Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
32
datasets available to search
ShareScore release 0.9.0
Dataset results
32 results for “Signal Conflict”
FIGURE 2 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 2. Syntopic species of Tropidurus found at the Reserva Particular do Patrimônio Natural Fazenda Pé da Serra, Serra do Arame, Ibotirama, Bahia, Brazil, and their respective habitats: (A, B) T. sertanejo, n. sp. (MZUSP 104274, allotype); (C, D) T. hispidus (MZUSP 104276); (E, F) T. pinima (MZUSP 104271).
FIGURE 6 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 6. Allotype of Tropidurus sertanejo, n. sp. (MZUSP 104274): (A) head in dorsal view; (B) head in ventral view; (C) head in lateral view; (D) dorsal body illustrating the spotted pattern typical of the new species; (E) ventral body showing the unpigmented underside of the thighs and cloacal flap characteristic of females.
FIGURE 5 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 5. Holotype of Tropidurus sertanejo, n. sp. (MZUSP 104273): (A) head in dorsal view; (B) head in ventral view showing intense pigmentation toward gular region; (C) head in lateral view; (D) dorsal body; (E) ventral body showing the typical dark flash marks on the underside of the thighs and cloacal flap of adult males.
FIGURE 15 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 15. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus on four mitochondrial (12S, 16S, CO1, Cyt b) and six nuclear loci (BACH1, kif24, NTF3, PRLR, PTPN, SNCAIP). Numbers associated to nodes refer to bootstrap values.
FIGURE 1. Taxonomic curve showing a in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 1. Taxonomic curve showing a steep, nonasymptotic increment in the number of species of the lizard genus Tropidurus described since 1820. Specimen of T. sertanejo, n. sp., MZUSP 104274 (allotype).
FIGURE 14 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 14. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus based on four nuclear (BACH1, kif24, NTF3, PRLR, PTPN, SNCAIP) loci. Numbers associated to nodes refer to bootstrap values.
FIGURE 13 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 13. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus based on four mitochondrial (12S, 16S, CO1, Cyt b) loci. Numbers associated to nodes refer to bootstrap values.
FIGURE 11 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 11. Boxplot showing variation in scale counts among Tropidurus species (ordinated by mean): (Tcat) T. catalanensis, (Tchr) T. chromatops, (Tcoc) T. cocorobensis, (Tery) T. erythrocephalus, (Teth) T. etheridgei, (This) T. hispidus, (Thyg) T. hygomi, (Timb) T. imbituba, (Tins) T. insulanus, (Tita) T. itambere, (Tmon) T. montanus, (Tmuc) T. mucujensis, (Tore) T. oreadicus, (Tpsa) T. psammonastes, (Tser) T. sertanejo, n. sp. (highlighted in dark gray.), (Ttor) T. torquatus.
FIGURE 4 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 4. Measurements used for morphometric analyses of Tropidurus. Abbreviations: AL, arm length; EOS, ear opening–snout distance; FAL, forearm length; FOL, foot length; HDL, hand length; HH, head height; HW, head width; SL, shank length; SVL, snout-vent length; THL, thigh length; TL, tail length.
FIGURE 3 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 3. Map on left shows the distribution of the Brazilian biomes and highlights the State of Bahia, predominantly covered by the semiarid Caatinga. Map on right (altimetric profile) shows the distribution of Tropidurus sertanejo, n. sp.: northernmost dot indicates the type locality (RPPN Fazenda Pé da Serra, Serra do Arame, Ibotirama, Bahia: 12° 08′ 45.21 S, 43° 03′ 20.83 W) and southernmost dot indicates the only known additional locality of occurrence of the new species (Caetité, Bahia: 14° 04′ 17.82 S, 42° 29′ 48.33″ W).
FIGURE 12 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 12. Scatterplot of LD1 and LD2 generated by the discriminant analysis performed on the scale counts of Tropidurus. See table 8 for corresponding summary statistics. Tropidurus sertanejo, n. sp., highlighted in dark gray.
FIGURE 10 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 10. Scatterplot of PC1 and PC2 generated by the principal component analyses and LD1 and LD2 generated by the size-free discriminant analyses performed on the log-transformed morphometric variables of Tropidurus. Tropidurus sertanejo, n. sp., highlighted in dark gray. See table 5 for corresponding summary statistics.
