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30 results for “long branches”
Text-fig. 5. Scanning electron microscope (SEM) images of megaspores with possible affinities to Isoetales (a–d) and megaspores of uncertain affinity (e–i); Torres Vedras locality, Portugal. a) Paxillitriletes reticulatus megaspore in lateral view showing long appendages on the flanges of the laesurae and the reticulate-spiny distal surface; b) Dijkstraisporites sp. megaspore in oblique lateral view showing long, sometimes dichotomizing, appendages on the equatorial flanges and bordering the laesurae; c, d) Tenellisporites sp. megaspore in proximal view (c) showing equatorial flanges and laesurae with short, broad, flattened and unbranched appendages; note numerous, spiny microspores adhering to the proximal face of the megaspore (d); e) Megaspore type sp. 2 in lateral view showing apical gula and ornamentation of scattered spines; f, g) Megaspore type sp. 3 in lateral (f) and proximal (g) view showing broad, often dichotomously branched appendages covering the megaspore surface; h, i) aff. Flabellisporites sp. megaspores in proximal (h) and lateral (i) view showing long, narrow appendages covering the megaspore surface. Specimens, TV39-S174619 (a), TV38-S170220 (b), TV38-S170221 (c, d), TV44-S174574 (e), TV44-S174575 (f), TV44-S174577 (g), TV38-S170223 (h), TV38-S170222 (i). Scale bars 100 Μm (a–c, e–i), 25 Μm (d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 5. Scanning electron microscope (SEM) images of megaspores with possible affinities to Isoetales (a–d) and megaspores of uncertain affinity (e–i); Torres Vedras locality, Portugal. a) Paxillitriletes reticulatus megaspore in lateral view showing long appendages on the flanges of the laesurae and the reticulate-spiny distal surface; b) Dijkstraisporites sp. megaspore in oblique lateral view showing long, sometimes dichotomizing, appendages on the equatorial flanges and bordering the laesurae; c, d) Tenellisporites sp. megaspore in proximal view (c) showing equatorial flanges and laesurae with short, broad, flattened and unbranched appendages; note numerous, spiny microspores adhering to the proximal face of the megaspore (d); e) Megaspore type sp. 2 in lateral view showing apical gula and ornamentation of scattered spines; f, g) Megaspore type sp. 3 in lateral (f) and proximal (g) view showing broad, often dichotomously branched appendages covering the megaspore surface; h, i) aff. Flabellisporites sp. megaspores in proximal (h) and lateral (i) view showing long, narrow appendages covering the megaspore surface. Specimens, TV39-S174619 (a), TV38-S170220 (b), TV38-S170221 (c, d), TV44-S174574 (e), TV44-S174575 (f), TV44-S174577 (g), TV38-S170223 (h), TV38-S170222 (i). Scale bars 100 Μm (a–c, e–i), 25 Μm (d).
Compositionally constrained sites drive long branch attraction
<p>Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from models with varying complexity and goodness of fit. Analyses of historical as well as current empirical datasets, such as alignments including Microsporidia, Nematoda or Platyhelminthes, have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies that are strongly supported. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets. Here, we introduce "compositional constraint analysis", a method to investigate the effect of site-specific amino acid diversity on phylogenetic inference, and show that more constrained sites with lower diversity and less constrained sites with higher diversity exhibit ostensibly conflicting signal under models ignoring across-site compositional heterogeneity and thus contribute to topological bias and long branch attraction artifacts. We demonstrate that more complex models accounting for across-site compositional heterogeneity can ameliorate this bias. We present CAT-PMSF, a pipeline for diagnosing and resolving phylogenetic bias resulting from inadequate modeling of across-site compositional heterogeneity based on the CAT model. CAT-PMSF is robust against long branch attraction in all alignments we have examined. We suggest using CAT-PMSF when convergence of the CAT model cannot be assured. We find evidence that compositionally constrained sites are driving long branch attraction in two metazoan datasets and recover evidence for Porifera as the sister group to all other animals.</p>
Compositionally constrained sites drive long branch attraction
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Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions
<p><span><span><span><span><span><span><span><span><span><span><span>Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (<b>new definition</b>), as the sister group of scorpions. Panscorpiones (<b>new name</b>) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.</span></span></span></span></span></span></span></span></span></span></span></p>
Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions
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TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
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FIGURE 1. Dictyanthus unicornus A. Branch segment with inflorescence and flower bud. B in Another remarkable new species of Dictyanthus (Apocynaceae, Asclepiadoideae, Asclepiadeae, Gonolobinae) with a long stylar head from Mexico
FIGURE 1. Dictyanthus unicornus A. Branch segment with inflorescence and flower bud. B. Detail of leaf base with colleters. C. Flower. D. Longitudinal section of the flower. E. Apex of the stylar head. F. Pollinaria. G. Fruit. Illustration of Quiyahuitl Colibrí Fernández Armendáriz, based on holotype J. F. Pío-León & M. G. Millán-Otero 375.
