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684 results for “Phylogenetic placement”
Figure 14 in An overview of labeonin relationships and the phylogenetic placement of the Afro-Asian genus Garra Hamilton, 1922 (Teleostei: Cyprinidae), with the description of five new species of Garra from Ethiopia, and a key to all African species
Figure 14. Garra tana, holotype, AMNH 223824, 108.3 mm standard length.
Data for: Phylogenetic placement and taxonomic revision of the enigmatic Brazilian genus Monochilus Fisch. & C. A. Mey. (Lamiaceae)
<p><em>Monochilus</em> (Lamiaceae) is an enigmatic genus endemic to Brazil with two rarely collected species currently recognized. Based on morphological features <em>Monochilus</em> is hypothesized to be closely related to <em>Amasonia</em> within subfamily Ajugoideae. However, <em>Monochilus</em> is one of the few genera within Lamiaceae never to be represented in a published molecular phylogenetic study and thus has an uncertain placement with the subfamily. During recent herbarium exploration in association with the Flora of Brasil 2020 project, new specimens of <em>Monochilus</em> <em>gloxinifolius</em> and <em>M</em>. <em>obovatus</em> were uncovered. Based on this material, a new phylogeny of Ajugoideae was constructed based on nuclear ribosomal ITS and the chloroplast markers matK and trnL-trnF. <em>Monochilus</em>, as previously hypothesized, is closely related to <em>Amasonia</em> and placed within Ajugoideae. We discuss the phylogenetic placement of the genus and provide a taxonomic revision with a description, distribution maps, an identification key, preliminary conservation assessments, photographic plates and comments on both the taxonomy and ecology of these two species. Additionally, we provide a lecotypification for <em>M</em>. <em>gloxinifolius</em>.</p>
Data from: Micromphale sect. Perforantia (Agaricales, Basidiomycetes); expansion and phylogenetic placement
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Data for: Phylogenetic placement and taxonomic revision of the enigmatic Brazilian genus Monochilus Fisch. & C. A. Mey. (Lamiaceae)
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Data from: APPLES: Scalable distance-based phylogenetic placement with or without alignments
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Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions
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Clarifying the phylogenetic placement of the Eupoinae Maddison, 2015 with ultra-conserved element data (Araneae, Salticidae)
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Phylogenetic double placement of mixed samples
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Data from: Aeschynomene chicocesariana, a striking new unifoliolate legume species from Brazilian Chapada Diamantina and its phylogenetic placement in the dalbergioid clade
Unifoliolate leaves are relatively rare in the species-rich dalbergioid clade of papilionoid legumes (Leguminosae, Papilionoideae). For the pantropical, diverse genus Aeschynomene (ca. 180 species), the only known record of unifoliolate species described so far is the savanna-inhabiting A. simplicifolia from Chapada dos Veadeiros in Goiás, Brazil. The current work provides a description, illustrations, and a distribution map of another unifoliolate species, Aeschynomene chicocesariana, which was newly discovered in the rupestrian grasslands of Chapada Diamantina in Bahia, Brazil. The new species readily differs from A. simplicifolia by having mostly single-stemmed, erect habit, leaves with considerably shorter, 1.5–4 mm long petioles, leaflet blades densely pubescent beneath and glabrescent above and inconspicuously veined on both surfaces and without a marginal vein, and much smaller, ca. 15 × 14 mm standard petal. Bayesian phylogenetic analyses of DNA sequence data (nuclear ribosomal ITS/5.8S and the plastid genes matK and trnL intron) have unequivocally placed A. chicocesariana with the rest of Aeschynomene species that are traditionally placed within sect. Ochopodium. This result concurs with the shared morphology of A. chicocesariana and members of that section.