Data for: Surviving the serenade: how conflicting selection pressures shape the early stages of sexual signal diversification
Open the record for dataset details and reuse information.
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
<p>This data depository contains analysis results from Parks, Wickett, and Alverson 2017 (Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta) (Mol. Biol. Evol. doi:10.1093/molbev/msx268)), and is made freely available to the research community.</p> <p>The file and subfolders here are as follows:</p> <p>gene_alignments<br> - contains compressed (tarred and gzipped) folders with all gene alignments at 0.2, 0.5 and 0.8 alignment column occupancy cutoffs. In each folder, there are also text files listing which gene alignments fall under which taxon occupancy subsetting strategy (i.e., 10-20% taxon occupancy, 40-60% taxon occupancy, 80-100% taxon occupancy, etc).</p> <p>gene_trees<br> - contains all (compressed) gene trees (bootstrapped versions, 100 bootstrap pseudo-replicates)) used in Astral analyses for each alignment column occupancy cutoff (0.2, 0.5, 0.8); nodes with less than 33% bootstrap support are collapsed.</p> <p>hmms.mafft_aligned<br> - contains (compressed) hmm specifications for each major diatom morphotype (radial and polar centrics, araphid and raphid pennates) from the 0.2 alignment column occupancy subset of the data. A summary of the sampling scheme and the hmm results/counts are also available in HMM_sampling.docx.</p> <p>mmetsp_nuclear_transcriptome_assemblies<br> - these are the compressed nuclear transcriptome assemblies that were done in-house (i.e., mostly MMETSP samples). Assemblies do not include organellar or rDNA loci.</p> <p>species_trees<br> - contains (compressed) species trees for all phylogenetic strategies and alignment column occupancy cutoff/data subset strategies.</p> <p>Suppl_1.MMETSP_basic_summaries.xlsx<br> - this an identical file to Parks, Wickett and Alverson 2017 supplementary file 1. This file contains taxon, strain and SRA information for all assembled taxa, and a variety of assembly metric information.</p> <p> </p>
Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting
Open the record for dataset details and reuse information.
Data from: Integrating incomplete fossils by isolating conflictive signal in saturated and non-independent morphological characters
Morphological characters are indispensable in phylogenetic analyses for understanding the pattern, process, and tempo of evolution. If characters are independent and free of systematic errors, then combining as many different kinds of characters as are available will result in the best-supported phylogenetic hypotheses. But since morphological characters are subject to natural selection for function and arise from the expression of developmental pathways, they may not be independent, a situation that may amplify any underlying homoplasy. Here, we use new dental and multi-locus genetic data from bats (Mammalia: Chiroptera) to quantify saturation and similarity in morphological characters and introduce two likelihood-based approaches to identify strongly conflicting characters and integrate morphological and molecular data. We implement these methods to analyze the phylogeny of incomplete Miocene fossils in the radiation of Phyllostomidae (New World Leaf-nosed Bats), perhaps the most ecologically diverse family of living mammals. Morphological characters produced trees incongruent with molecular phylogenies, were saturated, and showed rates of change higher than most molecular substitution rates. Dental characters encoded variation similar to that in other morphological characters, while molecular characters encoded highly dissimilar variation in comparison. Saturation and high rates of change indicate randomization of phylogenetic signal in the morphological data, and extensive similarity suggests characters are non-independent and errors are amplified. To integrate the morphological data into tree building while accounting for homoplasy, we used statistical molecular scaffolds and combined phylogenetic analyses excluding a small subset of strongly conflicting dental characters. The phylogenies revealed the Miocene nectar-feeding †Palynephyllum nests within the crown nectar-feeding South American subfamily Lonchophyllinae, while the Miocene genus †Notonycteris is sister to the extant carnivorous Vampyrum. These relationships imply new calibration points for timing of radiation of the ecologically diverse Phyllostomidae.
Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)
Open the record for dataset details and reuse information.
Data from: Integrating incomplete fossils by isolating conflictive signal in saturated and non-independent morphological characters
Open the record for dataset details and reuse information.
Conflicting phylogenetic signals in genomic data of the coffee family (Rubiaceae)
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.