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325 results for “molecular phylogenetic analysis”
Figure 1 from: Salvador RB, Brook FJ, Shepherd LD, Kennedy M (2020) Molecular phylogenetic analysis of Punctoidea (Gastropoda, Stylommatophora). Zoosystematics and Evolution 96(2): 397-410. https://doi.org/10.3897/zse.96.53660
Figure 1 Bayesian tree for the "Punctoidea", rooted by the Hygrophila. Numbers shown on nodes are BI posterior probabilities (0 to 1) followed by ML bootstrap values (0 to 100%). Scale bar is substitutions per site.
Data from: Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics
A phylogenetic analysis of mitochondrial and nuclear rDNA sequences from species of all the superfamilies of the insect order Orthoptera (grasshoppers, crickets and relatives) confirmed that although mitochondrial sequences provided good resolution of the youngest superfamilies, nuclear rDNA sequences were necessary to separate the basal groups. To try to reconcile these data sets into a single fully resolved orthopteran phylogeny, we adopted consensus and combined data strategies. The consensus analysis produced a partially resolved tree, lacking several well-supported features of the individual analyses. However, this lack of resolution was explained by an examination of resampled data sets that identified the likely source of error as the relatively short length of the individual mitochondrial data partitions. In a subsequent comparison in which the mitochondrial sequences were initially combined, we observed less conflict. We then used two approaches to examine the validity of combining all of the data in a single analysis; comparative analysis of trees recovered from resampled data sets and the application of a randomization test. The results did not point to significant levels of heterogeneity in phylogenetic signal between the mitochondrial and nuclear data sets, and we therefore proceeded with a combined analysis. Reconstructing phylogenies under the minimum evolution and maximum likelihood optimality criteria, we examined monophyly of the major orthopteran groups using nonparametric and parametric bootstrap analysis and Kishino-Hasegawa tests. Our analysis suggests that phylogeny reconstruction under the ML criteria is the most discriminating approach for the combined sequences. The results indicate that the caeliferan Pneumoroidea and Pamphagoidea (as previously suggested) are polyphyletic. The Acridoidea is redefined to include all pamphagoid families other than the Pyrgomorphidae, which we propose should be accorded superfamily status.
Data from: Molecular and morphological phylogenetic analysis of an insular radiation in Pacific black flies (Simulium)
Ecological adaptation within islands may have figured prominently in the insular radiation of black flies (subgenus Inseliellum) in the Society Islands, French Polynesia. To aid in understanding the sequence of ecological shifts in this group, we have constructed a phylogeny using morphology, the cytochrome oxidase I (COI) gene, and the small ribosomal subunit (12S) gene. The strong influence of COI on the combined analysis tree was evident from its contribution to the partitioned Bremer support (62%). The net effect of including 12S was to reduce overall tree support. Different character sets resolved different portions of the combined analysis tree, with COI resolving recent lineages, 12S resolving basal relationships and morphology supporting the monophyly of taxa possessing reduced larval feeding fans (oviceps group). The Partitionâ Homogeneity and Kashino-Hasegawa tests indicated significant incongruence between morphological and mitochondrial data. The Templeton test revealed that morphology and the combined (COI+12S) mitochondrial data were incongruent. This conflict stems primarily from disagreement over the monophyly of taxa with highly reduced larval feeding fans. Either 1) convergence in a subset of morphological characters, 2) low phylogenetic signal among mitochondrial sequences, or 3) lineage sorting causing the mitochondrial data to track an incorrect evolutionary history, may be responsible.
FIGURE 2 in Phylogenetic analysis of the Neotropical Pristimantis leptolophus species group (Anura: Craugastoridae): molecular approach and description of a new polymorphic species
FIGURE 2. Holotype of Pristimantis leopardus sp. nov. (MHUA-A 8865), SVL 17.5 mm, adult male.
FIGURE 4 in Coenura Bigot as a valid genus: A molecular and morphological phylogenetic analysis of Pelecorhynchus Macquart sensu lato (Diptera: Pelecorhynchidae)
FIGURE 4. Bayesian phylogeny showing the mean age of the clades. The blue bars are the 95 % HDI.
FIGURE 3 in Coenura Bigot as a valid genus: A molecular and morphological phylogenetic analysis of Pelecorhynchus Macquart sensu lato (Diptera: Pelecorhynchidae)
FIGURE 3. Bayesian phylogeny showing the posterior probabilities.
FIGURE 5. Haplotype analysis for C in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 5. Haplotype analysis for C. heros (TCS-network made in PopART 1.7).
FIGURE 6. Haplotype analysis for the Clade II in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 6. Haplotype analysis for the Clade II (TCS-network made in PopART 1.7).
