cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2122768
title: Data from: The mesic savannas of the Bateke Plateau: carbon stocks and floristic composition

description: The Bateke Plateau in the Republic of Congo is one of the last frontiers
 for ecology, with little known about its floristics and physiognomy.
 Despite occupying 89,800 km2 and its importance for local livelihoods, its
 ecology and ecosystem functions are poorly understood. Situated on
 Kalahari sands, the Bateke has a complex evolutionary history, mainly
 isolated from other savannas for much of its past, with currently
 unresolved ecological implications. Here we assess the biomass and
 floristic diversity of this savanna. We established four 25 ha permanent
 sample plots at two savanna sites, inventoried all trees, and assessed
 shrub, forb and grass species and biomass, and characterised the soils.
 Total plant carbon stocks (aboveground and belowground) were only 6.5 ±
 0.3 MgC/ha, despite precipitation of 1600 mm/yr. Over half the biomass was
 grass, with the remainder divided between trees and shrubs. The carbon
 stock of the system is mostly contained in the top layer of the soil (16.7
 ± 0.9 MgC/ha in 0-20 cm depth). We identified 49 plant species (4 trees,
 13 shrubs, 4 sedges, 17 forbs and 11 grass species), with an average
 species richness of 23 per plot. There is tree hyperdominance of
 Hymenocardia acida (Phyllanthaceae), and a richer herbaceous species
 composition dominated by Loudetia simplex and Hyparrhenia diplandra. The
 low carbon stocks and tree biodiversity, compared to other African
 savannas, is surprising considering the high rainfall. We speculate it is
 due to low nutrient soils, high fire frequency and the effect of a
 temporally variable and restricted connection to the main southern African
 savanna complex.
description: Nieto_Quintano_et_al_DATAplotsPlot level tree data (DBH&gt;10 cm) for 4 25-ha plots in the Bateke Plateau (plots LWR1 and LWR2 in Lefini Reserve and plots LLR1 and LLR2 in Lesio Louna Reserve)Nieto_Quintano_et_at_DATAsubplotsSpecies composition data (presence/absence) for 1-ha subplots, situated inside 4 plots of 25-ha (plots LWR1 and LWR2 in Lefini Reserve and plots LLR1 and LLR2 in Lesio Louna Reserve), located in the Bateke Plateau (Republic of Congo)Nieto_Quintano_et_al_DATASubplots_Grass_SaplingsSubplot level grass data (Above ground Carbon stocks) for 4 25-ha plots in the Bateke Plateau (plots LWR1 and LWR2 in Lefini Reserve and plots LLR1 and LLR2 in Lesio Louna Reserve), and Subplot level saplings/shrubs data (Above ground Carbon stocks) for 4 25-ha plots in the Bateke Plateau (plots LWR1 and LWR2 in Lefini Reserve and plots LLR1 and LLR2 in Lesio Louna Reserve).
DOI: 10.5061/dryad.q82nn
title: Data from: Opposing mechanisms drive richness patterns of core and transient bird species

description: Studies of biodiversity typically assume that all species are equivalent.
 However, some species in a community maintain viable populations in the
 study area, while others occur only occasionally as transient individuals.
 Here we show that North American bird communities can reliably be divided
 into core and transient species groups, and that the richness of each
 group is driven by different processes. The richness of core species is
 influenced primarily by local environmental conditions, while the richness
 of transient species is influenced primarily by the heterogeneity of the
 surrounding landscape. This demonstrates that the well-known effects of
 the local environment and landscape heterogeneity on overall species
 richness are the result of two sets of processes operating differentially
 on core and transient species. Models of species richness should focus on
 explaining two distinct patterns, those of core and transient species,
 rather than a single pattern for the community as a whole.
description: Core and transient
 species richness and environmental dataData.zipAnalysis codeScripts.zip
DOI: 10.5061/dryad.c7r8j
title: Data from: Relationships in the Lupinus albifrons species complex (Fabaceae) based on two highly variable chloroplast regions

