cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t85bf04
title: Data from: Species interactions limit the occurrence of urban-adapted birds in cities

description: Urbanization represents an extreme transformation of more natural systems.
 Populations of most species decline or disappear with urbanization, and
 yet some species persist and even thrive in cities. What determines which
 species persist or thrive in urban habitats? Direct competitive
 interactions among species can influence their distributions and resource
 use, particularly along gradients of environmental challenge. Given the
 challenges of urbanization, similar interactions may be important for
 determining which species persist or thrive in cities; however, their role
 remains poorly understood. Here we use a global dataset to test among
 three alternative hypotheses for how direct competitive interactions and
 behavioral dominance may influence the breeding occurrence of birds in
 cities. We find evidence to support the Competitive Interference
 Hypothesis: behaviorally dominant species were more widespread in urban
 habitats than closely-related subordinate species, but only in taxa that
 thrive in urban environments (hereafter, urban-adapted), and only when
 dominant and subordinate species overlapped their geographic ranges. This
 result was evident across diverse phylogenetic groups, but varied
 significantly with a country’s level of economic development.
 Urban-adapted, dominant species were more widespread than closely-related
 subordinate species in cities in developed, but not developing, countries;
 countries in economic transition showed an intermediate pattern. Our
 results provide evidence that competitive interactions broadly influence
 species responses to urbanization, and that these interactions have
 asymmetric effects on subordinate species that otherwise could be
 widespread in urban environments. Results further suggest that economic
 development might accentuate the consequences of competitive interactions,
 thereby reducing local diversity in cities.
description: Behavioural dominance
 dataDetails of behavioural
 dominance relationships among focal species pairs.urban.data.dominance.txtDataset used in analysisDataset used in analysis, corresponding to the R code.urban.data.for.analysis.csvFull raw datasetRaw dataset including all responses entered separately.urban.data.raw.responses.csvSubset of dataset for species pairs with quantitative dominance dataSubset of dataset for species pairs with either accessible, quantitative data on dominance relationships, or whose dominance relationships are based on the results of experiments. Dataset corresponds to a supplemental analysis (see R code line 2344).subset.quant.urban.data.for.analysis.csvR code for analysisR code for all analyses and figures.urban.analysis.RPhylogenyPhylogeny of focal species used in analyses, in Newick formaturban.tree.final
DOI: 10.25345/c5vq2sq44
title: MassIVE MSV000100601 - Isochrysis galbana microbiome members - Vreelandella alkaliphila and coculture with Sulfitobacter pontiacus
title: Study investigating the metabolomics profiles of a microalgal derived Vreelandella alkaliphila and Sulfitobacter pontiacus.
DOI: 10.48656/2704-0985
title: StoBerMan - Ein Instrument zur Erhebung von Bewegungsereignisbeschreibungen
title: StoBerMan - An instrument to elicit motion event descriptions
title: StoBerMan - Un instrument pour obtenir des descriptions d'événements de mouvement
title: StoBerMan - Uno strumento per la descrizione degli eventi di movimento
DOI: 10.5061/dryad.7j83s
title: Data from: Primate diversification inferred from phylogenies and fossils

