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312 results for “phylogenetic patterns”
Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria: phylogenetic data
<p>Alignments, trees and Biogeobears analyses related to the study: Leliaert F, Payo DA, Gurgel CFD, Schils T, Draisma SGA, Saunders GW, Kamiya M, Sherwood AR, Lin S-M, Huisman John M, Le Gall L, Anderson RJ, Bolton John J, Mattio L, Zubia M, Spokes T, Vieira C, Payri CE, Coppejans E, D'hondt S, Verbruggen H, De Clerck O. Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria. Journal of Biogeography. 2018;45(10):2299-313. doi:10.1111/jbi.13410</p> <p>Abstract: Biogeographical processes underlying Indo-Pacific biodiversity patterns have been relatively well studied in marine shallow water invertebrates and fishes, but have been explored much less extensively in seaweeds, despite these organisms often displaying markedly different patterns. Using the marine red alga Portieria as a model, we aim to gain understanding of the evolutionary processes generating seaweed biogeographical patterns. Our results will be evaluated and compared with known patterns and processes in animals. Species diversity estimates were inferred using DNA-based species delimitation methods. Historical biogeographical patterns were inferred based on a six-gene time-calibrated phylogeny, distribution data of 802 specimens, and probabilistic modelling of geographic range evolution. The importance of geographic isolation for speciation was further evaluated by population genetic analyses at the intraspecific level. We delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo-Malay Archipelago (IMA). Our phylogeny indicates that Portieria originated during the late Cretaceous in the area that is now the Central Indo-Pacific. The biogeographical history of Portieria includes repeated dispersal events to peripheral regions, followed by long-term persistence and diversification of lineages within those regions, and limited dispersal back to the IMA. Our results suggest that the long geological history of the IMA played an important role in shaping Portieria diversity. High species richness in the IMA resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both ‘centres of origin’ and ‘centres of accumulation’, and corroborate previous findings for invertebrates and fish that there is no single unifying model explaining the biological diversity within the IMA.</p>
Data from: Differential patterns of floristic phylogenetic diversity across a post-glacial landscape
<p>Abstract: Aim: In this study, we explored spatial patterns of phylogenetic diversity and endemism in the flora of Norway and tested hypothesized post-glacial environmental drivers of phylogenetic diversity, including temperature, precipitation, edaphic factors, and time since glacial retreat.<br> <br> Location: Norway.<br> <br> Taxon: Vascular plants (Trachaeophyta).<br> <br> Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history.<br> <br> Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway.<br> <br> Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.</p>
Supplementary Data for: A time-calibrated 'Tree of Life' of aquatic insects for knitting historical patterns of evolution and measuring extant phylogenetic biodiversity across the world
<p>This compendium of files includes the dated phylogenetic tree in Newick format (<strong>Data S1</strong>), the list of statistical routines used for the three empirical case studies (<strong>Data S2</strong>), and the high-resolution version of the figures in the supplementary materials and main text (<strong>Data S3</strong>) for the <em>Earth-Science Reviews</em> paper "A time-calibrated ‘Tree of Life’ of aquatic insects for knitting historical patterns of evolution and measuring extant phylogenetic biodiversity across the world", which is under consideration. The best-scoring molecular tree (<strong>Data S1</strong>) can be opened using freely available programs like R (R Development Core Team, 2021), Dendroscope (Huson and Scornavacca, 2012), and FigTree (Rambaut, 2018).</p> <p>Please, feel free to send an email to the maintainer Dr. Jorge García Girón (jogarg@unileon.es OR Jorge.Garcia-Giron@oulu.fi) if you face any trouble downloading, opening, or using these files.</p> <ul> <li>Huson, D. H., & Scornavacca, C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. <em>Systematic Biology</em>, <em>61(6)</em>, 1061–1067.</li> <li>R Development Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/</li> <li>Rambaut, A. (2018). FigTree. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. http://tree.bio.ed.ac.uk/software/figtree/</li> </ul>
