes, using RAxML. Trees are the consensus of 500 bootstrap replicates (RAxML_bipartitions.*).genetrees.zipGene alignmentsNucleotide alignments of 272 single copy genes.alignments.zipChloroplast treeRAxML bipartition tree from chloroplast alignment. 500 bootstrap replicates.chloroplast_RAxML.treChloroplast alignmentChloroplast alignment file.all.merged.fa.align-gb.68Concatenated nuclear treeRAxML bipartition (bootstraps=500) tree for the concatenated nuclear data.concatenated_nuclear_RAxML.treNuclear ASTRALII treeASTRAL-II species tree, based on 272 single copy gene trees. 400 bootstrap replicates.nuclear_astral.tre
DOI: 10.5061/dryad.q0g60
title: Data from: Predicting range-shift success potential for tropical marine fishes using external morphology

description: With global change accelerating the rate of species' range shifts,
 predicting which are most likely to establish viable populations in their
 new habitats is key to understanding how biological systems will respond.
 Annually, in Australia, tropical fish larvae from the Great Barrier Reef
 (GBR) are transported south via the East Australian Current (EAC),
 settling into temperate coastal habitats for the summer period, before
 experiencing near-100% mortality in winter. However, within 10 years,
 predicted winter ocean temperatures for the southeast coast of Australia
 will remain high enough for more of these so-called ‘tropical vagrants’ to
 survive over winter. We used a method of morphological niche analysis,
 previously shown to be an effective predictor of invasion success by
 fishes, to project which vagrants have the greatest likelihood of
 undergoing successful range shifts under these new climatic conditions. We
 find that species from the family of butterflyfishes (Chaetodontidae), and
 the moorish idol, Zanclus cornutus, are most likely to be able to exploit
 new niches within the ecosystem once physiological barriers to
 overwintering by tropical vagrant species are removed. Overall, the
 position of vagrants within the morphospace was strongly skewed,
 suggesting that impending competitive pressures may impact
 disproportionately on particular parts of the native community.
description: Smith et al_Images and
 Relative Warp ScoresImages of resident and
 vagrant fish species used for landmarking and output file of coordinates
 (relative warp scores) obtained from relative warp analysis
 (tpsRelw).
DOI: 10.5061/dryad.vd48c
title: Data from: Advances in finding Alba: the locus affecting life history and color polymorphism in a Colias butterfly

description: Although alternative life history strategies exist within many
 populations, very little is known about their genetic basis and
 mechanistic insight to these traits could greatly advance the
 understanding of eco-evolutionary dynamics. Many species of butterfly
 within the genus Colias exhibit a sex-limited wing color polymorphism,
 called Alba, which is correlated with an alternative life history
 strategy. Here we have taken the first steps in localizing the region
 carrying Alba in Colias croceus, a species with no genomic resources, by
 generating whole genome sequence of a single Alba mother and two
 sequencing pools, one for her Alba, and another for her orange, offspring.
 These data were used in a bulk segregant analysis wherein SNPs fulfilling
 the Mendelian inheritance expectations of Alba were identified. Then,
 using the conserved synteny in Lepidoptera, the Alba locus was assigned to
 chromosome 15 in Bombyx mori. We then identified candidate regions within
 the chromosome by investigating the distribution of Alba SNPs along the
 chromosome and the difference in nucleotide diversity in exons between the
 two pools. A region spanning ~5.7 Mbp at the 5’ end of the chromosome was
 identified as likely to contain the Alba locus. These insights set the
 stage for more detailed genomic scans and mapping of the Alba phenotype
 and demonstrate an efficient use of genomic resources in a novel species.
description: Alba
 scaffolds162 Alba gene model
 super-scaffolds (i.e. gene model super-scaffolds with an Alba SNP and
 constructed from B. mori proteins on B. mori chromosome
 15.Alba_scaffolds.fa
DOI: 10.5061/dryad.d4r50
title: Data from: A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius

description: The rapid evolution of insecticide resistance remains one of the biggest
 challenges in the control of medically and economically important pests.
 Insects have evolved a diverse range of mechanisms to reduce the efficacy
 of the commonly used classes of insecticides and finding the genetic basis
 of resistance is a major aid to management. In a previously unstudied
 population, we performed an F2 resistance mapping cross for the common bed
 bug, Cimex lectularius, for which insecticide resistance is increasingly
 widespread. Using 334 SNP markers obtained through RAD-sequencing, we
 constructed the first linkage map for the species, consisting of 14
 putative linkage groups (LG), with a length of 407 cM and an average
 marker spacing of 1.3 cM. The linkage map was used to reassemble the
 recently published reference genome, facilitating refinement and
 validation of the current genome assembly. We detected a major QTL on LG12
 associated with insecticide resistance, occurring in close proximity (1.2
 Mb) to a carboxylesterase encoding candidate gene for pyrethroid
 resistance. This provides another example of this candidate gene playing a
 major role in determining survival in a bed bug population following
 pesticide resistance evolution. The recent availability of the bed bug
 genome, complete with a full list of potential candidate genes related to
 insecticide resistance, in addition to the linkage map generated here,
 provides an excellent resource for future research on the development and
 spread of insecticide resistance in this resurging pest species.
description: Remove PCR
 duplicatesBash script to remove
 PCR duplicates using Stacks 1.21 clone_filter moduleremove_pcr_duplicates.shAlign RAD-seq readsAlign RAD-seq reads to bedbug reference genome using GSNAPpair_end_alignment.shStacks refmap pipelineMake Stacks catalogue from reference mapped datastacks_refmap.shQTL mapping for pyrethroid resistanceRscript that uses rqt_final_cross.csv to perform qtl mapping for pyrethroid resistance using R/qtlrqtl_mapping.RFinal cross dataFiltered and corrected linkage map data for use in QTL mappingbedbugs_cross_final_100316.csvConstruct linkage mapRscript for constructing a linkage map from filtered raw data (bedbugs_raw_filtered.csv) using Rqtlmake_genetic_map.RFiltered raw cross dataGenotype data output by Stacks that has been filtered to include loci only informative for QTL and linkage map analysis (i.e. ab/ab in both F1 parents)bedbugs_raw_filtered.csvStacks raw genotypesRaw genotypes from Stacks calling pipeline.stacks_raw_genotypes.tsvConvert stacks raw output to RqtlUtility tool to convert stacks raw output to Rqtl inputrqtl_format_conversion.RStacks catalogue outputRaw output data from Stacks catalogue - includes alleles, SNPs and RAD tags called from Stacks reference mapping pipeline.stacks_catalogue_output.zip
DOI: 10.34810/data1284
title: Partitura i enregistrament de "Sonata en Fa Major" Carles Baguer (1768-1808)

description: Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical, aquest dataset conté dos arxius: 
&lt;br&gt; Transcripció del manuscrit original de Carles Baguer
&lt;br&gt; Enregistrament de la peça interpretada per: 
&lt;br&gt;- Dani Espasa, piano de taula Miguel Slocker de 1831, cedit pel
Museu de la Música de Barcelona.
DOI: 10.5061/dryad.k23mq
title: Data from: Dental data perform relatively poorly in reconstructing mammal phylogenies: morphological partitions evaluated with molecular benchmarks

