cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dc195
title: Data from: Multiple sexual selection pressures drive the rapid evolution of complex morphology in a male secondary genital structure

description: The genitalia of internally fertilizing taxa represent a striking example
 of rapid morphological evolution. Although sexual selection can shape
 variation in genital morphology, it has been difficult to test whether
 multiple sexual selection pressures combine to drive the rapid evolution
 of individual genital structures. Here, we test the hypothesis that both
 pre- and postcopulatory sexual selection can act in concert to shape
 complex structural variation in secondary genital morphology. We
 genetically modified the size and shape of the posterior lobes of
 Drosophila melanogaster males and tested the consequences of morphological
 variation on several reproductive measures. We found that the posterior
 lobes are necessary for genital coupling and that they are also the
 targets of multiple postcopulatory processes that shape quantitative
 variation in morphology, even though these structures make no direct
 contact with the external female genitalia or internal reproductive organs
 during mating. We also found that males with smaller and less structurally
 complex posterior lobes suffer substantial fitness costs in competitive
 fertilization experiments. Our results show that sexual selection
 mechanisms can combine to shape the morphology of a single genital
 structure and that the posterior lobes of D. melanogaster are the targets
 of multiple postcopulatory selection pressures.
description: Master
 dataframeThis file contains male
 morphological measurements and pre- and post-copulatory reproductive
 measurements.MASTER_DATA.txtCourtship dataframeThis file contains the data used to calculate Courtship Index and Wing Extension Index.COURTSHIP.txtCompetition dataframeThis file contains the progeny counts used to analyze the competitive fertilizations experiments.COMPETITION.txtMovie S1Movie file that shows courtship and copulation behavior of a Canton S male mated with a white-eyed female.Movie_S1_SuppInfo.movMovie S2Movie file that shows courtship and copulation behavior of a Uas-Dcr-2; apGAL4; UAS-PoxnIR/elavGAL80 male mated with a white-eyed female.Movie_S2_SuppInfo.mov
DOI: 10.5061/dryad.bp106
title: Data from: Time-calibrated molecular phylogeny of pteropods

description: Pteropods are a widespread group of holoplanktonic gastropod molluscs and
 are uniquely suitable for study of long-term evolutionary processes in the
 open ocean because they are the only living metazoan plankton with a good
 fossil record. Pteropods have been proposed as bioindicators to monitor
 the impacts of ocean acidification and in consequence have attracted
 considerable research interest, however, a robust evolutionary framework
 for the group is still lacking. Here we reconstruct their phylogenetic
 relationships and examine the evolutionary history of pteropods based on
 combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA
 sequences and a molecular clock calibrated using fossils and the estimated
 timing of the formation of the Isthmus of Panama. Euthecosomes with
 uncoiled shells were monophyletic with Creseis as the earliest diverging
 lineage, estimated at 41–38 million years ago (mya). The coiled
 euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic
 contrary to the accepted morphology-based taxonomy; however, due to their
 high rate heterogeneity no firm conclusions can be drawn. We found strong
 support for monophyly of most euthecosome genera, but Clio appeared as a
 polyphyletic group, and Diacavolinia grouped within Cavolinia, making the
 latter genus paraphyletic. The highest evolutionary rates were observed in
 Heliconoides inflatus and Limacina bulimoides for both 28S and 18S
 partitions. Using a fossil-calibrated phylogeny that sets the first
 occurrence of coiled euthecosomes at 79–66 mya, we estimate that uncoiled
 euthecosomes evolved 51–42 mya and that most extant uncoiled genera
 originated 40–15 mya. These findings are congruent with a molecular clock
 analysis using the Isthmus of Panama formation as an independent
 calibration. Although not all phylogenetic relationships could be resolved
 based on three molecular markers, this study provides a useful resource to
 study pteropod diversity and provides general insight into the processes
 that generate and maintain their diversity in the open ocean.
description: Photographs of pteropod
 specimens.Photographs of pteropod
 specimens used for phylogenetic analyses in this study.Pteropod_photographs_AKBurridge.rar
DOI: 10.5061/dryad.r9c12
title: Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

