cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g02n5
title: Data from: Limited role of character displacement in the coexistence of congeneric Anelosimus spiders in a Madagascan montane forest

description: Evolutionary and ecological theory predicts that closely related and
 similar species should coexist infrequently because speciation is more
 likely to occur allopatrically than sympatrically, and because
 co-occurring species with similar traits may compete for limited
 resources, leading to competitive exclusion or character displacement.
 Here we study the unusual coexistence of 10 similar congeneric species of
 Anelosimus spiders within a small forest fragment in Madagascar. We asked
 if these species radiated in sympatry or allopatry, and if there was
 evidence for local-scale character displacement in body size and other
 species-level traits. We sampled ∼ 350 colonies (6346 individuals) along a
 2800 m transect. We identified colonies using morphology and DNA
 barcoding, and tested the monophyly of local and regional species
 assemblages with time-calibrated phylogenies. We used null model analysis
 and phylogenetic signal inference to test for patterns of segregation in
 body size, microhabitat, phenology, and seasonality of coexisting species.
 We found that all species belong to a Madagascan clade that radiated
 during the Pliocene, but that contemporary local assemblages are
 non-monophyletic. This is consistent with allopatric speciation during
 periods of global cooling and expansion of grasslands, and subsequent
 species assembly as forest fragments re-expanded and coalesced. We found
 no evidence for character displacement, except for overdispersion and even
 spacing in phenology: species were segregated by instars in a manner
 consistent with resource partitioning or maintenance of reproductive
 isolation. Overdispersion or even spacing in phenology may contribute to
 coexistence either through resource partitioning or mate recognition.
 However, there was no support for a scenario of resource partitioning and
 divergence of body size or other correlated morphological characters.
 These traits are better explained by evolutionary forces operating during
 speciation, rather than ecological forces operating during local community
 assembly.
description: AllDataforPhylogeny04Five locus concatenated DNA matrix used for phylogenetic analysesTreesForComparativeAnalyses_02Trees and data used for comparative analysesBarcodesDNA barcodes and barcoding tree
DOI: 10.5061/dryad.t0n42
title: Data from: Systematic revision of the pocket gopher genus Orthogeomys

description: Pocket gophers of the genus Orthogeomys show unusually high morphological
 and ecological diversity compared to other genera in the family Geomyidae.
 Whereas this diverse group once was divided into 3 genera (Merriam 1895),
 a revision by Russell (1968) recognized only Orthogeomys, with Merriam’s
 original genera relegated to subgeneric status as Heterogeomys,
 Macrogeomys, and Orthogeomys. Recent studies have called into question the
 monophyly of Orthogeomys, as well as the validity of 4 currently
 recognized Orthogeomys species. To date, the taxonomic validity of only 1
 of these species has been verified (Hafner et al. 2014). In this analysis,
 the first to include all 11 recognized species of the genus, we examine 3
 mitochondrial and 2 nuclear gene sequences (4,352 base pairs) and analyze
 cranial morphology to explore relationships within the genus. Our data
 support a taxonomic revision that restricts the genus Orthogeomys to a
 single species (O. grandis) and combines the subgenera Heterogeomys and
 Macrogeomys into the resurrected genus, Heterogeomys (7 species). In
 addition, 3 currently recognized species of Orthogeomys are synonymized as
 follows: O. cuniculus with O. grandis; H. thaeleri with H. dariensis; and
 H. matagalpae with H. cherriei. A synonymy and a key to the species of the
 genera Orthogeomys and Heterogeomys are provided.
description: S17734*BEAST analysis from
 trimmed, aligned sequences for the 5 genes, which yielded a total sequence
 length of 4,352 bp for 35 pocket gophers, with the 3 mitochondrial genes,
 Cytb, COI, and ND2 contributing 1,140, 1,460, and 488 bp, respectively,
 and the 2 nuclear genes, Bfib and IRBP, contributing 429 and 835 bp,
 respectively. Partition Finder indicated 3 partitions for the data: Cytb +
 COI (partition 1), ND2 (partition 2), and Bfib + IRBP (partition 3).
 Molecular substitution models suggested by jModelTest were GTR + I + G for
 partitions 1 and 2 and K80 + I for partition
 3.S1.– Species-tree
 analysis (*BEAST) with posterior probabilities.S1
 starbeast.pdfS2.–Results of a
 principal component analysis of 91 specimens representing the 7 species of
 the subgenus Macrogeomys.S2.pdfS3.–Results of a principal component analysis and a discriminant function analysis of 28 specimens representing the 3 small-sized species of the subgenus Macrogeomys (M. cherriei, M. matagalpae, and M. underwoodi).S3.pdfS4.–Results of a principal component analysis and a discriminant function analysis of 35 specimens representing the 3 medium-sized species of the subgenus Macrogeomys (M. dariensis, M. heterodus, and M. thaeleri).S4.pdfAligned sequence data
DOI: 10.5061/dryad.n9c88
title: Data from: Computational methods for tracking, quantitative assessment, and visualization of C. elegans locomotory behavior

