cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r2n58
title: Data from: Genetic history of a colonising population: Drosophila buzzatii (Diptera: Drosophilidae) in Australia

description: Drosophila buzzatii Patterson & Wheeler, a cactophilic species
 that feeds and breeds in the rotting tissues of various Opuntia cactus
 species, was inadvertently introduced to Australia from Argentina sometime
 during the period 1931–1936. After a bottleneck at introduction, its
 spread through the cactus distribution was probably very rapid as a result
 of natural dispersal from the site of introduction and from three other
 foci colonized from the introduction site by human intervention. By 1940,
 the Opuntia distribution and consequently that of D. buzzatii was reduced
 to spatially isolated populations, with probable further bottlenecking of
 at least some of the D. buzzatii populations. Allozyme data (primarily six
 polymorphic loci) from flies collected during April 1972 to February 1996
 at 67 localities were used to examine current population differentiation
 and relationships, as well as to infer aspects of their demographic
 history. Although there is significant isolation-by-distance, genetic
 relationships among the populations are not simply related to geographical
 distance, implying that genetic drift has contributed to population
 differentiation. However, the biotic and, to an extent, the physical
 environment are not the same in Australia as in Argentina. Consequently,
 exposure to novel environments has led to local adaptation and further
 population differentiation. Genetic variation and the structure of
 Australian populations apparently are determined by founder effects
 (drift) at the level of individual breeding sites (cactus rots), by
 diversifying selection among rots within a locality, as well as by drift
 and geographically varying selection among localities.
description: D
 buzzatii_GENEPOP_data_fileGenotypic data for seven
 allozyme loci for D. buzzatii flies collected at 67 localities, with a
 total of 195 samples (collections made more than once at 26 localities).
 File format - GENEPOPSupplementary Table
 1Identification of the 67
 localities (listed north to south), locality code numbers, geographical
 coordinates and sample size (number of genes assayed)
DOI: 10.5061/dryad.77f5q
title: Data from: Size-selectivity of predation by brown bears depends on the density of their sockeye salmon prey

description: Can variation in prey density drive changes in the intensity or direction
 of selective predation in natural systems? Despite ample evidence of
 density-dependent selection, the influence of prey density on predatory
 selection patterns has seldom been investigated empirically. We used 20
 years of field data on brown bears (Ursus arctos) foraging on sockeye
 salmon (Oncorhynchus nerka) in Alaska, to test the hypothesis that salmon
 density affects the strength of size-selective predation. Measurements
 from 41,240 individual salmon were used to calculate variance-standardized
 selection differentials describing the direction and magnitude of
 selection. Across the time series, the intensity of predatory selection
 was inversely correlated with salmon density; greater selection for
 smaller salmon occurred at low salmon densities as bears’ tendency to kill
 larger-than-average salmon was magnified. This novel connection between
 density dependence and selective predation runs contrary to some aspects
 of optimal foraging theory and differs from many observations of
 density-dependent selection because (1) the direction of selection remains
 constant while its magnitude changes as a function of density and (2)
 stronger selection is observed at low abundance. These findings indicate
 that sockeye salmon may be subject to fishery-induced size selection from
 both direct mechanisms and latent effects of altered predatory selection
 patterns on the spawning grounds, resulting from reduced salmon abundance.
description: Hansen Creek, Alaska
 Survey Data for sockeye salmon (Oncorhynchus nerka)These data are a
 compilation of daily stream surveys in conjunction with a long-term study
 of the evolutionary ecology of sockeye salmon (Oncorhynchus nerka) in
 Hansen Creek, a tributary of the Wood River system of Bristol Bay, Alaska.
 Data pertaining to tagged fish from 1990 to 1993 have been compiled from
 Dr. Ruggerone. Data from 1997-2012 are daily records of all dead salmon
 observed at the mouth of Hansen Creek and within the stream proper and
 have been collected primarily by Dr. Quinn. Mode of death and associated
 physical metadata are included.Cunningham Data for
 DRYAD.xlsx
DOI: 10.5061/dryad.74j5g
title: Data from: Timetree of Aselloidea reveals species diversification dynamics in groundwater