description: The perennial lupines of western North America, previously suggested to be
 monophyletic, comprise an apparently rapid and recent species radiation
 concentrated in the California Floristic Province. The Lupinus albifrons
 species complex consists of a number of closely related yet
 morphologically variable taxa within the larger group of perennial
 lupines. We used sequence data from two rapidly evolving noncoding
 chloroplast regions to analyze relationships in the perennial lupines,
 with special emphasis on the Lupinus albifrons species complex. Sampling
 from throughout the ranges of species thought to be closely related to
 Lupinus albifrons, we found that this group is characterized by high
 genetic diversity not only between species, but also within species and
 even within populations. The results of this study call into question the
 monophyly of the western North American perennials. Only two taxa clearly
 emerge as deserving recognition at the species or subspecies level based
 on the molecular data: Lupinus paynei from Simi Valley, California, and
 Lupinus excubitus from eastern California and the San Gabriel Mountains.
 Although some taxonomic conclusions can be extrapolated from this study,
 overall, these results warn against undersampling in phylogenetic studies
 of recently evolved groups.
description: S10975Maximum likelihood
 phylogeny based on chloroplast sequencesTCS haplotype
 networkHaplotype network
 constructed using chloroplast sequencesonly_coded_indels_95.graphaj_lf_align_w_indelsSequence alignment of petA–psbJ + trnL–ndhF, with indels removed from the alignment itself and coded as presence/absence as a fused dataset. The MrBayes parameters are also included as a Nexus block at the end.aj_lf_fused_indels.nex
DOI: 10.5061/dryad.dg8q0
title: Data from: Dating the species network: allopolyploidy and repetitive DNA evolution in American daisies (Melampodium sect. Melampodium, Asteraceae)

description: Allopolyploidy has played an important role in the evolution of the
 flowering plants. Genome mergers are often accompanied by significant and
 rapid alterations of genome size and structure via chromosomal
 rearrangements and altered dynamics of tandem and dispersed repetitive DNA
 families. Recent developments in sequencing technologies and bioinformatic
 methods allow for a comprehensive investigation of the repetitive
 component of plant genomes. Interpretation of evolutionary dynamics
 following allopolyploidization requires both the knowledge of parentage
 and the age of origin of an allopolyploid. Whereas parentage is typically
 inferred from cytogenetic and phylogenetic data, age inference is hampered
 by the reticulate nature of the phylogenetic relationships. Treating
 subgenomes of allopolyploids as if they belonged to different species
 (i.e., no recombination among subgenomes) and applying cross-bracing
 (i.e., putting a constraint on the age difference of nodes pertaining to
 the same event), we can infer the age of allopolyploids within the
 framework of the multi-species coalescent within BEAST2. Together with a
 comprehensive characterization of the repetitive DNA fraction using the
 RepeatExplorer pipeline, we apply the dating approach in a group of
 closely related allopolyploids and their progenitor species in the plant
 genus Melampodium (Asteraceae). We dated the origin of both the
 allotetraploid, M. strigosum, and its two allohexaploid derivatives, M.
 pringlei and M. sericeum, which share both parentage and the direction of
 the cross, to the Pleistocene (less than 1.4 Ma). Thus, Pleistocene
 climatic fluctuations may have triggered formation of allopolyploids
 possibly in short intervals, contributing to difficulties in inferring the
 precise temporal order of allopolyploid species divergence of M. sericeum
 and M. pringlei. The relatively recent origin of the allopolyploids likely
 played a role in the near-absence of major changes in the repetitive
 fraction of the polyploids’ genomes. The repetitive elements most affected
 by the post-polyploidization changes represented retrotransposons of the
 Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of
 Ty3-gypsy family.
description: Dryad_Repo_for_Submission.tarA compressed archive of nexus alignments, Beast XML files and MCC trees from the analyses performed in this study. The subfolders are clearly labeled to indicate file and analysis type associated with each file.Supplementary Appendices and TablesThe PDF file containing the supplementary appendices (S1-S4) and supplementary tables (S1-S7) as cited in the manuscript. A table of contents is provided within the file for easier access.McCann_et_al_Dating_polyploids_Supplementary_Information.pdf
DOI: 10.5061/dryad.3mk7f2q
title: Data from: Environmental coupling of heritability and selection is rare and of minor evolutionary significance in wild populations

