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57 results for “Taxonomic Alignment”
Aligned DNA sequence matrix for phylogenetic analyses in the article "Fifty years after: a taxonomic revision of the amphibian species from the Ecuadorian biodiversity hotspot Abra de Zamora, with description of two new Pristimantis species"
<p>The aligned matrices are in fasta format. Genes are arranged as follows:</p> <p>Subgenus Huicundomantis (Huicundomantis.fas):</p> <p>12S = 1–905</p> <p>16S = 906–1820</p> <p>RAG-1 = 1821–2463</p> <p> </p> <p>Genus Lynchius (Lynchius.fas):</p> <p>12S = 1–1028</p> <p>16S = 1029–2313</p> <p>RAG-1 = 2314–2925</p> <p> </p> <p>Pristimantis orestes group (Pristimantis_orestes.fas):</p> <p>12S = 1–964</p> <p>16S = 965–2041</p> <p>RAG-1 = 2042–2683</p>
Supplementary material 2 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Set of 13 Euler/X toolkit output Maximally Informative Relations: Explanation note: Set of 13 Euler/X toolkit output Maximally Informative Relations (MIR) and alignment visualizations for the input data files provided in Suppl. material 1. Each output file is saved in. csv (MIR) and. pdf (alingments) format, respectively. Dryad. doi: 10.5061/dryad.53mv1
Supplementary material 1 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Set of 13 Euler/X toolkit input data files: Explanation note: Set of 13 Euler/X toolkit input data files for all alignments produced for Minyomerus [JF2015] use case (Figs 3, 4). Each file is saved in txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the corresponding figures. Dryad. doi: 10.5061/dryad.53mv1
Data from: Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments
This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O'Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O'Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O'Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O'Brien & Wibmer (1982) was comprised solely of P. griseus Sleeper, 1960 sec. O'Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: M. bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., M. aeriballux [JF2015], sp. n., M. cracens [JF2015], sp. n., M. gravivultus [JF2015], sp. n., M. imberbus [JF2015], sp. n., M. reburrus [JF2015], sp. n., M. politus [JF2015], sp. n., M. puticulatus [JF2015], sp. n., M. rutellirostris [JF2015], sp. n., and M. trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places P. griseus sec. O'Brien & Wibmer (1982) within the genus as sister to M. rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of Minyomerus [JF2015], and its sole member P. griseus sec. Sleeper (1960) is moved to Minyomerus [JF2015] as M. griseus [JF2015], comb. n. In addition, the formerly designated type M. innocuus Horn, 1876 sec. Pierce (1913), syn. n. is changed to junior synonymy of M. microps (Say, 1831) [JF2015] which has priority. The genus is widespread throughout western North America, ranging from Canada to Mexico and Baja California. Apparent patterns of interspecific diversity of exterior and genitalic morphology, varying host plant ranges, overlapping and widely extending species distributions, suggest an early origin for Minyomerus [JF2015], with a diversification that likely followed the development of North American desert biomes. Three species in the genus – i.e., M. languidus Horn, 1876 [JF2015], M. microps [JF2015], and M. trisetosus [JF2015] – are putatively considered parthenogenetic.
Data from: Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments
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Figure 52 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 52 - Combined occurrence record and Maxent habitat modeling map for five species of Minyomerus [JF2015], as indicated in the legend. See also Fig. 50.
Figure 42 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 42 - Diagnostic features and terminalia of Minyomerus gravivultus [JF2015] A aedeagus, dorsal view B aedeagus, lateral view C labial prementum, ventral view D spermatheca E lamina of sternum VIII.
Figure 4 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 4 - Arrangement of five pairwise, logically consistent alignments for directly succeeding input taxonomies (1920–2015) with relevance to the Minyomerus [JF2015] revision, as shown in Fig. 2. See Fig. 1 and Suppl. material 2 for further explanation. A alignment of Blackwelder and Blackwelder (1948) and Green (1920) B alignment of Sleeper (1960) and Blackwelder and Blackwelder (1948) C alignment of Kissinger (1964) and Sleeper (1960) D alignment of O'Brien and Wibmer (1982) and Kissinger (1964) E alignment of Jansen and Franz (2015) and O'Brien and Wibmer (1982).
