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Figure 5. Agreement subtree cladogram obtained with the Ratchet algorithm for parsimonious analyses using the complete morphological matrix without gamete-related characters. Values above branches are bootstrap supports after 1000 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 5. Agreement subtree cladogram obtained with the Ratchet algorithm for parsimonious analyses using the complete morphological matrix without gamete-related characters. Values above branches are bootstrap supports after 1000 replicates; values under branches are Bremer relative supports.
Figure 1 in Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data
Figure 1. Maximum likelihood phylogenetic tree based on the resulting mitogenomes except control region for all known Crocodylia species. The mitogenomes employed have been identified by their accession number to the GenBank database. Ten species (two pythons, one lizard, five birds, two turtles) were used as outgroups to root the tree. The numbers on the nodes indicate ML bootstrap support (shown as a percentage) and Bayesian posterior probabilities. These letters (A, B and C) indicate the families in Crocodylia (Crocodylidae, Gavialidae and Alligatoridae). The head shapes and dentition in 'typical' examples of the three families of living Crocodylia (dorsal and side views) (Illustrations DSK, courtesy Weldon Owen Publishing)(Grigg & Kirshner, 2015).
Figure 2 in Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data
Figure 2. Time-calibrated phylogeny of the Crocodylia inferred from the complete mitogenomes. These letters (a and b) indicate the calibration points. The blue lines on nodes correspond to the 95% highest posterior density of the age of the node. The bottom axis is in millions of years (Myr). The climatic sequence of events including a global average δ 18O curve (right-hand axis) derived from benthic foraminifera which mirrors the major global temperature trends from the Palaeocene to the Pleistocene (Zachos et al., 2001, 2008). The establishment of ice sheets in the Northern Hemisphere is indicated by grey to black bars on top. Some key tectonic are listed (Zachos et al., 2001). These letters (A, B and C) indicate the families in Crocodylia (Crocodylidae, Gavialidae and Alligatoridae). The numbers on the nodes within Crocodylia indicate node numbers, corresponding to Table 3.
Figure 5 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 5. Phylogenetic relationships of control regions inferred by the maximum likelihood (ML) method. Statistical support is shown on the branches: bootstrap values (above) and posterior probability (below). BI, Bayesian inference; CR, control region.
Figure 1 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 1. Evolution of mitochondrial genomes in Antarctic notothenioids modified from Zhuang & Cheng (2010). Abbreviations: 12S, 12S ribosomal RNA; CR, control region; Cyt b, cytochrome b; E, tRNAGlu; F, tRNAPhe; ND, nicotinamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; T, tRNAThr.
Figure 4. A in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 4. A, linear representation of three types of gene content from the partial cytochrome b (Cyt b) to 12S rRNA in the mitochondrial (mt) genome of the mackerel icefish. Black and dark grey arrows respectively represent the first and the second duplicates. The first duplicate of the type-1 genome contains full-length nicotinamide adenine dinucleotide (reduced form) dehydrogenase subunit 6 (ND6) and tRNAGlu. Type-2 contains a half-sized ND6 only. Type-3 does not contain ND6 or tRNAGlu. B, PCR amplifications for detecting ND6 and tRNAGlu in the three types of mt genome of the mackerel icefish. PCR fragments between Cyt b and control region (CR) 2 (Cyt b-CR2) and between CR2 and CR3 (CR2-CR3) contain the first and second copies of ND6, respectively. The PCR fragment between ND5 and Cyt b (ND5-Cyt b) did not contain ND6 or tRNAGlu. M, size marker. Lanes 1, 2, 7, and 10 are type-1 individuals. Lanes 3, 4, 8 and 11 are type-2 individuals. Lanes 5, 6, 9, and 12 are type-3 individuals. Abbreviations: E, tRNAGlu; F, tRNAPhe; P, tRNAPro; T, tRNAThr.