F I G U R E 5 Phylogenetic study using the 5S in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 5 Phylogenetic study using the 5S rDNA sequences from Epinephelus fuscoguttatus, Epinephelus polyphekadion and the hybrid grouper
Data from: Functional and phylogenetic dimensions of tree biodiversity reveal unique geographic patterns
<p>Aim: Quantify tree functional and phylogenetic richness and divergence at the global scale, and explore the drivers underpinning these biogeographic patterns.</p> <p>Location: Global</p> <p>Time Period: Present</p> <p>Major taxa studied: Trees </p> <p>Methods: Using global tree occurrence data, we outlined species' observed ranges using individual alpha hulls to obtain per-pixel tree species composition. Using eight traits from a recent tree-trait database and a vascular-plant phylogeny we computed and mapped four pixel level biodiversity indices, including two metrics related to richness: phylogenetic richness and functional richness and two related to divergence: mean pairwise phylogenetic distance and Rao's quadratic entropy. To account for the effect of species richness, we also calculated standardized effect sizes accounting for richness for each pixel. We then explored the relations between richness and divergence and the latitudinal patterns of divergence both globally and across biomes. Finally, we used a random forest modeling approach to test for drivers of the different dimensions of diversity in trees.</p> <p>Results: In contrast to the latitudinal gradient in species richness, functional and phylogenetic divergence both peak in mid-latitude systems, exhibiting the highest values in temperate ecosystems and lowest values in boreal and tropical forests. This result holds for functional divergence when removing gymnosperms but the peak flattens for phylogenetic divergence. Phylogenetic richness is consistently lower than expected given the number of species, whereas functional richness has higher-than-expected values at mid-latitudes, mimicking functional divergence patterns. When considering the drivers of these diversity patterns, temperature and historical speciation rates consistently emerge as the strongest forces driving divergence, with negligible effects of human influence, soils or historical climate stability.</p> <p>Main Conclusions: Collectively, these results reveal unique similarities and disparities across biomes that are not apparent in any single dimension of biodiversity, highlighting the importance of considering multiple aspects of biodiversity in the management of natural ecosystems.</p>
Fig. 34. Phylogenetic network inferred from 1,476 in Morphology, Ciliary Pattern and Molecular Phylogeny of Trachelophyllum brachypharynx Levander, 1894 (Litostomatea, Haptoria, Spathidiida)
Fig. 34. Phylogenetic network inferred from 1,476 nucleotide characters of 69 litostomatean taxa, using the NeighborNet algorithm and the uncorrected distances. Numbers along the edges indicate bootstrap support values coming from 1,000 replicates. Only bootstraps> 50% and relevant to this study are shown. The scale bar indicates three substitutions per one thousand nucleotide positions.
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 known complete genomes of AlYVV from databank and two complete genomes determined in this study (indicated in black boxes). The tree was rooted on ToLCNDV (AB613826) as an out-group. The schematic representation of recombination events detected by RDP4. Arrows and blocks at the bottom correspond respectively to open reading frames (ORFs) and intergenic regions: pre-coat protein (AV2), coat protein (CP), replication-associated proteins (Rep and REn), transcriptional protein (TrAP), and AC4 region. AlYVV from different countries were colored differently. The colors of blocks represent the different ALYVV species and strains. Numbers at nodes indicate bootstrap confidence scores (1000 replicates).
Fig. 5 in Phylogenetic placement and microthrix pattern of Paranybelinia otobothrioides Dollfus, 1966 (Trypanorhyncha) from krill Nyctiphanes simplex Hansen, 1911
Fig. 5. Maximum Likelihood tree under the General Time Reversible model of selected trypanorhynchs including Paranybelinia otobothrioides. Major families, superfamilies, and orders are indicated. Numbers on the branches show nodal support.