description: A key challenge for biologists is to document and explain global patterns
 of diversification in a wide range of environments. Here, we explore
 patterns of continental-scale diversification in a groundwater
 species-rich clade, the superfamily Aselloidea (Pancrustacea: Isopoda).
 Our analyses supported a constant diversification rate during most of the
 course of Aselloidea evolution, until 4–15 Ma when diversification rates
 started to decrease. This constant accumulation of lineages challenges the
 view that groundwater species diversification in temperate regions might
 have been primarily driven by major changes in physical environment
 leading to the extinction of surface populations and subsequent
 synchronous isolation of multiple groundwater populations. Rather than
 acting synchronously over broad geographic regions, factors causing
 extinction of surface populations and subsequent reproductive isolation of
 groundwater populations may act in a local and asynchronous manner,
 thereby resulting in a constant speciation rate over time. Our phylogeny
 also revealed several cases of parapatric distributions among closely
 related surface-water and groundwater species suggesting that species
 diversification could also arise from a process of disruptive selection
 along the surface-subterranean environmental gradient. Our results call
 for re-evaluating the spatial scale and timing of factors causing
 diversification events in groundwater.
description: Online Appendix
 1Map
 of sampled sitesonline_appendix_1.pdfOnline Appendix 2COI datasetonline_appendix_2.pdfOnline Appendix 3PCR Primersonline_appendix_3.pdfOnline Appendix 4Molecular dating priorsonline_appendix_4.pdfOnline Appendix 5Evolutionary unit datasetonline_appendix_5.pdfOnline Appendix 6Plots of absolute diversification age estimates (Ma) for different Bayesian relaxed molecular clock modelsonline_appendix_6.pdfOnline Appendix 7Age (in Ma) of shifts in diversification rate inferred by birth-death-shift analyses on Multidivtime chronogramsonline_appendix_7.pdfData.nexData_table
DOI: 10.5061/dryad.bn281
title: Data from: Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)

description: Phylogenetic relationships among recently diverged species are often
 difficult to resolve due to insufficient phylogenetic signal in available
 markers and/or conflict among gene trees. Here we explore the use of
 reduced-representation genome sequencing, specifically in the form of
 restriction-site associated DNA (RAD), for phylogenetic inference and the
 detection of ancestral hybridization in non-model organisms. As a case
 study, we investigate Pedicularis section Cyathophora, a systematically
 recalcitrant clade of flowering plants in the broomrape family
 (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood
 and Bayesian concordance, were applied to data sets that included as many
 as 40,000 RAD loci. Both methods yielded similar topologies that included
 two major clades: a “rex-thamnophila” clade, composed of two species and
 several subspecies with relatively low floral diversity, and
 geographically widespread distributions at lower elevations, and a
 “superba” clade, composed of three species characterized by relatively
 high floral diversity and isolated geographic distributions at higher
 elevations. Levels of molecular divergence between subspecies in the
 rex-thamnophila clade are similar to those between species in the superba
 clade. Using Patterson’s D-statistic test, including a novel extension of
 the method that enables finer-grained resolution of introgression among
 multiple candidate taxa by removing the effect of their shared ancestry,
 we detect significant introgression among nearly all taxa in the
 rex-thamnophila clade, but not between clades or among taxa within the
 superba clade. These results suggest an important role for geographic
 isolation in the emergence of species barriers, by facilitating local
 adaptation and differentiation in the absence of homogenizing gene flow.
description: python script to
 simulate RAD sequencesUses the egglib python
 module to simulate RAD sequences evolving on a phylogeny under a
 coalescent model with or without introgression between
 lineages.sim_introgress.pysequences at NCBI SRA: SRR833563raw RADseq files for the 13 samples used in this studyaligned loci for introgression analyses: min4_wo.readloci.txtaligned RADseq loci in readable format produced by pyRAD and used as input for introgression analysesmin4_wo.readloci.txtTable_S1: specimen voucher informationspecimen voucher informationTable_S1.xlsTable_S2: BUCKy outputResults of Bayesian concordance analysis in BUCKy at two values for the prior alphaTable_S2.xlsTable_S3: D-statistic introgression resultsfour taxon D-statistic and five-taxon partitioned D-statistic results testing introgression on simulated and empirical dataTable_S3.xlstreebase accession number 14102Link to treebase data. ML and BCA trees: http://purl.org/phylo/treebase/phylows/study/TB2:S14102
DOI: 10.7927/adkr-bn17
title: IPCC AR6 Synthesis Report LR Figure 3.4 (a): Sea level rise: observations and projections 2020-2100, 2150, 2300 (relative to 1900)