Fig. 3 in Molecular Phylogenetic Analysis and Species Delimitation in the Pine Needle-feeding Aphid Genus Essigella (Hemiptera, Sternorrhyncha, Aphididae)
Fig. 3. Essigella specific differences in intron region 4 of EF-1α.
Supplementary material 1 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
List of sequences and GenBank accession number : Data type: molecular data
Supplementary material 3 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Pairwise genetic distance : Data type: molecular data
Supplementary material 2 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Illustration of morphological characters : Data type: species data
Figure 10 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 10 (a–b) Typical cascading stream habitat of Sumaterana crassiovis comb. n. at Taman Nasional Gunung Leuser, Provinsi Aceh. Sumaterana dabulescens sp. n. inhabits similar stream habitats. (c) Specimen of S. dabulescens sp. n. on a rock near a small cascade in its natural habitat at Taman Buru Linge Isaq, Provinsi Aceh. Photos by U. Arifin.
Figure 9 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 9 Geographical distribution of Sumaterana dabulescens sp. n. (purple squares; type locality purple arrow [1]: Jamat, Taman Buru Linge Isaq), S. crassiovis comb. n. (brown circles; type locality brown arrow [2]: Kerinci), and S. montana sp. n. (red triangles; type locality red [3]: Gunung Baru, Taman Nasional Kerinci-Seblat). The map was prepared using GeoMapApp (Ryan et al. 2009).
Figure 11 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 11 Tadpoles of Sumaterana crassiovis comb. n., ZMH.A12650, Provinsi Sumatera Barat (a–c) and S. dabulescens sp. n., MZB.AMPH.29411, Provinsi Aceh (d–f) showing dorsal, ventral, and lateral view. Scale 5 mm. Photos by U. Arifin.
Figure 5 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 5 Sumaterana gen. n. species: (a) S. crassiovis comb. n., ZMH.A14197, male, Provinsi Sumatera Barat; (b) S. dabulescens sp. n., MZB.AMPH.29396, male, holotype, Provinsi Aceh; (c) S. montana sp. n., ZMH.A14194, female, paratype, Provinsi Bengkulu. Photos by U. Arifin.
Figure 1 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 1 Sampling localities of adult and larva of Chalcorana crassiovis specimens for this study. Black circles represent localities of specimens which were examined. White triangles represent localities of specimens which were examined and measured. Red stars represent localities of specimens which were examined, measured, and sequenced. Type locality of C. kampeni shown by number 1 (Bandar Baru), number 2 (Kerinci) for C. crassiovis. Provinces are shown by alphabet: A Aceh, B Sumatera Utara, C Riau, D Sumatera Barat, E Jambi, F Bengkulu, G Sumatera Selatan, H Lampung. Borders between provinces are represented by black lines. The map was prepared using GeoMapApp (Ryan et al. 2009).
Figure 8 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 8 Morphological variation within Sumaterana crassiovis comb. n. (a) MZB.AMPH.29196, female, Provinsi Aceh, (b) Provinsi Sumatera Utara, (c) MZB.AMPH.29200, male, Provinsi Sumatera Barat, (d) ZMH.A14197, male, Provinsi Sumatera Barat, (e) MZB.AMPH.29320, male, Provinsi Sumatera Barat, (f) MZB.AMPH.29277, young male, Provinsi Bengkulu, (g) ZMH.A14151, male, Provinsi Sumatera Selatan, (h) ZMH.A14185 and MZB.AMPH.29296, male and female, Provinsi Lampung. Photos by U. Arifin, except for (b) by A. Irawan.
Figure 4 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 4 Variation of rear of thigh pattern and webbing on toes of the specimens within Clade 1A. Photographs were taken from ZMH.A14197, male, Provinsi Sumatera Barat (a, g); MZB.AMPH.29196, female, Provinsi Aceh (b); MZB.AMPH.29320, male, Provinsi Sumatera Barat (c); MZB.AMPH.29200, male, Provinsi Sumatera Barat (d–e); ZMH.A14170, female, Provinsi Sumatera Barat (f); ZMH.A14185, female, Provinsi Lampung (h). Photos by U. Arifin
Figure 7 from: Arifin U, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A (2018) Molecular phylogenetic analysis of a taxonomically unstable ranid from Sumatra, Indonesia, reveals a new genus with gastromyzophorous tadpoles and two new species. Zoosystematics and Evolution 94(1): 163-193. https://doi.org/10.3897/zse.94.22120
Figure 7 Pictures of dorsal (i), ventral (ii), palmar (iii), and plantar (iv) regions of the type species of Sumaterana crassiovis comb. n. (BMNH1947.2.4.1, female). Photos by U. Arifin.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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.