cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.74b5d
title: Data from: C4 photosynthesis promoted species diversification during the Miocene grassland expansion

description: Identifying how organismal attributes and environmental change affect
 lineage diversification is essential to our understanding of biodiversity.
 With the largest phylogeny yet compiled for grasses, we present an example
 of a key physiological innovation that promoted high diversification
 rates. C4 photosynthesis, a complex suite of traits that improves
 photosynthetic efficiency under conditions of drought, high temperatures,
 and low atmospheric CO2, has evolved repeatedly in one lineage of grasses
 and was consistently associated with elevated diversification rates. In
 most cases there was a significant lag time between the origin of the
 pathway and subsequent radiations, suggesting that the ‘C4 effect’ is
 complex and derives from the interplay of the C4 syndrome with other
 factors. We also identified comparable radiations occurring during the
 same time period in C3 Pooid grasses, a diverse, cold-adapted grassland
 lineage that has never evolved C4 photosynthesis. The mid to late Miocene
 was an especially important period of both C3 and C4 grass
 diversification, coincident with the global development of extensive, open
 biomes in both warm and cool climates. As is likely true for most “key
 innovations”, the C4 effect is context dependent and only relevant within
 a particular organismal background and when particular ecological
 opportunities became available.
description: diversification_sampling_matricesThis file is a compressed folder of the matrices containing sampling information for the diversification analyses. It includes input files for BiSSE that have C3/C4 species coding for all tips on our tree (C3=0, C4=1).nexus_filesAlignment files for each subclade.Poaceae_hyp1_allC4_maxcredMaximum credibility clade tree of Poaceae dated under calibration #1Poaceae_hyp2_allC4_maxcredMaximum credibility clade tree of Poaceae dated under calibration #2sampled_treescompressed file containing two phylip files each containing 200 Poaceae trees sampled from the posterior distribution, dated under calibration #1 and calibration #2 respectivelyC3_C4_codingthis text file provides character state information (C3 or C4 photosynthesis) for all taxa in study.
DOI: 10.5061/dryad.67f8v
title: Data from: Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex

description: Background: Determining the presence or absence of gene flow between
 populations is the target of some statistical methods in population
 genetics. Until recently, these methods either avoided the use of
 recombining genes, or treated recombination as a nuisance parameter.
 However, genes with recombination contribute additional information for
 the detection of gene flow (i.e. through linkage disequilibrium). Methods:
 We present three summary statistics based on the spatial arrangement of
 fixed differences, and shared and exclusive polymorphisms that are
 sensitive to the presence and direction of gene flow. Power and false
 positive rate for tests based on these statistics are studied by
 simulation. Results: The application of these tests to populations from
 the Drosophila simulans species complex yielded results consistent with
 migration between D. simulans and its two endemic sister species D.
 mauritiana and D. sechellia, and between populations D. mauritiana on the
 islands of the Mauritius and Rodrigues. Conclusions: We demonstrate the
 sensitivity of the developed statistics to the presence and direction of
 gene flow, and characterize their power as a function of differentiation
 level and recombination rate. The properties of these statistics make them
 especially suitable for analyzing high-throughput sequencing data or for
 their integration within the approximate Bayesian computation framework.
description: amyrel sim sech mau
 meljoc sim sech mau
 melnotch sim sech mau
 melobp sim sech mau
 melodysseus sim sech mau
 melOdysseus
 sim sech mau mel.fasotu sim sech mau
 melperiod sim sech mau
 melPGD sim sech mau
 melsqh sim sech mau
 melvermilion sim sech mau
 melwhite sim sech mau
 mel
DOI: 10.5061/dryad.jr66k
title: Data from: Modelling the dispersal of the two main hosts of the raccoon rabies variant in heterogeneous environments with landscape genetics