description: The nematode Caenorhabditis elegans provides a unique opportunity to
 interrogate the neural basis of behavior at single neuron resolution. In
 C. elegans, neural circuits that control behaviors can be formulated based
 on its complete neural connection map, and easily assessed by applying
 advanced genetic tools that allow for modulation in the activity of
 specific neurons. Importantly, C. elegans exhibits several elaborate
 behaviors that can be empirically quantified and analyzed, thus providing
 a means to assess the contribution of specific neural circuits to
 behavioral output. Particularly, locomotory behavior can be recorded and
 analyzed with computational and mathematical tools. Here, we describe a
 robust single worm-tracking system, which is based on the open-source
 Python programming language, and an analysis system, which implements
 path-related algorithms. Our tracking system was designed to accommodate
 worms that explore a large area with frequent turns and reversals at high
 speeds. As a proof of principle, we used our tracker to record the
 movements of wild-type animals that were freshly removed from abundant
 bacterial food, and determined how wild-type animals change locomotory
 behavior over a long period of time. Consistent with previous findings, we
 observed that wild-type animals show a transition from area-restricted
 local search to global search over time. Intriguingly, we found that
 wild-type animals initially exhibit short, random movements interrupted by
 infrequent long trajectories. This movement pattern often coincides with
 local/global search behavior, and visually resembles Lévy flight search, a
 search behavior conserved across species. Our mathematical analysis showed
 that while most of the animals exhibited Brownian walks, approximately 20%
 of the animals exhibited Lévy flights, indicating that C. elegans can use
 Lévy flights for efficient food search. In summary, our tracker and
 analysis software will help analyze the neural basis of the alteration and
 transition of C. elegans locomotory behavior in a food-deprived condition.
description: N2 On Food
 RecordingA sample tracker
 recording of a wild-type (N2) strain C. Elegans animal, moving freely on a
 150mm diameter agar plate with a bacterial lawn of E.
 Coli.N2_on_food.7zN2 Off Food RecordingA sample tracker recording of a wild-type (N2) strain C. Elegans animal, moving freely on a 150mm diameter agar plate.N2_off_food.7ztph-1 Strain On Food RecordingA sample tracker recording of a tph-1 mutant strain C. Elegans animal, moving freely on a 150mm diameter agar plate with a bacterial lawn of E. Coli.tph1_on_food.7ztph-1 Strain Off Food RecordingA sample tracker recording of a tph-1 mutant strain C. Elegans animal, moving freely on a 150mm diameter agar plate.tph1_off_food.7z
DOI: 10.5061/dryad.7g978
title: Data from: Varver: a database of microsatellite variation in vertebrates