description: Global mean sea level change in metres relative to 1900. The historical changes (black) are observed by tide gauges before 1992 and altimeters afterwards. The future changes to 2100 and for 2150 (coloured lines and shading) are assessed consistently with observational constraints based on emulation of CMIP, ice-sheet, and glacier models, and median values and likely ranges are shown for the considered scenarios. Relative to 1995–2014, the likely global mean sea level rise by 2050 is between 0.15–0.23 m in the very low GHG emissions scenario (SSP1-1.9) and 0.20– 0.29 m in the very high GHG emissions scenario (SSP5-8.5); by 2100 between 0.28–0.55 m under SSP1-1.9 and 0.63– 1.01 m under SSP5-8.5; and by 2150 between 0.37–0.86 m under SSP1-1.9 and 0.98–1.88 m under SSP5-8.5 (medium confidence). Changes relative to 1900 are calculated by adding 0.158 m (observed global mean sea level rise from 1900 to 1995–2014) to simulated changes relative to 1995–2014. The future changes to 2300 (bars) are based on literature assessment, representing the 17th–83rd percentile range for SSP1-2.6 (0.3–3.1 m) and SSP5-8.5 (1.7–6.8 m). Red dashed lines: Low-likelihood, high-impact storyline, including ice sheet instability processes. These indicate the potential impact of deeply uncertain processes, and show the 83rd percentile of SSP5-8.5 projections that include low-likelihood, high impact processes that cannot be ruled out; because of low confidence in projections of these processes, this is not part of a likely range.
DOI: 10.5061/dryad.v2k84
title: Data from: PyroClean: Denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation

description: [No abstract entered]
description: DatasetsThis .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript.
DOI: 10.5061/dryad.s449d
title: Data from: Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets

description: The orchid genus Maxillaria is one of the largest and most common of
 neotropical orchid genera, but its current generic boundaries and
 relationships have long been regarded as artificial. Phylogenetic
 relationships within subtribe Maxillariinae sensu Dressler (1993) with
 emphasis on Maxillaria s.l. were inferred using parsimony analyses of
 individual and combined DNA sequence data. We analyzed a combined matrix
 of nrITS DNA, the plastid matK gene and flanking trnK intron, and the
 plastid atpB-rbcL intergenic spacer for 619 individuals representing ca.
 354 species. The plastid rpoC1 gene (ca. 2600 bp) was sequenced for 84
 selected species and combined in a more limited analysis with the other
 data sets to provide greater resolution. In a well-resolved, supported
 consensus, most clades were present in more than one individual analysis.
 All the currently recognized minor genera of “core” Maxillariinae
 (Anthosiphon, Chrysocycnis, Cryptocentrum, Cyrtidiorchis, Mormolyca,
 Pityphyllum, and Trigonidium) are embedded within a polyphyletic
 Maxillaria s.l. Our results support the recognition of a more restricted
 Maxillaria, of some previously published segregate genera (Brasiliorchis,
 Camaridium, Christensonella, Heterotaxis, Ornithidium, Sauvetrea), and of
 several novel clades at the generic level. These revised monophyletic
 generic concepts should minimize further nomenclatural changes, encourage
 monographic studies, and facilitate more focused analyses of character
 evolution within Maxillariinae.
description: Maxillaria Fig1to7
 matrixCombined matrix of
 nrITS, matK, atpB-rbcL sequence dataMaxillaria
 Fig1to7.nexMaxillaria Fig1to7
 treeTreefile from max
 parsimony analysis of Maxillaria Fig1to7 matrix.Maxillaria
 Fig1to7.treMaxillaria figure8
 matrixMatrix of combined
 molecular data (nrITS, matK, atpB-rbcL, rpoC1) for 84 taxa, presented in
 figure 8.Maxillaria
 figure8.nexMaxillaria figure8
 treeTreefile for parsimony
 analysis of Maxillaria figure8 nexus file.Maxillaria
 figure8.tre
DOI: 10.5061/dryad.td20f
title: Data from: Ecological co-associations influence species’ responses to past climatic change: an example from a Sonoran Desert bark beetle