FIGURE 6 in A new species Cyrtodactytlus Gray (Squamata: Gekkonidae) from western Thailand and the phylogenetic placement of C. inthanon and C. doisuthep
FIGURE 6. Variation in dorsal pattern in Cyrtodactylus amphiptraeus sp. nov. in life. A. Adult holotype male (AUP-00696) from Tham Sri Fah Cave, Pop Pra District, Tak Province, Thailand. B. Adult paratype male (AUP-00698) from Tha Ra Rak waterfall, Pop Pra District, Tak Province, Thailand. C. General view of the adult paratype female (ZMMU R-16626) from Tha Ra Rak waterfall, Pop Pra District, Tak Province, Thailand. D. Close-up of the head of the same specimen showing green iris. E. Adult male (not collected) hiding in crevice near Tha Ra Rak waterfall, Pop Pra District, Tak Province, Thailand. F. Juvenile specimen (not collected) from Tha Ra Rak waterfall, Pop Pra District, Tak Province, Thailand. Photos by C. Suwannapoom (A–B), N.A. Poyarkov (C–D), and P. Pawangkhanant (E–F).
FIGURE 7 in A new species Cyrtodactytlus Gray (Squamata: Gekkonidae) from western Thailand and the phylogenetic placement of C. inthanon and C. doisuthep
FIGURE 7. Karstic habitat of Cyrtodactylus amphipetraeus sp. nov. at the type locality of Tha Pha Pum, Tham Sri Fah Cave, Tak Province, Thailand.
FIGURE 5 in A new species Cyrtodactytlus Gray (Squamata: Gekkonidae) from western Thailand and the phylogenetic placement of C. inthanon and C. doisuthep
FIGURE 5. Holotype of adult male Cyrtodactylus amphipetraeus sp. nov. (AUP-00696). A. Dorsal view of body showing nuchal loop, dorsal band, and caudal patterns (in preservative). B. Lateral view of head showing greenish coloration of iris. C. Gular region showing mental, postmental, and chin scales arrangement. D. Dorsal view of top of head. E. Precloacal and femoral region showing scale sizes and pore arrangements, and plantar view of feet showing subdigital lamellae morphology. Photos by C. Suwannapoom.
FIGURE 4 in A new species Cyrtodactytlus Gray (Squamata: Gekkonidae) from western Thailand and the phylogenetic placement of C. inthanon and C. doisuthep
FIGURE 4. Boxplot comparisons of discrete meristic characters among the species of clade 2 of the Cyrtodactylus sinyinensis group. Light blue circle is the mean and the black horizontal bars is the median. Asterisks denote species bearing statistically significant mean differences from C. amphipetraeus sp. nov.
FIGURE 3. A in A new species Cyrtodactytlus Gray (Squamata: Gekkonidae) from western Thailand and the phylogenetic placement of C. inthanon and C. doisuthep
FIGURE 3. A. PCA of the species of clade 1 of the Cyrtodactylus sinyeensis group based on meristic characters. B. DAPC of same. C. Histograms of the factor loadings of the characters contributing the most to the variation along PC1, PC2, and PC3.
FIGURE 2 in A new species Cyrtodactytlus Gray (Squamata: Gekkonidae) from western Thailand and the phylogenetic placement of C. inthanon and C. doisuthep
FIGURE 2. BEAST maximum clade credibility tree of the Cyrtodactylus sinyineensis group based on ND2 and its flanking tRNAs.
FIGURE 1 in A new species Cyrtodactytlus Gray (Squamata: Gekkonidae) from western Thailand and the phylogenetic placement of C. inthanon and C. doisuthep
FIGURE 1. Distribution of the species of the Cyrtodactylus sinyineensis group in Thailand and Myanmar.
Data from: INSTRAL: discordance-aware phylogenetic placement using quartet scores
Phylogenomic analyses have increasingly adopted species tree reconstruction using methods that account for gene tree discordance using pipelines that require both human effort and computational resources. As the number of available genomes continues to increase, a new problem is facing researchers. Once more species become available, they have to repeat the whole process from the beginning because updating species trees is currently not possible. However, the de novo inference can be prohibitively costly in human effort or machine time. In this paper, we introduce INSTRAL, a method that extends ASTRAL to enable phylogenetic placement. INSTRAL is designed to place a new species on an existing species tree after sequences from the new species have already been added to gene trees; thus, INSTRAL is complementary to existing placement methods that update gene trees.