description: Understanding how genetic variation is maintained within a species is
 important in ecology, evolution, conservation and population genetics.
 Tremendous efforts have been made to evaluate the patterns of genetic
 variation in natural populations of various species. For this purpose,
 microsatellites have played a major role since the 1990s. Here we describe
 a comprehensive database, varver (Variation in Vertebrates) that provides
 complete information regarding microsatellite variation in natural
 populations of vertebrates. For each species, varver includes basic
 information of the species, a list of publications reporting the
 microsatellite variation, and tables of genetic variation within and
 between populations (heterozygosity and FST). The geographic location and
 rough sampling range are also shown for each sampled population. The
 database should be useful for researchers interested in not only specific
 species but also comparing multiple species. We discuss the utility of
 microsatellite data, particularly for meta-analyses that involve multiple
 microsatellite loci from various species. We show that in such analyses,
 it is extremely important to correct for biases caused by differences in
 mutation rate, mainly due to repeat unit and number. It is an important
 task to understand how genetic variation is maintained within a species in
 ecology, evolution, conservation and population genetics. A tremendous
 amount of effort has been made to evaluate the patterns of genetic
 variation in natural populations of various species. For this purpose,
 microsatellites have played the major role since 1990'. We here
 develop a comprehensive database that provide full information of
 microsatellite variations in natural populations of vertebrates, named
 VarVer. For each species, VarVer includes basic information of the
 species, a list of publications that reported microsatellite variation,
 and tables of genetic variation within and between populations
 (heterozygosity and Fst). The geographic location and rough sampling range
 are also shown for each sampled population. The database should be useful
 for not only researchers who are interested in specific species but also
 those who are interested in comparing multiple species. We discuss how
 useful microsatellite data are particularly for meteanalyses that involve
 a number of microsatellite loci from various species. In such analyses, we
 show that it is extremely important to correct for biases caused by the
 difference in the mutation rate, mainly due to the repeat unit and number.
description: All HTML files of
 VarVer.VarVer.zip
DOI: 10.5061/dryad.p6598
title: Data from: Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore

description: Ecological and environmental heterogeneity can produce genetic
 differentiation in highly mobile species. Accordingly, local adaptation
 may be expected across comparatively short distances in the presence of
 marked environmental gradients. Within the European continent, wolves
 (Canis lupus) exhibit distinct north–south population differentiation. We
 investigated more than 67-K single nucleotide polymorphism (SNP) loci for
 signatures of local adaptation in 59 unrelated wolves from four previously
 identified population clusters (northcentral Europe n = 32, Carpathian
 Mountains n = 7, Dinaric-Balkan n = 9, Ukrainian Steppe n = 11). Our
 analyses combined identification of outlier loci with findings from
 genome-wide association study of individual genomic profiles and 12
 environmental variables. We identified 353 candidate SNP loci. We examined
 the SNP position and neighboring megabase (1 Mb, one million bases)
 regions in the dog (C. lupus familiaris) genome for genes potentially
 under selection, including homologue genes in other vertebrates. These
 regions included functional genes for, for example, temperature regulation
 that may indicate local adaptation and genes controlling for functions
 universally important for wolves, including olfaction, hearing, vision,
 and cognitive functions. We also observed strong outliers not associated
 with any of the investigated variables, which could suggest selective
 pressures associated with other unmeasured environmental variables and/or
 demographic factors. These patterns are further supported by the
 examination of spatial distributions of the SNPs associated with
 universally important traits, which typically show marked differences in
 allele frequencies among population clusters. Accordingly, parallel
 selection for features important to all wolves may eclipse local
 environmental selection and implies long-term separation among population
 clusters.
description: 59_EuropeanWolvesSingle nucleotide polymorphism (SNP) raw data files for 59 individuals in PLINK-format.59_EuropeanWolvesSingle nucleotide polymorphism (SNP) raw data files for 59 individuals in PLINK-format.Sample ID and locations for 59 European wolvesSample identification, sample locations and population cluster memberships for all individuals.
DOI: 10.5061/dryad.th18q
title: Data from: Dynamic NF-κB and E2F interactions control the priority and timing of inflammatory signalling and cell proliferation

