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.
20
datasets available to search
ShareScore release 0.9.0
Dataset results
20 results for “Concatenated tree”
Fig. 27. Maximum likelihood tree from the concatenated data set with COI, 28S and 18S in Revision of the Merodon bombiformis group (Diptera: Syrphidae) - rare and endemic African hoverflies
Fig. 27. Maximum likelihood tree from the concatenated data set with COI, 28S and 18S rRNA gene sequences.
Fig. 3. Phylogenetic trees obtained from a concatenated dataset with a in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 3. Phylogenetic trees obtained from a concatenated dataset with a total length of 1,277 bp, consisting of seven mitochondrial genes (16S, tRNA-Ala, tRNA-Leu, tRNA-Asn, tRNA-Gln, tRNA-Pro, and COI). The trees were built based on maximum likelihood (ML, left) and Bayesian inference (BI, right). Values at nodes indicate bootstrap scores from ML and posterior probabilities from BI. Outgroups are only shown in the ML tree with both the support values. Scale bars indicate the number of nucleotide substitutions per site. OTUs sequenced in this study are in bold face. Each letter in parentheses after non-bold OTUs denotes the source: C, Chichvarkhin (2017b); F, Foltz and Rocha- Olivares (unpublished); K, Knott et al. (2018); L, Lopes et al. (2016); M, Matsubara et al. (2004); W, Wada et al. (1996). Circles indicate species listed as Setihenricia in Chichvarkhin and Chichvarkhina (2017). Triangles indicate species morphologically identified as Setihenricia in this study (see Fig. 4A).
FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription
FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4-trnS and trnM-trnV sequence data of the analysed dataset of Pottiaceae subfam. Pottioideae, partitioned between DNA sequence and indel data. Posterior probability from BI is displayed above the branches; bootstrap support (656 replications) from ML analysis is displayed below the branches.
Fig. 2. Maximum Likelihood species tree from the concatenated 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 2. Maximum Likelihood species tree from the concatenated 50 % complete dataset consisting of 4561 loci. Values on the branch indicate Shimodaira Hasegawalike approximate likelihood ratio test and ultrafast bootstrap. Abbreviations as in Fig. 1.
FIGURE 4 Maximum Clade Credibility Tree inferred using a concatenate COI, 16S, 28S and 18S alignment using BEAST. Node bars are 95 in The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
FIGURE 4 Maximum Clade Credibility Tree inferred using a concatenate COI, 16S, 28S and 18S alignment using BEAST. Node bars are 95% Higher Posterior Density, scale bar is in million years ago (Ma), starting from present 0. Numbers above bars = node age; numbers below bars (bold) = posterior probability of the node.
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers> 50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. Letters A and B correspond to clades referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–2 and 4–6.
Figure 3. COI–28S concatenated maximum-likelihood tree reconstructed using GARLI 2.0 in Unmasking Aurelia species in the Mediterranean Sea: an integrative morphometric and molecular approach
Figure 3. COI–28S concatenated maximum-likelihood tree reconstructed using GARLI 2.0. Numbers adjacent to nodes show the bootstrap support values. The scale indicates the number of substitutions per site. Reference sequences from GenBank are in bold.
FIGURE 1. The best-scoring RAxML tree constructed from a concatenated ITS, tef1 in Combination of morphological and molecular data support Pestalotiopsis eleutherococci (Sporocadaceae) as a new species
FIGURE 1. The best-scoring RAxML tree constructed from a concatenated ITS, tef1-α, and tub2 dataset of Pestalotiopsis species. The tree is rooted with Truncatella laurocerasi (ICMP 11214) and T. angustata (CBS 144025). The asterisk at P. jesteri indicates its ambiguous status on Index Fungorum (2022). The type delivered sequences are indicated in bold and marked with T. The new isolates are in blue. The asterisk at P. intermedia indicates a misidentification.
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I in New species of Trichomycterus (Siluriformes: Trichomycteridae) lacking pelvic fins from Paranapanema basin, southeastern Brazil
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I (COI) and 16S genes, showing the relationships of Trichomycterus pascuali within Trichomycterinae. Numbers on branches of tree denote bootstrap (B) values.
FIGURE 7. Comparison concatenated tree ITS2 – 28S rDNA D2 in Description of two new species closely related to Doryctobracon areolatus (Szépligeti, 1911) (Hymenoptera, Braconidae), based on morphometric and molecular analyses
FIGURE 7. Comparison concatenated tree ITS2 – 28S rDNA D2 (UPGMA) produced from the nucleotide sequences (A), cluster analysis of the Mahalanobis distance (UPGMA) calculated from the shape of the wings components (B). (DAAP = Doryctobracon areolatus from Amapá, DAGO = D. areolatus from Goiás, DATO = D. areolatus from Tocantins, DASP = D. areolatus from São Paulo, YSAP = Doryctobracon whartoni sp. nov. (yellow stigma) from Amapá; BSAP = Doryctobracon adaimei sp. nov. (brown stigma) from Amapá, BSGO = D. adaimei sp. nov. from Goiás, BSTO = D. adaimei sp. nov. from Tocantins.