description: Evolutionary radiations are prominent and pervasive across many plant
 lineages in diverse geographical and ecological settings; in neotropical
 rainforests there is growing evidence suggesting that a significant
 fraction of species richness is the result of recent radiations.
 Understanding the evolutionary trajectories and mechanisms underlying
 these radiations demands much greater phylogenetic resolution than is
 currently available for these groups. The neotropical tree genus Inga
 (Leguminosae) is a good example, with ~300 extant species and a crown age
 of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives
 only poor phylogenetic resolution among species. Here we explore the use
 of larger-scale nuclear gene data obtained though targeted enrichment to
 increase phylogenetic resolution within Inga. Transcriptome data from
 three Inga species were used to select 264 nuclear loci for targeted
 enrichment and sequencing. Following quality control to remove probable
 paralogs from these sequence data, the final dataset comprised 259,313
 bases from 194 loci for 24 accessions representing 22 Inga species and an
 outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci
 concatenated or a subset of 60 loci in a gene-tree/species-tree approach
 yielded highly resolved phylogenies. We used coalescent approaches to show
 that the same targeted enrichment data also have significant power to
 discriminate among alternative within-species population histories in the
 widespread species I. umbellifera. In either application, targeted
 enrichment simplifies the informatics challenge of identifying orthologous
 loci associated with de novo genome sequencing. We conclude that targeted
 enrichment provides the large volumes of phylogenetically-informative
 sequence data required to resolve relationships within recent plant
 species radiations, both at the species level and for within-species
 phylogeographic studies.
description: Inga_transcriptomesTrinity assemblies of transcriptomes from expanding young leaves of Inga umbellifera (BCI_104), Inga sapindoides (BCI_97) and Inga spectabilis (BCI_190)INGA.zipInga_phylogenies.tarPhylogenies generated with the bait captured data, Sanger sequence and plastid data.Inga_sequence.tarSequences assembled from captures reads. Nexus files as used to generate the phylogenies.
DOI: 10.5061/dryad.c471f
title: Data from: Asgard archaea illuminate the origin of eukaryotic cellular complexity

description: The origin and cellular complexity of eukaryotes represent a major enigma
 in biology. Current data support scenarios in which an archaeal host cell
 and an alphaproteobacterial (mitochondrial) endosymbiont merged together,
 resulting in the first eukaryotic cell. The host cell is related to
 Lokiarchaeota, an archaeal phylum with many eukaryotic features. The
 emergence of the structural complexity that characterizes eukaryotic cells
 remains unclear. Here we describe the ‘Asgard’ superphylum, a group of
 uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin-
 and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in
 phylogenomic analyses, and their genomes are enriched for proteins
 formerly considered specific to eukaryotes. Notably, thorarchaeal genomes
 encode several homologues of eukaryotic membrane-trafficking machinery
 components, including Sec23/24 and TRAPP domains. Furthermore, we identify
 thorarchaeal proteins with similar features to eukaryotic coat proteins
 involved in vesicle biogenesis. Our results expand the known repertoire of
 ‘eukaryote-specific’ proteins in Archaea, indicating that the archaeal
 host cell already contained many key components that govern eukaryotic
 cellular complexity.
description: Datasets and tree files
 accompanying publication about Asgard archaea.Bins, tree files for
 figures and phylogenetic datasets and results (sequence selection as
 fasta, alignments and trimmed alignments, tree files) for the publication
 about Asgard archaea.AsgardDatasets_Nature_v2.tgz
DOI: 10.5061/dryad.50m70
title: Data from: Inferring diversification rate variation from phylogenies with fossils