Data from: Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies
Gobioidei is one of the largest suborders of teleost fishes, with nearly 2000 extant species currently recognized. They have a worldwide distribution and show a spectacular variety in morphology, ecology, and behavior. Despite their importance, phylogenetic relationships among many groups of gobioids (including some of the major lineages) still remain poorly understood. In this study, we analyze sequence data of five molecular markers (two mitochondrial and three nuclear) averaging 6000 bp for 222 species of gobioids. Our study is the first to include both multiple nuclear and mitochondrial genes to reconstruct a comprehensive multilocus phylogeny of gobioids encompassing most major lineages representing the overall diversity of one of the most speciose vertebrate lineages. Two separate datasets are produced and used to specifically address the phylogenetic placement of Rhyacichthyidae and Odontobutidae, and the phylogenetic relationships among the lineages of Gobioidei. Our results strongly support that the initial split in the gobioid tree separated a clade containing Rhyacichthyidae + Odontobutidae as the sister group of all other lineages. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae + Odontobutidae clade, followed by the Butidae as sister to the Gobiidae. Additionally, several major monophyletic groups are confidently identified within the two major Gobiidae subclades, the gobiine-like gobiids and the gobionelline-like gobiids. Robustness of the phylogenetic trees inferred here is significantly higher than that of previous studies, hence our results provide the most compelling molecular phylogenetic hypothesis of Gobioidei thus far. For the first time, we provide a comprehensive sampling of European gobies that traditionally have been divided into "transverse" and "sand gobies". We show that the European gobies cluster in three distinct lineages, the Pomatoschistus-, Aphia-, and Gobius-lineages. The former resolved within the gobionelline-like gobiids and the latter two within the gobiine-like gobiids. These findings have significant implications for our understanding of the phylogeographic origin of European gobies in the light of the closure of the Paratethys. A rogue taxon analysis identified Kraemeria as an unstable taxon decreasing support at the base of the gobiine-like gobiids. Removal of this rogue taxon significantly increased phylogenetic resolution in that part of the tree and revealed additional insights into early bursts of cladogenesis of the gobiine-like gobiids.
FIGURES 15–18 in A basal phylogenetic placement for the salticid spider Eupoa, with descriptions of two new species (Araneae: Salticidae)
FIGURES 15–18. Analyses using all genes for both small sample of salticoids (28S + 18S + 16S-ND1 + CO1) and large sample (28S + 16S-ND1 + CO1). The salticoid taxa in the large sample are unnamed; they are those used by Maddison & Needham (2006). 15 Small sample, majority rule consensus tree of 9900 trees sampled from 10 million generation Bayesian analysis; shown are estimated posterior probabilities; 16 Small sample, single most parsimonious tree found (treelength 7375 steps); shown are bootstrap values (Felsenstein 1985), 1000 replicates; 17 Large sample, majority rule consensus tree of 9900 trees sampled from 10 million generation Bayesian analysis, with estimated posterior probabilities; 18 Large sample, strict consensus of 2 most parsimonious trees found (treelength 22326 steps).
FIGURES 8–14 in A basal phylogenetic placement for the salticid spider Eupoa, with descriptions of two new species (Araneae: Salticidae)
FIGURES 8–14. Eupoa jingwei Maddison & Zhang, new species. 8–10 Palp of male holotype (8 ventral-prolateral view, 9 retrolateral, 10 ventral-retrolateral; 11–12 Male holotype; 13 epigynum of female paratype, ventral view; 14 palpus of female paratype. Scale bars 0.2mm.
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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
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