FIGURE 2. Dictyanthus unicornus A. Branch with leaves. B. Leaves and flower bud. C in Another remarkable new species of Dictyanthus (Apocynaceae, Asclepiadoideae, Asclepiadeae, Gonolobinae) with a long stylar head from Mexico
FIGURE 2. Dictyanthus unicornus A. Branch with leaves. B. Leaves and flower bud. C. Top view of flower. D. Lateral view of flower. E. Fruit. Credits: J. F. Pío-León.
◂Fig. 9 Scanning electron microscopy images of branches of Ramisyllis kingghidorahi n. sp. A–F Midbody branching regions with segments of different morphologies, as long as wide with long dorsal cirri in A–C, much longer with short dorsal cirri in D, E and F Details of cirri alternation in length. A, C, E–F In dorsal view; B and D in ventral view. Scale bars: 200 µm A, C, 100 µm B, F, 400 µm D, and 500 µm E in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan
◂Fig. 9 Scanning electron microscopy images of branches of Ramisyllis kingghidorahi n. sp. A–F Midbody branching regions with segments of different morphologies, as long as wide with long dorsal cirri in A–C, much longer with short dorsal cirri in D, E and F Details of cirri alternation in length. A, C, E–F In dorsal view; B and D in ventral view. Scale bars: 200 µm A, C, 100 µm B, F, 400 µm D, and 500 µm E
◂Fig. 8 Light microscope images of living specimens of Ramisyllis kingghidorahi n. sp. A Branching point. B, E–G Posterior ends showing pygidia. C, D, H, I Midbody segments in regions of long dorsal cirri. Arrows point to the ventral blood vessel in H and the digestive tract in I.A, D, E, and I in dorsal view. B, C, F and H in ventral view. G In lateral view. Scale bars: 500 µm A, E, 200 µm B, C, D, 100 µm F, H, I, and 50 µm G in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan
◂Fig. 8 Light microscope images of living specimens of Ramisyllis kingghidorahi n. sp. A Branching point. B, E–G Posterior ends showing pygidia. C, D, H, I Midbody segments in regions of long dorsal cirri. Arrows point to the ventral blood vessel in H and the digestive tract in I.A, D, E, and I in dorsal view. B, C, F and H in ventral view. G In lateral view. Scale bars: 500 µm A, E, 200 µm B, C, D, 100 µm F, H, I, and 50 µm G
Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira–Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia + the Asian clade, Baisseeae + milkweeds, and Periplocoideae + the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value.
FIGURE 11. Cynoglossum wallichii G. Don. Different growth habits. A Plant with single stem branching from below with long inflorescences and elliptical leaves. B Smaller plant branching from the base with ovate leaves. C in A revision of the genus Cynoglossum L. (Boraginaceae Juss.) in Nepal and notes on the widespread Asian species
FIGURE 11. Cynoglossum wallichii G. Don. Different growth habits. A Plant with single stem branching from below with long inflorescences and elliptical leaves. B Smaller plant branching from the base with ovate leaves. C Specimen with single stem, terminal and young, still more or less congested inflorescence and very narrow leaves (A M. Weigend 9169; B. Miyamoto et al. 20210115; C Lowndes 1-082).
FIGURE 1. Rhizoclonium pachydermum. A. Entire filament. Note the long, almost unbranched filaments. B. Basal region. Note the basal branches and the holdfast. C. Long, almost unbranched filaments. D in Occurrence of true branches in Rhizoclonium (Cladophorales, Ulvophyceae) and the reinstatement of Rhizoclonium pachydermum Kjellman
FIGURE 1. Rhizoclonium pachydermum. A. Entire filament. Note the long, almost unbranched filaments. B. Basal region. Note the basal branches and the holdfast. C. Long, almost unbranched filaments. D. Showing the number of nuclei. Scale bars: A, C = 500 µm B, D = 100 µm.
FIGURE 2. Dasyphyllum diamantinense. A. Habit. B. Branch with long spines. C in Dasyphyllum diamantinense (Asteraceae, Barnadesioideae): a new species from the Chapada Diamantina, Bahia State, Brazil
FIGURE 2. Dasyphyllum diamantinense. A. Habit. B. Branch with long spines. C. Apex of a fertile branch. D. Fertile branch. E. Lateral view of the capitula. F. Frontal view of the capitula, with tubulose corolla. Photos by C.N. Fraga.