description: Dynamic cellular systems reprogram gene expression to ensure appropriate
 cellular fate responses to specific extracellular cues. Here we
 demonstrate that the dynamics of Nuclear Factor kappa B (NF-κB) signalling
 and the cell cycle are prioritised differently depending on the timing of
 an inflammatory signal. Using iterative experimental and computational
 analyses, we show physical and functional interactions between NF-κB and
 the E2 Factor 1 (E2F-1) and E2 Factor 4 (E2F-4) cell cycle regulators.
 These interactions modulate the NF-κB response. In S-phase, the NF-κB
 response was delayed or repressed, while cell cycle progression was
 unimpeded. By contrast, activation of NF-κB at the G1/S boundary resulted
 in a longer cell cycle and more synchronous initial NF-κB responses
 between cells. These data identify new mechanisms by which the cellular
 response to stress is differentially controlled at different stages of the
 cell cycle.
description: Peak RelA Nuclear
 Amplitude for HeLa CellsPeak RelA Nuclear
 Amplitude for HeLa Cells following TNF stimulation arranged by virtual
 synchronization of cell cycle. Single cell traces upon which the peak
 amplitude data is based are also included021009 061109 061109e
 combined.xls020611 ALL
 CELLS_SK-N-ASPeak RelA Nuclear
 Amplitude for SK-N_AS Cells following TNF stimulation arranged by virtual
 synchronization of cell cycle. Single cell traces upon which the peak
 amplitude data is based are also includedHeLa FUCCI
 ANALYSISAnalysis of cell cycle
 transition from G1 to S using Fucci vectors in HeLa cells as well as
 analysis of mean Mitosis length in the cell type090909 HeLa FUCCI r2
 ANALYSIS.xls120210 AS FUCCI O+G CTRL
 ANALYSISAnalysis of cell cycle
 transition from G1 to S using Fucci vectors in SK-N-AS cells as well as
 analysis of mean Mitosis length in the cell typeEffect of TNFalpha on
 HeLa and SK-N-AS cell cycle lengthCell cycle lengths for
 SK-N-AS and HeLa cells without and with TNFalpha stimulation. Effect
 extension on cell cycle following stimulation is also shown at G1 and S
 phases.Origin
 cc.opjRelA-DsRedxp E2F1-Venus
 BAC stables Representitive cell tracesRelA-DsRedexpress and
 E2F1-Venus BAC stables Representative cell traces separated into cell
 cycle phases by virtual synchronization.Representitive cell
 traces.xlsxRelA-DsRedxp E2F1-Venus
 BAC stables FCS molecular fluoresence DataMolecular fluorescence
 counts in single cells of RelA-DsRedxp E2F1-Venus BAC stables and
 correlation data.C11_nuc_table.xlsxRelA-DsRedxp E2F1-Venus BAC stables FCS Autocorrolation and cross-corrolation dataRelA-DsRedxp E2F1-Venus BAC stables FCS autocorrolation and cross-corrolation dataC11_TNF.xlsxBAC BAC Stable cell phase Meta data_DryadTraces of BAC-BAC E2F-1-Venus and Rel-A-dsRedexpress sorted into different cell cycle phases.
DOI: 10.5061/dryad.sf6s9
title: Data from: Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae)

description: The anomaly zone, defined by the presence of gene tree topologies that are
 more probable than the true species tree, presents a major challenge to
 the accurate resolution of many parts of the Tree of Life. This
 discrepancy can result from consecutive rapid speciation events in the
 species tree. Similar to the problem of long-branch attraction, including
 more data via loci concatenation will only reinforce the support for the
 incorrect species tree. Empirical phylogenetic studies often employ
 coalescent-based species tree methods to avoid the anomaly zone, but to
 this point these studies have not had a method for providing any direct
 evidence that the species tree is actually in the anomaly zone. In this
 study, we use 16 species of lizards in the family Scincidae to investigate
 whether nodes that are difficult to resolve place the species tree within
 the anomaly zone. We analyze new phylogenomic data (429 loci), using both
 concatenation and coalescent-based species tree estimation, to locate
 conflicting topological signal. We then use the unifying principle of the
 anomaly zone, together with estimates of ancestral population sizes and
 species persistence times, to determine whether the observed phylogenetic
 conflict is a result of the anomaly zone. We identify at least three
 regions of the Scindidae phylogeny that provide demographic signatures
 consistent with the anomaly zone, and this new information helps reconcile
 the phylogenetic conflict in previously published studies on these
 lizards. The anomaly zone presents a real problem in phylogenetics, and
 our new framework for identifying anomalous relationships will help
 empiricists leverage their resources appropriately for investigating and
 overcoming this challenge.
description: anomalous_skinks_data.tarData files and results from analyses for the 429 loci used. These results were used for summaries presented in the paper.
DOI: 10.18167/dvn1/8g8ahy
title: Paracou forest permanent plots details

