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115 results for “ultraconserved elements”
Data from: Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history
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Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the Euphonia and Chlorophonia finches (Passeriformes: Fringillidae)
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Data from: Ultraconserved element phylogenomics and biogeography of the agriculturally important mason bee subgenus Osmia (Osmia)
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Data for: Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo River
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Ultraconserved element data for phylogenomic analysis and four-gene Sanger dataset for phylogenetic analysis of Tenkana, a new genus of plexippine jumping spider (Salticidae, Plexippini, Plexippina)
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Unraveling the myotis norass: Ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
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Ultraconserved element data for phylogenomic placement of the jumping spider genus Iranattus Prószyński, 1992 (Salticidae, Plexippini, Plexippina)
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Data from: A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements
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Ultraconserved elements support the elevation of a new avian family, Eurocephalidae, the white-crowned shrikes
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Data from: What is an eared nightjar? Ultraconserved elements clarify the evolutionary relationships of Eurostopodus and Lyncornis nightjars (Aves: Caprimulgidae)
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Ultraconserved element data for phylogenomic analysis of Ghatippus paschima jumping spider (Salticidae, Plexippini, Plexippina)
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Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards
<p>Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses, and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyze next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with ultraconserved elements and two morphological matrices. In unweighted maximum likelihood and Bayesian combined-evidence analyses, morphological signal was dwarfed by the ultraconserved elements, and some node support values were reduced relative to ultraconserved element-only analyses. Increasing the weight of morphological characters allowed those data to influence the tree, but weighting subjectivity should be considered in future analyses. More attempts should be made to simultaneously analyze genomic and morphological datasets.</p>
Data from: Protein-encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera, Calyptratae)
<p>The diverse superfamily Oestroidea with more than 15,000 known species includes among others, blow flies, flesh flies, bot flies, and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2,077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10–550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent-based analyses produced well-resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae, all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.</p>
Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees
<p>Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree and RAxML. We study their performance in the phylogenomic framework of > 800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus <i>Pseudapis</i>, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (MFP). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for <i>Pseudapis</i> s. l. and map the distribution of distinct morphological features of the group.</p>
Phylogenomic analysis of ultraconserved elements resolves the evolutionary and biogeographic history of Segmented Trapdoor Spiders
<p>The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2,765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92–113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders.</p>
Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.
Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.
Supplementary material 1 from: Jasso-Martínez JM, Brady SG, Kula RR (2023) Phylogenetic affinities of the non-cyclostome subfamilies Amicrocentrinae and Dirrhopinae (Hymenoptera, Braconidae) confirmed by ultraconserved element data. Journal of Hymenoptera Research 96: 1017-1030. https://doi.org/10.3897/jhr.96.111012
Maximum likelihood tree resulting from the 50% complete matrix without collapsed clades and with full names of the terminal taxa
Fig. 6 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 6. Proposed Introgression Pathways identified using quartet asymmetry tests. Sixty-three quartets indicated significant deviation from expectations under incomplete lineage sorting. Pathways are identified by letters with number of supporting quartets in parentheses. Branch lengths are time-calibrated as in Fig. 1.
Fig. 5 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 5. Measures of population structure and diversity of the Nearctic Myotis species. (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPS. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis. Samples marked by * in A and D are individuals with discordant positions on the trees and are discussed further in the text.
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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.
Annotated Behaviour and Observability Dataset (ABODe)
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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.