description: Phylogenetic trees underpin reconstructions of evolutionary history and
 tests of evolutionary hypotheses. They are inferred from both molecular
 and morphological data, yet the relative value of morphology has been
 questioned in this context due to perceived homoplasy, developmental
 linkage, and nonindependence of characters. Nevertheless, fossil data are
 limited to incomplete subsets of preserved morphology, and different
 regions are treated as equivalent. Through meta-analysis of 40 data sets,
 we show here that the dental and osteological characters of mammals convey
 significantly different phylogenetic signals, and that osteological
 characters are significantly more compatible with molecular trees.
 Furthermore, the application of simplified paleontological filters
 (retaining only dental data) results in significantly greater loss of
 phylogenetic signal than random character ablation. Although the mammal
 fossil record is largely comprised of teeth, dental data alone are
 generally found to be less reliable for phylogenetic reconstruction given
 their incongruence with osteological and molecular data. These findings
 highlight the need for rigorous meta-analyses of distributions of
 homoplasy in morphological data. These tests, and consequent refinements
 to phylogenetic analyses that they permit, promise to improve the quality
 of all macroevolutionary studies that hinge on accurate trees.
description: Supplementary
 DataDetails of the datasets
 included in the meta-analyses and the results for individual
 datasetsSupplementaryR3.xlsx
DOI: 10.5061/dryad.vh810
title: Data from: Deciphering a survival strategy during the interspecific competition between Bacillus cereus MSM-S1 and Pseudomonas sp. MSM-M1

description: Interspecific competition in bacteria governs colony growth dynamics and
 pattern formation. Here, we demonstrate an interesting phenomenon of
 interspecific competition between Bacillus cereus MSM-S1 and Pseudomonas
 sp. MSM-M1, where secretion of an inhibitor by Pseudomonas sp. is used as
 a strategy for survival. Although B. cereus grows faster than Pseudomonas
 sp., in the presence of Pseudomonas sp. the population of B. cereus
 reduces significantly, whereas Pseudomonas sp. do not show any marked
 alteration in their population growth. Appearance of a zone of inhibition
 between growing colonies of two species on nutrient agar prevents the
 expanding front of the MSM-S1 colony from accessing and depleting
 nutrients in the region occupied by MSM-M1, thereby aiding the survival of
 the slower growing MSM-M1 colonies. To support our experimental results,
 we present simulations, based on a chemotactic model of colony growth
 dynamics. We demonstrate that the chemical(s) secreted by Pseudomonas sp.
 is responsible for the observed inhibition of growth and spatial pattern
 of the B. cereus MSM-S1 colony. Our experimental results are in excellent
 agreement with the numerical results and confirm that secreted inhibitors
 enable Pseudomonas sp. to survive and coexist in the presence of faster
 growing B. cereus, in a common niche.
description: Growth Characteristics
 of S1 and M1 in Nutrient BrothThis file contains the
 data and calculations in support of the Figure 1aGrowth characteristics
 of S1 and M1 on Nutrient agar platesThis file contains the
 data and calculations in support of figure 1bCompetitive growth
 patterns of S1 and M1 in Nutrient brothThis file contains data
 and calculations in support of figure 2aComparative growth
 characteristics of S1 on Nutrient agar plateThis file contains data
 and calculations in support of figure 2bComparative growth
 pattern of M1 on Nutrient agar plateThis file contains data
 and calculations in support of figure 2cFile S1_supporting
 Information_BCetalThis file contains
 supporting Information on Methods, Results and Reaction-Diffusion
 Model
DOI: 10.5061/dryad.2nh23
title: Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs

description: Understanding patterns of dispersal and connectivity among marine
 populations can directly inform fisheries conservation and management.
 Advances in high-throughput sequencing offer new opportunities for
 estimating marine connectivity. We used Restriction-site Associated DNA
 sequencing to examine dispersal and realized connectivity in the sea
 scallop Placopecten magellanicus, an economically important marine
 bivalve. Based on 245 individuals sampled range-wide at 12 locations from
 Newfoundland to the Mid-Atlantic Bight we identified and genotyped 7163
 Single Nucleotide Polymorphisms; 112 (1.6%) were identified as outliers
 potentially under directional selection. Bayesian clustering revealed a
 discontinuity between northern and southern samples and latitudinal clines
 in allele frequencies were observed in 42.9% of the outlier loci and in
 24.6% of neutral loci. Dispersal estimates derived using these clines and
 estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0
 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for
 neutral loci. Our analysis suggests restricted dispersal compared to the
 species range (&gt;2000 km) and that dispersal and effective
 connectivity differ. These observations support the hypothesis that
 limited effective dispersal structures scallop populations along eastern
 North America. These findings can help refine the appropriate scale of
 management and conservation in this commercially valuable species.
description: VanWyngaardenM_etal_GeogDistMatrixThis file contains matrices of pairwise geographic distances (km; shortest distance and estimated ocean current-based distance) between 12 populations of the sea scallop, Placopecten magellanicus, used along with 7163 RAD-seq derived SNPs to estimate isolation-by-distance and dispersal distances among populations. Population names and geographic coordinates can be found in Table 1 of the associated publication.VanWyngaardenM_etal_PopStructure_GeogDist.xlsxVanWyngaardenM_etal_RADseq_SNPsThis VCF file contains 7216 RAD-seq derived SNPs detected among 12 Northwest Atlantic Ocean populations of the sea scallop, Placopecten magellanicus. The program stacks v0.9999 was used to call variants; parameters can be found in Table S1 of the associated publication.VanWyngaardenM_etal_PopStructure_SNPMap4b.vcf
DOI: 10.5061/dryad.p35r2
title: Data from: The landscape of anthropogenic mortality: how African lions respond to spatial variation in risk

description: 1. Demography and conservation status of many wild organisms are
 increasingly shaped by interactions with humans. This is particularly the
 case for large, wide ranging carnivores. 2. Using 206 mortality records
 (1999-2012) of lions in Hwange National Park, Zimbabwe, we calculated
 mortality rates for each source of anthropogenic mortality, modelled risk
 of anthropogenic mortality across the landscape accounting for time lions
 spent in different parts of the landscape, and assessed whether subsets of
 the population were more at risk. 3. Anthropogenic activities caused 88%
 of male and 67% of female mortalities; male mortality being dominated by
 trophy hunting while the sources for female mortality were more varied
 (snaring, retaliatory killing, hunting). 4. Landscapes of anthropogenic
 mortality risk revealed that communal subsistence farming areas,
 characterized by high risk (due to retaliatory killing) but avoided by
 lions, are population sinks. Trophy hunting areas and areas within
 protected areas bordering communal farmland, where bush-meat snaring is
 prevalent, form ‘ecological traps’ (or ‘attractive sinks’). 5. Lions
 avoided risky areas, suggesting they may make behavioural decisions based
 on perceptions of risk. Experienced adults used risky areas less and
 incorporated lower proportions of them in their home ranges than young
 individuals, suggesting that the latter may either be naïve or forced into
 peripheral habitats. Synthesis and applications: This paper contributes to
 an understanding of the way in which carnivore populations are affected by
 anthropogenic mortality across the conservation landscape. This is
 critical to designing focussed, appropriate and cost effective
 conservation management strategies. Agricultural areas are intuitively
 identified by conservationists as being risky for carnivores due to
 retaliatory or pre-emptive killing, with threats largely mitigated against
 by improving livestock protection. However, parts of protected areas may
 also form less easily identified ‘attractive sinks’ for carnivores. In
 particular, trophy hunting adjacent to national parks needs careful
 management to avoid damaging effects of overhunting. Law enforcement is
 needed to reduce the effects of bush-meat poaching on predators and other
 wildlife in protected areas. To be most effective, resource limited
 anti-poaching activities should prioritise wildlife rich areas close to
 human settlement as these tend to be hotspots for bush-meat poaching.
description: Data_for_landscape_of_anthro_mortalityGPS positions, random positions, mortality data used in Resource Selection Function analysis to determine the landscape of use, as described in the methods section of Loveridge et al 2016 The landscape of anthropogenic mortality: how African lions respond to spatial variation in risk
DOI: 10.5061/dryad.j29f5
title: Data from: Sequencing improves our ability to study threatened migratory species: genetic population assignment in California's Central Valley Chinook salmon