description: Ecologically interacting species may have phylogeographic histories that
 are shaped both by features of their abiotic landscape, and by biotic
 constraints imposed by their co-association. The Baja California peninsula
 provides an excellent opportunity to examine the influence of abiotic vs.
 biotic factors on patterns of diversity in plant-insect species. This is
 because past climatic and geological changes impacted the genetic
 structure of plants quite differently to that of co-distributed
 free-living animals (e.g., herpetofauna and small mammals). Thus,
 ‘plant-like’ patterns should be discernible in host-specific insect
 herbivores. Here we investigate the population history of a monophagous
 bark beetle, Araptus attenuatus, and consider drivers of phylogeographic
 patterns in light of previous work on its host plant, Euphorbia lomelii.
 Based on mitochondrial and nuclear markers, we found that the evolutionary
 history of A. attenuatus exhibits similarities to host plant that are
 attributable to both biotic and abiotic processes. Southward range
 expansion and recent colonization of continental Sonora peninsula appear
 to be unique to this taxon pair, and likely reflect influences of the host
 plant. On the other hand, abiotic factors with landscape-level influences
 on suites of co-distributed taxa, such as Plio- and Pleistocene-aged
 marine incursions in the region, also left genetic signatures in beetle
 populations. Superimposed on these similarities, bark beetle-specific
 patterns and processes were also evident. Taken together, this work
 illustrates that the evolutionary history of species-specific insect
 herbivores may represent a mosaic of influences, including—but not limited
 to—those imposed by the host plant.
description: Garrick_et_al_MolEcol_DRYADRaster file used for ecological niche modelingRaster files used for ecological niche modeling File 1: 'araptus.curr.asc' Timescale: Present-day, class: RasterLaye, dimensions: 960, 720, 691200 (nrow, ncol, ncell), resolution: 0.008333, 0.008333 (x, y), extentL-115, -109.0002, 22, 29.99968 (xmin, xmax, ymin, ymax). File 2: 'araptus.lgm.asc' Timescale: Last Glacial Maximum, class: RasterLayer, dimensions: 960, 720, 691200 (nrow, ncol, ncell), resolution: 0.008333, 0.008333 (x, y), extent: -115, -109.0002, 22, 29.99968 (xmin, xmax, ymin, ymax)araptus.zip
DOI: 10.5061/dryad.pv6df
title: Data from: Efficient exploration of the space of reconciled gene trees