description: Predicting the geographic spread of wildlife epidemics requires knowledge
 about the movement patterns of disease hosts or vectors. The field of
 landscape genetics provides valuable approaches to study dispersal
 indirectly, which in turn may be used to understand patterns of disease
 spread. Here, we applied landscape genetic analyses and spatially explicit
 models to identify the potential path of raccoon rabies spread in a
 mesocarnivore community. We used relatedness estimates derived from
 microsatellite genotypes of raccoons and striped skunks to investigate
 their dispersal patterns in a heterogeneous landscape composed
 predominantly of agricultural, forested and residential areas. Samples
 were collected in an area covering 22 000 km2 in southern Québec, where
 the raccoon rabies variant (RRV) was first detected in 2006. Multiple
 regressions on distance matrices revealed that genetic distance among male
 raccoons was strictly a function of geographic distance, while dispersal
 in female raccoons was significantly reduced by the presence of
 agricultural fields. In skunks, our results suggested that dispersal is
 increased in edge habitats between fields and forest fragments in both
 males and females. Resistance modelling allowed us to identify likely
 dispersal corridors used by these two rabies hosts, which may prove
 especially helpful for surveillance and control (e.g. oral vaccination)
 activities.
description: Skunk raw
 dataIncludes all data from
 striped skunk individuals sampled in the study: geographic coordinates,
 sex, year of sampling, and multilocus genotype.Skunk_rawdata.xlsxRaccoon raw dataIncludes data from all raccoon individuals sampled in this study: geographic coordinates, sex, year of sampling, and multilocus genotype.Raccoon_rawdata.xlsxSkunk MRM dataData used for MRM analyses in striped skunks. For each individual pairwise comparisons, geographic and genetic distances, habitat proportions, edge density, and number of barriers (rivers and highways) are provided.Skunk_MRMdata.xlsxRaccoon MRM dataData used for MRM analyses in raccoons. For each individual pairwise comparisons, geographic and genetic distances, habitat proportions, edge density, and number of barriers (rivers and highways) are provided.Raccoon_MRMdata.xlsx
DOI: 10.5061/dryad.5sv39
title: Data from: The translational landscape of the splicing factor SRSF1 and its role in mitosis

description: The shuttling Serine/Arginine rich (SR) protein SRSF1 (previously known as
 SF2/ASF) is a splicing regulator that also activates translation in the
 cytoplasm. In order to dissect the gene network that is translationally
 regulated by SRSF1, we performed a high-throughput deep sequencing
 analysis of polysomal fractions in cells overexpressing SRSF1. We
 identified approximately 1,500 mRNAs that are translational targets of
 SRSF1. These include mRNAs encoding proteins involved in cell cycle
 regulation, such as spindle, kinetochore and M phase proteins, which are
 essential for accurate chromosome segregation. Indeed, we show that
 translational activity of SRSF1 is required for normal mitotic
 progression. Furthermore, we found that mRNAs that display alternative
 splicing changes upon SRSF1 overexpression are also its translational
 targets; strongly suggesting that SRSF1 couples pre-mRNA splicing and
 translation. These data provide insights on the complex role of SRSF1 in
 the control of gene expression at multiple levels and its implications in
 cancer.
description: Supplementary file
 1-SRSF1 translational targetsData containing list of
 1576 mRNAs that showed a 1.85-fold increase in polysomal-association in
 response to SRSF1 overexpression (translational targets tab). Data are
 supplied as an excel spreadsheet. Descriptions of columns are included in
 additional tab (descriptions of columns). Negative controls tab contains
 information on cellular abundance of mRNAs used as negative controls in
 all validation experiments.Supplementary file
 1.xlsxSupplementary file
 2-SILAC analysis following SRSF1 overexpressionList of proteins
 identified in SILAC experiment (SILAC tab). Data are supplied as an excel
 spreadsheet. Descriptions of columns are included in the additional tab
 (description of columns tab).Supplementary file
 2.xlsxSupplementary file
 3-Alternative splicing changes following SRSF1
 overexpressionList of 382
 SRSF1-regulated cassette exons determined by exon arrays (cassette exons
 tab) and list of SRSF1-regulated cassette exons with SRSF1-clip-tags CLIP
 tag over casette exon (clip tag over cassette exon tab). Data are supplied
 as an excel spreadsheet.Supplementary file
 3.xlsxSupplementary file
 4-SRSF1 translational consensus motif positionsBed file containing
 positions and sequences of the SRSF1 consensus motif in hg18 assembly of
 human genome. Data are supplied as a tab-delimited text
 file.CLIP_454_M2.hg18.005.ucsc.bed
DOI: 10.5061/dryad.5f0h8
title: Data from: Calculating structural complexity in phylogenies using ancestral ontologies