Long-term Efficacy and Safety Research of Left Bundle Branch Pacing
ClinicalTrials.gov study NCT05600699. IPD Sharing: UNDECIDED. Countries: 1. Publications: 5.
Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae
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Supplementary material for: Long branch attraction biases in phylogenetics
<p>Long branch attraction is a prevalent form of bias in phylogenetic estimation but the reasons for it are only partially understood. We argue here that it is largely due to differences in the sizes of the model spaces corresponding to different trees. Trees with long branches together allow much more flexible internal branch-length parameter estimation. Consequently, although each tree has the same number of parameters, trees with long branches together have larger effective model spaces. The problem of long branch attraction becomes particularly pronounced with partitioned data. Formulation of tree estimation as model selection leads us to propose bootstrap bias corrections as cross-checks on estimation when long branches end up being estimated together. </p>
Data from: Testing hypotheses of chaetognath origins: long branches revealed by 18S ribosomal DNA
Many hypotheses regarding the phylogenetic position of the Chaetognatha (arrow worms) have been proposed; these organisms are problematic primarily because their morphology offers few unambiguous systematic characters that ally them with other taxa. Early researchers proposed a plethora of phylogenetic placements for the Chaetognatha, grouping them with such divergent taxa as acanthocephalans and mollusks, but more traditional hypotheses posit that chaetognaths are, in fact, deuterostomes. Recently, Telford and Holland (1993, Mol. Biol. Evol. 10:660--676) and Wada and Satoh (1994, Proc. Natl. Acad. Sci. USA 91:1801--1804) disputed the deuterostome affinities of chaetognaths based on 18S nuclear ribosomal RNA (rDNA) gene sequence data. By employing published 18S rDNA gene sequence data, I extended these previous analyses by testing specific hypotheses of chaetognath affinities to nematodes, mollusks, acanthocephalans, and deuterostomes. Both parsimony and neighbor-joining analyses supported the monophyly of a chaetognath--nematode clade. Faith's T-PTP test and winning-sites analyses were employed to discriminate among competing hypotheses. The possibility of long-branch attraction accounting for the chaetognath--nematode relationship was explored by analyzing alternative four-taxon trees. An evolutionary scenario for the origin of the chaetognath lineage from a vermiform benthic organism is presented.
Data from: Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes
Background: Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (2009; BMC Evol Biol 9: 134) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) + Leptopodomorpha (shore bugs) + Cimicomorpha (assassin bugs and relatives) + Pentatomomorpha (stink bugs and relatives), thereby suggesting that fully aquatic hemipterans evolved independently at least twice. Based on these results, Hua et al. (2009) elevated the Pleoidea to a new infraorder, the Plemorpha. Results: Our reanalysis suggests that the lack of support for the monophyly of the true water bugs (including Pleoidea) by Hua et al. (2009) likely resulted from inadequate taxon sampling. In particular, long-branch attraction (LBA) between the distant outgroup taxa and Pleoidea, as well as LBA among taxa in the ingroup, made Nepomorpha appear to be polyphyletic. We used three complementary strategies to test and alleviate the effects of LBA: (1) the removal of distant outgroups from the analysis; (2) the addition of closely related outgroups; and (3) the addition of a mitochondrial genome from a second family of Pleoidea. We also performed likelihood-ratio tests to examine the support for monophyly of Nepomorpha with different combinations of taxa included in the analysis. Furthermore, we found that specimens of Helotrephes sp. were misidentified as Paraplea frontalis (Fieber, 1844) by Hua et al. (2009). Conclusions: All analyses that included the addition of more taxa significantly and consistently supported the placement of Pleoidea within the Nepomorpha (i.e., supported the monophyly of the traditional true water bugs). Our analyses further support a close relationship between Notonectoidea and Pleoidea within Nepomorpha, and the superfamilies Nepoidea, Ochteroidea, Naucoroidea, and Pleoidea are resolved as monophyletic in all trees with strong support. Our results also confirmed that monophyly of Nepomorpha clearly is not refuted by the mitochondrial genome data.
Supporting data for: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae
<p>This is supporting sequence data for the paper: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae. It contains DNA and protein sequences as well as gene trees for 2135 loci for the investigation of the phylogenetic placement of the parasitic Rafflesiaceae and Apodannthaceae.</p>
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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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OpenNeuro
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