description: Time-calibrated phylogenies of living species have been widely used to
 study the tempo and mode of species diversification. However, it is
 increasingly clear that inferences about species diversification —
 extinction rates in particular — can be unreliable in the absence of
 paleontological data. We introduce a general framework based on the
 fossilized birth-death process for studying speciation-extinction dynamics
 on phylogenies of extant and extinct species. Our model assumes that
 phylogenies can be modeled as a mixture of distinct evolutionary rate
 regimes and that a hierarchical Poisson process governs the number of such
 rate regimes across a tree. We implemented the model in BAMM, a
 computational framework that uses reversible jump Markov chain Monte Carlo
 to simulate a posterior distribution of macroevolutionary rate regimes
 conditional on the branching times and topology of a phylogeny. The
 implementation we describe can be applied to paleontological phylogenies,
 neontological phylogenies, and to phylogenies that include both extant and
 extinct taxa. We evaluate performance of the model on datasets simulated
 under a range of diversification scenarios. We find that speciation rates
 are reliably inferred in the absence of paleontological data. However, the
 inclusion of fossil observations substantially increases the accuracy of
 extinction rate estimates. We demonstrate that the inferences are
 relatively robust to at least some violations of model assumptions,
 including heterogeneity in preservation rates and misspecification of the
 number of occurrences in paleontological datasets.
description: bamm-fossilIncludes BAMM extension to paleontological data, plus simulations and processing code.BAMM-fossil.zip
DOI: 10.5061/dryad.h1n02
title: Data from: Reliability of fish size estimates obtained from a multibeam imaging sonar

description: Multibeam imaging sonars have considerable potential for use in fisheries
 surveys because the video-like images are easy to interpret and contain
 information about fish size, shape, and swimming behavior, as well as
 characteristics of occupied habitats. We examined images obtained using a
 DIDSON multibeam sonar for Atlantic sturgeon Acipenser oxyrinchus, striped
 bass Morone saxatilis, white perch M. americana, and channel catfish
 Ictalurus punctatus of known size (20 - 141 cm) to determine the
 reliability of length estimates. For ranges up to 11 m, percent
 measurement error (sonar estimate - total length)/total length X 100
 varied by species but was not related to the fish's range or aspect
 angle (orientation relative to the sonar beam). Least-square mean percent
 error was significantly different from 0.0 for Atlantic sturgeon (x
 ̅=-8.34, SE=2.39) and white perch (x ̅=14.48, SE=3.99) but not striped
 bass (x ̅= 3.71, SE=2.58) or channel catfish (x ̅=3.97, SE=5.16).
 Underestimating lengths of Atlantic sturgeon may be due to difficulty in
 detecting the snout or the longer dorsal lobe of the heterocercal tail.
 White perch was the smallest species tested and it had the largest percent
 measurement errors (both positive and negative) and the lowest percentage
 of images classified as good or acceptable. Automated length estimates
 using Echoview software varied with position in the view-field. Estimates
 tended to be low at more extreme azimuthal angles (fish's angle
 off-axis within the view-field) but mean and maximum estimates were highly
 correlated with total length. Software estimates were also biased by fish
 images partially outside the view-field and when acoustic crosstalk
 occurred (when a fish perpendicular to the sonar and at relatively close
 range is detected in the side lobes of adjacent beams). These sources of
 bias are apparent when files are processed manually and can be filtered
 out when producing automated software estimates. Multibeam sonar estimates
 of fish size should be useful for research and management if these
 potential sources of bias and imprecision are addressed.
description: 2007-10-31_140001_HF_Clip1DIDSON data file. See Table 1 in Hightower et al.2007-10-31_172000_HF_Clip2DIDSON data file. See Table 1 in Hightower et al.2007-11-01_160549_HF_Clip3DIDSON data file. See Table 1 in Hightower et al.2007-11-02_082740_HF_Clip4DIDSON data file. See Table 1 in Hightower et al.2007-11-02_101000_HF_Clip5DIDSON data file. See Table 1 in Hightower et al.2007-11-01_113000_HF_Clip6DIDSON data file. See Table 1 in Hightower et al.2007-11-02_101000_HF_Clip7DIDSON data file. See Table 1 in Hightower et al.2007-11-01_160549_HF_Clip8DIDSON data file. See Table 1 in Hightower et al.2007-10-31_162000_HF_Clip9DIDSON data file. See Table 1 in Hightower et al.2007-11-01_141000_HF_Clip10DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.6vb720f
title: Data from: Flower preferences and pollen transport networks for cavity nesting solitary bees: implications for the design of agri-environment schemes