description: Complexity is an important aspect of evolutionary biology, but there are
 many reasonable concepts of complexity, and its objective measurement is
 an elusive matter. Here we develop a simple measure of complexity based on
 counts of elements, incorporating the hierarchical information as
 represented in anatomical ontologies. Neomorphic and transformational
 characters are used to identify novelties and individuated morphological
 regions, respectively. By linking the characters to terms in an anatomical
 ontology a node-driven approach is implemented, where a node ontology and
 a complexity score are inferred from the optimization of individual
 characters on each ancestral or terminal node. From the atomized vector of
 character scorings, the anatomical ontology is used to integrate the
 hierarchical structure of morphology in terminals and ancestors. These
 node ontologies are used to calculate a measure of complexity that can be
 traced on phylogenetic trees and is harmonious with usual phylogenetic
 operations. This strategy is compared with a terminal-driven approach,
 where the complexity scores are calculated only for terminals, and
 optimized as a continuous character on the internal nodes. These ideas are
 applied to a real dataset of 166 araneomorph spider species scored for 393
 characters, using the Spider Ontology (SPD); complexity scores and
 transitions are calculated for each node and branch, respectively. This
 result in a distribution of transitions skewed towards simplification; the
 transitions in complexity have no apparent correlation with character
 branch lengths. The node-driven and terminal-driven estimations are
 generally correlated in the complexity scores, but have higher divergence
 in the transition values. The structure of the ontology is used to provide
 complexity scores for organ systems and body parts of the focal groups.
description: Data from: Calculating
 structural complexity in phylogenies using ancestral
 ontologiesSee
 README.txtcomplexity_dryad_data_package.zip
DOI: 10.5061/dryad.ck0mp
title: Data from: The Probable Datum Method (PDM): a technique for estimating the age of origination or extinction of nannoplankton

description: Accurate interpretation of origination and extinction of fossil species is
 crucial to answering a variety of questions in paleontology. Fossil
 datums, the observed age of first or last occurrences, are subject to
 sampling error as a result of preservation and low abundances near range
 endpoints. This sampling error can cause local range offset, an age
 difference between the observed first or last occurrence of a species and
 its true origination or extinction. Here we develop and test a new
 technique, the Probable Datum Method (PDM) that can be used to assess the
 extent of local range offset for nannofossil species. The PDM estimates
 the original abundance of a taxon and its probable true age of first or
 last occurrence. The PDM uses a model in which original abundance is
 related to count abundance through preservation and the counting process.
 This model is empirically parameterized, including an experimental
 determination of false positive and error rates of a nannofossil count.
 The model is simulated then inverted to estimate likely original abundance
 and true datum age from count abundance data. We first test the PDM in a
 positive control experiment with known parameter values. This experiment
 shows the PDM is robust and returns known values accurately. Next we apply
 the method to the origination of nannoplankton after the
 Cretaceous/Paleogene boundary to test whether first occurrences were
 synchronous between widely-spaced locations. The PDM results suggest that
 observed diachrony of K/Pg originations cannot be explained by the effects
 of range offset, rather in some cases they indicate truly diachronus first
 occurrences between localities. Although the technique was developed to
 analyze nannoplankton ranges, the statistical nature of the PDM, its
 experimentally derived parameters and parsimonious nature should make it
 applicable to many micropaleontological studies that interpret patterns of
 origination and extinction.
description: Schueth et al
 Supplementary MaterialsSupplementary appendices
 for the Probable Datum Method manuscript. Included are: positive control
 appendix, sensitivity analysis, comparison with other methods,
 etc.PDM code files and
 readmeIncluded in this package
 are all code required to run the PDM and a readme file to explain how to
 implement the PDM for use.PDM code
 files.zip
DOI: 10.7927/sr9v-1q31
title: IPCC AR6 Synthesis Report SPM.4 (a) and LR Figure 3.3 (a) (Burning embers): Global Reasons for Concern in AR5 vs. AR6