Figure 37 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 37 - Diagnostic features and terminalia of Minyomerus bulbifrons [JF2015] A aedeagus, dorsal view B aedeagus, lateral view C spermatheca D lamina of sternum VIII E labial prementum, ventral view.
Figure 35 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 35 - Diagnostic features and terminalia of Minyomerus puticulatus [JF2015] A aedeagus, dorsal view B aedeagus, lateral view C labial prementum, ventral view D lamina of sternum VIII E spermatheca.
Figure 40 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 40 - Diagnostic features and terminalia of Minyomerus politus [JF2015] A aedeagus, dorsal view B aedeagus, lateral view C spermatheca D lamina of sternum VIII.
Figure 30 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 30 - Diagnostic features and terminalia of Minyomerus caseyi [JF2015] A labial prementum, ventral view B spermatheca C lamina of sternum VIII D aedeagus, lateral view E aedeagus, ventral view.
Figure 3 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 3 - Arrangement of eight pairwise, logically consistent alignments for directly succeeding input taxonomies (1831–1920) with relevance to the Minyomerus [JF2015] revision, as shown in Fig. 1. The alignments and visualizations were produced using the Euler/X toolkit for concept Taxonomy, as detailed in Franz et al. (2015a, 2015b). For each pairwise alignment, congruent concept regions (originating in T2 and/or T1) are shown as grey rectangles, concepts regions unique to the later taxonomy (T2) are shown as green rectangles, and concept regions unique to the earlier taxonomy (T1) are shown as yellow octagons. Articulations of inverse proper inclusion (>) and overlap (>>) are also shown. For further detail see Suppl. material 2. A alignment of Boheman (1833) and Say (1831) B alignment of LeConte (1859) and Boheman (1833) C alignment of Horn (1876) and LeConte (1859) D alignment of Casey (1888) and Horn (1876) E alignment of Sharp (1891) and Casey (1888) F alignment of Pierce (1909) and Sharp (1891) G alignment of Pierce (1913) and Pierce (1909) H alignment of Boheman (1920) and Say (1913).
Figure 48 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 48 - Diagnostic features and terminalia of Minyomerus rutellirostris [JF2015] A aedeagus, dorsal view B aedeagus, lateral view C labial prementum, ventral view D spermatheca E lamina of sternum VIII.
Figure 49 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 49 - Single most parsimonious cladogram representing the preferred phylogeny of species of Minyomerus [JF2015], and select outgroup taxa (L = 82, CI = 65, RI = 82). Characters 7, 33, 38, 39, 41, 43, and 46 are mapped under ACCTRAN optimization; all others are unambiguously optimized. Black squares indicate non-homoplasious character state changes, whereas white squares indicate homoplasious character state changes. The numbers above and below the squares represent character numbers and states, respectively. Bootstrap (upper value) and Bremer support (lower value) values can be found at the left ends of the branches.
Figure 28 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 28 - Diagnostic features and terminalia of Minyomerus cracens [JF2015] A aedeagus, lateral view B aedeagus, dorsal view C labial prementum, ventral view D lamina of sternum VIII E spermatheca F spermatheca, variant.
Figure 8 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 8 - Diagnostic features and terminalia of Minyomerus constrictus [JF2015] A aedeagus, dorsal view B aedeagus, lateral view C labial prementum, ventral view D spermatheca E lamina of sternum VIII.
Figure 26 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 26 - Diagnostic features and terminalia of Minyomerus reburrus [JF2015] A labial prementum, ventral view B lamina of sternum VIII C spermatheca D spermatheca, variant.
Figure 32 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 32 - Diagnostic features and terminalia of Minyomerus trisetosus [JF2015] A labial prementum, ventral view B spermatheca C lamina of sternum VIII.
Figure 45 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Figure 45 - Diagnostic features and terminalia of Minyomerus griseus [JF2015] A aedeagus, dorsal view B aedeagus, lateral view C labial prementum, ventral view D spermatheca E lamina of sternum VIII.
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