description: Biodiversity arises from the balance between speciation and extinction.
 Fossils record the origins and disappearance of organisms, and the
 branching patterns of molecular phylogenies allow estimation of speciation
 and extinction rates, but the patterns of diversification are frequently
 incongruent between these two data sources. I tested two hypotheses about
 the diversification of primates based on ~600 fossil species and 90%
 complete phylogenies of living species: 1) diversification rates increased
 through time; 2) a significant extinction event occurred in the Oligocene.
 Consistent with the first hypothesis, analyses of phylogenies consistently
 supported increasing speciation rates and negligible extinction rates. In
 contrast, fossils showed that while speciation rates increased, speciation
 and extinction rates tended to be nearly equal, resulting in zero net
 diversification. Partially supporting the second hypothesis, the fossil
 data recorded a clear pattern of diversity decline in the Oligocene,
 although diversification rates were near zero. The phylogeny supported
 increased extinction ~34 Ma, but also elevated extinction ~10 Ma,
 coinciding with diversity declines in some fossil clades. The results
 demonstrated that estimates of speciation and extinction ignoring fossils
 are insufficient to infer diversification and information on extinct
 lineages should be incorporated into phylogenetic analyses.
description: Supplementary
 MaterialsAppendix to accompany
 the manuscript: Primate diversification dynamics inferred from fossils and
 phylogenies.Supplementary materials for
 Primate diversification round
 3.docxTable S1. Model fit
 resultsTable S1. Full results
 of RPANDA model comparisons with four different time-calibrated
 trees.Raw data on fossil
 taxonomy and agesRaw data on fossil
 taxonomy, first and last appearance dates (FAD, LAD, respectively), and
 number of occurrences, with ages and references from PBDB and the
 literature search performed in this study.Table S3. Raw data on
 fossils.xlsxTable S4. PBDB raw
 dataRaw data and references
 downloaded from Paleobiology DatabaseR code for Herrera
 Primate diversificationR code to run RPANDA
 phylogenetic diversification analysis, and fossil data preparation for
 PYRATE as well as analyses with PALEOTREEPhylogenetic trees from
 Springer et al. 2012Raw tree files of four
 phylogenetic trees from Springer et al. 2012 for all primates with
 different age calibration assumptionsspringer_trees.tre
DOI: 10.48656/tw59-yn81
title: StoBerMan - Ein Instrument zur Erhebung von Bewegungsereignisbeschreibungen
title: StoBerMan - An instrument to elicit motion event descriptions
title: StoBerMan - Un instrument pour obtenir des descriptions d'événements de mouvement
title: StoBerMan - Uno strumento per la descrizione degli eventi di movimento
DOI: 10.5061/dryad.344852tm
title: Data from: Identifying insecticide resistance genes in mosquito by combining AFLP genome scan and 454 pyrosequencing

description: AFLP-based genome scans are widely used to study the genetics of
 adaptation and to identify genomic regions potentially under selection.
 However, this approach usually fails to detect the actual genes or
 mutations targeted by selection due to the difficulty to obtain the
 sequences from AFLP fragments. Here we combine classical AFLP outlier
 detection to 454 sequencing of AFLP fragments obtained from chosen
 individuals to obtain the sequence of outliers. We applied this approach
 to the study of resistance to Bacillus thuringiensis israelensis (Bti)
 toxins in the dengue vector Aedes aegypti. A genome scan of Bti-resistant
 and Bti-susceptible Aedes aegypti laboratory strains was performed based
 on 432 AFLP markers. Fourteen outliers were detected using two different
 population genetics algorithms, a frequentist and a Bayesian approach. Out
 of these, 11 were successfully sequenced. Three contained transposable
 elements (TEs) sequences. The 10 outliers that could be mapped at a unique
 location in the reference genome were located on different supercontigs,
 underlying the multigenic basis of resistance to Bti toxins. One outlier
 was in the vicinity of a gene coding for an aminopeptidase potentially
 involved in Bti toxin binding. Patterns of sequence variability of this
 gene showed significant deviation from neutrality in the resistant strain
 but not in the susceptible strain, even after taking into account the
 known demographic history of the selected strain. This gene is a promising
 candidate for future functional analysis.
description: 454 AFLP fragments
 sequencing454 complete (CR) and
 incomplete reads (IR) for 22 AFLP profiles of susceptible individuals
 (Bora-Bora strain: Ae) and Bti resistant individuals (LiTOX
 strain)fichiers base de donnees
 publication.zipSequences of a candidate
 gene for Bti resistance in Aedes aegyptiBatch of aligned
 sequences (Sanger) of exon 2 (1004 bp) of puromycin-sensitive
 aminopeptidase (AAEL012918) from 11 susceptible individuals (Bora-Bora
 strain) and 12 Bti-resistant individuals (LiTOX strain)BatchAAEL012918.sqnAFLP ProfilesAFLP profilesAFLPprofiles.zip
DOI: 10.5061/dryad.n40h2
title: Data from: A suite of genetic markers useful in assessing wildcat (Felis silvestris ssp.) - domestic cat (Felis silvestris catus) admixture