Figure 3 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 3. Map of the mackerel icefish mitochondrial (mt) genome as a circular diagram. The map represents the mt genome of a type-1 individual in which ND6 and tRNAGlu were transposed to a position between tRNAThr and tRNAPro flanked by intergenic spacers (UN3 and UN4), and the ND6- to -CR segment was duplicated once. Fourteen protein-coding genes, two rRNA genes, and noncoding regions are labelled with abbreviations. Twenty-four tRNA genes are shown by a one-letter amino acid code. Different codons used by each of tRNALeu and tRNASer are shown in parentheses. Genes transcribed from the heavy strand and light strand are respectively presented outside and inside the circle. Heavy- and light-strand replication origins are represented by OH and OL, respectively. Abbreviations: 12S, 12S ribosomal RNA; 16S, 16S ribosomal RNA; A, tRNAAla; ATP, ATP synthase; C, tRNACys; CO, cytochrome oxidase; Cyt b, cytochrome b; D, tRNAAsp; E, tRNAGlu; F, tRNAPhe; G, tRNAGly; H, tRNAHis; I, tRNAIle; K, tRNALys; L, tRNALeu; M, tRNAMet; N, tRNAAsn; ND, nicotiamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; Q, tRNAGln; R, tRNAArg; S, tRNASer; T, tRNAThr; V, tRNAVal; W, tRNATrp; Y, tRNATyr.
Rhizophora complete chloroplast genome sequences
<p>Historical processes of long-distance migration and ocean-wide expansion feature the global biogeographic pattern of <i>Rhizophora</i> species. Throughout the Indian Ocean, <i>R. stylosa</i> and <i>R. mucronata</i> appear as a young phylogenetic group with expansion of <i>R. mucronata</i> towards the Western Indian Ocean (WIO) driven by the South Equatorial Current. Nuclear microsatellites revealed genetic patterns and breaks, however, estimating propagule dispersal routes requires maternally inherited cytoplasmic markers. Here, we examine the phylogeography of 21 <i>R. mucronata</i> provenances across a >4,200 km coastal stretch in the WIO using <i>R. stylosa</i> as outgroup. Full length chloroplast genome (164,474 bp) and nuclear ribosomal RNA cistron (8,033 bp) sequences were assembled. Boundaries, junction point, sequence orientation and stretch between LSC/IRb/SSC/IRa/LSC showed no differences with the <i>R. stylosa</i> chloroplast genome. A total of 58 mutations in <i>R. mucronata</i> encompassing transitions/transversions, insertion-deletions and mononucleotide repeats revealed three major haplogroups. Haplonetwork, Bayesian ML and Approximate Bayesian Computation (ABC) analyses supported discrete historical migration events. An ancient haplogroup A in the Seychelles and eastern Madagascar was as divergent from other <i>R. mucronata</i> haplogroups as it was from <i>R. stylosa</i>. A star-like haplonetwork referred to recent range expansion of haplogroup B from northern Madagascar towards the African mainland coastline, including a single variant spanning >1,800 km across the Mozambique Channel Area. Populations south of Delagoa Bight contained haplogroup C and originate from a unique bottleneck dispersal event. Divergence estimates of pre- and post-Last Glacial Maximum illustrated a recent emergence of WIO <i>Rhizophora </i>mangroves compared to other oceans. Connectivity patterns could be aligned with directionality of major ocean currents. Madagascar and the Seychelles each harbored haplogroups A and B, albeit among spatially separated populations, explained from a different migration era. Likewise, the Aldabra Atoll harbored spatially distinct haplotypes. Nuclear ribosomal cistron (8,033bp) variants corresponded to haplogroups and confirmed admixtures in the Seychelles and Aldabra. These findings shed new light on the origins and dispersal routes of <i>R. mucronata</i> lineages that have shaped their contemporary populations in large regions of the WIO, which may be important information for defining marine conservation units, both at ocean scale and at level of small islands.</p>
FIGURE 5. a—Waveform showing the complete 1.5 in Platylomia kohimaensis n. sp.-a new cicada species (Hemiptera: Cicadidae) from the Naga Hills in the Eastern Himalayas
FIGURE 5. a—Waveform showing the complete 1.5 minute call recording, note the middle part where call is paused (inbox—section stretched to reveal waveform pattern), b—a portion of the recorded timbalisation stretched to revel the pattern of waveform in the form of regular echemes repeating at the rate of 8 echemes per second, c—Frequency spectrogram of the call showing frequency components (arrow showing main frequency components in each echeme).
Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights into Phylogenetic Relationships of Onagraceae
<p>This is all the alignments which used to constructed a phylogenetic tree in our study about Onagraceae. The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, which comprises 22 genera widely distributed from boreal to tropical areas. In the present study, we report and characterize the complete chloroplast genome sequences of 13 species in <em>Circaea</em>,<em> Chamaenerion</em>, and <em>Epilobium</em> using a next-generation sequencing method. We also retrieved plastome sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete plastomes of Onagraceae showed a typical quadripartite structure and encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The results show that chloroplast genomes are basically conserved in gene arrangement across the family. Whereas, a large segment of inversion was detected in the LSC region of all samples in the<em> Oenothera </em>subsect. <em>Oenothera</em>. An inverted repeat (IR) contraction was found in <em>Circaea</em> and<em> Ludwigia </em>samples. We also compared chloroplast genomes across the Onagraceae samples and revealed similarities in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference (BI) methods. The generic relationship of Onagraceae was well resolved by the complete plastome sequences, showing potential value in inferring phylogeny within the family. <em>Oenothera </em>phylogeny was better resolved than other densely sampled genera. Biparental transmission may be the main cause of higher variation in the genus<em> Oenothera</em>.</p>
A complete view of the atmospheric hydrologic cycle
<p>fig01.zip: Inside this zip there are 4 files which were used to make Figure 1. The 3 csv files are used to plot the trajectory pathways from their starting positions to the ending locations. The variable 'ntopo' in the single netcdf file represents the ocean basin and global landmass mask.</p> <p>fig02_03_04.zip: In this zip there are 192 netcdf files and were used to produce Figure 2, 3 and 4. Each file is for a month and consists of evaporation, precipitation, meridional and zonal overturning stream function within and between the three major ocean basins and the global landmass. Here atl = Atlantic Ocean, pac=Pacific Ocean,ind = Indian Ocean, and lnd = global landmass.</p> <p>fig05.zip: In this zip there are also 192 netcdf files that were used to produce Figure 5.</p> <p>fig06.zip: Consists of 16 nectdf files that represent average residence time (days) of the atmospheric waters travelling from the surface evaporative regions to the precipitation areas. This residence time was calculated from the points where net evaporation exceeds a monthly mean value of 0.2 mm/day.</p> <p>table1.zip: This zip file was used to calculate the atmospheric freshwater transport within and between the ocean basins and land.</p>
Supplementary material 9 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure S5. Phylogenetic relationships of Gobioninae based on complete mitochondrial genomes using Bayesian analyses
Supplementary material 7 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure S3. Putative secondary structures of the 22 tRNA genes identified in the mitochondrial genome of M. elongatus
Complete mitochondrial genome of the hawthorn moth Scythropia crataegella (Linnaeus, 1767) (Lepidoptera: Scythropiidae)
<p>Currently, only a limited number of mitochondrial genomes (mitogenomes) are available in the superfamily Yponomeutoidea. In the present study, we report on the complete mitogenome of the hawthorn moth <em>Scythropia crataegella </em>(Linnaeus, 1767), the first species in the family Scythropiidae to enrich the catalog of Yponomeutoidea mitogenomes. The <em>S. crataegella </em>mitogenome was 15,350 bp in size and consisted of the set of genes and major non-coding A+T-rich region that are typical of insect mitogenomes. The <em>COI</em> gene had a CGA start codon; however, the other PCGs began with ATN codons. The A/T content was 80.3% in PCGs, 81.8% in tRNAs, 85.3% in <em>lrRNA</em>, 87.3% in <em>srRNA</em>, 81.8% in the whole genome, and 95.8% in the A+T-rich region. Phylogenetic analyses based on the concatenated sequences of 13 PCGs and two rRNA genes placed Scythropiidae, represented by <em>S. crataegella</em>, as a sister group to Yponomeutidae, represented by <em>Yponomeuta sedellus</em>; however, the nodal support for this group was very low (bootstrap support = 18%), indicating that extended taxon diversity is required for further robust phylogenetic inference in Yponomeutoidea.</p>
FIGURE 11 in Complete mitogenome and phylogenetic significance of Metoecus javanus (Pic, 1913) (Coleoptera: Ripiphoridae) from Southwest China, with notes on morphological traits of adult and immature stages
FIGURE 11. Ecological photos of M. javanus and its wasp hosts. A Male adult of M. javanus (Lincang). B Female of M. javanus (Chuxiong). C Vespa velutina: host of population from Nujiang. D Vespa bicolor: host of population from Lincang.
