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1,344 results for “: phylogenomics”

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dryad36/100

Data for: Phylogenomics of Aralia sect. Aralia (Araliaceae)

Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. Aralia sect. Aralia is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial conflicts among nuclear genes, yet different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) Aralia californica of western North America is sister to the eastern Asian clade consisting of A. cordata and A. continentalis in the nuclear tree, and (2) the eastern North American A. racemosa forms a clade with A. bicrenata from southwestern North America, and the North American A. racemosa - A. bicrenata clade is then sister to the eastern Asian clade consisting of A. glabra (Japan), A. fargesii (C China), and A. apioides and A. atropurpurea (the Hengduan Mountains). Aralia cordata is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and Aralia continentalis is redefined with a narrower distribution in Northeast China, eastern Russia and peninsular Korea.

opencc-zeroJan 2023View details →

dryad36/100

Data from: Morphometrics and phylogenomics reveal a new species of Heuchera (Saxifragaceae) in northeastern México

Here I describe a new species narrowly endemic to high-altitude limestone outcrops of the Sierra Madre Oriental, Coahuila, Mexico, together with a phylogenomic and morphometric evaluation of the Heuchera species of northeastern Mexico. Originally thought to be a disjunct population of Heuchera sanguinea, the new species is phylogenetically and morphologically most similar to Heuchera lakelae; from which it is distinguished based on morphometric characters and other morphological attributes, phylogenetic placement, geographic range, phenology, and ecological preferences.

opencc-zeroJan 2023View details →

dryad36/100

Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Coloration is an important phenotypic trait for taxonomic studies and has been widely used for identifying insect species and populations. However, coloration can be a poor diagnostic character for insect species that exhibit high polymorphism in this trait, which can lead to over-splitting of taxonomic units. In orchid bees, color variation has been interpreted by different taxonomists as either polymorphism associated with Mullerian mimicry complexes or diagnostic traits for species identification. Despite this uncertainty, integrative approaches that incorporate multiple independent datasets to test the validity of hair coloration as a character that identifies independent evolutionary units have not been used. Here, we use phylogenomic data from Ultraconserved Elements (UCEs) to explore whether color phenotypes in the widespread orchid bee species complexes Eulaema meriana and Eulaema bombiformis (Hymenoptera: Apidae: Euglossini) correspond to independent lineages or polymorphic trait variation within species. We find that lineages within both species are structured according to geography and that color morphs are generally unassociated with evolutionarily independent groups except for populations located in the Atlantic Forest of Brazil. We conclude that there is compelling evidence that E. atleticana and E. niveofasciata are subspecies of E. meriana and E. bombiformis, respectively, and not different species as previously suggested. Therefore, we recognize Eulaema meriana atleticana comb. n. and Eulaema bombiformis niveofasciata comb. n. and discuss their morphological characteristics. We make recommendations on the use of color traits for orchid bee taxonomy and discuss the significance of subspecies as evolutionary units relevant for conservation efforts.

opencc-zeroJan 2023View details →

dryad36/100

Data from: A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion

PREMISE: The ~140 species of Lonicera are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well-supported phylogeny of Lonicera will allow us to trace the evolutionary history of organ fusion. METHODS: We inferred the phylogeny of Lonicera using Restriction-site Associated DNA Sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion-related traits. RESULTS: RADSeq data yielded a well-resolved and well-supported phylogeny. The two traditionally recognized subgenera (Periclymenum and Chamaecerasus), three of the four sections (Isoxylosteum, Coeloxylosteum, and Nintooa), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section Isika was strongly supported as paraphyletic. Nintooa, a clade of ~22 mostly vine-forming species, including L. japonica, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules. CONCLUSIONS: We provide the most comprehensive and well-supported phylogeny of Lonicera to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in-depth developmental and functional analyses.

opencc-zeroFeb 2023View details →

dryad36/100

Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acari: Eriophyoidea)

Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acari; their higher-level phylogeny, however, remains unresolved due to the availability of limited number of morphological characters, some of which are suspected as homoplasy. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships. Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within the Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that the Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms. This study demonstrates the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.

