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1,344 results for “: phylogenomics”
A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)
<p><strong>The premise of the study: </strong>The true blueberries, (<em>Vaccinium</em> sect. <em>Cyanococcus</em>; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from 9 to 24 and much confusion regarding species boundaries, this ecologically and economically valuable group remains inadequately understood at a basic evolutionary and taxonomic level. As a first step toward understanding the evolutionary history and taxonomy of this species complex, we present the first phylogenomic hypothesis of the known diploid blueberries.</p> <p><strong>Methods</strong>: We used flow cytometry to verify the ploidy of putative diploid taxa and a target-enrichment approach to obtain a genomic dataset for phylogenetic analyses.</p> <p><strong>Results</strong>: Despite evidence of gene flow, we found that a primary phylogenetic signal is present. Monophyly for all morphospecies was recovered, with two notable exceptions: one sample of <em>V. boreale</em> was consistently nested in the V<em>. myrtilloides</em> clade, and <em>V. caesariense</em> was nested in the <em>V. fuscatum</em> clade. One diploid taxon, <em>Vaccinium pallidum</em>, is implicated as having a homoploid hybrid origin.</p> <p><strong>Conclusions</strong>: This foundational study represents the first attempt to elucidate evolutionary relationships of the true blueberries of North America with a phylogenomic approach and sets the stage for multiple avenues of future study such as a taxonomic revision of the group, the verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny.</p>
Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification
<p class="MsoNormal"><strong><span>Premise</span></strong></p> <p class="MsoNormal"><span>Bryophytes, land plants defined by a free-living gametophyte and an unbranched sporophyte, form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. </span><span>Our understanding of the evolutionary history of hornworts, liverworts and mosses has been significantly reshaped by inferences from molecular data, highlighting extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, and the degree to which the observed homoplasy represents error or biological processes, remain poorly resolved.</span></p> <p class="MsoNormal"><strong><span>Methods</span></strong></p> <p class="MsoNormal"><span>Using the GoFlag probe set, we sampled 405 exons representing 228 nuclear genes for 531 species from 51 of the 53 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.</span></p> <p class="MsoNormal"><strong><span>Results</span></strong></p> <p class="MsoNormal"><span>The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses. Most orders originated in the Jurassic or earlier and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene tree topology. </span></p> <p class="MsoNormal"><strong><span>Conclusions</span></strong></p> <p class="MsoNormal"><span>We sampled hundreds of homologous loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution, and these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of bryophytes and for investigating the transformations of traits in this important group of plants.</span></p>
Data from: hiding in plain sight: phylogenomics reveals a new branch on the Noctuoidea tree of life
<p>We analyze anchored hybrid enrichment data (AHE) from densely sampled tribes and subfamilies of Notodontidae (Prominent Moths). Notodontidae are monophyletic except for an assemblage of genera related to <em>Thacona</em> Walker (=<em>Scrancia</em> Holland), which had been recognized at either the tribal or subfamilial rank within Notodontidae. We elevate and re-describe Scranciidae, stat. nov. as a family distinct from the six currently recognized noctuoid families (Noctuidae, Erebidae, Euteliidae, Nolidae, Notodontidae, and Oenosandridae). Scranciidae include 22 genera comprising approximately 100 species—distributed in Africa, Asia, and Australia. We re-interpret morphological synapomorphies previously proposed for Notodontidae (including Scranciidae) and for the trifid Noctuoidea more broadly. Deep-level relationships within Noctuoidea are not well resolved outside the clade comprising the four quadrifid families (Noctuidae, Erebidae, Euteliidae, and Nolidae). The phylogenetic position of Scranciidae relative to Notodontidae, Oenosandridae, and the quadrifids varied markedly depending on data type (amino acid vs. nucleotide) and analytical framework (maximum likelihood, multi-species coalescent, and parsimony). We discuss the possible roles of missing data and short branch lengths in resolving the placement of Scranciidae. In the topology best supported by the most available data, Scranciidae are sister to the remaining Noctuoidea, highlighting their phylogenetic significance. We provide a provisional list of the genera included in Scranciidae.</p>
Data for: The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats
<p>A species tree is a central concept in evolutionary biology whereby a single-branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) – a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that proximate chromosomal regions tended to have more similar phylogenetic histories. While we found no clear relationship between local tree similarity and recombination rates in house mice, we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.</p>
Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)
<p>Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships, and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.</p>
Data from: Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)
<p>Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well-supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modelling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnSGGA-rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had strong impact on topological results in the Pacific clade.</p>
Treefile of a Klebsormidiophyceae phylogenomic analysis based on 845 loci
Open the record for dataset details and reuse information.