description: The wildcat (Felis silvestris ssp.) is a conservation concern largely due
 to introgressive hybridization with its congener F. s. catus, the common
 domestic cat. Because of a recent divergence and entirely overlapping
 ranges, hybridization is common and pervasive between these taxa
 threatening the genetic integrity of remaining wildcat populations.
 Identifying pure wildcats for inclusion in conservation programs using
 current morphological discriminants is difficult because of gross
 similarity between them and the domestic, critically hampering
 conservation efforts. Here we present a vetted panel of microsatellite
 loci and mitochondrial polymorphisms informative for each of the five
 naturally evolved wildcat subspecies and the derived domestic cat. We also
 present reference genotypes for each assignment class. Together, these
 marker sets and corresponding reference genotypes allow for the
 development of a genetic rational for defining ‘units of conservation’
 within a phylogenetically based taxonomy of the entire F. silvestris
 species complex. We anticipate this marker panel will allow conservators
 to assess genetic integrity and quantify admixture in managed wildcat
 populations and to be a starting point for more in-depth analysis of
 hybridization.
description: ST1Genotyped
 individualsST2 3 &
 4Supplementary Table 2:
 Mitochondrial sequence alignment showing variable sites. Supplementary
 Table 3: Synopsis alignment of Felis silvestris phylogenetically
 informative mitochondrial sites. Supplementary Table 4: Primer sequences
 for mitochondrial amplification of F. silvestris ssp. informative
 sites.ST5Supplementary Table 5:
 STR genotypes ascertained in range-wide survey. Header rows indicate cat
 chromosome location of STR loci with distances given according to
 conventions used in PHASE (STEPHENS 2004). Alleles are indicated by
 base-pair length. Missing data is denoted by -9. Individual cats are
 listed by LGD code in column one. Refer to Supplemental Table 1 for
 additional information regarding provenance and taxonomic assignment. Data
 is provided for 77 loci, however only the 36 that amplified most
 completely across different runs were further characterized and used in
 published analysis (DRISCOLL et al. 2007). A limited examination of
 alternative locus combinations (data not shown) that include loci other
 than the published 36 indicates similar levels of performance. For future
 studies requiring the greatest genetic resolution these additional data
 could be considered.ST6Supplementary Table 6:
 Locus by locus tabulation of allele frequencies broken down by results of
 categorical genetic assignments.J_of_H_Wildcat_Genetic_Diagnostics_supplement_final(3)Supplementary material
DOI: 10.5061/dryad.c5m42
title: Data from: Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection

description: Molecular evolutionary rate heterogeneity—the violation of a molecular
 clock—is a prominent feature of many phylogenetic datasets. It has
 particular importance to systematists not only because of its biological
 implications, but also for its practical effects on our ability to infer
 and date evolutionary events. Here we show, using both maximum likelihood
 and Bayesian approaches, that a remarkably strong increase in substitution
 rate in the vittarioid ferns is consistent across the nuclear and plastid
 genomes. Contrary to some expectations, this rate increase is not due to
 selective forces; the vittarioids bear no signature of the change in the
 relative strengths of selection and drift that one would expect if the
 rate increase was caused by altered fixation rates. Instead, the
 substitution rate increase appears to stem from an elevated supply of
 mutations, perhaps limited to the vittarioid ancestral branch. This
 generalized rate increase is accompanied by extensive fine-scale
 heterogeneity in rates across loci, genomes, and taxa. Our analyses
 demonstrate the power and flexibility of trait-free investigations of rate
 heterogeneity within a model selection framework, emphasize the importance
 of explicit tests for signatures of selection prior to invoking
 selection-related or demography-based explanations for patterns of rate
 variation, and illustrate some unexpected nuances in the behavior of
 relaxed clock methods for modeling rate heterogeneity, with implications
 for our ability to confidently date divergence events. In addition, our
 data provide strong support for the monophylly of Adiantum, and for the
 position of Calciphilopteris in the cheilanthoid ferns, two relationships
 for which convincing support was previously lacking.
description: codon_all_genesNexus file for the codon-based analyses.Dryad_BASEML_results_summaryOutputs from BASEML runs (part of the PAML package).Dryad_CODEML_results_summaryOutputs from CODEML (part of the PAML package).nucleotide_all_dataNexus file for nucleotide-model based analyes (including a block of recoded indels).SI_Appendix1PAMLparser, a Python script for organizing PAML outputs (from both CODEML and BASEML) and reformated them in tab-delimited files.SI_Fig1Phylogeny of the gapCp "retained clones." Includes gapC, gapCp "short," and gapCp "long" sequences.SI_Table1Primers used in amplification and sequencing.SI_Table2Voucher table and sequence data for the broad gapCp and gapC family sequences.SI Table 3SI_Fig2SI_Fig3
DOI: 10.5061/dryad.h4qn5
title: Data from: Enlarged multilocus dataset provides surprisingly younger time of origin for the Plethodontidae, the largest family of salamanders

