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9 results for “phylogenetic network analysis”
FIGURE 1. Phylogenetic relationship between Metarhizium synnematis GZUHXCHL12 in Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis
FIGURE 1. Phylogenetic relationship between Metarhizium synnematis GZUHXCHL12 and its allies based on ITS-5.8S rDNA sequence data. Bootstrap values (1,000 replicates) are indicated above the nodes.
FIGURE 3 in Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis
FIGURE 3. Metarhizium synnematis (holotype) A. Synnema on a lepidopteran cocoon. B. Upper part of a synnema. C. Phialides covering the surface of the synnema in a hymenium with conidia aggregating in sticky masses. D. Phialides. E. Conidia. Scale bars: A = 10 mm, B = 100 μm, C–E = 10 μm.
FIGURE 2 in Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis
FIGURE 2. Minimum spanning network displaying the relationship among Metarhizium synnematis, Neotyphodium sp., Akanthomyces sp. and Metarhizium sp.
Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis
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Data from: Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis
The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.
Data from: The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes
The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera Zalesskya, Iegosigopteris, and Petcheropteris are all considered synonymous with Thamnopteris; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.
FIGURE 4 in Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis
FIGURE 4. Reconstruction of Neighbor-Net network of Metarhizium synnematis and Metarhizium sp.
Data from: The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes
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Data from: Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis
Open the record for dataset details and reuse information.
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Allen Brain Atlas
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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
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