description: Effective conservation and management of migratory species requires
 accurate identification of unique populations, even as they mix along
 their migratory corridors. While telemetry has historically been used to
 study migratory animal movement and habitat use patterns, genomic tools
 are emerging as a superior alternative in many ways, allowing large-scale
 application at reduced costs. Here, we demonstrate the usefulness of
 genomic resources for identifying single-nucleotide polymorphisms (SNPs)
 that allow fast and accurate identification of the imperiled Chinook
 salmon in the Great Central Valley of California. We show that 80
 well-chosen loci, drawn from a pool of over 11,500 SNPs developed from
 restriction site-associated DNA sequencing, can accurately identify
 Chinook salmon runs and select populations within run. No other SNP panel
 for Central Valley Chinook salmon has been able to achieve the high
 accuracy of assignment we show here. This panel will greatly improve our
 ability to study and manage this ecologically, economically, and socially
 important species and demonstrates the great utility of using genomics to
 study migratory species.
description: Meek_et_al_EandE_LocusMapNamesAndSequenceFile contains the Sequence ID and corresponding Map ID for loci used in the linkage map. The sequence provided is for one of the two alleles at each locus.Meek_et_al_EandE_Sequence_DataFile contains the sequences for the 24,198 SNP loci discovered. Sequence names are followed by "_1" or "_2" to denote the two different alleles of the same locus.Meek_et_al_EandE_Seq_Count_dataFile contains the sequence counts for each individual in the RAD-seq study at each SNP locus, showing the counts for both allele 1 and allele 2, separated by a comma.
DOI: 10.5061/dryad.125
title: Data from: Elevated substitution rates estimated from ancient DNA sequences

description: Ancient DNA sequences are able to offer valuable insights into molecular
 evolutionary processes, which are not directly accessible via modern DNA.
 They are particularly suitable for the estimation of substitution rates
 because their ages provide calibrating information in phylogenetic
 analyses, circumventing the difﬁcult task of choosing independent
 calibration points. The substitution rates obtained from such datasets
 have typically been high, falling between the rates estimated from
 pedigrees and species phylogenies. Many of these estimates have been made
 using a Bayesian phylogenetic method that explicitly accommodates
 heterochronous data. Stimulated by recent criticism of this method, we
 present a comprehensive simulation study that validates its performance.
 For datasets of moderate si ze, i t produces accurate estimates of rates,
 while appearing robust to assumpti ons about demographic history. We then
 analyse a large collection of 749 ancient and 727 modern DNA sequences
 from 19 species of animals, plants and bacteria. Our new estimates conﬁrm
 that the substitution rates estimated from ancient DNA sequences are
 elevated above long-term phylogenetic levels.
description: Nene Data
 Setnene_mt.const.xmlBison Data Setbison.bsp.xmlCave Bear Data Setcavebear.const.xmlBrown Bear Data Setbrownbear.const.xmlBowhead Whale Data Setbowheadwhale.const.xmlCave Lion Data Setcavelion.const.xmlCow Data Setcow.bsp.xmlCave Hyaena Data Setcavehyaena.bsp.xmlMuskox Data Setmuskox.const.xmlMaize Data Setmaize.const.xmlTuco-Tuco Data Settucotuco.const.xmlHorse Data Sethorse.expon.xmlWoolly Mammoth Data Setwoollymammoth.const.xmlArctic Fox Data SetBEAST input files for ancient DNA data sets. Substitution models were selected by comparison of Akaike Information Criterion scores, and coalescent priors were chosen using Bayes Factor analysis.arcticfox.const.xmlAdelie Penguin Data SetBEAST input files for ancient DNA data sets. Substitution models were selected by comparison of Akaike Information Criterion scores, and coalescent priors were chosen using Bayes Factor analysis.adeliepenguin.const.xmlChlorobium Data Setchlorobium.expon.xmlData Sets and Population Genetic StatisticsSummary and neutrality statistics, model abbreviations, and data sources.rsbl20070377supp1.docBoar Data Setboar.const.xmlMoa Data Setmoa.const.xmlAurochs Data SetBEAST input files for ancient DNA data sets. Substitution models were selected by comparison of Akaike Information Criterion scores, and coalescent priors were chosen using Bayes Factor analysis.aurochs.bsp.xml