description: Deep phylogenetic relationships of the largest salamander family
 Plethodontidae have been difficult to resolve, probably reflecting a rapid
 diversification early in their evolutionary history. Here, data from 50
 independent nuclear markers (total 48,582 bp) are used to reconstruct the
 phylogeny and divergence times for plethodontid salamanders, using both
 concatenation and coalescence-based species tree analyses. Our results
 robustly resolve the position of the enigmatic eastern North American
 four-toed salamander (Hemidactylium) as the sister taxon of
 Batrachoseps + Tribe Bolitoglossini, thus settling a long-standing
 question. Furthermore, we statistically reject sister taxon status of
 Karsenia and Hydromantes, the only plethodontids to occur outside the
 Americas, leading us to new biogeographic hypotheses. Contrary to previous
 long-standing arguments that plethodontid salamanders are an old lineage
 originating in the Cretaceous (more than 90 Ma), our analyses lead to the
 hypothesis that these salamanders are much younger, arising close to the
 K-T boundary (∼66 Ma). These time estimates are highly stable using
 alternative calibration schemes and dating methods. Our data simulation
 highlights the potential risk of making strong arguments about
 phylogenetic timing based on inferences from a handful of nuclear genes, a
 common practice. Based on the newly obtained timetree and ancestral area
 reconstruction results, we argue that (i) the classic “Out of Appalachia”
 hypothesis of plethodontid origins is problematic; (ii) the common
 ancestor of extant plethodontids may have originated in northwestern North
 America in the early Paleocene; (iii) origins of Eurasian plethodontids
 likely result from two separate dispersal events from western North
 America via Beringia in the late Eocene (∼42 Ma) and the early Miocene
 (∼23 Ma), respectively.
description: Shen_et_al_Supplementary_MaterialsThis zip package includes data matrices and resulting trees, as well as supplementary tables and figures.
DOI: 10.5061/dryad.s27v5b0
title: Data from: Ecological crossovers of sexual signalling in a migratory bird

description: Environmental shifts may induce sudden reversals in the relative quality
 or sexual attractiveness of mates (ecological cross-overs) leading to
 non-directional sexual selection. Studies on such ecological cross-overs
 induced by environmental shifts during the non-breeding season are
 particularly rare. We studied the interactive effects between wintering
 conditions and a male white wing patch on the breeding success of breeding
 pairs and the local survival of females in a migratory passerine
 population over a 32-year period. After dry winters, females paired with
 large-patched males were more likely to survive than those paired with
 small-patched males, and vice versa after moist winters. Moreover, after
 dry winters, large-patched males succeeded in attracting females that laid
 large clutches, while small-patched males bred with females that laid
 small clutches, and vice versa after moist winters. This phenomenon led to
 a difference in fledgling numbers only during years with dry winters and
 high precipitation during the breeding season. The selection on this male
 trait and its signalling value to females thus depended on a complex
 interaction between conditions both at the wintering and breeding grounds.
 We show that it is important to consider conditions during the
 non-breeding season when examining the effects of sexual ornaments on
 fitness.
description: DATA_Teerikorpi_etal_2018The data set is composed of one excel file with two data sheets. One sheet is for population level analyses and the other one is for individual level analysis. Data includes an environmental variable (NAO index) describing environmental conditions at the wintering areas of pied flycatchers in Sub-Saharan Africa (1983-2014) and phenotypic (wing patch size) information of male pied flycatcher individuals caught during the breeding seasons (1983-2014) in Turku and Siuntio, Finland.DATA_Ecological_crossovers_Teerikorpi_etal_2018.xlsSAS_codes_Teerikorpi_etal.2018SAS codes for the analyses conducted in Teerikorpi et al. 2018SAS_codes_Ecological_crossovers_Teerikorpi_etal.2018.docx
DOI: 10.5061/dryad.g4f84
title: Data from: Breeding system evolution influenced the geographic expansion and diversification of the core Corvoidea (Aves: Passeriformes)

