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591 results for “phylogenomic data”
Research data for UCE phylogenomics of sawflies and woodwasps
<p>Input files, scripts and newick tree files for the ongoing project on reconstructing a comprehensive phylogeny and biogeography for sawflies and woodwasps (Hymenoptera). </p>
Data set: Australia's hidden radiation - phylogenomic analysis reveals rapid Miocene radiation of blindsnakes
<p>This repository contains the additional raw data to accompany our paper entitled "Australia’s hidden radiation: phylogenomic analysis reveals rapid Miocene radiation of blind snakes."</p> <p>This project is part of the AusARG Initiative funded by BioPlatforms Australia.</p> <p>Raw sequences data can be downloaded from the BioPlatforms downloads portal: https://data.bioplatforms.com/dataset?q=ticket%3ABPAOPS-1196</p> <p><strong>Information about files</strong></p> <ol> <li>ASTRAL_tree_SqCL_AHE.tre - output from ASTRAL-III just with SqCL data + outgroups</li> <li>ASTRAL_tree_SqCL_AHE_Ramphotyphlops.tre - same with above but also including additional <em>Ramphotyphlops </em>genes.</li> <li>mcmctree_1.txt - mcmcfile output from MCMCTree analysis using all SkewT or SkewNormal distribution priors.</li> <li>mcmctree_2.txt - mcmcfile output from MCMCTree analysis using SkewT, SkewNormal, and cauchy distribution priors. **This is the tree used in our publication**</li> <li>mcmctree_strategy1.tre - output phylogeny 1</li> <li>mcmctree_strategy2.tre - output phylogeny 2</li> <li>IQTREE_gcf_scf.nex - gene concordance and site factors for mcmctree_strategy2.tre</li> </ol> <p>tree_data/ folder contains concatenated gene trees (IQTREE) and corresponding shortcut coalescent method (ASTRAL-III) tree.</p> <p>Should there be questions regarding the code and data set, please contact the corresponding author.</p>
Data from: Paule et al. (2020) Phylogenomic insights into the Fascicularia-Ochagavia group (Bromelioideae, Bromeliaceae). Botanical Journal of the Linnean Society (doi: 10.1093/botlinnean/boz085)
<p>DNA sequence alignments as well as the input and output files which specify the different data partitioning schemes used for phylogenetic analyses in Paule et al. (2020) Phylogenomic insights into the Fascicularia-Ochagavia group (Bromelioideae, Bromeliaceae). Botanical Journal of the Linnean Society (doi: 10.1093/botlinnean/boz085).</p>
Data from: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees
The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing the phylogenetic affinities of ants and bees helps us understand and reconstruct patterns of social evolution as well as fully appreciate the biological implications of the switch from carnivory to pollen feeding (pollenivory). Despite recent advancements in aculeate phylogeny [4–11], considerable uncertainty remains regarding higher level relationships within Aculeata, including the phylogenetic affinities of ants and bees [5–7]. We used ultraconserved element (UCE) phylogenomics [7,12] to resolve relationships among stinging wasp families, gathering sequence data from > 800 UCE loci and 187 samples, including 30 out of 31 aculeate families. We analyzed the 187-taxon data set using multiple analytical approaches, and we evaluated several alternative taxon sets. We also tested alternative hypotheses for the phylogenetic positions of ants and bees. Our results present a highly supported phylogeny of the stinging wasps. Most importantly, we find unequivocal evidence that ants are the sister group to bees+apoid wasps (Apoidea) and that bees are nested within a paraphyletic Crabronidae. We also demonstrate that taxon choice can fundamentally impact tree topology and clade support in phylogenomic inference.
Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
<p>Recent high-throughput sequencing endeavors have yielded multi-gene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of <i>Mesodinium</i> and to generate the most taxonomically-rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multi-protein dataset, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. <i>Mesodinium</i> always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of <i>Mesodinium</i> – <i>M. rubrum</i>, <i>M. major</i>, and <i>M. chamaeleon</i> - being more closely related to each other than to the heterotrophic member, <i>M. pulex</i>. The well-supported position of <i>Mesodinium</i> as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination - particularly for <i>Mesodinium</i> species where expression from stolen prey nuclei appears to dominate – requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.</p>
Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
<p>Recent high-throughput sequencing endeavors have yielded multi-gene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of <i>Mesodinium</i> and to generate the most taxonomically-rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multi-protein dataset, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. <i>Mesodinium</i> always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of <i>Mesodinium</i> – <i>M. rubrum</i>, <i>M. major</i>, and <i>M. chamaeleon</i> - being more closely related to each other than to the heterotrophic member, <i>M. pulex</i>. The well-supported position of <i>Mesodinium</i> as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination - particularly for <i>Mesodinium</i> species where expression from stolen prey nuclei appears to dominate – requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.</p>
Code and sequence data pertaining to: A phylogenomic perspective on interspecific competition
<p>Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbor trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harboring phylogenetic signal and demonstrate its application through a proof of principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.</p>
Data from: Phylogenomics of American pika (Ochotona princeps) lineage diversification
<p>Quaternary climate oscillations have profoundly influenced current species distributions. For many montane species, these fluctuations were a prominent driver in species range shifts, often resulting in intraspecific diversification, as has been the case for American pikas (<em>Ochotona princeps</em>). Range shifts and population declines in this thermally-sensitive lagomorph have been linked to historical and contemporary environmental changes across its western North American range, with previous research reconstructing five mitochondrial DNA lineages. Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of <em>O. princeps</em> monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81mya), including a new Central Rocky Mountain lineage. We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on <em>O. princeps</em> lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.</p>
Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis
<p>Parrots (Order: Psittaciformes) are a diverse clade that are easily distinguishable from other birds. Despite the clear characters that define the Psittaciformes (hooked bills, zygodactylous feet, and plumage that is often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification a fraught endeavor for over a century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- and species-level relationships. However, despite these significant advances, major gaps in taxon sampling and uncertainty in relationships remained due to inferring phylogenetic relationships with short fragments of DNA. Recent work using genome-wide molecular markers with nearly complete parrot species-level sampling has brought clarity to many of the remaining outstanding questions on taxonomic relationships. Here, we build on this work by including four additional species to present a taxonomic revision of Psittaciformes better aligned with its evolutionary tree. We infer maximum likelihood and time-calibrated phylogenies for parrots, present accounts for 106 genera, compare how our findings relate to previous work, and highlight future areas of research. The family-group nomenclature we propose reflects deep evolutionary divergences with diagnosable synapomorphies that are commensurate across comparable ranks in psittaciform clades. We erect three new family-group names at the rank of tribe (Brotogerini Smith, Thom and Joseph, 2024; Neophemini Schodde, Smith, Thom and Joseph, 2024; Bolbopsittacini Smith, Thom and Joseph, 2024). We elevate one tribe to subfamily rank for the cacatuid genus <em>Probosciger</em> and we restrict usage of the recently introduced tribe Touitini to its type-genus <em>Touit</em>. At shallower taxonomic scales, recognition of more rather than fewer genera addresses issues of paraphyly or high discordance in morphological and genomic characters at those levels. We support many reinstatements of older generic names advocated in recent decades and we further reinstate five valid, available generic names not widely used in recent literature if at all (<em>Licmetis</em>, <em>Gymnopsittacus</em>, <em>Clarkona</em>, <em>Suavipsitta</em>, <em>Cardeos</em>). We advocate the retention of <em>Vini</em> Lesson, 1833 over <em>Coriphilus</em> Wagler, 1832 based on preliminary examination showing substantially more frequent usage of the former. We redraw generic limits in some other cases (e.g., <em>Bolborhynchus</em> parrotlets and allies) and this includes recognizing fewer genera than recently proposed for the <em>Psittacula</em> <em>sensu lato</em> ringneck parakeets. Our revised classification of parrots addresses many longstanding taxonomic questions including those that have arisen through the acquisition of genetic data. It provides context for the temporal origins of psittaciform clades and the taxonomic and phenotypic diversification throughout their evolutionary history. We hope that it will be a benchmark guiding further taxonomic study as well as for downstream analyses in many other fields.</p>
