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36 results for “time-calibration”
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>
Figure 5 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 5. Ancestral area reconstruction produced by means of the RASP–Bayesian binary Markov Chain Monte Carlo method and based on the occurrence of Verbesina L. (Heliantheae–Asteraceae) species. Nodes with a predicted dispersal component are circled in blue, and those with a significant vicariance component are circled in green. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.
Figure 4 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 4. Time-calibrated Bayesian inference tree generated using concatenated internal and external transcribed spacer data. The values at the nodes indicate mean divergence dates, and the horizontal bars indicate 95% highest posterior density ranges for the age at each node. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.
Figure 3 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 3. Bayesian inference tree of combined internal and external transcribed spacer data. Posterior probabilities> 0.9 are given above the branches. The red text indicates South American species. Leaf figures indicate opposite and alternate phyllotaxy. Chromosome numbers are based on Moreira & Cavalcanti (2020) and Panero & Strother (2021). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NA, North America; NIC, Nicaragua; PER, Peru; SA, South America; VEN, Venezuela.
Figure 2 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 2. Total distribution of Verbesina in North America, Central America, the Caribbean, and South America. (Data accessed from GBIF, https://www.gbif.org/).
Figure 1 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 1. Morphological characters in Verbesina. A, Tree of Verbesina floribunda Gardner; B, subshrubby habit of V. bipinnatifida Baker; C, capitulum of V. luetzelburgii Mattf.; D, capitulum of V. bipinnatifida; E, cypsela of V. bipinnatifida; F, cypsela of V. floribunda; G, scanning electron micrograph (SEM) of the verrucous cypsela surface of V. macrophylla (Cass.) S.F.Blake; H, inflorescence of V. macrophylla; I, pinnatipartite leaf of V. macrophylla; J, SEM of the scalariform cypsela surface of V. glabrata Hook. & Arn.; K, inflorescence of V. glabrata; L, entire leaf of V. glabrata. Vouchers: C, G.L. Moreira et al. 118 (CEN); D–E, G.L. Moreira et al. 116 (CEN); F, G.L. Moreira et al. 101 (CEN). Scale bars: C, 8 mm; D, 4 mm; E, 2 mm; F, 4 mm; G and J, 200 μm. Photographs: G. L. Moreira.
Fig. 1 in Phylogenetic relationships and time-calibration of the South American fossil and extant species of southern beeches (Nothofagus)
Fig. 1. Strict consensus tree from Implied Weight Analysis (IWA) (k = 8). Dashed cladogram branches indicate fossil taxa. Consistency Index (CI): 0.51; Retention Index (RI): 0.78. Shaded circles (a–c) indicate the three possible placements of the two taxa Nothofagus alpina and Nothofagus elongata before pruning as indicated by IterPCR. Green/brown and black leaves are representatives of living and fossil species, respectively. Abbreviations: NCA, New Caledonia; NGU, New Guinea; NZE, New Zealand; SAU, Southern Australia; SSA, Southern South America; TAS, Tasmania.
A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade
<p><strong>Background.</strong> Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group. </p> <p><strong>Methods.</strong> Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data. </p> <p><strong>Results.</strong> Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (<em>Lemmus</em> and <em>Myopus</em>) and bog lemmings (<em>Synaptomys</em>), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ~6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.</p>
Genus level DNA sequence data for three genes (matK, rbcL, trnH-psbA) for the paper: A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability
<p>This data file contains the consensus DNA sequences in fasta format, of 64 tree genera found in Mediterranean Europe, following the checklist of Médail et al. (2019). </p> <p>The data are used in a manuscript submitted for publication to Botany Letters and currently under revision. The manuscript is entitled: "<em>A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability</em>". Its authors are: Marwan Cheikh Albassatneh, Marcial Escudero, Loic Ponge<sup>*</sup>, Anne-Christine Monnet, Juan Arroyo, Toni Nikolic, Gianluigi Bacchetta, Francesca Bagnoli, Panayotis Dimopoulos, Agathe Leriche, Frédéric Médail, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Arndt Hampe, Bruno Fady.</p>
Time-calibrated phylogeny of Neotropical Freshwater Fishes
<p>The Neotropical Freshwater Fish (NFF) fauna exhibits the greatest phenotypic disparity and species richness among all continental aquatic vertebrate faunas, with more than 6,345 species distributed across the mostly tropical regions of Central and South America. The two several decades have seen a proliferation of molecular phylogenies, often at the species level, covering almost all 875 valid NFF genera. This study presents the most comprehensive genome-wide, time-calibrated phylogenetic hypothesis of NFF species to date, based on DNA sequences generated over decades through collaborative efforts of the multinational ichthyological research community. Our purpose is to compile an extensive dataset and organize it systematically, allowing for continuous refinement and expansion, thereby enabling researchers to evaluate macroevolutionary hypotheses in the NFF. Using thousands of DNA sequences from dozens of studies, we compiled a supermatrix of 51 markers across 5,984 taxa, comprising 3,167 species representing 50% of NFF species, and estimating divergence times based on a fossil-calibrated phylogenomic tree of fishes. We used this dataset to infer the most species-rich time-calibrated phylogeny of the NFF taxa to date, summarizing the collective efforts of the ichthyological research community since the midpoint of the last century. We hope this dataset provides a framework for forthcoming evolutionary studies of the NFF fauna, documenting macro-scale patterns in the world's most diverse continental vertebrate fauna.</p>
A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade
Open the record for dataset details and reuse information.