description: &lt;a href="https://paracou.cirad.fr/"&gt;Paracou Research Station&lt;/a&gt;. Plots size, location and type. &lt;a href="https://umr-ecofog.cirad.fr/organisation/dispositifs-experimentaux/guyafor-reseau-de-parcelles-forestieres"&gt;Guyafor network&lt;/a&gt;
DOI: 10.5061/dryad.qd0c2
title: Data from: A time-calibrated road map of Brassicaceae species radiation and evolutionary history

description: The Brassicaceae include several major crop plants and numerous important
 model species in comparative evolutionary research such as Arabidopsis,
 Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary
 hypothesis needs to be placed in a temporal context, reliably dated major
 splits within the evolution of Brassicaceae are essential. We present a
 comprehensive time-calibrated framework with important divergence time
 estimates based on whole-chloroplast sequence data for 29 Brassicaceae
 species. Diversification of the Brassicaceae crown group started at the
 Eocene-to-Oligocene transition. Subsequent major evolutionary splits are
 dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene
 transition, with increasing drought and aridity and transient glaciation
 events. The age of the Arabidopsis thaliana crown group is 6 million years
 ago, at the Miocene and Pliocene border. The overall species richness of
 the family is well explained by high levels of neopolyploidy (43% in
 total), but this trend is neither directly associated with an increase in
 genome size nor is there a general lineage-specific constraint. Our
 results highlight polyploidization as an important source for generating
 new evolutionary lineages adapted to changing environments. We conclude
 that species radiation, paralleled by high levels of neopolyploidization,
 follows genome size decrease, stabilization, and genetic diploidization.
description: Brassicaceae species
 check-listBrassicaceae
 species-checklist for cytogenetically investigated taxa and respective
 chromosome numbers (data export from BrassiBase:
 http://brassibase.cos.uni-heidelberg.de/).Supplemental Data Set
 1.xlsxBrassicaceae life-cycle
 data.Species list with data
 for Brassicaceae life cycle.Supplemental Data Set
 2.xlsxBrassicaceae genome size
 estimatesSpecies list for genome
 size estimates of Brassicaceae species.Supplemental Data Set
 3.xlsxPlant material
 sourcesSources of plant
 material and sequence data used for chloroplast genome
 analysis.Supplemental Data Set
 4.xlsxAlignments and
 partitionsNUCLEOTIDE ALIGNMENT(s)
 and annotattions/partitionsSupplemental Data Set
 5.txt
DOI: 10.5061/dryad.qg3ft
title: Data from: Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Background: Downy mildews are the most speciose group of oomycetes and
 affect crops of great economic importance. So far, there is only a single
 deeply-sequenced downy mildew genome available, from Hyaloperonospora
 arabidopsidis. Further genomic resources for downy mildews are required to
 study their evolution, including pathogenicity effector proteins, such as
 RxLR effectors. Plasmopara halstedii is a devastating pathogen of
 sunflower and a potential pathosystem model to study downy mildews, as
 several Avr-genes and R-genes have been predicted and unlike Arabidopsis
 downy mildew, large quantities of almost contamination-free material can
 be obtained easily. Results: Here a high-quality draft genome of
 Plasmopara halstedii is reported and analysed with respect to various
 aspects, including genome organisation, secondary metabolism, effector
 proteins and comparative genomics with other sequenced oomycetes.
 Interestingly, the present analyses revealed further variation of the RxLR
 motif, suggesting an important role of the conservation of the dEER-motif.
 Orthology analyses revealed the conservation of 28 RxLR-like core
 effectors among Phytophthora species. Only six putative RxLR-like
 effectors were shared by the two sequenced downy mildews, highlighting the
 fast and largely independent evolution of two of the three major downy
 mildew lineages. This is seemingly supported by phylogenomic results, in
 which downy mildews did not appear to be monophyletic. Conclusions: The
 genome resource will be useful for developing markers for monitoring the
 pathogen population and might provide the basis for new approaches to
 fight Phytophthora and downy mildew pathogens by targeting core
 pathogenicity effectors.
description: Tree_for_submission