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2,620 results for “Molecular Phylogeny”
Data from: A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity
Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes. Each clade includes several new species and potentially new genera. Collectively, our data uncover a rich and undescribed diversity that appears to be especially prevalent in Australia. Our work highlights the need for a major taxonomic revision of the family and for generating a robust molecular phylogeny using multi-gene approaches in order to resolve the relationships among clades.
Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were constructed: dataset 1, which included 12 loci totalling 9927 bp for 94 taxa, and dataset 2, which supplemented dataset 1 with 10 additional loci for 10 taxa, for a total of 22 loci and 16 167 bp. Maximum likelihood analyses strongly supported the monophyly of Gracillariidae and most previously recognized subfamilies and genus groups. On this basis, we propose a new classification consisting of eight subfamilies, four of which are newly recognized or resurrected: Acrocercopinae Kawahara & Ohshima subfam. n.; Gracillariinae Stainton; Lithocolletinae Stainton; Marmarinae Kawahara & Ohshima subfam. n.; Oecophyllembiinae Réal & Balachowsky; Parornichinae Kawahara & Ohshima subfam. n.; Ornixolinae Kuznetzov & Baryshnikova stat. rev.; and Phyllocnistinae Zeller. The subfamily Gracillariinae is restricted to the monophyletic group comprising Gracillaria Haworth and closely related genera. We also formally transfer Acrocercops scriptulata Meyrick to Ornixolinae and use the name Diphtheroptila Vári, creating Diphtheroptila scriptulata comb. n. An exploratory mapping of larval host-use traits on the phylogeny shows strong conservation of modes of leaf mining but much higher lability of associations with host plant orders and families, suggesting that host shifts could play a significant role in gracillariid diversification.
Data from: Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses
There are 14 species of marmots distributed across the Holarctic, and despite extensive systematic study, their phylogenetic relationships remain largely unresolved. In particular, comprehensive studies have been lacking. A well-supported phylogeny is needed to place the numerous ecological and behavioral studies on marmots in an evolutionary context. To address this situation, we obtained complete cytochrome (cyt) b sequences for 13 of the species and partial sequence for the 14th. We employed a statistical approach to both phylogeny estimation and hypothesis testing using parsimony and maximum likelihood based methods. We conducted statistical tests on a suite of previously proposed hypotheses of phylogenetic relationships and biogeographic histories. The cyt b data strongly support the monophyly of Marmota and a western montane clade in the Nearctic. The results are consistent with an initial diversification in North America followed by an invasion and subsequent rapid diversification in the Palearctic. These analyses reject the two major competing hypotheses of M. broweri's phylogenetic relationships: namely, that it is the sister species to camtschatica of eastern Siberia and that it is related closely to caligata of the Nearctic. The Alaskan distribution of M. broweri is best explained as a reinvasion from the Palearctic but a Nearctic origin can not be rejected. Several other conventionally recognized species groups can also be rejected. Social evolution has been homoplastic, with large colonial systems evolving in two groups convergently. The cyt b data do not provide unambiguous resolution of several basal nodes in the Palearctic radiation, leaving some aspects of pelage and karyotypic evolution equivocal.
FIGURE 178 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURE 178. Maximum Likelihood best tree of the 28S gene dataset from 44 Platystictidae taxa, including 19 representatives of the subfamily Platystictinae from Sri Lanka. Bootstrap support and posterior probabilities are shown if less than 100%. Specimen details are provided in Table 3 of Appendix 1.
FIGURE 179 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURE 179. Maximum Likelihood best tree of the 16S+28S gene dataset from 44 Platystictidae taxa, including 19 representatives of the subfamily Platystictinae from Sri Lanka. Bootstrap support and posterior probabilities are shown if less than 100%. Specimen details are provided in Table 3 of Appendix 1.
FIGURE 177 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURE 177. Maximum Likelihood best tree of the 16S gene dataset from 44 Platystictidae taxa, including 19 representatives of the subfamily Platystictinae from Sri Lanka. Bootstrap support and posterior probabilities are shown if less than 100%. Specimen details are provided in Table 3 of Appendix 1.
FIGURE 176 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURE 176. Maximum Likelihood best tree of the COI gene dataset from 45 Platystictidae taxa, including 21 representatives of the subfamily Platystictinae from Sri Lanka. Bootstrap support and posterior probabilities are shown if less than 100%. Specimen details are provided in Table 3 of Appendix 1.
FIGURE 175 in Taxonomy and molecular phylogeny of the Platystictidae of Sri Lanka (Insecta: Odonata)
FIGURE 175. Bayesian inference of the combined 16S+28S+COI dataset from 46 Platystictidae taxa, represented by 62 specimens. Sri Lankan Platystictinae are represented by 21 species and 37 specimens. Posterior probabilities are shown if less than 100%. For Sri Lankan taxa the individual species-groups are indicated by the dark grey bars. The bars on the right indicate the distribution of individual specimens, the bars of Sri Lankan and Indian specimens are highlighted with light grey. Specimen details are provided in Table 3 of Appendix 1.
FIGURE 8 in Description and molecular phylogeny of Tethya hibernica sp. nov. (Porifera, Demospongiae) from Northern Ireland with remarks on the European species of the genus Te t h y a *
FIGURE 8. Distribution maps of T. aurantium, T. citrina, and T. norvegica compiled from various sources (Sarà, 1987; Sara & Gaino, 1987; Sarà et al., 1989; Sara, 1990; Sarà & Manara, 1991; Bavestrello et al., 1992; Sarà et al., 1992; Bavestrello & Sarà, 1994; Corriero et al., 1996; Sarà, 1998; Pansini & Longo, 2003). The occurrance of T. norvegica on the British Isles will have to be proven carefully (see text for details).