opencc-zeroFeb 2023View details →

dryad36/100

Target-capture probes for phylogenomics of the Caenogastropoda

Target-capture approaches have facilitated a rapid growth in the field of phylogenomics but few probe sets exist for mollusks, an exceptionally rich phylum with unparalleled ecological and morphological diversity. We designed and tested the first universal probe set using Phyluce to capture ultraconserved elements (UCEs) and exon loci from the Subclass Caenogastropoda – one of six major lineages of gastropods. The probe set consists of 29,441 probes (8,872 for UCEs and 20,569 for exons) designed to target 1,142 UCE loci and 1,933 exon loci (3,075 total). In silico analyses of our probe set yielded an average of 2,110 loci from genomes and 1,389 loci from transcriptomes of diverse caenogastropods, respectively. After screening these loci to remove those that matched multiple contigs, an average of 1,686 loci from genomes and 785 loci from transcriptomes were retained. Phylogenetic analyses of the loci extracted from transcriptomes produced well-supported trees very similar to those published based on transcriptomic analyses. Although there are few caenogastropod genomes to analyze, phylogenetic relationships estimated from the analysis of loci extracted from genomes recover similar phylogenetic relationships and indicate that the loci targeted with this probe set are informative for resolving deep phylogenetic relationships. An in vitro analysis of the probe set with the Epitoniidae, a diverse caenogastropod family of uncertain affinity and with poorly resolved evolutionary relationships, recovered an average of 1,710 loci and produced a well-resolved phylogeny. Although preliminary, the analysis of loci captured by our probe set for a small number of epitoniid taxa produced a well-resolved tree indicating that this probe set is also able to resolve relationships at shallower hierarchical scales. Together, the in silico and in vitro analyses indicate that target-capture enrichment with this probe set is a useful tool for reconstructing phylogenetic relationships across taxonomic levels and evolutionary time scales.

opencc-zeroMar 2023View details →

dryad36/100

Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree

Euglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being the most elusive. Ploeotids make up most of this backbone diversity—yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show they are non-monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships between these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single-cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place Decastava in Alistosa; while Hemiolia branches with Liburna, establishing the novel clade Karavia. We describe Hemiolia limna, a freshwater-dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: Chelandium granulatum nov. gen. nov. sp. branches as sister to Olkasia, and Gaulosia striata nov. gen. nov. sp. remains an orphan taxon.

opencc-zeroDec 2022View details →

zenodo36/100

Phylogenomic inference of the higher classification of velvet ants (Hymenoptera: Mutillidae)

The family Mutillidae (Hymenoptera) is a species-rich group of aculeate wasps that occur worldwide. The higher-level classification of the family has historically been controversial due, in part, to the extreme sexual dimorphism exhibited by these insects and their morphological similarity to other wasp taxa that also have apterous females. Modern hypotheses on the internal higher classification of Mutillidae have been exclusively based on morphology and, further, they include Myrmosinae as a mutillid subfamily. In contrast, several molecular-based family-level studies of Aculeata recovered Myrmosinae as a nonmutillid taxon. To test the validity of these morphology-based classifications and the phylogenetic placement of the controversial taxon Myrmosinae, a phylogenomic study of Mutillidae was conducted using ultraconserved elements (UCEs). All alignments, tree files, XML file, and contig assemblies (SPAdes and Trinity) used for (or produced by) this study are included here. A specimen data table is also included.

opencc-by-4.0Mar 2023View details →

dryad36/100

Phylogenomics resolves the Himalayan endemic Brachymeniopsis gymnostoma (Bryophyta, Funariaceae), rediscovered after almost a century, as a species of Entosthodon

Traits of the spore-bearing generation have historically provided the basis for systematic concepts across the phylogenetic spectrum and depth of mosses. Whether taxa characterized by a simple sporophytic architecture are closely related or emerged from independent reduction is often ambiguous. Phylogenomic inferences in the Funariaceae, which hold the model taxon Physcomitrium patens, revealed that several such shifts in sporophyte complexity occurred, mostly within the Entosthodon-Physcomitrium complex. Here, we report the rediscovery, nearly 100 years after its description, of the Chinese endemic and monospecific genus Brachymeniopsis, which is characterized by, among other traits, its short sporophytes lacking the sporangial peristome teeth controlling spore dispersal. Phylogenomic inferences reveal that its sole species, B. gymnostoma arose within the clade of Entosthodon sensu stricto, a genus with typically long-exerted capsules. We therefore propose to transfer B. gymnostoma to the genus Entosthodon, as E. gymnostomus. Furthermore, Clavitheca poeltii, the sole species of the genus, is morphologically highly similar to E. gymnostomus, and should also be transferred to Entosthodon, but is retained as a distinct taxon, E. poeltii, until additional populations allow for testing the robustness of the observed divergence in costa and seta length between the Nepalese and Chinese populations.