description: Birds vary greatly in their life-history strategies, including their
 breeding systems, which range from brood parasitism to a system with
 multiple non-breeding helpers at the nest. By far the most common
 arrangement, however, is where both parents participate in raising the
 young. The traits associated with parental care have been suggested to
 affect dispersal propensity and lineage diversification, but to date tests
 of this potential relationship at broad temporal and spatial scales have
 been limited. Here, using data from a globally distributed group of
 corvoid birds in concordance with state-dependent speciation and
 extinction models, we suggest that pair breeding is associated with
 elevated speciation rates. Estimates of transition between breeding
 systems imply that cooperative lineages frequently evolve biparental care,
 whereas pair breeders rarely become cooperative. We further highlight that
 these groups have differences in their spatial distributions, with pair
 breeders over-represented on islands, and cooperative breeders mainly
 found on continents. Finally, we find that speciation rates appear to be
 significantly higher on islands compared to continents. These results
 imply that the transition from cooperative breeding to pair breeding was
 likely a significant contributing factor facilitating dispersal across
 tropical archipelagos, and subsequent world-wide phylogenetic expansion
 among the core Corvoidea.
description: core Corvoidea -
 polytomy resolved trees (763 species)CC_763_trees.nexcore Corvoidea - molecular data only trees (604 species)CC_604_trees.nexcore Corvoidea supermatrixcore_corvoidea_supermatrix.nex
DOI: 10.5061/dryad.m0s82c3
title: Data from: The unexpected genetic mating system of the red‐backed toadlet (Pseudophryne coriacea): a species with prolonged terrestrial breeding and cryptic reproductive behaviour

description: Molecular technologies have revolutionised our classification of
 animal-mating systems, yet we still know very little about the
 genetic-mating systems of many vertebrate groups. It is widely believed
 that anuran amphibians have the highest reproductive diversity of all
 vertebrates, yet genetic mating systems have been studied in less than one
 percent of all described species. Here, we use SNPs to quantify the
 genetic-mating system of the terrestrial breeding red-backed toadlet
 Pseudophryne coriacea. In this species, breeding is prolonged
 (approximately 5 months), and males construct subterranean nests in which
 females deposit eggs. We predicted that females would display extreme
 sequential polyandry because this mating system has been reported in a
 closely-related species (P. bibronii). Parentage analysis revealed that
 mating success was heavily skewed towards a subset of males (30.6% of
 potential sires), and that nearly all females (92.6%) mated with one male.
 In a high percentage of occupied nests (37.1%) the resident male was not
 the genetic sire, and very few nests (4.3%) contained clutches with
 multiple paternity. Unexpectedly, these results show that sequential
 polyandry is rare. They also show that there is a high frequency of nest
 takeover and extreme competition between males for nest sites, but that
 males rarely sneak matings. Genetic analysis also revealed introgressive
 hybridisation between P. coriacea and the red-crowned toadlet (P.
 australis). Our study demonstrates a high level of mating system
 complexity and it shows that closely-related anurans can vary dramatically
 in their genetic-mating system.
description: Hamming distance matrix
 - Pseudophyne coriaceaSNP Hamming distance
 values between siblings, adults and offspring from a population of
 Pseudophryne coriacea .O'BrienEtAl_HammingDistanceValues.xlsxSNP scoring data - Pseudophryne coriaceaO'BrienEtAl_SNPscoring.xlsx