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2,620 results for “Molecular Phylogeny”
Fig. 1 in Taxonomic revision of Bergera J.Koenig ex L. (Rutaceae) based on the molecular phylogeny and morphology
Fig. 1. Bayesian tree, based on nuclear ITS data of representatives of Bergera J.Koenig ex L. and Clausena Burm.f., Murraya elongata DC. ex Hook.f. and Merrillia caloxylon Swingle. Branch lengths are proportional to the number of nucleotide changes (indicated above branches with Bayesian posterior probabilities, PP); bootstrap support (BS) values for maximum likelihood (ML) are given below the branches.
Fig. 3 in Taxonomic revision of Bergera J.Koenig ex L. (Rutaceae) based on the molecular phylogeny and morphology
Fig. 3. Bergera alternifolia (Kurz) F.J.Mou comb. nov. A. Holotype, S. Kurz 2010, CAL0000213357 (Botanical Survey of India, CAL). B. Cultivated plant. C. Leaves of cultivated plant. D. Flowers. Photos taken by Yoshiaki Takaya and Hla Myoe Min in Myanmar.
FIG. 3 in Morphological description and molecular phylogeny of two diatom clones from the genus Ulnaria (Kützing) Compère isolated from an ultraoligotrophic lake at the Pole of Cold in the Northern Hemisphere, Republic of Sakha (Yakutia), Russia
FIG. 3. — Cells in the culture Ulnaria pilum Kulikovskiy & Lange-Bertalot LAB55 attached to substrate: A, LM, mucilage strands are stained by Alcian blue in single cell; B, LM, cell aggregates; C, SEM, there are no traces of mucilage on the unattached ends of cells, tree closed girdle bands of each valve are pointed by arrowheads; D, SEM, attachment occurs with mucilage excreted through the pore field. Scale bars: A, B, 50 µm; C, 5 µm; D, 1 µm.
FIG. 2 in Morphological description and molecular phylogeny of two diatom clones from the genus Ulnaria (Kützing) Compère isolated from an ultraoligotrophic lake at the Pole of Cold in the Northern Hemisphere, Republic of Sakha (Yakutia), Russia
FIG. 2. — Ulnaria pilum Kulikovskiy & Lange-Bertalot LAB59: A, LM; B, SEM, external view and central area; C, internal view and central area; D, SEM, external view and the valve apex; E, internal view and the valve apex, rimoportula is located at an oblique angle relative to the central sternum; F, SEM, external view, two small spines at the apex. Scale bars: A, 50 µm; B-E, 5 µm; F, 1 µm.
A new molecular phylogeny of salps (Tunicata: Thalicea: Salpida) and the evolutionary history of their colonial architecture
<p>Salps are marine pelagic urochordates with a complex life cycle including a solitary and colonial stage composed of asexually-budded individuals. These colonies develop into species-specific architectures with distinct zooid orientations, including transversal, oblique, linear, helical, and bipinnate chains; as well as whorls, and clusters. The evolutionary history of salp colony architecture has remained obscured due to the lack of a homology-based ontology to characterize architectures, as well as a lack of phylogenetic taxon sampling and resolution of critical nodes. We (1) collected and first-time sequenced eight species of salps, (2) inferred the phylogenetic relationships among salps, and (3) reconstructed the evolutionary history of salp colony architecture. We collected salp specimens via offshore SCUBA diving, dissected tissue samples, extracted their DNA, amplified their 18S gene, and sequenced them using Sanger technology. We inferred a new molecular phylogeny using both Maximum Likelihood and Bayesian approaches. Using this phylogeny, we reconstructed the ancestral states of colony architecture using a Bayesian ordered Markov model informed by the presence and absence of specific developmental mechanisms that lead to each architecture. We find that the ancestral salp architecture is either oblique or linear, with every other state being derived. Moreover, linear chains have evolved independently at least three times. While transversal chains are developmentally basal and hypothesized to be ancestral, our phylogenetic topology and reconstructions strongly indicate that they are evolutionarily derived through the loss of zooid torsion. These traits are likely critical to multijet locomotory performance and evolving under natural selection. Our work showcases the need to study the broader diversity of salp species in order to gain a comprehensive understanding of their organismal biology, evolutionary history, and ecological roles in pelagic ecosystems.</p>
Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny
<p class="western">The processes responsible for the formation of Earth's most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely-sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea), and investigate the role of time, macroevolutionary processes and biome-shift dynamics in shaping the LDG in this ancient insect superfamily. We used process-based biogeographic models to jointly infer ancestral ranges and speciation times, and to characterise within-biome dispersal and biome-shift dynamics across the cosmopolitan distribution of Coenagrionoidea. We also investigated temporal and biome-dependent variation in diversification rates. Our results uncover a tropical origin of pond damselflies and featherlegs ~ 105 Ma, while highligthing uncertainty of ancestral ranges within the tropics in deep time. Even though diversification rates have declined since the origin of this clade, global climate change and biome-shifts have slowly increased diversity in warm- and cold-temperate areas, where lineage turnover rates have been relatively higher. This study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies and their relatives, while diversification dynamics have instead resulted in the formation of ephemeral species in temperate regions. Biome-shifts, although limited by tropical niche conservatism, have been the main factor reducing the steepness of the LDG in the last 30 Myr. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may become less pronounced. Our results support recent calls to unify biogeographic and macroevolutionary approaches to increase our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.</p>
Fig. 1 in Morphology and Molecular Phylogeny of Pseudocyrtohymenides lacunae nov. gen., nov. spec. (Ciliophora: Oxytrichidae) from South Korea
Fig. 1. Pseudocyrtohymenides lacunae nov. gen., nov. spec. (A, B), living specimens and (C–E), after protargol impregnation. (A, B), ventral (A) and dorsal (B) views of representative specimens; arrow denotes contractile vacuole. (C, D), ventral (C) and dorsal (D) views of the holotype specimen. (E), ventral views showing the variation of frontal-ventral-transverse cirri. AZM, adoral zone of membranelles; DK1, dorsal kinety 1; EM, endoral membrane; G, cortical granules; LMR, left marginal cirral row; Ma, macronuclear nodules; Mi, micronuclei; PM, paroral membrane; RMR, right marginal cirral row; TC, transverse cirri. Scale bars: 50 µm.
Fig. 2 in Morphology and Molecular Phylogeny of Pseudocyrtohymenides lacunae nov. gen., nov. spec. (Ciliophora: Oxytrichidae) from South Korea
Fig. 2. Pseudocyrtohymenides lacunae nov. gen., nov. spec. (A–E), living specimens; (F–K), after protargol impregnation. (A, D), ventral views of representative specimens. (B, C, E), dorsal views showing cortical granules and dorsal bristles. (F–K), dorsal (F, J) and ventral (G–I, K) views showing infraciliature and nuclear apparatus. AZM, adoral zone of membranelles; CV, contractile vacuole; DB, dorsal bristle; DK1–4, dorsal kineties 1–4; EM, endoral membrane; FC, frontal cirrus; G, cortical granules; LMR, left marginal cirral row; Ma, macronuclear nodules; Mi, micronuclei; PM, paroral membrane; RMR, right marginal cirral row; TC, transverse cirri; VC, ventral cirri. Scale bars: 100 µm in A–D and 50 µm in F–G.
Fig. 3 in Morphology and Molecular Phylogeny of Pseudocyrtohymenides lacunae nov. gen., nov. spec. (Ciliophora: Oxytrichidae) from South Korea
Fig. 3. Phylogenetic tree of SSU rRNA gene sequences, showing the position of Pseudocyrtohymenides lacunae nov. spec. on the basis of Maximum Likelihood (ML) and Bayesian Inference (BI). Bootstrap values of ML and posterior probabilities of BI were denoted on each interior branch. If the values of the bootstrap and the posterior probability were less than 50% and 0.50, respectively, they were excluded. The scale bar represents one nucleotide substitution per 100 nt.
