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FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 dataset rooted according to the result for the COI dataset. Support values are shown as jackknife from parsimony analysis and bootstrap from maximum likelihood respectively separated by /. * indicates 100% values for each support measure.
FIGURE 1. The three sympatric Thoracophelia spp. from Dillon Beach. A, Thoracophelia dillonensis. B in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data
FIGURE 1. The three sympatric Thoracophelia spp. from Dillon Beach. A, Thoracophelia dillonensis. B, Pectinate branchiae of T. dillonensis. C, Thoracophelia williamsi. D, Bifurcated branchiae with pinnules of T. williamsi. E, Thoracophelia mucronata. F, Bifurcated branchiae of T. mucronata. Scale bars all 1 mm.
Figure 4 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 4: Maximum likelihood phylogenetic tree inferred from the alignment of ITS1 sequences. Support values are shown as in Figure 3. The ribotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Alaria esculenta was used as an outgroup to root the tree. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site).
Figure 3 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 3: Maximum likelihood phylogenetic tree inferred from the alignment of the combined cox3 and tatC–tLeu sequences. Bootstrap values and Bayesian posterior probabilities>50% are shown, and "-" indicates a value <50%. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site). Refer to Uwai et al. (2006a) for explanation of the haplotype names and classification of the clades I to IV. The haplotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Lessoniopsis littoralis was used as an outgroup to root the tree.
Figure 2 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 2: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of ITS1 sequences. The color areas in the pie charts are proportional to the ribotype frequency in the map. Small circles indicate undetected ribotypes. Each line connecting ribotypes represents one base mutation. The ribotypes detected in the Chinese samples in the present study are indicated in the ribotype network by the same colors as those in the map.
Figure 1 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 1: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of the combined cox3 and tatC–tLeu sequences. The color areas in the pie charts are proportional to the haplotype frequency in the map. Refer to Uwai et al. (2006a) and Table 3 for explanation of the haplotype names and classification of the clades I to IV, which are enclosed by boxes with lines of different patterns. Small circles indicate undetected haplotypes. Each line connecting haplotypes represents one base mutation. The haplotypes detected in the Chinese samples in the present study are indicated in the haplotype network with the same colors as those in the map.
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches.
Integrative taxonomic analysis to reveal the species status of Bombus flavidus, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction as well as patterns of color polymorphism
<p>Bumble bees, due to their morphological monotony and color diversity, have presented difficulties with species delimitation. Recent bumble bee declines have made it ever more imperative to resolve the status of species to address conservation concerns. Some of the taxa found to be most threatened are the often-rare socially parasitic bumble bees, which have additional trophic requirements. Among the socially parasitic bumble bees,<i> Bombus flavidus</i> Eversmann has contentious species status. While multiple separate species allied with <i>Bombus flavidus</i> have been suggested, until recently, recognition of two species, a Nearctic <i>Bombus fernaldae</i> (Franklin) and Palearctic <i>B. flavidus,</i> was favoured. Limited genetic data, however, suggested that even these could be a single widespread species, <i>B. flavidus</i>. We addressed the species status of this lineage using an integrative taxonomic approach, combining <i>COI</i> and nuclear sequencing, wing morphometrics and secretions used for mate attraction. We also explore patterns of color polymorphism that have previously confounded taxonomy in this lineage. Our results support the conspecific status of <i>Bombus fernaldae</i> and <i>Bombus flavidus,</i> however, sampling specimens from across the range of these two taxa revealed a distinct population within this broader species confined to eastern North America. This makes the distribution of the social parasite <i>B. flavidus</i> the broadest of any bumble bee, broader than the known distribution of any non-parasitic bumble bee species. Analysis of color phenotypes revealed that color polymorphisms are retained across the range of the species, but may be influenced by local mimicry complexes. Following these results, <i>Bombus flavidus</i> Eversmann, 1852<i> </i>is synonymized with <i>Bombus fernaldae </i>(Franklin, 1911) <b>syn. nov.</b> and a subspecific status, <i>Bombus flavidus </i><i>appalachiensis</i> <b>ssp. nov.</b>, is assigned to the distinct lineage ranging from the Appalachians to the eastern boreal regions of the United States and far southeastern Canada.</p>
Data from: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago
<p><span>This study aimed to reveal the evolutionary timescale and processes underlying the diversity of <em>Rubus</em> in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, <em>R. chamaemorus</em>, <em>R. pedatus</em>, <em>R. vernus</em>, <em>R. pseudojaponicus</em>, and <em>R. ikenoensis</em>, were found to belong to anciently diverged lineages; in particular, <em>R. ikenoensis</em> formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. <em>Malachobatus</em>, <em>Chamaebatus</em>, and sects. <em>Pungentes</em>, <em>Idaeanthi</em>, and <em>Parvifolii</em> (subg. <em>Idaeobatus</em>), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, <em>R. sieboldii</em> has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. <em>Microphylli</em>, <em>Corchorifolii</em>, <em>Peltati</em>, and <em>Rosifolii</em> (subg. <em>Idaeobatus</em>), and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, <em>R. sumatranus</em>, <em>R. peltatus</em>, <em>R. corchorifolius</em>, and <em>R. chingii</em>, was incongruent among gene trees. At the lower taxonomic levels, <em>R. illecebrosus</em>, <em>R. grayanus</em>, and the thornless species of sect. <em>Microphylli</em> showed earlier divergence.</span></p>
Supplementary material 2 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132
Maximum likelihood model parameters: Explanation note: Model parameters used in the maximum likelihood approach to phylogenetic reconstruction.