description: Global Reasons for Concern (RFCs), comparing AR6 (2022, thick embers) and AR5 (2014, thin embers) assessments. Diagrams are shown for each RFC, assuming low to no adaptation (i.e., adaptation is fragmented, localised and comprises incremental adjustments to existing practices). However, the transition to a very high risk level has an emphasis on irreversibility and adaptation limits. The horizontal line denotes the present global warming of 1.1°C which is used to separate the observed, past impacts below the line from the future projected risks above it. Lines connect the midpoints of the transition from moderate to high risk across AR5 and AR6.
DOI: 10.5061/dryad.d1nb6
title: Data from: Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

description: Background: Estimating divergence times in phylogenies using a molecular
 clock depends on accurate modeling of nucleotide substitution rates in DNA
 sequences. Rate heterogeneity among lineages is likely to affect
 estimates, especially in lineages with long stems and short crowns
 (“broom” clades) and no internal calibration. We evaluate the performance
 of the random local clocks model (RLC) and the more routinely employed
 uncorrelated lognormal relaxed clock model (UCLN) in situations in which a
 significant rate shift occurs on the stem branch of a broom clade. We
 compare the results of simulations to empirical results from analyses of a
 real rate-heterogeneous taxon – Australian grass trees (Xanthorrhoea) –
 whose substitution rate is slower than in its sister groups, as determined
 by relative rate tests. Results: In the simulated datasets, the RLC model
 performed much better than UCLN: RLC correctly estimated the age of the
 crown node of slow-rate broom clades, whereas UCLN estimates were
 consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN
 returned significantly younger crown ages than RLC (mean estimates
 respectively 3-6 Ma versus 25-35 Ma). In both real and simulated datasets,
 Bayes Factor tests strongly favored the RLC model over the UCLN model.
 Conclusions: The choice of an unsuitable molecular clock model can
 strongly bias divergence time estimates. In particular, for data predicted
 to have more rate variation among than within clades, dating with RLC is
 much more likely to be accurate than with UCLN. The choice of clocks
 should be informed by the biology of the study group (e.g., life-form) or
 assessed with relative rate tests and post-hoc model comparisons.
description: Monocots_cpDNAData files for phylogenetic analyses of monocots in RAxML and BEAST using cpDNA alignment with varying combinations of DNA partitioning and clock models.Xanthorrhoeaceae_cpDNAxml files for dating analyses of Xanthorrhoeaceae in BEAST using cpDNA alignment with varying combinations of tree growth models (Yule and birth-death) and clock models (RLC and UCLN).Xanthorrhoeaceae_rpb2xml files for dating analyses of Xanthorrhoeaceae in BEAST using rpb2 alignment with varying combinations of DNA partitioning, clock and tree growth models.Appendix 1 simulationsZip file containing (1) files used for simulations including scripts for simulating broom-and-bush trees, (2) a tree file containing the 10 trees selected for further analysis, (3) xml files used for analysis of simulated alignments in BEAST under combinations of tree growth (Yule and BD) and clock (RLC and UCLN) models, and (4) annotated MCC trees resulting from the BEAST analyses.Appendix 2 cpDNA accessionsTable of taxa sequenced for ndhF and trnL-trnF (chloroplast DNA) with GenBank accession numbersAppendix 3 rpb2 accessionsTable of taxa sequenced for rpb2 (nuclear DNA) with GenBank accession numbers
DOI: 10.5061/dryad.1580p
title: Data from: How the aridification of Australia structured the biogeography and influenced the diversification of a large lineage of Australian cicadas