Data for phylogenomic analysis of chelicerate gene family evolution
<p>We used phylogenomics to investigate patterns of gene family evolution across ticks and other chelicerates, which include a diverse array of parasites. We used phylogenetic profiling and trait-association tests to predict gene families that may enable parasitic species to feed on hosts undetected for prolonged periods (>1 day). This release accompanies the pub, “<a href="https://doi.org/10.57844/arcadia-4e3b-bbea">Comparative phylogenomic analysis of Chelicerates points to gene families associated with long-term suppression of host detection</a>." Please see the pub for more information.</p> <ul> <li>chelicerata-v1-10062023.zip contains the outputs from NovelTree that are needed as inputs for phylogenetic profiling.</li> <li>annotated.zip contains gene annotations used to do orthogroup filtering.</li> <li>tx2gene.tsv has presence/absence of expression for each Amblyomma americanum transcript. </li> <li>chelicerate_proteome_preprocessing_outputs.zip contains the outputs of chelicerate protein data curation.</li> <li>chelicerata-v1-parameterfile.json & chelicerata-v1-samplesheet.csv were inputs for setting up the initial NovelTree run.</li> <li>2024-06-24-all-chelicerate-noveltree-proteins.fasta has the full set of chelicerate protein sequences.</li> <li>summary_of_noveltree_results.zip contains summary figures from the outputs of the NovelTree run.</li> <li>chelicerate-samples.tsv is the sample sheet used in proteome curation upstream of NovelTree.</li> </ul>
Molecular data from "Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex)"
<p><strong>Phylogenetic_dataset.csv</strong>: Unfiltered DArTseq data used in phylogenetic analyses. Readable by 'dartR' (Gruber et al. 2018).</p> <p><strong>Population_dataset.csv</strong>: Unfiltered DArTseq data used in population-level analyses. Readable by 'dartR' (Gruber et al. 2018).</p> <p><strong>Reference.csv</strong>: Spreadsheet listing individuals included in molecular analyses. Includes vouchers, species, name of each sample in DArTseq data sets, and GenBank accession numbers (GB) for mitochondrial data. ABTC stands for Australian Biological Tissue Collection; AA and CCM for field numbers of uncatalogued specimens. Other collection acronyms follow Sabaj (2019). We refrain from assigning individuals that were not included in the molecular analyses to any given species.</p>
Data from: Phylogenomics of elongate-bodied Springtails reveals independent transitions from aboveground to belowground habitats in deep time
<p>Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of palaeontological data. To overcome this limitation, we conducted a genome-based macroevolutionary study of an ancient, diversified, and widespread lineage of soil fauna, the elongate-bodied springtails (class Collembola, order Entomobryomorpha). To build the first robust backbone phylogeny of this previously refractory group, we sampled representatives of major higher taxa (6 out of 8 families, 11 out of 16 subfamilies) of the order with an emphasis on the most problematic superfamily Tomoceroidea, applied whole-genome sequencing (WGS) methods, and compared the performance of different combinations of datasets (universal single-copy orthologues/USCO versus ultraconserved elements/UCE) and modelling schemes. The fossil-calibrated timetree was used to reconstruct the evolution of body size, sensory organs, and pigmentation to establish a time frame of the ecomorphological divergences. The resultant trees based on different analyses were congruent in most nodes. Several discordant nodes were carefully evaluated by considering method fitness, morphological information, and topology test. The evaluation favoured the well-resolved topology from analyses using USCO amino acid matrices and complex site-heterogeneous models (CAT+GTR and LG+PMSF (C60)). The preferred topology supports the monophyletic superfamily Tomoceroidea as an early-diverging lineage and a sister relationship between Entomobryoidea and Isotomoidea. The family Tomoceridae was recovered as monophyletic, while Oncopoduridae was recovered as paraphyletic, with <em>Harlomillsia</em> as a sister to Tomoceridae and hence deserving a separate family status as Harlomillsiidae Yu and Zhang <strong>fam. n.</strong> Ancestral Entomobryomorpha were reconstructed as surface-living, supporting independent origins of soil-living groups across the Palaeozoic–Mesozoic, and highlighting the ancient evolutionary interaction between aboveground and belowground fauna.</p>
Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq
<p><span>Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus </span><em>Torreya</em><span>. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for </span><em>Torreya</em><span>. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of </span><em>Torreya</em><span> that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern </span><em>Torreya</em><span> from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the "Out of NA" pattern common to gymnosperms and in contrast to the "Out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on </span><em>T. jackii</em><span>, suggesting differential lineage sorting of plastid genomes among </span><em>Torreya</em><span> species or plastid genome capture in </span><em>T. jackii</em><span>.</span></p>