opencc-zeroApr 2023View details →

dryad36/100

Phylogenomics resolves major relationships of Catocala underwing moths

<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> Underwing moths in the genus Catocala Shrank are among the most charismatic Lepidoptera. Catocala is also one of the most diverse genera in the speciose family Erebidae, but a phylogenetic framework for the genus is lacking. We reconstruct the first comprehensive molecular phylogeny for Catocala based on 685 anchored hybrid enrichment loci sampled from 173 species. Phylogenetic analysis unambiguously recovers Catocala and Catocala + Ulotrichopus as monophyletic with strong support and resolves many backbone relationships within Catocala. Our results confirm the classification of previously proposed taxonomic subgroups of Catocala, including seven based on recent molecular/morphological evidence, and ten based on early twentieth-century morphological research. Mapping of larval host plant use onto the tree shows Fabaceae to be the likely ancestral host plant family for Catocala (96.3% probability) and Catocala + Ulotrichopus (83.9% probability). There were at least 18 independent larval host plant shifts to nine plant families, the most common shift being from Fabaceae to Fagaceae. Larval host plant use appears to have played a critical role in the evolutionary history of Catocala, with several rapid diversification events propelled by shifts to novel larval host plants, particularly in the North American Catocala fauna. </div> </div> </div> </div>

opencc-zeroApr 2023View details →

dryad36/100

Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite a recent surge in interest in these mushrooms due to emerging evidence that psilocybin, the main psychoactive compound, is a promising therapeutic for a variety of mental illnesses, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny for Psilocybe using shotgun sequencing of 71 fungarium specimens, including 23 types, and conducting phylogenomic analysis using 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4–5 possible horizontal transfers to other mushrooms between 40 and 9mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the cluster that corresponds to a deep split within the genus, possibly consistent with the independent acquisition of the cluster. By mining genomic data beyond markers for phylogenetic inference, we gained novel insights into the evolutionary origins of psilocybin biosynthesis that have implications for understanding the functional role of this powerful chemical and can inform translational applications for human well-being.

opencc-zeroMay 2023View details →

dryad36/100

Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum

Placozoa is an ancient phylum of extraordinarily unusual animals: miniscule, ameboid creatures that lack most fundamental animal features. Despite high genetic diversity, only recently have the second and third species been named. While prior genomic studies suffer from incomplete placozoan taxon sampling, we more than double the count with protein sequences from seven key genomes and produce the first nuclear phylogenomic reconstruction of all major placozoan lineages. This leads us to the first complete Linnaean taxonomic classification of Placozoa, over a century after its discovery: This may be the only time in the 21st century when an entire higher taxonomy for a whole animal phylum is formalized. Our classification establishes 2 new classes, 4 new orders, 3 new families, 1 new genus, and 1 new species, namely classes Polyplacotomia and Uniplacotomia; orders Polyplacotomea, Trichoplacea, Cladhexea, and Hoilungea; families Polyplacotomidae, Cladtertiidae, and Hoilungidae; and genus Cladtertia with species Cladtertia collaboinventa, nov. Our likelihood and gene content tree topologies refine the relationships determined in previous studies. Adding morphological data into our phylogenomic matrices suggests sponges (Porifera) as the sister to other animals, indicating that modest data addition shifts this node away from comb jellies (Ctenophora). Furthermore, by adding the first genomic protein data of the exceptionally distinct and branching Polyplacotoma mediterranea, we solidify its position as sister to all other placozoans; a divergence we estimate to be over 400 million years old. Yet even this deep split sits on a long branch to other animals, suggesting a bottleneck event followed by diversification. Ancestral state reconstructions indicate large shifts in gene content within Placozoa, with Hoilungia hongkongensis and its closest relatives having the most unique genetics.