description: Predicting the rate of adaptation to environmental change in wild
 populations is important for understanding evolutionary change. However,
 predictions may be unreliable if the two key variables affecting the rate
 of evolutionary change, heritability and selection, are both affected by
 the same environmental variable. To determine how general such an
 environmentally induced coupling of heritability and selection is, and how
 this may influence the rate of adaptation, we made use of freely
 accessible, open data on pedigreed wild populations to answer this
 question at the broadest possible scale. Using 16 populations from 10
 vertebrate species, which provided data on 50 traits (body mass,
 morphology, physiology, behaviour and life history), we found evidence for
 an environmentally induced relationship between heritability and selection
 in only 6 cases, with weak evidence that this resulted in an increase or
 decrease in expected selection response. We conclude that such a coupling
 of heritability and selection is unlikely to strongly affect evolutionary
 change even though both heritability and selection are commonly postulated
 to be environment dependent.
description: Flycatcher_LD_filePhenotype (laying date) file for Pied flycatchers (Ficedula hypoleuca) in the Hoge Veluwe, NLPedigree_flycatchersPedigree file linking to the phenotype file.
DOI: 10.5061/dryad.3bc76
title: Data from: Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

description: Speciation often involves repeated episodes of genetic contact between
 divergent populations before reproductive isolation (RI) is complete.
 Whole-genome sequencing (WGS) holds great promise for unravelling the
 genomic bases of speciation. We have studied two ecologically divergent,
 hybridizing species of the ‘model tree’ genus Populus (poplars, aspens,
 cottonwoods), Populus alba and P. tremula, using &gt;8.6 million
 single nucleotide polymorphisms (SNPs) from WGS of population pools. We
 used the genomic data to (i) scan these species’ genomes for regions of
 elevated and reduced divergence, (ii) assess key aspects of their joint
 demographic history based on genomewide site frequency spectra (SFS) and
 (iii) infer the potential roles of adaptive and deleterious coding
 mutations in shaping the genomic landscape of divergence. We identified
 numerous small, unevenly distributed genome regions without fixed
 polymorphisms despite high overall genomic differentiation. The joint SFS
 was best explained by ancient and repeated gene flow and allowed
 pinpointing candidate interspecific migrant tracts. The direction of
 selection (DoS) differed between genes in putative migrant tracts and the
 remainder of the genome, thus indicating the potential roles of adaptive
 divergence and segregating deleterious mutations on the evolution and
 breakdown of RI. Genes affected by positive selection during divergence
 were enriched for several functionally interesting groups, including
 well-known candidate ‘speciation genes’ involved in plant innate immunity.
 Our results suggest that adaptive divergence affects RI in these
 hybridizing species mainly through intrinsic and demographic processes.
 Integrating genomic with molecular data holds great promise for revealing
 the effects of particular genetic pathways on speciation.
description: it_s1_10_10_29808Joint SFS between P. alba and P. tremula in Italy made with dadi from Pool-seq data, 24 individuals for each species downsampled to 10 diploid individuals, 29808 SNPRAD_it_s1Joint SFS for 20 P. alba and24 P. tremula in Italy for RAD-seq data made with dadi, downsampled to 15 and 15 individuals for a total of 8876 SNPs.script_inference_anneal2_newton_mis_0Script allowing to carry out demographic models comparisons using ∂a∂i on genomic data.dadi_define_modelsDefinition of the different 38 models of divergence used in our inferences with ∂a∂i. We corrected a typo in the definition of five models: IM2N2M2Pex; AM2N2M2Pex; PAM2N2M2Pex; SC2N2M2Pex; PSC2N2M2Pex. Parameters nu1 and nu2 were replaced by nua1 and nua2 in the more ancient timeDoSDirection of selection (DoS) script:
DOI: 10.5061/dryad.8616
title: Data from: Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)