Alignment of 845 loci for phylogenomic analysis of Klebsormidiophyceae
<p>Improved alignment with more informative loci (845)</p>
Data sets for phylogenomic analyses in: Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data
<p>Ants are the most ubiquitous and ecologically dominant arthropods on Earth, and understanding their phylogeny is crucial for deciphering their character evolution, species diversification, and biogeography. Although recent genomic data have shown promise in clarifying intrafamilial relationships across the tree of ants, inconsistencies between molecular datasets have also emerged. Here I re-examine the most comprehensive published Sanger-sequencing and genome-scale datasets of ants using model comparison methods that model among-site compositional heterogeneity to understand the sources of conflict in phylogenetic studies. My results under the best-fitting model, selected on the basis of Bayesian cross-validation and posterior predictive model checking, identify contentious nodes in ant phylogeny whose resolution is <a>modelling-dependent. </a>I show that the Bayesian infinite mixture CAT model outperforms empirical finite mixture models (C20, C40 and C60) and that, under the best-fitting CAT-GTR+G4 model, the enigmatic <a><em>Martialis</em> </a><em>heureka</em> is sister to all ants except Leptanillinae, rejecting the more popular hypothesis supported under worse-fitting models, that place it as sister to Leptanillinae. These analyses resolve a lasting controversy in ant phylogeny and highlight the significance of model comparison and adequate modelling of among-site compositional heterogeneity in reconstructing the deep phylogeny of insects.</p>
Artifactual orthologs and the need for diligent data exploration in complex phylogenomic datasets: A museomic case study from the Andean flora
<p>The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap to our understanding of the World's richest flora, we present the first phylogeny of <em>Freziera</em> (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in <em>Freziera</em>, including a significant proportion of paralogous loci and a high degree of gene tree discordance. Via gene tree filtering, by-eye observation of gene trees, and detailed examination of warnings from recently improved assembly pipelines, we identified that cryptic paralogs (i.e., the presence of only one copy of a multi-copy gene due to assembly errors) were a major source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These cryptic paralogs likely result from limitations in data collection that are common in museomics, combined with a history of genome duplication; they may be common in plant phylogenomic datasets. After accounting for cryptic paralogs as source of gene tree error, we identified a significant, but non-specific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve <em>Freziera</em> into nine well-supported subclades whose histories have been shaped by myriad evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, and point to the need to test for multiple sources of gene tree discordance via careful examination of empirical datasets.</p>
Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)
<p>Here, we present the Ion Torrent® next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include <em>Galeorhinus galeus</em> (17,487 bp; GenBank accession number ON652874), <em>Mustelus asterias</em> (16,708; ON652873), <em>Mustelus mosis</em> (16,755; ON075077), <em>Mustelus palumbes</em> (16,708; ON075076), and <em>Triakis megalopterus</em> (16,746 bp; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes (<em>tRNA<sup>Leu</sup></em><sup> </sup>and <em>tRNA<sup>Ser</sup> </em>are duplicated), except for <em>G</em>. <em>galeus</em> which contains 23 tRNA genes where <em>tRNA<sup>Thr</sup> </em>is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories.</p>
Data for: Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny
<p>Sequence alignments and gene trees for: Braun et al. "Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny." See README file for detailed description of all files.</p>
Data from: phylogenomics of the Neogastropoda: the backbone hidden in the bush
<p>The molluscan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economics of coastal countries. Neogastropoda underwent intensive cladogenesis in early stages of diversification, generating a 'bush' at the base of their evolutionary tree, that has been hard to resolve even with high throughput molecular data. In the present study we analyze a comprehensive exon capture dataset of 1,817 loci (79.6% data occupancy), comprising 112 taxa of 48 (out of 60) recent Neogastropoda families with a variety of phylogenetic inference methods to resolve their relationships. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolve most backbone nodes, three prove problematic. First, uncertain placement of Cancellariidae, as a sister group of either a Ficoidea-Tonnoidea clade, or of the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major grouping the 'core Neogastropoda'. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analysed loci phylogenetic signal in relation with potential biases, and propose most probable resolutions in the two latter recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to the differential paralog loss short after the whole genome duplication, and should be resolved with a curated set of longer loci.</p>
Data from: Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs
<p>Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly-studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes (SAGs), and only a single formal described species, <em>Eupelagonema oceanica</em>. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows these two cells represent distinct subclades within eupelagonemids, each different from <em>E. oceanica</em>. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data, and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.</p>
Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics
<p>Studying the historical biogeography and life history transitions from eusocial colony life to social parasitism contributes to our understanding of the evolutionary mechanisms generating biodiversity in eusocial insects. The bulldog ants in the genus <em>Myrmecia</em> are a well-suited system for testing competing evolutionary hypotheses about how their species diversity was assembled through time because the genus is endemic to Australia with the single exception of the species <em>Myrmecia apicalis </em>inhabiting the Pacific Island of New Caledonia and because at least one social parasite species exists in the genus. However, the evolutionary mechanisms underlying the disjunct biogeographic distribution of <em>M. apicalis</em> and the life history transition(s) to social parasitism remain unexplored. To study the biogeographic origin of the isolated, oceanic species <em>M. apicalis</em> and to reveal the origin and evolutionary history of social parasitism in the genus, we reconstructed a comprehensive phylogeny of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements (UCEs) as molecular markers to generate a comprehensive molecular genetic dataset consisting of 2,287 loci per taxon on average for 66 out of the 93 known <em>Myrmecia </em>species as well as for the sister lineage <em>Nothomyrmecia macrops</em> and selected outgroup taxa. Our time-calibrated phylogeny inferred that: (i) stem myrmeciine ants originated during the Paleocene ~58 Ma ago; (ii) the current disjunct biogeographic distribution of <em>M. apicalis </em>was driven by long-distance dispersal from Australia to New Caledonia during the Miocene ~14 Ma ago; (iii) the single social parasite species, <em>M. inquilina</em>, exploits three host species and evolved directly from one of the known host species, <em>M. nigriceps</em>, most likely via the intraspecific route of social parasite evolution in sympatry; and (iv) 5 of the 9 previously established taxonomic species groups are non-monophyletic. We suggest minor changes to reconcile the molecular phylogenetic results with the taxonomic classification. Our study enhances our understanding of the evolution and biogeography of Australian bulldog ants in the genus <em>Myrmecia</em>, contributes to our knowledge about the evolution of social parasitism in ants, and provides a solid phylogenetic foundation for future inquiries </p>
Specimens from Brand et al. 2021, "Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits"
<p>The deposited folders contain image and video material of free-living flatworm specimens that were documented in vivo. These data support the following publication:</p> <p>Jeremias N. Brand, Gudrun Viktorin, R. Axel W. Wiberg, Christian Beisel, Lukas Schärer.<br> Large-scale phylogenomics of the genus<em> Macrostomum</em> (Platyhelminthes) reveals cryptic diversity and novel sexual traits.<br> Molecular Phylogenetics and Evolution. Volume 166. 2022. <a href="https://doi.org/10.1016/j.ympev.2021.107296">https://doi.org/10.1016/j.ympev.2021.107296</a></p> <p>For more information about these specimens see also http://macrostomorpha.info.</p>
Alignments used for the phylogenies in "Caryophylliids (Anthozoa, Scleractinia) have a mitochondrial gene rearrangement: lesson learned from mitochondrial and nuclear phylogenomics"
<p>"mitochondrial_caryotree.phy": concatenated alignment of mitochondrial data in phylip format; "mitochondrial_caryotree.partitions.txt": indication of start/stop positions of each partition in the mitochondrial data alignment; "nuclear_caryotree_55taxa-50p.phylip": alignment of nuclear exons and ultraconserved elements in phylip format.</p>
UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction
<p><span><span><span><span><span><span><span><span><span><span><span>The genus <i>Cryptopone</i> Emery contains 25 species of litter and soil ants, 5 of which occur in the Americas. <i>Cryptopone</i><i>gilva </i>occurs in the southeastern U.S.A. and cloud forests of Mesoamerica, exhibiting an uncommon biogeographic disjunction observed most often in plants. We used phylogenomic data from ultraconserved elements (UCEs), as well as mitogenomes and legacy markers, to investigate phylogenetic relationships, species boundaries, and divergence dates among New World <i>Cryptopone</i>. Species delimitation was conducted using a standard approach and then tested using model-based molecular methods (SNAPP, BPP, SODA, and bPTP). We found that <i>Cryptopone</i> as currently constituted is polyphyletic, and that all the South American species belong to <i>Wadeura</i> Weber, a separate genus unrelated to <i>Cryptopone</i>. A single clade of true <i>Cryptopone</i> occurs in the Americas, restricted to North and Central America. This clade is composed of four species that originated ~4.2 million years ago. One species from the mountains of Guatemala is sister to the other three, favoring a vicariance hypothesis of diversification. The taxonomy of the New World <i>Cryptopone</i>and <i>Wadeura</i> are revised. Taxonomic changes are: <i>Wadeura</i> Weber is <b>resurrected</b>, with <b>new combinations</b> <i>W. guianensis</i>Weber, <i>W. holmgreni</i> (Wheeler), and <i>W. pauli</i> (Fernandes & Delabie); <i>C. guatemalensis</i> (Forel) (<b>rev. stat.</b>) is raised to species, and includes <i>C. obsoleta</i> (Menozzi) (<b>syn. nov.</b>). The following <b>new species</b> are described: <i>Cryptopone gilvagrande</i>, <i>C. gilvatumida</i>, and <i>Wadeura holmgrenita</i>. <i>Cryptopone hartwigi</i> is transferred to <i>Fisheropone</i> (<b>n. comb.</b>). <i>Cryptopone mirabilis</i> (Mackay & Mackay 2010) is a junior synonym of <i>Centromyrmex brachycola</i> (Roger) (<b>syn. nov.</b>).</span></span></span></span></span></span></span></span></span></span></span></p>
Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere
<p><span>Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. An unparalleled transformation of forest dynamics began with the rapid diversification of major lineages within 15 million years following the K-Pg extinction. Innovations related to seed and pollen dispersal are implicated in triggering waves of continental radiations, while fungal symbioses fortified a competitive edge underground. We detected introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, further amplifying global proliferation.</span></p>
Highly resolved papilionoid legume phylogeny based on plastid phylogenomics
<p>Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera of evolution and morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. An ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.</p>
ScienceDex guides
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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.