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.
17
datasets available to search
ShareScore release 0.9.0
Dataset results
17 results for “plastome phylogeny”
Linked collectors and determiners for: Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World.
Natural history specimen data linked to collectors and determiners held within, "Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4">https://bionomia.net/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4">https://gbif.org/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4</a>. Formatted as a Frictionless Data package.
Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees
<p><strong>Aim</strong>: Miombo woodlands form a characteristic vegetation type covering 2.7 million km<sup>2</sup> in southern and eastern Africa. Despite their wide geographical extent, their origin, floristic and spatial evolution through time remain understudied. To fill this gap, we studied the evolution of <em>Brachystegia</em> trees, one of the most representative genera of these woodlands (20 species), also represented in Guineo-Congolian rain forests (8 species).</p> <p><strong>Location</strong>: Tropical Africa, Guineo-Congolian forests and Zambezian savannahs.</p> <p><strong>Methods</strong>: We used a genome skimming approach to sequence the plastomes of 45 <em>Brachystegia</em> samples, covering 25 of the 29 existing species, and one outgroup (<em>Julbernardia paniculata</em>). The phylogeny of the plastomes was reconstructed and time-calibrated. We tested if the genetic divergence between lineages reflected taxonomic and/or geographic distances using Mantel tests. Finally, we inferred the evolutionary history of <em>Brachystegia</em> based on the age and spatial distribution of its lineages.</p> <p><strong>Results</strong>: Surprisingly, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. Two main clades separate woodland and rain forest species, which diverged during the late Miocene-Pliocene (95% HPD = 2.78-8.59 Ma). In miombo woodlands, three subclades occur in parapatry along an East-West axis, ranging from Angola to East Africa. Their divergence started from the Plio-Pleistocene (95% HPD = 1.17-3.69 Ma). Divergence dates (TMRCA) within miombo subclades decrease from East Africa (1.53 Ma) to Angola (0.76 Ma).</p> <p><strong>Main Conclusions</strong>: <em>Brachystegia</em> plastomes appear unreliable to identify species, probably due to species introgression leading to recurrent chloroplast captures. However, they prove very informative for tracking the past dynamics of the genus, and suggest a historical westwards expansion of miombo <em>Brachystegia</em>, and possibly of miombo vegetation, during the Plio-Pleistocene. Further investigations using nuclear DNA are needed to assess the species tree as well as speciation and hybridisation events between species. </p>
Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)
<p><strong>Background and Aims</strong> <em>Rhododendron </em>is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of <em>Rhododendron </em>in the Himalaya–Hengduan Mountains where the genus is most diverse.</p> <p><strong>Methods </strong>We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the <em>Rhododendron </em>species native to the Himalaya–Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of <em>Rhododendron</em>, especially the two species-rich subgenera <em>Rhododendron</em> and <em>Hymenanthes </em>that comprise >90 % of <em>Rhododendron </em>species in the Himalaya–Hengduan Mountains.</p> <p><strong>Key Results </strong>The full plastid dataset produced a well-resolved and supported phylogeny of <em>Rhododendron</em>. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies strongly suggested that reticulation events may have occurred in the deep lineage history of the genus. Within <em>Rhododendron</em>, subgenus <em>Therorhodion </em>diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core <em>Rhododendron</em>. Diversification in subgenus <em>Rhododendron </em>accelerated c. 16.6 Mya and then became fairly continuous. Conversely, <em>Hymenanthes </em>diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya–Hengduan Mountains, subgenus <em>Rhododendron </em>contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in <em>Hymenanthes </em>contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification.</p> <p><strong>Conclusions </strong>The 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for <em>Rhododendron</em>, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of <em>Rhododendron</em>.</p>
Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
<p>Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available <em>de novo</em> genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation. </p>
A plastome phylogeny of Rumex (Polygonaceae) illuminates the divergent evolutionary histories of docks and sorrels
<p>The genus <em>Rumex</em> L. (Polygonaceae) provides a unique system for investigating the evolutionary development of sex determination and molecular rate evolution. Historically, <em>Rumex</em> has been divided, both taxonomically and colloquially into two groups: 'docks' and 'sorrels'. A well-resolved phylogeny can help evaluate a genetic basis for this division. Here we present a plastome phylogeny for 34 species of <em>Rumex</em>, inferred using maximum likelihood criteria. The historical 'docks' (<em>Rumex</em> subgenus <em>Rumex</em>) were resolved as monophyletic. The historical 'sorrels' (<em>Rumex</em> subgenera <em>Acetosa</em> and <em>Acetosella</em>) were resolved together, though not monophyletic due to the inclusion of <em>R. bucephalophorus</em> (<em>Rumex</em> subgenus <em>Platypodium</em>). <em>Emex</em> is supported as its own subgenus within <em>Rumex</em>, instead of resolved as sister taxa. We found remarkably low nucleotide diversity among the docks, consistent with recent diversification in that group, especially as compared to the sorrels. Fossil calibration of the phylogeny suggested that the common ancestor for <em>Rumex</em> (including <em>Emex</em>) has origins in the lower Miocene (22.13 MYA). The sorrels appear to have subsequently diversified at a relatively constant rate. The origin of the docks, however, was placed in the upper Miocene, but with most speciation occurring in the Plio-Pleistocene.</p>
Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
Open the record for dataset details and reuse information.
Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)
Open the record for dataset details and reuse information.
A plastome phylogeny of Rumex (Polygonaceae) illuminates the divergent evolutionary histories of docks and sorrels
Open the record for dataset details and reuse information.
Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees
Open the record for dataset details and reuse information.
Fig. 4 in Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)
Fig. 4 An evolutionary scenario for the cox1 intron acquisitions in the tribe Hyoscyameae. Purple dots indicate mitochondrial cox1 intron acquisitions by horizontal gene transfer. The paraphyly of the genus Scopolia is supported by plastid and nuclear markers (see text and Fig. 3)
Fig. 1 in Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)
Fig. 1 The chloroplast genome of Scopolia carniolica. Large and small single-copy regions (LSC and SSC, respectively) and inverted repeats (IR) are indicated. Genes inside and outside the circle indicate clockwise and counterclockwise transcription directions, respectively. Gene positions are color-coded according to functional categories of genes. The
Fig. 3 in Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)
Fig. 3 Maximum likelihood phylogenetic trees of the tribe Hyoscyameae. A Tree based on the complete chloroplast genomes. The last inverted repeat region was removed to avoid sequence overrepresentation. The alignment length is 134,327 nt. B Tree based on nuclear ITS2 sequences. The seven individuals of Atropa
Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae)
<p>Dwarf mistletoes are a group of morphologically-reduced aerial shoot parasites of Pinaceae and Cupressaceae found in the northern hemisphere and equatorial east Africa. Though diagnosable by a suite of morphological traits, phylogenetic knowledge of species relationships has been limited to studies employing either comprehensive sampling of one or two genes, or more sequence data but limited taxonomic sampling. We used genome skimming data to assemble 3kb of the nuclear ribosomal cistron and up to 45kb of the plastome to clarify the phylogenetic root of the genus, species monophyly, and relationships among infraspecific taxa. Genomic differentiation among taxa was variable; however, we found strong support for reciprocally monophyletic New World and Old World lineages and congruent nrDNA and plastome topologies at the species level and below, and most taxonomic sections and at the species level and below. Plastome gene content was stable across the genus with minimal pseudogenization or loss, with the notable exception of <i>cemA</i>. These findings form the basis of our re-evaluation of historical biogeographical hypotheses, species and subspecies-level taxonomy, and plastome evolution in <i>Arceuthobium. </i>More broadly, this work provides a foundation for future clade-focused comparative and biosystematics studies of <i>Arceuthobium.</i></p>
Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae)
Open the record for dataset details and reuse information.
Data from: Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set
PREMISE OF THE STUDY: Major relationships within Lamiidae, an asterid clade with ∼40000 species, have largely eluded resolution despite two decades of intensive study. The phylogenetic positions of Icacinaceae and other early-diverging lamiid clades (Garryales, Metteniusaceae, and Oncothecaceae) have been particularly problematic, hindering classification and impeding our understanding of early lamiid (and euasterid) character evolution. METHODS: To resolve basal lamiid phylogeny, we sequenced 50 plastid genomes using the Illumina sequencing platform and combined these with available asterid plastome sequence data for more comprehensive phylogenetic analyses. KEY RESULTS: Our analyses resolved basal lamiid relationships with strong support, including the circumscription and phylogenetic position of the enigmatic Icacinaceae. This greatly improved basal lamiid phylogeny offers insight into character evolution and facilitates an updated classification for this clade, which we present here, including phylogenetic definitions for 10 new or converted clade names. We also offer recommendations for applying this classification to the Angiosperm Phylogeny Group (APG) system, including the recognition of a reduced Icacinaceae, an expanded Metteniusaceae, and two orders new to APG: Icacinales (Icacinaceae + Oncothecaceae) and Metteniusales (Metteniusaceae). CONCLUSIONS: The lamiids possibly radiated from an ancestry of tropical trees with inconspicuous flowers and large, drupaceous fruits, given that these morphological characters are distributed across a grade of lineages (Icacinaceae, Oncothecaceae, Metteniusaceae) subtending the core lamiid clade (Boraginales, Gentianales, Lamiales, Solanales, Vahlia). Furthermore, the presence of similar morphological features among members of Aquifoliales suggests these characters might be ancestral for the Gentianidae (euasterids) as a whole.
Data from: Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set
Open the record for dataset details and reuse information.
Fig. 2 in Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)
Fig. 2 Similarity plot comparing Scopolia carniolica chloroplast genome to other members of the tribe Hyoscyameae. The Y-axis represents the sequence identity (within the range 70–100%) from pairwise comparisons between the chloroplast genomes of Scopolia carniolica and other species of the tribe using the VISTA program. Coding and non-coding regions are in green and gray colors, respectively. The percent identities
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.