Supplementary material 4 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132
Patterns of COI sequence variation: Explanation note: Patterns of COI sequence variation. Graphs and discussion of patterns of nucleotide substitions in the COI data-set.
Supplementary material 1 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132
Aligned and concatenated partial sequences of COI and 28S rDNA: Explanation note: Aligned and concatenated partial sequences of COI and 28S rDNA in nexus format. Aligned partial sequences of COI and 28S rDNA from each acanthocephalan population have been concatenated. Gaps are indicated by '-'. The first 585 characters in each block correspond to COI and the remainder to 28S rDNA. The file contains data for all nine Echinorhynchus samples and the outgroup taxon, Acanthocephalus lucii. This nexus file was used in all phylogenetic analyses.
Supplementary material 3 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132
Nucleotide substitutions: Explanation note: Substitutions of nucleotides (transitions/transversions) for 28S rDNA (below the diagonal) and COI sequence data (above the diagonal).
FIGURE 3 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 3. Larva of Simulium lampangense. A. Cephalic apotome, dorsal view. B. Mandible, apex. C. Hypostoma. D. Head capsule showing postgenal cleft, ventral view. Scale bars = 0.1 mm for A and D and 0.05 mm for B and C.
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 (ECP1) sequences of five nominal species and unknown (Unk) larvae in the Simulium multistriatum species group in Thailand. Bootstrap values for neighbor-joining and maximum likelihood and posterior probability of Bayesian analysis are shown above or near the branches. -- denotes bootstrap support less than 50%. Scale bar represents 0.03 substitutions per nucleotide position.
FIGURE 1 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 1. Bayesian tree based on cytochrome c oxidase subunit I (COI) sequences of six nominal species and unknown (Unk) larvae in the Simulium multistriatum species group in Thailand. Bootstrap values for neighbor-joining and maximum likelihood (ML) and posterior probability of Bayesian analysis are shown above or near the branches. -- denotes bootstrap support less than 50%. Scale bar represents 0.03 substitutions per nucleotide position.
Monotropoid Ericaceae 102-locus nuclear sequences matrices and plastid locus sequence matrix
<p>Monotropoideae (Ericaceae) is a wholly leafless and holomycotrophic group of primarily temperate herbs with centers of diversity in western North America and east Asia. The eleven genera are structurally diverse and also vegetatively reduced, making relationships difficult to assess based on morphology. Previous molecular analyses have focused primarily on segments of the ribosomal RNA repeat and yielded sometimes conflicting topologies. We employed a genomic sampling approach to obtain 102 nuclear loci and plastid coding loci for nine of the genera, as well as sampling ITS-26S and plastid <em>rps2</em> for a broader set of accessions via PCR and Sanger sequencing Data filtering for character completeness had a clear effect on relationships and branch support. Nuclear and plastid loci agree on a topology that resolves <em>Allotropa</em> and <em>Hemitomes</em> as sisters and <em>Monotropsis</em> sister to <em>Eremotropa</em>+<em>Monotropa</em>+<em>Monotropastrum</em>, relationships that were unclear from previous analyses. <em>Hypopitys</em> should be recognized as distinct from <em>Monotropa</em>, with previous ambiguity in <em>rps2</em> relationships here explained by the existence of plastid and mitochondrial paralogs. Comparison of branch lengths between nuclear and plastid loci reveals increased rates of change in plastid sequences in most cases, especially in <em>Monotropsis</em> and <em>Monotropa</em>, but the reverse situation in <em>Pityopus</em>, with nuclear branches being unusually long, possibly indicating cryptic diversity. Parallel shifts in plant form to a ground-level floral display correlate with shifts from capsular to berry fruits and reduction in species ranges. The optimal tree from molecular data requires significant parallelism and/or reversal in morphological features due to the placement of <em>Allotropa</em> and <em>Hemitomes</em>.</p>
FIGURE 6 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 6. Distribution of the five species of the N. melanoleuca complex. A full list of voucher specimens beyond those included in multivariate analyses and Appendix 2 is available on request from the first author.
FIGURE 1 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 1. Maximum likelihood mitochondrial phylogeny of the Naja melanoleuca complex. Node support values indicate % bootstrap support; support values for the most distal nodes not shown. Country abbreviations: CAR = Central African Republic, DRC = Democratic Republic of Congo, KZN = KwaZulu-Natal Province, South Africa, RoC = Republic of Congo. Mitochondrial candidate species (CS) are shown in the same colours as in Figures 2–4. For specimen information see Appendix 1.
FIGURE 5 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 5. Naja (Boulengerina) guineensis sp. nov. Left and top right: holotype, MNHN 1921.0485, dorsal and ventral view and side view of head. Note extensive mottling of throat and anterior ventral side and limited posterior extent of lighter ventral markings. Bottom right: live adult specimen measuring approximately 200 cm total length, from Sekondi-Takoradi, Western Region, Ghana, displaying dark suffusion of throat and anterior venter (not preserved; photo L. Chirio).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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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.