opencc-zeroMay 2023View details →

dryad36/100

Phylogenomics and deep convergence in cockroach hind-wing morphology

Despite regular advances in Blattodea systematics, several relationships remain controversial or untested in formal phylogenetic reconstructions. This common situation for understudied metazoan groups limits our power to answer questions about phenotypic evolution. In this study, we infer the evolutionary history of Blattodea using newly sampled taxa that improve phylogenetic resolution while also illuminating the evolutionary history of an unusual phenotype—the apically folded hind-wing. Taxa newly sequenced include those with a hind-wing apical fold (Anaplecta pulchella, A. pygmaea, A. sp. cf. malaysensis, Diplopterina parva, Prosoplecta semperi, Anaplectoidea klossi, and Oulopteryx illuminata sp. nov. that we describe herein, including its male genitalia) and other rare taxa (Dipteretrum hamstroemi, Duchailluia togoensis, Lauraesilpha mearetoi, Buboblatta vlasaki). The phylogenetic design utilizes 41 genes over 91 species in total, analyzed in a maximum likelihood and coalescent framework. To quantify the phylogenetic uncertainty of the analysis, support for various topologies is assessed. We find unambiguous support for the surprising position of Neotropical Oulopteryx (Oulopterygidae) as sister to New Caledonian/Australian Tryonicidae. This, and other phylogenetic findings, reveal that the apically folded hind-wing may have arisen nine times in Blattodea. Further investigations are needed, notably with an increased taxonomic sampling, to demonstrate stronger support for the placement of rogue taxa (e.g., Anaplecta) and to investigate the evolutionary correlates of wing evolution.

opencc-zeroMay 2023View details →

dryad36/100

Phylogenomic analyses reveal an allopolyploid origin of core Didymocarpinae (Gesneriaceae) followed by rapid radiation

Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.

opencc-zeroMay 2023View details →

dryad36/100

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.

opencc-zeroMay 2023View details →

zenodo36/100

Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera)

Genomes, alignments and tree files of the study "Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera). Molecular Phylogenetics and Evolution, https://doi.org/10.1016/j.ympev.2024.108113".

opencc-by-4.0Jan 2023View details →

dryad36/100

Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a 'spectacular failure' due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an fbranch analysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.

opencc-zeroDec 2022View details →

dryad36/100

Data for: Preliminary phylogenomic analyses reveal multiple reversions to nocturnal behavior and morphology within the primarily diurnal tribe Adesmiini (Coleoptera: Tenebrionidae)

The darkling beetle tribe Adesmiini (Tenebrionidae: Pimeliinae) is a prominent part of the African and western Palearctic desert faunas, with most species being day-active fast-running detritivores. Taxonomic diversity within the tribe is highest in the southern part of the Afrotropical realm (all genera present), while only the species-rich genus Adesmia occurs north of the Sahara. Despite containing conspicuous diurnal species, such as the fog-basking beetle Onymacrisunguicularis (a focal taxon in ecological research for decades), Adesmiini has undergone few modern taxonomic or phylogenetic studies. Hence, generic concepts and the evolution of diurnal behaviors and morphologies, rare in the primarily nocturnal family Tenebrionidae, remain poorly explored. To investigate evolutionary relationships and the origin of diurnal activity within the tribe, a genomic dataset of 529 protein-coding genes across 43 species spanning 10 of 11 Adesmiini genera was assembled and analyzed. The resulting phylogeny for the tribe does not support the monophyly of many current Adesmiini genera (i.e. Adesmia, Metriopus, Onymacris, Physadesmia, and Stenocara). Ancestral state reconstruction of diurnal activity, using eye shape as a proxy and supplemented by literature and collection records, supports the hypothesis that Adesmiini were primitively diurnal, followed by at least four shifts to nocturnal or crepuscular activity.

opencc-zeroJun 2023View details →

dryad36/100

Data for: Phylogenomic analyses of the Neotropical Artocarpeae (Moraceae) reveal a history of introgression and support the reinstatement of Acanthinophyllum

This molecular study of the Neotropical Artocarpeae, the closest living allies of the Asia-Pacific breadfruit genus, uses phylogenetic and network analyses to untangle the evolutionary history of this difficult group. Results paint a picture of a rapid radiation, with introgression between sympatric species confounding attempts to reconstruct a well-supported bifurcating tree. While bifurcating trees were markedly at odds with morphology, multifurcating phylogenetic network analyses recovered multiple histories, with clearer traces of morphological alliances. The sole unambiguous finding is the sister relationship between Clarisia sect. Acanthinophyllum and the rest of the Neotropical Artocarpeae; as a result, the genus Acanthinophyllum is reinstated.

opencc-zeroJun 2023View details →

dryad36/100

Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis

A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivali group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America.

opencc-zeroJun 2023View details →

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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.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record