FIGURE 9 in Complete mitogenome and phylogenetic significance of Metoecus javanus (Pic, 1913) (Coleoptera: Ripiphoridae) from Southwest China, with notes on morphological traits of adult and immature stages
FIGURE 9. Pupa of M. javanus. A–C Mature pupa, female (A ventral view; B dorsal view; C lateral view). D–F Pupa of early stages, sex undetermined (D ventral view; E head; F pronotum) (Scale bar: A–D: 5 mm; E, F: 1 mm).
FIGURE 10 in Complete mitogenome and phylogenetic significance of Metoecus javanus (Pic, 1913) (Coleoptera: Ripiphoridae) from Southwest China, with notes on morphological traits of adult and immature stages
FIGURE 10. Mature larva of M. javanus. A Habitus (lateral view). B–D Head and thorax (B lateral view; C dorsal view; D ventral view). E Head. F Left V spiracle (unmarked arrows represent fleshy tubercles, scale bar: A, B–D: 5 mm; E–F: 2 mm).
FIGURE 8. Male genitalia. A–C Tergite IX, IX in Complete mitogenome and phylogenetic significance of Metoecus javanus (Pic, 1913) (Coleoptera: Ripiphoridae) from Southwest China, with notes on morphological traits of adult and immature stages
FIGURE 8. Male genitalia. A–C Tergite IX, IX (T9, T10) and sternite IX (S9) of male adult (A left view; B ventral view; C dorsal view). D–G Aedeagus (D dorsal view; E ventral view; F left view; G right view). H Median lobe (left view). I Aedeagus, separated (left on dorsal view) J–M Phallobase and parameres (J dorsal view; K ventral view; L left view; M right view) (Scale bar: A–G, H–M, 1 mm).
FIGURE 6 in Complete mitogenome and phylogenetic significance of Metoecus javanus (Pic, 1913) (Coleoptera: Ripiphoridae) from Southwest China, with notes on morphological traits of adult and immature stages
FIGURE 6. Adult morphology of M. javanus. A–C Male habitus (A dorsal view; B ventral view; C lateral view). D–F Female habitus (D dorsal view; E ventral view; F lateral view) (Scale bar: 5 mm).
FIGURE 4 in Complete mitogenome and phylogenetic significance of Metoecus javanus (Pic, 1913) (Coleoptera: Ripiphoridae) from Southwest China, with notes on morphological traits of adult and immature stages
FIGURE 4. Phylogenetic trees of M. javanus (Nujiang) and 16 Tenebrionoidea species based on 13 mitochondrial PCGs and two rRNA genes. Inferred phylogenetic relationships among Tenebrionoidea based on nucleotide sequences of concatenated set of 13 PCGs and two rRNAs (rrnL and rrnS) using BI and ML analyses. Batocera lineolata and Massicus raddei were used as outgroups. Topology came from BI analysis, with numbers on each branch indicating Bayesian posterior probabilities (BBP)/ ML bootstrap values.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.