Fig. 2 in Phylogenetic placement and microthrix pattern of Paranybelinia otobothrioides Dollfus, 1966 (Trypanorhyncha) from krill Nyctiphanes simplex Hansen, 1911
Fig. 2. Surface ultrastructure of the scolex and tentacular armature of Pa. otobothrioides. (A) Dorso-ventral view of the scolex dissected from the blastocyst showing the distal bothrial surface without complete median separation. (B) Pedunculus scolecis showing 2 bothria with free lateral and posterior margins. (C) Apical view of the scolex bothrial surfaces. (D) Capilliform filitriches. (E) External tentacle surface, metabasal armature with solid uncinate hooks. (F) Distal bothrial surface showing (G) hamulate spinitriches and (H) lineate spinitriches. Scale bars: (A,C) 100 μm; (D–H) 50 μm.
Fig. 35. Character 50, dorsal thigh color pattern. A in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)
Fig. 35. Character 50, dorsal thigh color pattern. A: State 0, pale with dark spots (quinquivittatus, AMNH 124069). B: State 1, solid dark (petersi, AMNH 111000). Note that the pale spot is confined to the inguinal regions and does not extend onto the dorsal surface of the thigh. C: State 2, dark with pale spots/ bands (aurotaenia, AMNH live exhibit). D: State 3, solid pale (terribilis, AMNH live exhibit). E: State 4, brown with dark brown bands/blotches (inguinalis, LACM 42409). F: State 5, dark with pale longitudinal stripe (flavopictus, AMNH 88642).
FIGURE 37 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 37 | Patterns of PBS value distribution of myologycal characters per taxonomic level in the phylogeny based on phenotypic data (Figs. 35, 36). Green bars indicate positive PBS values and red bars indicate negative PBS values. Bar for tribes include only non-monogeneric tribes. Taxon legends: A) Characiformes; B) Siluriformes; C) Siluriphysi; D) Gymnotiformes; E) Sternopygoidei; F) Rhamphichthyoidea; G) Sternopygoidea; H) Gymnotidae; I) Hypopomidae; J) Rhamphichthyidae; K) Sternopygidae; L) Apteronotidae; M) Steatogeninae; N) Eigenmanniinae; O) Sternarchorhynchinae; P) Microsternarchini; Q) Gymnotus; R) Brachyhypopomus; S) Akawaio + Hypopomus; T) Gymnorhamphichthys; U) Iracema + Rhamphichthys; V) Steatogenys; W) Hypopygus; X) Sternopygus; Y) Archolaemus + remaining Eigenmanniinae genera (except Japigny) Z) Distocyclus + remaining Eigenmanniinae genera (except Archolaemus and Japigny); A1) Eigenmannia + Rhabdolichops; B1) Rhabdolichops; C1) R. eastwardi + Rhabdolichops spp.; D1) Eigenmannia spp.; E1) Adontosternarchus; F1) Megadontognathus + Apteronotus; G1) Apteronotus; H1) A. cuchillejo + A. spp.1; I1) ((Porotergus + Tenebrosternarchus, Sternarchogiton) + (Compsaraia + "A." bonapartii)); J1) (Porotergus + Tenebrosternarchus, Sternarchogiton); K1) (Tenebrosternarchus, Sternarchogiton); L1) (Compsaraia + "A." bonapartii); M1) Compsaraia; N1) Pariosternarchus + Sternarchella; O1) Sternarchella; P1) Orthosternarchus + Sternarchorhamphus; Q1) Platyurosternarchus + Sternarchorhynchus; R1) Platyurosternarchus; S1) Sternarchorhynchus; T1) G. curupira + Gymnotus subgroups; U1) Gymnotus spp.2,3, 4, 5; V1) Gymnotus spp.3; W1) Gymnotus spp.4; X1) Gymnotus spp.5; Y1) Gymnotus spp.6; Z1) Gymnotus spp.7; A2) B. beebei + Brachyhypopomus subgroups; B2) B. draco + Brachyhypopomus spp.2; C2) Brachyhypopomus spp.3; D2) Hypopygus spp.; E2) Rhabdolichops spp.; F2) Adontosternarchus spp.; G2) Apteronotus spp.1; H2) Apteronotus spp.2 + Apteronotus spp.3; I2) Apteronotus spp.2; J2) Apteronotus spp.3; K2) "A." bonapartii; L2) Sternarchorhynchus spp.