description: The capelin (Mallotus villosus) is a widespread marine fish species for
 which previous work has identified geographically distinct mtDNA clades,
 the frontiers of which are well within adult and larval dispersal
 capabilities. Here, we use AFLPs to test for the presence of nuclear gene
 flow among clades. In addition, we evaluate genetic structuring within one
 clade, the Northwest Atlantic (NWA). We found that each of the mtDNA
 clades corresponds with a unique nuclear DNA genetic cluster. Within the
 NWA clade, we detected individuals with small but significant amounts of
 genetic ancestry from other clades, likely due to historical
 introgression. Further support for historical introgression comes from
 analyses of variance in locus-specific differentiation, which support
 introgression between some clades and divergence without gene flow between
 others. Within the NWA, we identified two genetic clusters that correspond
 to sites in geographically adjacent areas. However, these clusters differ
 primarily at ‘outlier’ loci, and a genetic subdivision (K = 2) was not
 supported by genetic clustering programs using neutral loci. Significant
 neutral FST differentiation was found only between sites that otherwise
 differed at outlier loci. Thus, these populations may be in the initial
 stages of ‘isolation by adaptation’. These results suggest strong
 between-clade reproductive isolation despite opportunities for gene flow
 and support the hypothesis that selection can contribute to divergence in
 otherwise ‘open’ systems.
description: colbeck_allsitesAFLP datafile for all sites used in phylogeographic analysiscolbeck_introgressionAFLP data file from analysis of between clade introgressioncapelin_274_ind_134_loci
DOI: 10.6084/m9.figshare.30170305.v1
title: A global image-based data repository of killer whale interactions with elasmobranchs - Metadata

description: Killer whales (<i>Orcinus orca</i>) are cosmopolitan apex predators that interact with numerous species, including sharks, skates, and rays (subclass Elasmobranchii). Interactions between killer whales and elasmobranchs have garnered attention from the scientific community, but the dynamics of these events are poorly understood, as interactions are often challenging to observe. In this study, we collated imagery of interactions between killer whales and elasmobranchs to create the first image-based repository of interspecific interactions between marine predators. A total of 320 photos and videos from 82 unique interactions were collected from 12 countries. A minimum of 18 elasmobranch species across 16 genera were identified from the imagery. Furthermore, 10 different interaction types were documented, encompassing both predatory and non-predatory behavior. This dataset can provide insight into various research topics, including killer whale predation techniques, elasmobranch behavior, and the identification of individual killer whales that specialize in elasmobranch prey. As a new and openly accessible resource, this dataset provides the foundation to support future ecological and behavioral research on killer whale and elasmobranch interactions.
DOI: 10.5061/dryad.9r5v7
title: Data from: Deciphering the evolutionary history and developmental mechanisms of a complex sexual ornament: the abdominal appendages of Sepsidae (Diptera)