description: Gene trees record the combination of gene-level events, such as
 duplication, transfer and loss, and species-level events, such as
 speciation and extinction. Gene tree-species tree reconciliation methods
 model these processes by drawing gene trees into the species tree using a
 series of gene and species level events. The reconstruction of gene trees
 based on sequence alone almost always involves choosing between
 statistically equivalent or weakly distinguishable relationships that
 could be much better resolved based on a putative species tree. To exploit
 this potential for accurate reconstruction of gene trees the space of
 reconciled gene trees must be explored according to a joint model of
 sequence evolution and gene tree-species tree reconciliation. Here we
 present amalgamated likelihood estimation (ALE), a probabilistic approach
 to exhaustively explore all reconciled gene trees that can be amalgamated
 as a combination of clades observed in a sample of gene trees. We
 implement the ALE approach in the context of a reconciliation model
 (Szöllősi et al., 2013), which allows for the duplication, transfer and
 loss of genes. We use ALE to efficiently approximate the sum of the joint
 likelihood over amalgamations and to find the reconciled gene tree that
 maximizes the joint likelihood among all such trees. We demonstrate using
 simulations that gene trees reconstructed using the joint likelihood are
 substantially more accurate than those reconstructed using sequence alone.
 Using realistic gene tree topologies, branch lengths and alignment sizes,
 we demonstrate that ALE produces more accurate gene trees even if the
 model of sequence evolution is greatly simplified. Finally, examining 1099
 gene families from 36 cyanobacterial genomes we find that joint
 likelihood-based inference results in a striking reduction in apparent
 phylogenetic discord, with resp. 24%,59% and 46% percent reductions in the
 mean numbers of duplications, transfers and losses per gene family. The
 open source implementation of ALE is available from
 https://github.com/ssolo/ALE.git.
description: real_alignmentsAlignments constructed using MUSCLE and GBLOCKS for 1099 cyanobacterial gene families with from version 5 of the HOGENOM database.real_treesFor each cleaned alignment an MCMC sample was obtained using PhyloBayes. For each family we subsequently sampled reconciled gene trees using ALEsample. For each ALEsample sample we computed "real" trees for each gene family by finding the tree that maximised conditional clade probabilities based on the sample.real_ale.ale files based on PhyloBayes samples for real alignments.real_mlrecALEml output for real ales.sequence_mlrecALEml output fro PhyML trees based on real alignments.simulated_alignmentsSimulated alignments based on real trees.simulated_ale.ale files based on PhyloBayes samples using the SIMPLE sequnce evolution model for simulated alignments.simulated_mlrecALEml output for simulated ales.
DOI: 10.5061/dryad.0nj49
title: Data from: Historical changes in northeastern US bee pollinators related to shared ecological traits

description: Pollinators such as bees are essential to the functioning of terrestrial
 ecosystems. However, despite concerns about a global pollinator crisis,
 long-term data on the status of bee species are limited. We present a
 long-term study of relative rates of change for an entire regional bee
 fauna in the northeastern United States, based on &gt;30,000 museum
 records representing 438 species. Over a 140-y period, aggregate native
 species richness weakly decreased, but richness declines were significant
 only for the genus Bombus. Of 187 native species analyzed individually,
 only three declined steeply, all of these in the genus Bombus. However,
 there were large shifts in community composition, as indicated by 56% of
 species showing significant changes in relative abundance over time.
 Traits associated with a declining relative abundance include small
 dietary and phenological breadth and large body size. In addition, species
 with lower latitudinal range boundaries are increasing in relative
 abundance, a finding that may represent a response to climate change. We
 show that despite marked increases in human population density and large
 changes in anthropogenic land use, aggregate native species richness
 declines were modest outside of the genus Bombus. At the same time, we
 find that certain ecological traits are associated with declines in
 relative abundance. These results should help target conservation efforts
 focused on maintaining native bee abundance and diversity and therefore
 the important ecosystems services that they provide.
description: Bee Species Trait
 DataEcological traits used
 in the analysis for all bee speciesBartomeus_Traits_Data.csvHistorical Bee Specimen DataThis file contains all bee specimen records included in the final analysis.Bartomeus_Specimen_Data.csv
DOI: 10.25824/redu/mh6bov
title: Dados sobre a síntese e funcionalização de indolizinas para a obtenção de novas estruturas heterocíclicas

description: Nos dados fornecidos constam as caracterizações realizadas dos análogos sintetizados no trabalho. Os dados brutos também foram fornecidos em zip., bem como os dados já tratados.