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122 results for “Incongruence”
Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence
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Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data
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Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
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Data from: Pervasive phylogenomic incongruence underlies evolutionary relationships in eyebrights (Euphrasia, Orobanchaceae)
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Data from: Low-copy nuclear genes reveal new evidence of incongruence in relationships within Malvaceae s.l.
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Data from: Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification
The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria.
Data from: Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: the monophyly of characiform fishes
Phylogenomic studies using genome‐wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non‐monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
Fig. 5 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 5. Color phenotypes and phyloheatmap of the morphological characters of E. meriana and E. atleticana, visualized using the (A) mtDNA and (B) UCE phylogenies. Circles at the end of individual names indicate the color phenotype of that individual. Names above the phyloheatmaps indicate the character that was measured. BL, Body length; HW, Head width; ID, Intertegular distance;WTII,Width of colored bands on tergum II; WTIII,Width of colored bands on tergum III. In this phyloheatmap, each column of the measured characters was standardized to have the same variance prior to analysis.The scale below indicates how much each value deviates from the mean.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.
Fig. 4 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 4. Chronogram of the phylogenetic relationships in the E. meriana and E. bombiformis species complexes estimated using BEAST2 and 500 UCE loci. All nodes had a posterior probability of 1. The arrow indicates the node used for calibration of the tree and acronyms correspond to geographic regions outlined in Fig. 1. CA, Central America; CR, Choco Region; AM, Amazon Forest; AF, Atlantic Forest. In the calibration point, M = mean age, and S = confidence interval.
Fig. 2 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 2. Phylogenetic relationships of the E. meriana and E. bombiformis species complexes based on (A) mitochondrial data (mtDNA; CO1 and Cytb) and (B) ultraconserved elements (UCE; 2022 loci). The mtDNA phylogeny was estimated using Bayesian inference in BEAST2, posterior probabilities on nodes were all above 0.9 except for nodes with asterisks (*). The UCE phylogeny was estimated with maximum likelihood using IQ-TREE and a concatenated 100% completeness matrix. Support values on nodes indicate ultrafast bootstrap (UFB) and SH-like (SH) approximate likelihood ratio test scores (SH-aLRT). All support values were above 95/95 except for nodes indicated with asterisks (* or **). One of the E. cingulata individuals (TA12) was pruned to improve the cophylogenetic visualization.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.
Fig. 1 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 1. Geographic distribution of the different color phenotypes in the E. meriana and E. bombiformis species complexes. (A) Colored areas in the map indicate approximate distribution for both species complexes as well as the different areas that correspond to lineages recovered in López-Uribe et al. (2014), including Central America (green), Choco region (orange), Amazon Forest (blue), and Brazilian Atlantic Forest (pink). (B) Photos of color phenotypes are shown for each species and the geographic region in which that phenotype is present. Photos of E. meriana and E. bombiformis by NashTurley, photos of E. niveofasciata and E. atleticana by Marcelo de Oliveira Gonzaga.
Fig. 3 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 3. Maximum clade credibility (MCC) species tree of the phylogenetic relationships in the E. meriana and E. bombiformis species complexes estimated under the multi-species coalescent model (MSC) using *BEAST in BEAST2.The species tree was estimated using the 50 most informative UCE loci from the 100% completeness dataset. Nodes without labels had posterior probabilities <0.5.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.
Fig. 6 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 6. Scatterplots of first against second principal component of the morphological measurements of the (A) E. bombiformis and (B) E. meriana complexes. Insets display boxplots of the first principal component between groups outlined by geographic regions: CA, Central America (Green); CR, Choco Region (Orange); AM, Amazon Forest (Blue); AF, Atlantic Forest (Pink). The letters above boxplots represent groups that are statistically differentiated after a Tukey′s honest significant test. Colors represent individuals grouped by geographic regions.
Fig. 20 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 20. Phaneropterinae group (continued). Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credit: Arthur Anker.
Fig. 17 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 17. Pseudophyllinae group: supertribe 'Pseudophylliti'. Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credit: Nigel Voaden.
Fig. 19 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 19. Phaneropterinae group (partial). Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credits are as follows: (Barbitistes ocskayi) (Charpentier, 1850) Orthoptera species file online and (Phaneroptera sp. (Serville, 1831)) Arthur Anker.
Fig. 15 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 15. Tettigoniinae group:Terpandrini,Austrosaginae, and HolarcticTettigoniinae.Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credit: Joseph Mugleston.
Fig. 14 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 14. Tettigoniinae group: Requenini, Hexacentrinae, Meconematini, Australian Nedubini, Phisidini (sans Arachnoscelis), Arytropteridini, and Hetrodinae. Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credits are as follows: (Hexacentrus sp.) (Serville, 1831) Hojun Song, (Oediphisis sp.) (Jin, 1992) Arthur Anker, (Hetrodes sp.) (Fischer von Waldheim, 1833) Joseph Mugleston.
Fig. 16 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 16. Early Phaneropteroid clade lineages and Mecopodinae group.Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credits are as follows: (Ischnomela sp.) (Stål, 1873) Joseph Mugleston, (Eumecopoda sp.) (Hebard, 1922) Hojun Song.
Fig. 13 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 13. Conocephalinae group: Euconchophorini, Agraeciini, and Copiphorini. Vertical bars indicate subtribes, tribes, and subfamilies. Paraphyletic groups are marked with an asterisk. Posterior probability values over 90 are marked with a circle at the node. Photo credit: Joseph Mugleston.
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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.