Supplementary data for: McFadden et al., Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics
<p class="MsoNormal">The anthozoan sub-class Octocorallia includes over 3500 nominal species of soft corals and gorgonian sea fans, many of which serve as critical foundation species in benthic marine ecosystems in shallow waters to the deep sea. Despite their familarity and ecological importance, the diversity and taxonomy of octocorals remain poorly known. All of the orders, subordinal groups and a majority of families have been recognized to be poly- or paraphyletic, but poor resolution of the deeper nodes in mitochondrial or single-locus nuclear gene trees have hindered formal revision of the higher level taxonomy of the group. We used sequence data from target-capture of 739 ultraconserved and exon loci to reconstruct a fully resolved phylogeny for 185 octocoral taxa representing 55 of 63 currently recognized families. We use this phylogeny, supplemented with a gene tree for mitochondrial <em>mtMutS</em> for an additional 107 taxa, to guide a revision of the families and orders of Octocorallia. We: (1) elevate the anthozoan sub-classes Octocorallia and Hexacorallia to the rank of Class; (2) replace the three currently recognized orders of Octocorallia (Alcyonacea, Pennatulacea, Helioporacea) with two new orders reflecting reciprocally monophyletic major clades; and (3) revise all families with the exception of the 15 recognized families of sea pens, which we accommodate within a new superfamily. The revised classification of Octocorallia thus comprises 79 families, including 18 that are newly described and three that have been reinstated or elevated in rank. In addition, two new genera are described and another three reinstated. We leave the family assignment of 46 of 411 genera as <em>incertae sedis</em> until further molecular or morphological data can be obtained to confirm their phylogenetic affinities.</p>
Data for: Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers
<p>Supporting data for "Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers" submitted by A Pandey and EL Braun. File is a gzipped tarball including protein multiple sequence alignments, phylogenetic trees, and other supporting data; see included README for details.</p>
Data for: Resolving the avian tree of life from top to bottom: The promise and potential boundaries of the phylogenomic era
<p>This data package includes multiple sequence alignments, information about base compositional variation, and phylogenetic analyses that support Figures 7 and 8 in Braun et al. (2019). There is a README in SuppInfo_Braun_et_al_chapter_Kraus_volume.tar.gz that provides a detailed description of the files in this data package.</p> <p>Braun, E.L., Cracraft, J., Houde, P. (2019). Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era. In: Kraus, R. (eds) Avian Genomics in Ecology and Evolution. Springer, Cham. https://doi.org/10.1007/978-3-030-16477-5_6</p>
Data for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae"
<p>Data and code for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae". Preprint available at bioRxiv: https://doi.org/10.1101/2022.09.07.506897.</p>
Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria
<p>Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread Horizontal Gene Transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic datasets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic datasets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated datasets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic datasets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.</p>
Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
<p>Demonstrating the process of transregional biogeography and mechanisms underlying evolutionary radiations is crucial to understanding biological evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique disjunct distribution and complex trait variations, using a solid phylogenetic framework, to investigate how geographical and climatic factors interact with functional traits to trigger plant evolutionary radiations. We constructed the first highly supported and dated phylogenetic framework using 79 protein-coding genes obtained from 81 plastomes, representing 63 species and all major clades, and found that most extant species originated from asynchronous diversification of two lineages undergoing repeated expansion and retraction, at middle and high latitudes of the Northern Hemisphere between East Asia and North America, during the Eocene to Pleistocene (driven by geologic and climatic dynamics). In accordance with these drivers, interactions of flora between central-eastern China and Japan occurred frequently after the Late Tertiary. We found that resource limitation and range fragmentation likely accelerated the diversification of Hydrangeeae, which supports the resource-use hypothesis. Our study sheds light on the evolutionary radiation and assembly of flora within East Asia, and the East Asian-North American disjunction, through integration of phylogenomic and biogeographic data with functional trait and ecological data.</p>
Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq
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