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1,751 results for “molecular phylogenetics”
Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
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Data from: Out of Africa to Madagascar - then back? Molecular phylogenetics and biogeography of tribe Tarchonantheae (Asteraceae: Tarchonanthoideae)
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Files for phylogenetic analyses and molecular diagnosis between Diplomystidae catfish species
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Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
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The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade
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Phylogenetic position of Centroglossa and Dunstervillea (Ornithocephalus clade: Oncidiinae: Orchidaceae) based on molecular and morphological data
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Data from: Molecular phylogenetics of Distephanus supports the recognition of a new tribe, Distephaneae (Asteraceae)
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FIGURE 18 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 18. Highest maximum-likelihood tree (-ln = 8673.71) from the 2760 aligned nuclear RAG-1 DNA positions. The maximum-likelihood analysis chose one of the 62 equally parsimonious trees. Bootstrap values are presented above branches and comparative parsimony decay indices are presented below branches in bold (Macey 2005). Branches that appear in parsimony analyses have the parsimony decay index plotted. Branches with no parsimony cost but are not present in strict consensus trees are listed as a "0" decay value. Branches that conflict with the parsimony analysis have a negative decay value representing the number of parsimony steps cost to obtain the maximum-likelihood branch. Bold italic bootstraps are those that differ from parsimony analysis. A dash above a branch is one that had a bootstrap value above 50% in the parsimony analysis but does not in this analysis. Outgroups (Laudakia, Bufoniceps, and Trapelus), and Phrynocephalus clades and lineages previously identified are labeled to the right as A–M (clades that are broken are numbered).
PLATE VIII. Outgroup taxa and Phrynocephalus mimicry adaptations. (A) Laudakia caucasia; (B) habitat of A, Big Balkan Mountains, Turkmenistan; (C) Trapelus sanguinolentus; (D) habitat of C, Repetek, Karakum Desert, Turkmenistan; (E) P. turcomanus illustrating false large head with eyes on body-back; and (F) P. mystaceus illustrating false enlarged mouth with red capillary-beds. in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE VIII. Outgroup taxa and Phrynocephalus mimicry adaptations. (A) Laudakia caucasia; (B) habitat of A, Big Balkan Mountains, Turkmenistan; (C) Trapelus sanguinolentus; (D) habitat of C, Repetek, Karakum Desert, Turkmenistan; (E) P. turcomanus illustrating false large head with eyes on body-back; and (F) P. mystaceus illustrating false enlarged mouth with red capillary-beds.
PLATE VI in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE VI. Species of the northern Tibetan Plateau. (A) P. hongyuanensis; (B) habitat of A, near Waqên, northeastern Tibet in Sichuan Province; (C) P. roborowskii-1; (D) habitat of C, Chaka Depression, Qinghai Province; (E) P. vlangalii-1; and (F) habitat of E, near Heimahe, south side of Qinghai Lake, Qinghai Province.
FIGURE 4 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 4. Strict consensus of three equally parsimonious trees of 4425 steps from the 1595 included (839 informative) aligned mitochondrial DNA positions. Bootstrap values are presented above branches and decay indices are presented below branches in bold. Outgroups (Laudakia, Bufoniceps, and Trapelus), and well-supported Phrynocephalus clades and lineages are identified to the right as A–M.
PLATE VII. Species of the low elevation deserts in China (A-D) and northern Caspian Basin in Russia (E-F). (A) P. przewalskii-3; (B) habitat of A, Shapatou (foreground), Yellow River, Gobi Desert, Ningxia; (C) P. salenskyi-1; (D) habitat of C, near Jimsar, Junggar Depression, Xinjiang; (E) P. guttatus; and (F) habitat of E, west side of Caspian Sea in Dagestan. in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE VII. Species of the low elevation deserts in China (A-D) and northern Caspian Basin in Russia (E-F). (A) P. przewalskii-3; (B) habitat of A, Shapatou (foreground), Yellow River, Gobi Desert, Ningxia; (C) P. salenskyi-1; (D) habitat of C, near Jimsar, Junggar Depression, Xinjiang; (E) P. guttatus; and (F) habitat of E, west side of Caspian Sea in Dagestan.
PLATE IV in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE IV. Small species inhabiting hard substrates in the Caspian Basin of Turkmenistan. (A) P. rossikowi; (B) habitat of A, along the Amu-Darya River; (C) P. raddei; (D) habitat of C, Karakum Desert, north of Ashkhabad; (E) P. bannikovi; and (F) habitat of E, Big Balkan Mountains.
