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1,344 results for “: phylogenomics”
The closest relative of Archaeplastida is revealed by phylogenomic analyses that include Microheliella maris
<p>By clarifying the phylogenetic positions of "orphan" protists (unicellular micro-eukaryotes with no affinity to extant species/lineages), we may uncover the novel affiliation between two (or more) major lineages in eukaryotes. <em>Microheliella maris</em> was an orphan protist, which failed to be placed within the previously described species/lineages by pioneering phylogenetic analyses. In this study, we analyzed a 319-gene alignment and demonstrated that <em>M. maris</em> represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name "Pancryptista" for Cryptista plus <em>M. maris</em>. The 319-gene analyses also indicated that <em>M. maris</em> is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called as "CAM clade" here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of <em>M. maris</em> and Rhodelphidia) and the particular phylogenetic 'signal' most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies.</p>
Data from: Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines)
[No abstract entered]
Data from: Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea to resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino-acid data provide implicit support for the respective optimal topologies. By analyzing the nucleotide data, we found that the 3rd codon positions are more saturated than the 1st and 2nd codon positions, and excluding these from the analyses leads to a topology congruent with that obtained using amino-acid data. Further, we determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a non-stationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoids the effects of synonymous mutations that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants. These analyses indicate that the discrepancy between the nucleotide-based and the amino acid-based trees is caused by the lineage specific, parallel compositional bias, or synonymous mutations driving codon-usage bias, as well as saturation in the 3rd codon positions. While genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein coding gene data and their amino-acids translations, by analyzing data modeling compositional bias, and by excluding nucleotide noisy signals due to saturation or codon-usage bias. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.
Data from: An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)
[No abstract entered]
A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae
<p>Premise</p> <p>Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated: (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) integration of plastome data from off-target reads with existing plastome datasets; and (4) how do the novel inferencescoincide with infra-familial classification </p> <p>Methods</p> <p>We generated two large datasets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid dataset was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees, and also usingmaximum likelihood analyzes from concatenated and partitioned data.</p> <p>Results</p> <p>The nuclear, plastome, and extended-plastid datasets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling made for the order to date, which includes seven never-before sequenced genera.</p> <p>Conclusions</p> <p>We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered a Pontederiaceae-Haemodoraceae and a Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes synonymization of <em>Tapheocarpa </em>in <em>Commelina.</em></p>
Supplementary material 2 from: Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE (2022) Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics 14. Classification of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205: 3-58. https://doi.org/10.3897/phytokeys.205.85866
Table S2
Supplementary material 4 from: Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE (2022) Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics 14. Classification of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205: 3-58. https://doi.org/10.3897/phytokeys.205.85866
Supplementary tree file
Supplementary material 3 from: Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE (2022) Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics 14. Classification of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205: 3-58. https://doi.org/10.3897/phytokeys.205.85866
Figure S1
Supplementary material 1 from: Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE (2022) Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics 14. Classification of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205: 3-58. https://doi.org/10.3897/phytokeys.205.85866
Table S1
Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)
<p>Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is typically targeted in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (<em>Micropterus</em>) are an iconic lineage of freshwater fishes that include some of the world's most popular species for recreational fishing and rank among the world's most invasive vertebrate species. Despite their popularity, previous studies to delimit species and lineages in <em>Micropterus</em> suffer from insufficient geographic coverage and uninformative molecular markers. Phylogenomic analyses of ddRAD data result in the delimitation of 19 species in <em>Micropterus</em>, which includes 14 described species, the undescribed but fairly well-known Altamaha Bass, Bartram's Bass, and Choctaw Bass, and two additional undescribed species currently classified as Smallmouth Bass (<em>M. dolomieu</em>). We also provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: <em>Micropterus salmoides</em> is retained for the Florida Bass and <em>Micropterus nigricans </em>is elevated from synonymy for the Largemouth Bass. Our findings provide a resolved phylogeny of all <em>Micropterus </em>species, insight into the role of introgression in the history of <em>Micropterus</em> diversification, and a robust delimitation of species that differs from current taxonomic classifications and the list of North American fishes maintained by the American Fisheries Society. The new understanding of diversity, distribution, and systematics of Blass Basses will serve as an important basis for the management and conservation of this charismatic and economically important clade of fishes.</p>
Fig. 11 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 11. Holotype of Cryptopone gilvatumida (unique specimen identifier CASENT0631951).
Fig. 10 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 10. Holotype of Cryptopone gilvagrande (unique specimen identifier CASENT0614525).
FIGURE 9. Ovipositor, holotype adult S in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)
FIGURE 9. Ovipositor, holotype adult S. nuevoguatemalae. Photo Dan Weissman.
FIGURE 8. Left hind leg tibia, holotype female S in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)
FIGURE 8. Left hind leg tibia, holotype female S. nuevoguatemalae. Photo Dan Weissman.
FIGURE 7. Holotype adult female S in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)
FIGURE 7. Holotype adult female S. nuevoguatemalae. Photo Dan Weissman.
FIGURE 10. Face, holotype adult female S in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)
FIGURE 10. Face, holotype adult female S. nuevoguatemalae. Photo Dan Weissman.
FIGURE 2 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 2. Species-level topology of Strigopoidea and Cacatuoidea. Support values come from the maximum likelihood tree. Nodes have ultrafast bootstrap values of ≥95% otherwise noted.
FIGURE 13 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 13. Photographs (not to scale) of an adult male Psephotellus dissimilis (left photo: David Cook) of Australia and Poicephalus meyeri (right photo: John Missing) of Africa and showing broadly similar plumage patterning that includes most unusual but similar shades of green on the underparts, dark brownish upperparts and a prominent patch of yellow about the wing coverts and bend of the wing. See text for discussion. Photographs reproduced with permission from the photographers.
FIGURE 5 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 5. Time-calibrated phylogeny of Amoropsittacini and Touitini. Support values come from the maximum likelihood tree. Nodes have ultrafast bootstrap values of ≥95% otherwise noted.
Fig. 1 in Phylogenomics and deep convergence in cockroach hind-wing morphology
Fig. 1 Phylogeny of Blattodea (a) and wing morphology illustration (b). a The phylogeny presented is the final species tree resulting from a number of topology tests and inference methods (IQ-TREE and ASTRAL). Node support values represent bootstrap frequency (3000 replicates from concatenation analyses of all three modified alignments; left) and gene concordance factors among the 41 loci (right). Taxa in bold have hind wings with a very large apical folding area (b – i, and b – ii). The apical region in Diploptera may not be homologous to those of other taxa so we use another symbol and did not count them as addi-
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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)
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.