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26 results for “NUMTs”
Figure 2 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 2. Tree topologies resulting from the analysis of COI-like cloned sequences from Lysmata seticaudata and mtDNA COI gene fragments for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML) and Bayesian inference (BI). Numbers above or below the branches represent the bootstrap values obtained from the ML analysis in TREEFINDER, and posterior probabilities from the BI analysis in MrBayes.
TABLE 1 in A new wave of Mesoamerican bumblebees? Revising the weisi-complex to reject numts and pseudospecies (Apidae: Bombus)
<p><b>TABLE 1.</b> Collections from which material has been examined.</p><table><tbody><tr><th>Abbreviation</th><th>Address</th></tr></tbody><tbody><tr><th>AMNH</th><td>American Museum of Natural History, New York, USA</td></tr><tr><th>BMEC</th><td>Bohart Museum of Entomology, University of California, Davis, California, USA</td></tr><tr><th>CAS</th><td>California Academy of Sciences, San Francisco, California, USA</td></tr><tr><th>CNIN</th><td>Colección Nacional de Insectos, Universidad Nacional Autónoma de México, D.F, México</td></tr><tr><th>ECOAB</th><td>El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México</td></tr><tr><th>EMEC</th><td>Essig Museum Entomological Collection, University of California, Berkeley, California, USA</td></tr><tr><th>INHS</th><td>Illinois Natural History Survey, Champaign, Illinois, USA</td></tr><tr><th>LACM</th><td>Natural History Museum of Los Angeles, Los Angeles, California, USA</td></tr><tr><th>MNHP</th><td>Museum National d’Histoire Naturelle, Paris, France</td></tr><tr><th>MZFC</th><td>Museo de Zoología, Facultad de Ciencia UNAM, D. F. Mexico</td></tr><tr><th>NHMUK</th><td>Natural History Museum, London, UK</td></tr><tr><th>SDEI</th><td>Senckenberg Deutsches Entomologisches Institut, Senckenberg, Germany</td></tr><tr><th>SEMC</th><td>Snow Entomological Museum Collection, Lawrence, Kansas, USA</td></tr><tr><th>UCRC</th><td>University of California Riverside Entomology Research Museum, Riverside, California, USA</td></tr><tr><th>UDLAP</th><td>Universidad de las Américas, Puebla, México</td></tr><tr><th>USDA-ARS</th><td>Bee Biology and Systematics Laboratory, Utah State University, Logan, Utah, USA</td></tr><tr><th>USNM</th><td>United State National Entomological Collection, Washington DC, USA</td></tr><tr><th>VAB</th><td>Van Asperen de Boer, Amsterdam, Netherlands (now in Naturalis)</td></tr><tr><th>ZMHB</th><td>Museum für Naturkunde an der Humboldt-Universität, Berlin, Germany</td></tr><tr><th>ZMUC</th><td>Zoological Museum University of Copenhagen, Denmark</td></tr><tr><th>ZSM</th><td>Zoologische Staatssammlung München, Germany</td></tr></tbody></table>
Fig. 11 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)
Fig. 11. Re-interpretation of sequences from Fig. 10, re-drawn with the percentage of nucleotides A and T at codon position 3 (AT3%) for each sequence given after the sequence label. Sequences are classified: (a) in purple – earlier-diverging groups of sequences without unique morphology that often have lower AT3% and shorter sequences that appear to duplicate species as pseudospecies in Fig. 10 – these sequences are interpreted as older, more divergent numts; (b) red – remaining sequences with low AT3% (<95%) – these are interpreted as younger, less divergent numts; (c) orange – sequences from the red group but with the highest AT3% available for some taxa, selected to retain these taxa in the analysis; (d) grey and brown – sequences that are duplicate haplotypes for the black and orange sequences above and often shorter; (e) black – likely orthologous sequences with high AT3% (≥ 95%) and unique haplotypes.
Fig. 10 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)
Fig. 10. Default interpretation of MrBayes estimate of phylogeny as a metric tree (outgroup B. festivus Smith, 1861, not shown) for the subgenus Alpigenobombus Skorikov, 1914, from COI-like sequences from GenBank and BOLD databases with additions from the authors, analysed with Bayesian Poissontree-process (PTP) models for assessing support for species' gene coalescents by maximum likelihood (PTP scores are shown above branches: scores approaching 1, and where branches change from blue to red, indicates where the most likely species' gene coalescents are identified for 17 candidate species). The scale bar is calibrated in substitutions per nucleotide site. Each sequence is labelled with: sequence length; a morphological taxon name; a code consisting of a sequence identifier from the project database and a specimen identifier from the online database; its country and (for larger countries) state or province of origin.
Fig. 18 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)
Fig. 18. Most likely ancestral ranges reconstructed for all extant currently recognised species from the dispersal model in Fig. 17, using the model DIVALIKE+J in S-BioGeoBEARS from a sample of 10000 trees from BEAST used to make the estimates of species phylogenies from the six genes in Fig. 16. Letters represent the area units in Fig. 17: letter combinations at terminals show species' current distributions (key lower left show the colour codes used for the principal areas of endemism, other colours not in the key represent combinations of areas e.g., darker green for area combination CDE, with black for a mixture of other areas); letter combinations at nodes show the most likely reconstructions for ancestral distributions; pies at nodes indicate the percentage of solutions for that node in which solutions occur (area E does not occur alone in any ancestor distribution). Numbers on the x-axis are ages in Ma before present. Outgroup shown in grey.
Data from: Towards eradicating the nuisance of Numts and noise in molecular biodiversity assessment
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