Supplementary material 7 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878
Figure S5. Time-calibrated tree of European butterflies Section IV: Nymphalidae Part II: Subfamilies Libytheinae, Danainae & Satyrinae
Supplementary material 4 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878
Figure S2. Time-calibrated tree of European butterflies Section I: Papilionidae, Hesperiidae & Pieridae
Supplementary material 6 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878
Figure S4. Time-calibrated tree of European butterflies Section III: Nymphalidae Part I: Subfamilies Limenitidinae, Heliconiinae, Apaturinae & Nymphalinae
Supplementary material 1 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878
Table listing of European butterfly species with higher taxonomy, voucher codes and accession numbers for the sequences used to build the phylogeny.
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 in The phylogenetIc posItIon and taxonomIc status of the RaInbow Tree Snake Gonyophis margaritatus (Peters, 1871) (Squamata: ColubrIdae)
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 (Drummond et al. 2012) with node support values representing posterior probability (left) and bootstrap support (right) from inferred Maximum Likelihood tree. Dashes for bootstrap values indicate low support or not supported by ML tree. Family Colubridae and subfamily Colubrinea are highlighted by red arrows. Taxa in genera Gonyosoma, Rhadinophis, Gonyophis, and Rhynchophis are highlighted in the red square on the tree.
Figure 4. Time-calibrated phylogeny from BEAST2 in Origin and evolution of the Haustoriidae (Amphipoda): a eulogy for the Haustoriidira
Figure 4. Time-calibrated phylogeny from BEAST2. Green diamonds represent calibration points: 1, closure of the Okefenokee Trough (1.75 Mya); 2, proposed migration to Europe by H. arenarius (~5 Mya); 3, Pontocaspian gammarid clade radiation (9–83 Mya); 4,Niphargidae–Pseudoniphargidae split (38–215 Mya); 5, Crangonyctidae-Pseudocrangonyctidae split (38–215 Mya).
A complete time-calibrated multi-gene phylogeny of the European butterflies - data
<p>The datasets used for the article on phylogenetic relationships of European butterflies, including the treefile for all European species, as well as the posterior distributions of ages of each node.</p>
Fig. 3 in Time-calibrated molecular phylogeny reveals a Miocene-Pliocene diversification in the Amazon miniature killifish genus Fluviphylax (Cyprinodontiformes: Cyprinodontoidei)
Fig. 3 Time-calibrated phylogeny of the Cyprinodontoidei and Fluviphylax obtained from the Bayesian dating analysis in Beast v.1.8. Bars represent maximum and minimum date estimates for each node, and the numbers are node divergence mean ages. Arrows indicate the nodes
Fig. 1 in Time-calibrated molecular phylogeny reveals a Miocene-Pliocene diversification in the Amazon miniature killifish genus Fluviphylax (Cyprinodontiformes: Cyprinodontoidei)
Fig. 1 Distribution map of Fluviphylax: F. obscurus (white dot), F. palikur (orange dot), F. pygmaeus (yellow dot), F. simplex (blue dot), F. zonatus (red dot), Fluviphylax sp. A (green dot), Fluviphylax sp. B (brown dot), and Fluviphylax sp. C (purple dot)
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