description: Over the last 30 million years, Australia’s landscape has undergone
 dramatic cooling and drying due to the establishment of the Antarctic
 Circumpolar Current and change in global CO2 levels. Studies have shown
 that many Australian organisms went extinct during these major cooling
 events, while others experienced adaptive radiations and increases in
 diversification rates as a result of exploiting new niches in the arid
 zone. Despite the many studies on diversification and biogeography in
 Australia, few have been continent-wide and none have focused on a group
 of organisms adapted to feeding on plants. We studied 162 species of
 cicadas in the Australian Pauropsalta complex, a large generic lineage
 within the tribe Cicadettini. We asked whether there were changes in the
 diversification rate of Pauropsalta over time and if so: 1) which clades
 were associated with the rate change? 2) did timing of rate shifts
 correspond to known periods of dramatic historical climate change, 3) did
 increases in diversification rate along select lineages correspond to
 adaptive radiations with movement into the arid zone? To address these
 questions, we estimated a molecular phylogeny of the Pauropsalta complex
 using ∼ 5300 bp of nucleotide sequence data distributed among five loci
 (one mtDNA locus and four nDNA loci). We found that this large group of
 cicadas did not diversify at a constant rate as they spread through
 Australia; instead the signature of decreasing diversification rate
 changed roughly around the time of the expansion of the east Antarctic ice
 sheets ∼ 16 Ma and the glaciation of the northern hemisphere∼3 Ma. Unlike
 other Australian taxa, the Pauropsalta complex did not explosively radiate
 in response to an early invasion of the arid zone. Instead multiple groups
 invaded the arid zone and experienced rates of diversification similar to
 mesic-distributed taxa. We found evidence for relictual groups, located in
 pre-Mesozoic habitat, that have not diversified and continue to reside on
 mesic hosts in isolated “habitat islands”. Future work should focus on
 groups of similar ages with similar distribution patterns to determine
 whether this tempo and pattern of diversification and biogeography is
 consistent with evidence from other phytophagous insects.
description: Owen_et_al_mtDNA_nDNANexus file that includes mtDNA and nDNA alignment with a partition block at the bottom of the file.Owen_et_al_nDNAonlyNexus file that contains only the nDNA alignment. The file contains a partition block at the bottom of the file.
DOI: 10.5061/dryad.h68jd
title: Data from: Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k SNP array

description: With the access to draft genome sequence assemblies and whole-genome
 re-sequencing data from population samples, molecular ecology studies will
 be able to take truly genome-wide approaches. This now applies to an avian
 model system in ecological and evolutionary research: Old World
 flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb
 collared flycatcher genome assembly and identified 13 million SNPs in
 population re-sequencing of this species and its sister species, pied
 flycatcher. Here we developed a custom 50K Illumina iSelect flycatcher SNP
 array with markers covering 30 autosomes and the Z chromosome. By using a
 number of selection criteria for inclusion in the array, both genotyping
 success rate and polymorphism information content (mean marker
 heterozygosity = 0.41) were high. We used the array to assess linkage
 disequilibrium (LD) and hybridization in flycatchers. LD declined quickly
 to the background level at an average distance of 17 kb but the extent of
 LD varied markedly within the genome and was more than 10-fold higher in
 ‘genomic islands’ of differentiation than in the rest of the genome.
 Genetic ancestry analysis identified 33 F1 hybrids but no later-generation
 hybrids from sympatric populations of collared flycatchers and pied
 flycatchers, contradicting earlier reports of backcrosses identified from
 much fewer number of markers. With an estimated divergence time as
 recently as &lt;1 million years ago, this suggests strong selection
 against F1 hybrids and unusually rapid evolution of reproductive
 incompatibility in an avian system.
description: Collared_Pied_Hybrid_Genotype_plinkDryad_MER14-0028.zip