Fig. 8 Maximum parsimony strict-consensus tree for the concatenated 3 in Sky island diversification in the Merodon rufus group (Diptera, Syrphidae)-recent vicariance in south-east Europe
Fig. 8 Maximum parsimony strict-consensus tree for the concatenated 3′-end and 5′-end mtCOI and 28S rRNA genes. Filled circles denote unique changes and open circles non-unique changes. 72 trees, length = 1935 steps, CI = 34, RI = 64
Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 in A multigene phylogeny demonstrates that Tuber aestivum and Tuber uncinatum are conspecific
Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 are indicated. The tree is rooted with MAC (T. macrosporum) and MAG (T. magnatum)
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 in Trichoderma changiae (Hypocreales), a new species isolated from a native orchid in Taiwan
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 sequences using Maximum-likelihood analysis. The new species Trichoderma changiae is highlighted in bold blue. Bootstrap values above 50% from RAxML-HPC2 on XSEDE (left) and posterior probabilities above 0.95 from Bayesian analysis (right) are displayed at the nodes. The scale bar represents 0.05 substitutions per nucleotide position. Trichoderma vulgatum was used as the outgroup. "T" denotes type strains.
Data from: Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
Data from: Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts
Open the record for dataset details and reuse information.
Data from: Concatenated alignments and the case of the disappearing tree
BackgroundAnalyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of generating genetic diversity, there are open questions as to whether concatenation amplifies or averages phylogenetic signals residing in individual genes. Here we investigate concatenations of prokaryotic and eukaryotic datasets to investigate possible sources of incongruence in phylogenetic trees and to examine the level of overlap between individual and concatenated alignments.ResultsWe analyzed prokaryotic datasets comprising 248 invidual gene trees from 315 genomes at three taxonomic depths spanning gammaproteobacteria, proteobacteria, and prokaryotes (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual gene trees from 85 genomes at two taxonomic depths: across plants-animals-fungi and within fungi. Consistent with previous findings, the branches in trees made from concatenated alignments are, in general, not supported by any of their underlying individual gene trees, even though the concatenation trees tend to possess high bootstrap proportions values. For the prokaryote data, this observation is independent of phylogenetic depth and sequence conservation. The eukaryotic data show much better agreement between concatenation and single gene trees. LGT frequencies in trees were estimated using established methods. Sequence length in individual alignments, but not sequence divergence, was found to correlate with the generation of branches that correspond to the concatenated tree.ConclusionsThe weak correspondence of concatenation trees with single gene trees gives rise to the question where the phylogenetic signal in concatenated trees is coming from. The eukaryote data reveals a better correspondence between individual and concatenation trees than the prokaryote data. The question of whether the lack of correspondence between individual genes and the concatenation tree in the prokaryotic data is due to LGT or phylogenetic artefacts is remains unanswered. If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence.
Concatenated DNA matrix and BEAST tree used for phylogenetic, dating, biogeographic and diversification analyses of Caribbean Podocarpus
<p><b>Aim </b>The Progression Rule, that older lineages inhabit older islands and colonize newer ones as they emerge, has seldom been tested in the Caribbean due to its geological complexity. Here we use the conifer genus <i>Podocarpus</i> to explore this hypothesis. We infer the evolutionary history, biogeography, and diversification rates of this genus under a hypothesis testing framework.</p> <p><b>Location</b> The Caribbean archipelago (Antilles)</p> <p><b>Methods</b> We present the most comprehensive sampling for Caribbean <i>Podocarpus</i> to date in a Bayesian dated phylogenetic tree using a genotyping by sequencing DNA matrix of 67,589 bp. We inferred ancestral ranges and inter-island divergence patterns using several models available. We explored diversification rates associated with island colonization, and checked for diversification rate shifts in the phylogeny.</p> <p><b>Results</b> Caribbean <i>Podocarpus</i> is the result of colonization from the Andes during the Eocene to Oligocene (ca. 45-31 Ma). Lesser Antillean species originated during the Oligocene from the Andes or the Greater Antilles, depending on the model of choice. Vicariance can explain the divergence of Cuban and Hispaniolan species, with subsequent dispersals into Jamaica. Despite the availability of new habitat opportunities, which might promote cladogenesis, insular <i>Podocarpus</i> did not show higher diversification rates than continental taxa.</p> <p><b>Main</b> <b>conclusions </b>The conditions for progression rule were not met because colonization of younger islands (Lesser Antilles) occurred from the continent, or because suitable habitat in the partially emerged younger islands was likely present at the time older islands (Greater Antilles) were colonized. An improved paleogeographic knowledge of the Caribbean will allow testing this hypothesis in multiple lineages. Our finding that diversification rates did not increase with island colonization might be common in other Caribbean lineages. Genotyping by sequencing proved promising to reveal complex historical assembly processes of vicariance and dispersal at a fine phylogenetic scale.</p> <p> </p>
Data from: Concatenated alignments and the case of the disappearing tree
Open the record for dataset details and reuse information.
Concatenated DNA matrix and BEAST tree used for phylogenetic, dating, biogeographic and diversification analyses of Caribbean Podocarpus
Open the record for dataset details and reuse information.
Data from: When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny
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.