Molecular phylogeny of Urvillea (Paullinieae, Sapindaceae) and its implications in stem vascular diversity
<ul> <li>Background and Aims: The tribe Paullinieae have the highest diversity of vascular variants among the seed plants. The developmental diversity is better understood in the speciose genera <em>Paullinia </em>and <em>Serjania, </em>however, the phylogeny and diversity of vascular variants in the smaller genera of Paullinieae remain understudied. Here we investigate the evolution of development of stem vasculatures in the small genus <em>Urvillea.</em></li> <li>Methods: We generate the first molecular phylogeny of <em>Urvillea </em>derived from 11 markers using a maximum likelihood and Bayesian approach. In combination with phylogenetic reconstruction, stochastic character mapping is used to assess evolutionary changes in stem ontogenies, determined from developmental anatomy of stems collected in the field or from herbarium and wood collections. </li> <li>Key Results: <em>Urvillea </em>is supported as a monophyletic group and sister to <em>Serjania. </em>There are five stem ontogenies in <em>Urvillea, </em>including a regular anatomy and four vascular variants. Most stem ontogenies initiate with lobed stems. Lobed adult stems are conserved in <em>Urvillea</em>, but this ontogeny was lost multiple times. A reversal to regular anatomy occurred in non-climbing species. Phloem wedges, fissured stems and ectopic cambia evolved independently once. Phloem wedges is an intermediate developmental stage in the formation of fissured stems, which is characterized by a continuous fragmentation of vascular tissues. Lobed stems may generate constriction zones and lobes may split or not. </li> </ul> <ul> <li>Conclusions: <em>Urvillea </em>stands out as the third most diverse genus in number of vascular variants within Paullinieae, but only one ontogeny (fissured stems) is exclusive for the genus. Differential cambial activity and ectopic cambia are the main ontogenetic processes generating stem diversity. The evolutionary history of vascular variants demonstrates the large developmental lability of the cambium in such a small genus and corroborates a scenario of repeated evolution of complex anatomies within Paullinieae lianas.</li> </ul>
Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)
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A new molecular phylogeny of salps (Tunicata: Thalicea: Salpida) and the evolutionary history of their colonial architecture
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Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny
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Revisiting the multispecies coalescent model fit with an example from a complete molecular phylogeny of the Liolaemus wiegmannii species group (Squamata: Liolaemidae)
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Fig. 1. Part 2 in Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea), with implications for taxonomy and evolutionary scenarios
Fig. 1. Part 2. See legend on preceding page.
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
<p><span><span><span><span><span><span><span><span><span><span><span>Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior onBayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effectof the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyze datasets containing both populations and species variation when its computational-efficiency is needed.</span></span></span></span></span></span></span></span></span></span></span></p>
Fig. 1 in Five new Palaearctic species of Docosia (Diptera: Mycetophilidae), with updated molecular phylogeny of the genus
Fig. 1. Docosia svanetica Kurina sp. nov., paratype (ZFMK-DIP-00067331), habitus.
Figure 4 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers
Figure 4. Hemipenis of Philodryas chamissonis (MNHN 3807) in A and B, Tropidodryas serra (MNRJ 7354) in C and D, and Xenoxybelis argenteus (BMNH 1994.7000) in E and F. Photographs in A, C, and E are in sulcate views, and photographs in B, D, and F are in asulcate views. Scale bars: 5 mm.
Figure 3 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers
Figure 3. Hemipenes of Chlorosoma viridissimum (MUSM 2403) in A and B, and Incaspis amaru (FHGO 4749) in C and D. Photographs in A and C are in sulcate views, and photographs in B and D are in asulcate views. Scale bars: 5 mm.
Figure 2 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers
Figure 2. Maximum likelihood (ML) tree estimated using RAxML, showing only the relationships of Incaspidini (1), Tropidodryadini (2), and Philodryadini (3). Terminal names on the left are presented following nomenclature in current literature, while generic and tribal arrangements on the right show our changes in the classification of Philodryadini. Numbers above and below branches indicate posterior probability and bootstrap support values, respectively. Bootstrap values below 70% and posterior probabilities below 85% are not shown.
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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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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.
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