FIGURE 5 in Description and molecular phylogeny of Tethya hibernica sp. nov. (Porifera, Demospongiae) from Northern Ireland with remarks on the European species of the genus Te t h y a *
FIGURE 5. SEM images of T. hibernica spicule morphology. A. Typical megasters. B. Acanthostrongylasters, which represent the major group of micrasters (>95%). C. Acanthotylasters (rarest group of micrasters). D. Oxyasters, which are slightly more frequent than tylasters.
FIGURE 1 in Description and molecular phylogeny of Tethya hibernica sp. nov. (Porifera, Demospongiae) from Northern Ireland with remarks on the European species of the genus Te t h y a *
FIGURE 1. Geographic location of Rathlin Island (star in right map) within the British Isles between Northern Irleand and Mull of Kintyre (Scotland). The insert map (left) displays Rathlin Island with coordinates and the collection point of the type specimens of T. hibernica (filled circle).
FIGURE 3. A in Description and molecular phylogeny of Tethya hibernica sp. nov. (Porifera, Demospongiae) from Northern Ireland with remarks on the European species of the genus Te t h y a *
FIGURE 3. A. Schematic overview on the skeletal arrangement in the cortex (light grey) and the choanoderm (dark grey) in a contracted specimen of T. hibernica. B. Micrograph of tissue slice preparations. Main megascleres form bundles, which fan near the surface. Auxiliary megascleres are present in-between bundles in the choanoderm. Megasters are mainly present throughout the whole cortex. Micrasters are present throughout the sponge, with a prominent layer supporting the outer and inner pinacoderm layers. The lacuna system of the ectoderm is not dominant due to the contracted state of the specimens investigated. For details on the spicules refer to Figures 4 and 5.
FIGURE 4 in Description and molecular phylogeny of Tethya hibernica sp. nov. (Porifera, Demospongiae) from Northern Ireland with remarks on the European species of the genus Te t h y a *
FIGURE 4. Megascleres (strongyloxeas) of T. hibernica. A. SEM image collage of a main megasclere, presenting typical geometry and diameters of both ends and a middle section. B. Size distribution of auxiliary megascleres (filled triangles; n = 70) and main megascleres (filled circles, n = 40), which form distinct groups of normal distributions (Kolmogorov-Smirnov test), significantly separated by spicule length (p <0.001; independent t-test).
FIGURE 2 in Description and molecular phylogeny of Tethya hibernica sp. nov. (Porifera, Demospongiae) from Northern Ireland with remarks on the European species of the genus Te t h y a *
FIGURE 2. In vivo images of T. hibernica types from the type location at Rathlin Island. Both specimens have been used for morphological description and DNA sequencing. A. Expanded holotype (Mc3037) with open oscules (arrow heads). B. Contracted holotype (Mc3037) with closed oscules, after contraction stimulation by extensive artificial water current. C. Paratype (Mc2748), with external buds (arrow heads). Mind the colour variation from brownish to yellowish between the two specimens.
FIGURE 1. Locus specific phylogenies for COI, 12S in Molecular and morphological evaluation of the aphid genus Hyalopterus Koch (Insecta: Hemiptera: Aphididae), with a description of a new species
FIGURE 1. Locus specific phylogenies for COI, 12S, EF-1α, and Buchnera 16S. All trees are from analyses performed with MRBAYES, with node support given as posterior probabilities. Collection data for each specimen are provided in Table 1 and models of sequence evolution used for each gene are provided in Table 2.
FIGURE 10 in A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny
FIGURE 10. Phylogeny of nobleobatrachian frogs represented by selected species and constructed using sequences from 9 genes. The tree is rooted with Rana temporaria (not shown). Support values (ML bootstrap/Bayesian posterior probability/MP bootstrap) are indicated at nodes. Bayesian and MP support values are not given in cases where those phylogenies conflicted with the ML phylogeny.
FIGURE 9 in A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny
FIGURE 9. (A) Bayesian and (B) maximum parsimony phylogenies of nobleobatrachian frogs represented by selected genera and constructed using sequences from 17 genes. The trees are rooted with Ranidae (not shown). Support values (Bayesian posterior probabilities or MP bootstrap values) are indicated at nodes.
FIGURE 8 in A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny
FIGURE 8. Maximum likelihood phylogeny of nobleobatrachian frogs represented by selected genera and constructed using sequences from 17 genes. The tree is rooted with Ranidae (not shown). Bootstrap support values are indicated at nodes. Higher classification is indicated to the right.
FIGURE 6 in A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny
FIGURE 6. High-resolution tomographs of terraranan frogs representing two families (left, dorsal view; right, ventral view). (A–B) Brachycephalidae, Ischnocnema guentheri (KU 92816); (C–D) Craugastoridae, Haddadus binotatus (KU 92808). Scale bars = 5 mm.
FIGURE 5 in A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny
FIGURE 5. Habitat of Ceuthomantis smaragdinus at 1540 m on Mt. Kopinang, Guyana. The holotype was found about 5 m from the stream in the foreground in Figure 5A; the paratype was found on a leaf about 10 m away from the other side of the stream slightly to the left of the middle of Figure 5B. Photographs by D. B. Means.
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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.