description: Male abdomen appendages are a novel trait found within Sepsidae (Diptera).
 Here we demonstrate that they are likely to have evolved once, were lost
 three times, and then secondarily gained in one lineage. The developmental
 basis of these appendages was investigated by counting the number of
 histoblast cells in each abdominal segment in four species: two that
 represented the initial instance of appendage evolution, one that has
 secondarily gained appendages, and one species that did not have
 appendages. Males of all species with appendages have elevated cell counts
 for the fourth segment, which gives rise to the appendages. In Perochaeta
 dikowi, which reacquired the trait, the females also have elevated cell
 count on the fourth segment despite the fact that females do not develop
 appendages. The species without appendages has similar cell counts in all
 segments regardless of sex. These results suggest that the basis for
 appendage development is shared in males across all species, but the
 sexual dimorphism is regulated differently in P. dikowi.
description: M.fasciculatus cell
 countsCell counts for all
 histoblast nests in both males and females of the species Meroplius
 fasciculatus.P.dikowi cell
 countsCell counts for all
 histoblast nests in both males and females of the species Perochaeta
 dikowi.T.biloba cell
 countsCell counts for all
 histoblast nests in both males and females of the species Themira biloba.
 Anterior Dorsal (A), Posterior dorsal (P) and Ventral (V) were all counted
 twice as described in the methods.S.punctum cell
 countsCell counts for each
 histoblast nest in the species S. punctum, including both males and
 females. Counts are organized by sex, segment number, and then nest. The
 nest abbreviations are A, anterior dorsal; P, posterior dorsal and V,
 ventral. Contact Julia Bowsher for questions regarding this
 file.sepsidae_matrixThis is a Mesquite file that contains the character matrix. Contact Rudolf Meier for questions regarding this file.brush+250bootThis is a Mesquite file that contains the appendage character sets for the bootstrap analysis. Contact Rudolf Meier for questions regarding this file.brush+250boot+best_likelihoodThis is a Mesquite file that contains the tree sets for the likelihood analysis. Contact Rudolf Meier for questions regarding this file.brush+250boot+best_parsimonyThis is a Mesquite file that contains the tree sets for the parsimony analysis. Contact Rudolf Meier for questions regarding this file.brush+250boot+best_stepmatrixThis is a Mesquite file that contains the stepmatrix. Contact Rudolf Meier for questions regarding this file.brush+250boot+bestThis is a Mesquite file. Contact Rudolf Meier for questions regarding this file.
DOI: 10.5061/dryad.k89b2ps8
title: Data from: Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast

description: In addition to genetic differences between individuals due to nucleotide
 sequence variation, epigenetic changes experienced by genotypes due to DNA
 methylation may also contribute to population niche width, an intriguing
 possibility that remains essentially untested. Using the nectar-living
 yeast Metschnikowia reukaufii as study subject, we examine the hypothesis
 that changes in genome-wide DNA methylation patterns underly the ability
 of this fugitive species to exploit a broad resource range in its
 heterogeneous patchy environment. Data on floral nectar characteristics
 and use by M. reukaufii in the wild were combined with laboratory
 experiments and methylation sensitive amplified polymorphism (MSAP)
 analyses designed to detect epigenetic responses of single genotypes to
 variations in sugar environment that mimicked those occurring naturally in
 nectar. Metschnikowia reukaufii exploited a broad range of resources,
 occurring in nectar of 48% of species and 52% of families surveyed, and
 its host plants exhibited broad intra- and interspecific variation in
 sugar-related nectar features. Under experimental conditions, sugar
 composition, sugar concentration, and their interaction influenced
 significantly the mean probability of MSAP markers experiencing a
 transition from unmethylated to methylated state. The methylation
 inhibitor 5-Azacytidine had strong inhibitory effects on M. reukaufii
 proliferation in sugar-containing media, and a direct relationship existed
 across sugar x concentration experimental levels linking inhibitory effect
 of 5-Azacytidine and mean per-marker probability of genome-wide
 methylation. DNA methylation polymorphisms induced by variable sugar
 environments allowed genotypes to grow successfully in extreme sugar
 environments, and the broad population niche width of M. reukaufii was
 largely made possible by environmentally-induced epigenetic changes
 enabling genotype plasticity in resource use.
description: Metschnikowia reukaufii
 MSAP fingerprintsMethylation sensitive
 amplified polymorphism (MSAP)fingerprints of the Metschnikowia reukaufii
 strains used in this study obtained under control and experimental
 conditions in media differing in sugar composition and
 concentration.Metschnikowia_reukaufii_MSAP_fingerprints.xlsxMetschnikowia reukaufii growth experimentsRaw results of the Metschnikowia reukaufii growth experiments, involving replica-plating the five strains in experimental media with and without 5-Azacytidine, and differing also in sugar composition (sucrose, glucose or fructose) and sugar concentration (20%, 30%, 40% or 50%). Colony growth was scored on an ordinal scale from 0 (no growth) to 4 (maximum growth, thickest and broadest colony) on days 2, 7, 12 and 17 after plating.Metschnikowia_reukaufii_growth_experiments.xlsx