FIGURE 35 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 35 | Strict consensus of MPT's resulting from parsimony analysis of character matrix in Peixoto et al. (2019), concatenated with dorsolateral head musculature characters of this study [Score: 795; RI: 0.92; CI: 0.37], with numbered dorsolateral head musculature characters (below branches) and respective characters states (above branches. Black circles indicate homoplasy-free characters and white circles indicate homoplastic characters. Taxon legends: Gymnotus spp.1 (G. panamensis, G. maculosus, and G. cylindricus); Gymnotus spp.2 (G. varzea, G. pantanal, G. obscurus, G. chaviro); Gymnotus spp.3 (G. ucamara, G. sylvius, G. sp, G. omamorum, G. mamiraua, G. bahianus); Gymnotus spp.4 (G. choco and G. ardilai); Gymnotus spp.5 (G. carapo and G. arapaima); Gymnotus spp.6 (G. tigre and G. hehni); Gymnotus spp.7 (G. stenoleucus, G. pedanopterus, G. pantherinus, G. jonasi, G. javari, G. coropinae, G. coatesi, G. cf. anguilaris, and G. cataniapo); Brachyhypopomus spp.1 (B. sp., B. accidentalis, and B. diazi); Brachyhypopomus spp.2 (B. pinnicaudatus; B. sp. 2); Brachyhypopomus spp.3 (B. bullocki and B. brevirostris); Rhabdolichops spp. (R. jegui and R. cf. stewarti); Adontosternarchus spp. (A. nebulosus, A. devenanzii, A. clarkae, A. balaenops); Apteronorus spp.1 (A. caudimaculosus and A. albifrons); Apteronorus spp.2 (A. magdalenensis and A. cuchillo); Apteronorus spp.3 (A. leptorhynchus and A. eschemeyeri); Sternarchorhynchus spp. (S. starski, S. hagedornae, S. galibi, S. sp.).
FIGURE 25 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 25 | Lateral view of dorsolateral musculature of Apteronotus bonapartii (Apteronotidae), MPEG 3038, 217.5 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 31 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 31 | Lateral view of dorsolateral musculature of Compsaraia compsa (Apteronotidae), MZUSP 56206, 123.4 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 34 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 34 | Same tree as in Fig. 33, with numbered dorsolateral head musculature characters (below branches) and respective character states (above branches). Black squares indicate homoplasy-free characters and white squares indicate homoplastic characters. Table on left indicates support values for each node: BR (Relative Bremer support), BST (Bootstrap), and JCK (Jackknife). Taxon legends as in Fig. 33.
FIGURE 32 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 32 | Lateral view of dorsolateral musculature of Tenebrosternarchus preto (Apteronotidae), MPEG 22758, 268.5 mm LEA. A= anterolateral fibers of the levator arcus palatini; P= posterolateral fibers of the levator arcus palatini. Remaining anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 36 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 36 | Strict consensus of MPT's resulting from parsimony analysis of character matrix in Peixoto et al. (2019), concatenated with dorsolateral head musculature characters of this study [Score: 795; RI: 0.92; CI: 0.37]. PBS values for general morphological characters and myological characters are indicated below each branch. Circle size is arbitrary; gray indicate neutral values of PBS for myologycal characters. Taxon legends as in Fig. 35.
FIGURE 28 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 28 | Lateral view of dorsolateral musculature of Sternarchella terminalis (Apteronotidae), MPEG 3481, 155.3 mm TL [regenerated]. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 21 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 21 | Lateral view of dorsolateral musculature of Distocyclus conirostris (Sternopygidae), MZUSP 23316, 242.2 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 4 mm.
FIGURE 18 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 18 | Lateral view of dorsolateral musculature of Rhamphichthys hahni (Rhamphichthyidae), MZUSP 24736, 479.5 mm TL. Anatomical abbreviations in Tab. 1. Scale bar = 20 mm.
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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.
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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.
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.