PLATE III. Species of southern Tibet and soft substrate habitats in the Caspian Basin. (A) P. theobaldi; (B) habitat of A, near Yangbajain, north of Lhasa, southern Tibet; (C) P. sogdianus; (D) P. interscapularis; (E) P. mystaceus; and (F) habitat of D and E, Karakum Desert. north of Ashkhabad, Turkmenistan. in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE III. Species of southern Tibet and soft substrate habitats in the Caspian Basin. (A) P. theobaldi; (B) habitat of A, near Yangbajain, north of Lhasa, southern Tibet; (C) P. sogdianus; (D) P. interscapularis; (E) P. mystaceus; and (F) habitat of D and E, Karakum Desert. north of Ashkhabad, Turkmenistan.
PLATE V in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE V. Large species inhabiting hard substrates in the Caspian Basin of Turkmenistan (A-D) and Kazakhstan (E-F). (A) P. golubewii; (B) habitat of A, near Bami, southern edge of Karakum Desert; (C) P. turcomanus; (D) habitat of C, southern edge of Karakum Desert; (E) P. helioscopus; and (F) habitat of E, Barsakel'mes Island, Aral Sea.
PLATE II in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE II. Species of the Helmand Basin in Afghanistan and Iranian Plateau. (A) P. luteoguttatus; (B) P. clarkorum; (C) P. ornatus; (D) habitat of A and B, Registan Desert, Afghanistan; (E) P. scutulatus; and (F) habitat of E, near Khabr, southern Iran.
PLATE I in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE I. Species of the Arabian Peninsula and Iranian Plateau. (A) P. arabicus-2; (B) habitat of A, near Al Ashkhara, Oman; (C) P. longicaudatus; (D) habitat of C, near Al Hij, Bar Al Hikman Peninsula, Oman; (E) P. maculatus-2; and (F) habitat of E, near Sirjan, southern Iran.
A comprehensive sampling of species sheds light on the molecular phylogenetics of Calothecinae (Poaceae, Pooideae): evidence for a new subtribe and multiple genera within the Chascolytrum clade
The circumscription of subtribe Calothecinae has undergone several changes since its description. Currently, three genera are considered in the subtribe: <i>Chascolytrum</i>, <i>Laegaardia </i>and <i>Paramochloa</i>, although no phylogenetic evidence for the placement of the two last genera was published so far. In this study we aim to evaluate the circumscription of Calothecinae and the infrageneric classification recently proposed for <i>Chascolytrum </i>using a more comprehensive sampling of taxa and molecular markers. We included species of all genera of Calothecinae, plus two South American species of <i>Trisetum s.l.</i> that have been suggested to be related to <i>Chascolytrum</i>, and representatives from subtribes Agrostidinae, Echinopogoninae, Brizinae, Torreyochloinae, Phalaridinae and Koeleriinae. We performed Bayesian and Maximum Likelihood analyses using a total of six molecular markers, including four plastid DNA regions (<i>atpF-atpH, matK, rps16</i> intron, and <i>trnL-trnF</i>) and two ribosomal nuclear regions (ITS and ETS). Our results revealed that neither Calothecinae nor <i>Chascolytrum </i>are monophyletic considering their last circumscription. <i>Trisetum brasiliense</i> and <i>T. bulbosum</i> appeared nested to <i>Chascolytrum</i>, and are formally included in Calothecinae as <i>incertae sedis</i>. More studies are needed to confirm their taxonomic position. Based on morphological characters, <i>Laegaardia </i>and <i>Paramochloa </i>are transferred to the new subtribe Paramochloinae, and <i>Chascolytrum </i>is splitted in nine different genera, of which two are newly described: <i>Boldrinia </i>(gen. nov.), <i>Calotheca, Chascolytrum, Erianthecium, Lombardochloa, Microbriza, Poidium, Rhombolytrum</i>, and <i>Rosengurttia </i>(gen. nov.).
The asymptotic behavior of bootstrap support values in molecular phylogenetics
<p>The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic datasets whether or not the inferred trees and clades are correct. Here we study the asymptotic behavior of bootstrap support for the ML tree in large datasets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are nonnested and misspecified. The bootstrap is found to have qualitatively different dynamics from Bayesian inference, and does not exhibit the polarized behavior of posterior model probabilities, consistent with the empirical observation that the bootstrap is more conservative than Bayesian probabilities. Nevertheless bootstrap support similarly shows fluctuations among large datasets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus in large datasets strong support for wrong trees or models is likely to occur. Our analysis provides a partial explanation for the high bootstrap support values for incorrect clades observed in empirical data analysis.</p>
FIGURE 4 in A morphological and molecular phylogenetic analysis of relationships between genera of the nematode sub-family Cloacininae (Stossich) (Strongyloidea Chabertiidae) parasitic in kangaroos, wallabies and rat-kangaroos (Marsupialia Macropodoidea)
FIGURE 4. Morphological phylogenetic analysis of the genera of the Cloacininae. Numerals represent bootstrap values.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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