description: Floral foraging resources are valuable for pollinator conservation on
 farmland, and their provision is encouraged by agri-environment schemes in
 many countries. Across Europe, wildflower seed mixtures are widely sown on
 farmland to encourage pollinators, but the extent to which key pollinator
 groups such as solitary bees exploit and benefit from these resources is
 unclear. We used high-throughput sequencing of 164 pollen samples
 extracted from the brood cells of 6 common cavity nesting solitary bee
 species (Osmia bicornis, Osmia caerulescens, Megachile versicolor,
 Megachile ligniseca, Megachile centuncularis and Hylaeus confususi) which
 are widely distributed across the UK and Europe. We documented their
 pollen use across 19 farms in southern England, UK, revealing their forage
 plants and examining the structure of their pollen transport networks. Of
 the 32 plant species included currently in sown wildflower mixes, 15 were
 recorded as present within close foraging range of the bees on the study
 farms, but only Ranunculus acris L. was identified within the pollen
 samples. Rosa canina L. was the most commonly found of the 23 plant
 species identified in the pollen samples, suggesting that, in addition to
 providing a nesting resource for Megachile leafcutter bees, it may be an
 important forage plant for these species. Higher levels of connectance and
 nestedness were characteristic of pollen transport networks on farms with
 abundant floral resources, which may increase resilience to species loss.
 Our data suggest that plant species promoted currently by agri-environment
 schemes are not optimal for solitary bee foraging. If a diverse community
 of pollinators is to be supported on UK and European farmland, additional
 species such as Rosa canina should be encouraged to meet the foraging
 requirements of solitary bees.
description: Supporting Raw
 DataThis excel contains
 supporting raw data for the manuscript, including: GPS coordinates &
 key for all nest boxes, bee emergence data, flower unit abundance data
 & flower unit key, pollen DNA output data and farm summary
 dataDNA
 DataThis set of files
 contains the DNA sequence data to support the manuscript. The key for the
 pollen samples, including nest box location & farm is contained in the
 raw data excelDNA_Data.zip
DOI: 10.5061/dryad.31614
title: Data from: Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants

description: A new view is emerging of the interplay between mutation at the genomic
 level, substitution at the population level, and diversification at the
 lineage level. Many studies have suggested that rate of molecular
 evolution is linked to rate of diversification, but few have evaluated
 competing hypotheses. By analyzing sequences from 130 families of
 angiosperms, we show that variation in the synonymous substitution rate is
 correlated among genes from the mitochondrial, chloroplast, and nuclear
 genomes and linked to differences in traits among families (average height
 and genome size). Within each genome, synonymous rates are correlated to
 nonsynonymous substitution rates, suggesting that increasing the mutation
 rate results in a faster rate of genome evolution. Substitution rates are
 correlated with species richness in protein-coding sequences from the
 chloroplast and nuclear genomes. These data suggest that species traits
 contribute to lineage-specific differences in the mutation rate that drive
 both synonymous and nonsynonymous rates of change across all three
 genomes, which in turn contribute to greater rates of divergence between
 populations, generating higher rates of diversification. These
 observations link mutation in individuals to population-level processes
 and to patterns of lineage divergence.
description: PlantRateEstimationThis online data supplement contains the assoicated data and replicatable analyses to estimate branch rates for sister-pair analyses from the paper "Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants" Bromham, Lindell, Hua, Xia, Lanfear, Robert, Cowman, Peter F.
DOI: 10.5061/dryad.3vk1g
title: Data from: The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways

description: The neural fate commitment of pluripotent stem cells requires the
 repression of extrinsic inhibitory signals and the activation of intrinsic
 positive transcription factors. However, how these two events are
 integrated to ensure appropriate neural conversion remains unclear. Here,
 we showed that Pou3f1 is essential for the neural differentiation of mouse
 embryonic stem cells (ESCs), specifically during the transition from
 epiblast stem cells (EpiSCs) to neural progenitor cells (NPCs). Chimeric
 analysis showed that Pou3f1 knockdown leads to a markedly decreased
 incorporation of ESCs in the neuroectoderm. By contrast,
 Pou3f1-overexpressing ESC derivatives preferentially contribute to the
 neuroectoderm. Genome-wide ChIP-seq and RNA-seq analyses indicated that
 Pou3f1 is an upstream activator of neural lineage genes, and also is a
 repressor of BMP and Wnt signaling. Our results established that Pou3f1
 promotes the neural fate commitment of pluripotent stem cells through a
 dual role, activating internal neural induction programs and antagonizing
 extrinsic neural inhibitory signals.
description: GSE54569RNA-seq was performed to examine Oct6 function in ESC neural differentiation at Day2, Day4 and Day6 after dox induction. On Day4 EB, ChIP-seq assay was ultilized to characterize the targets of Oct6.microarray screening duiring ES neural differentiationMicroarray was performed to screen the genes differentially expressed during mESC neural differentiation in serum-free medium.microarray screening out of Oct6.zip
DOI: 10.5061/dryad.kt5nq
title: Data from: Extreme QTL mapping of germination speed in Arabidopsis thaliana

description: Seed germination is a key life history transition for annual plants and
 partly determines lifetime performance and fitness. Germination speed, the
 elapsed time for a nondormant seed to germinate, is a poorly understood
 trait important for plants’ competitiveness and fitness in fluctuating
 environments. Germination speed varied by 30% among 18 Arabidopsis
 thaliana populations measured, and exhibited weak negative correlation
 with flowering time and seed weight, with significant genotype effect (P
 &lt; 0.005). To dissect the genetic architecture of germination speed,
 we developed the extreme QTL (X-QTL) mapping method in A. thaliana. The
 method has been shown in yeast to increase QTL mapping power by
 integrating selective screening and bulk-segregant analysis in a very
 large mapping population. By pooled genotyping of top 5% of rapid
 germinants from ~100 000 F3 individuals, three X-QTL regions were
 identified on chromosomes 1, 3 and 4. All regions were confirmed as QTL
 regions by sequencing 192 rapid germinants from an independent F3
 selection experiment. Positional overlaps were found between X-QTLs and
 previously identified seed, life history and fitness QTLs. Our method
 provides a rapid mapping platform in A. thaliana with potentially greater
 power. One can also relate identified X-QTLs to the A. thaliana physical
 map, facilitating candidate gene identification.
description: Cumulative_germination_count_of_natural_accessionsThis file provides triplicate raw data of cumulative germination counts in 18 accessions phenotyped for their germination speed. Tab 1 shows germination counts of the two parental accessions (Bs-2 and Col-0), and Tab 2 shows germination counts of a worldwide collection of 16 accessions.Dryad1_Cumulative_germination_counts_accession.xlsxAthaliana_Isothermal_Array_Probe_SequenceAll custom-designed probes featured on the A.thaliana Isothermal SNP array. The array was manufactured by Agilent Biotech in CGH 8*60K format. The mean Tm value of the probes is 55 degree Celsius. The nomenclature of the probes follows the "Allele source_Chromosome_Position" format. The two alternatives of the allele source are "C" stands for Col-0 allele, and "NC" stands for non-Col-0 allele. The position information of the probes follows TAIR 8 coordinate.Dryad2_Athaliana_Isothermal_Array_Probe_Sequence.xlsxTimeSeries_GerminationCohort_ArrayGenotypeRaw microarray genotyping data derived by the Agilent feature extraction software, with built-in rank invariant normalization. Data from the manufacturer-supplied quality-control probes are not included. Cohorts (early, medium, late, and all germinants) are genotyped in two biologcal replicates (rep1 and rep2), and with dye-swap hybridization replicates (Cy3 and Cy5).