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Figure 4 from: Arimoto K, Arimoto H (2020) The genus Nipponodrasterius Kishii (Coleoptera, Elateridae, Agrypninae), a junior synonym of the genus Gamepenthes Fleutiaux (Coleoptera, Elateridae, Elaterinae), with review of the Japanese Gamepenthes species. ZooKeys 1004: 109-127. https://doi.org/10.3897/zookeys.1004.56201
Figure 4 Gamepenthes spp., head and prothorax AG. ornatus, male [GO003] BG. ornatus, female [GO002] CG. versipellis, male [GV006] DG. versipellis, female [GV007] EG. pictipennis, male [GP010] FG. yoshidai, male [GY001] A–D dorsal view E, F lateral view.
Figure 2 from: Arimoto K, Arimoto H (2020) The genus Nipponodrasterius Kishii (Coleoptera, Elateridae, Agrypninae), a junior synonym of the genus Gamepenthes Fleutiaux (Coleoptera, Elateridae, Elaterinae), with review of the Japanese Gamepenthes species. ZooKeys 1004: 109-127. https://doi.org/10.3897/zookeys.1004.56201
Figure 2 Gamepenthes spp., color variation AG. pictipennis, male [GP003] BG. pictipennis, male [GP012] CG. pictipennis, male, holotype of Nipponodrasterius alpicolaDG. pictipennis, female [GP010] EG. versipellis, female [GV007].
Figure 6 from: Arimoto K, Arimoto H (2020) The genus Nipponodrasterius Kishii (Coleoptera, Elateridae, Agrypninae), a junior synonym of the genus Gamepenthes Fleutiaux (Coleoptera, Elateridae, Elaterinae), with review of the Japanese Gamepenthes species. ZooKeys 1004: 109-127. https://doi.org/10.3897/zookeys.1004.56201
Figure 6 Gamepenthes pictipennis, male, apex of left paramere of aedeagus A, B [GP006] C, D [GP007] E, F [GP009] G, H [GP012] I, J holotype of Nipponodrasterius alpicolaA, C, E, G, I dorsal side B, D, F, H, J ventral side.
Figure 1 from: Arimoto K, Arimoto H (2020) The genus Nipponodrasterius Kishii (Coleoptera, Elateridae, Agrypninae), a junior synonym of the genus Gamepenthes Fleutiaux (Coleoptera, Elateridae, Elaterinae), with review of the Japanese Gamepenthes species. ZooKeys 1004: 109-127. https://doi.org/10.3897/zookeys.1004.56201
Figure 1 Gamepenthes spp., male, habitus, dorsal view AG. ornatus [GO003] BG. pictipennis [GP010] CG. similis [GS003] DG. versipellis [GV006] EG. yoshidai [GY001].
FIGURE 5 in Rediscovering the poorly-known Neotropical katydid Hyperomerus crassipes Redtenbacher, 1891 (Orthoptera: Tettigoniidae: Conocephalinae: Agraeciini) description of male reveals the synonymic status of Uchuca Giglio-Tos, 1898
FIGURE 5. Map with the records of all Hyperomerus Redtenbacher species.
FIGURES 82 in Notes on the genus Astenus Dejean, 1833 in the Mediterranean and adjacent regions. A new species from Turkey, seven new synonyms, and additional records (Coleoptera: Staphylinidae: Paederinae)
FIGURES 82. Distributions of Astenus henrii sp. n. (open circles).
Data from: Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase
While synonymous mutations were long thought to be without phenotypic consequences, there is growing evidence they can affect gene expression, protein folding and ultimately the fitness of an organism. In only a few cases have the mechanisms by which synonymous mutations affect the phenotype been elucidated. We previously identified 48 mutations in TEM-1 β-lactamase that increased resistance of Escherichia coli to cefotaxime, 10 of which were synonymous. To better understand the molecular mechanisms underlying the beneficial effect of synonymous mutations, we made a series of measurements for a panel containing the 10 synonymous together with 10 non-synonymous mutations as a reference. Whereas messenger levels were unaffected, we found that total and functional TEM protein levels were higher for 5 out of 10 synonymous mutations. These observations suggest that some of these mutations act on translation or a downstream process. Similar effects were observed for some small-benefit non-synonymous mutations, suggesting a similar causal mechanism. For the synonymous mutations, we found that the cost of resistance scales with TEM protein levels. A resistance landscape for four synonymous mutations revealed strong epistasis: None of the combinations of mutations exceeded the resistance of the largest-effect mutation and there were synthetically neutral combinations. By considering combined effects of these mutations, we could infer that functional TEM protein level is a multi-dimensional phenotype. These results suggest that synonymous mutations may have beneficial effects by increasing the expression of an enzyme with low substrate activity, which may be realized via multiple, yet unknown, post-transcriptional mechanisms.
Data from: How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework
First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.
Data from: Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions
Plants are the primary producers of the terrestrial ecosystems that dominate much of the natural environment. Occurring approximately 480 MYA (Sanderson 2003; Kenrick et. al. 2012), the evolutionary transition of plants from an aquatic to a terrestrial environment was accompanied by several major developmental innovations. The freshwater charophyte ancestors of land plants have a haplobiontic life cycle with a single haploid multicellular stage, whereas land plants, which include the bryophytes (liverworts, hornworts, and mosses) and tracheophytes (also called vascular plants, namely, lycopods, ferns, and seed plants), exhibit a marked alternation of generations with a diplobiontic life-cycle with both haploid and diploid multicellular stages and where the embryo remains attached to, and is nourished by, the gametophyte (Haig 2008). The interjection of a multicellular diploid phase into the land plant life cycle was an important adaptation that enabled long-distance dispersal via mitotic spores where water-borne male gametes have restricted motility in dry terrestrial environments. Despite the similarity among land-plant life-cycles, they differ in one significant aspect: in the three bryophyte groups, the haploid gametophytic stage is the dominant vegetative stage, whereas in vascular plants the diploid sporophyte dominates. A common assumption, and one implied by the tradition of referring to bryophytes as "lower plants" - in contrast to the "higher plants", the tracheophytes - is that the bryophytes and their life-cycle are primitive (Kato and Akiyama 2005). However, without a strong phylogenetic hypothesis of land-plant relationships, it is not clear which (if either) of the gametophyte or sporophyte was the dominant ancestral vegetative state present in the earliest land plants (Renzaglia et al. 2007; Qiu et al. 2012). Early land plants have a relatively poor fossil record with few intermediate forms (Kenrick and Crane 1997; Wellman et al. 2003; Clarke et al. 2011), so most of the evidence for early land plant evolution has been based upon the patterns of morphological change that are implied by phylogenetic trees of relationships among extant land plant and algal groups. In this context, several recent studies based on large molecular data sets have converged upon a phylogenetic solution to land plant origins wherein tracheophytes are derived from bryophyte ancestors (Karol et al. 2001; Qiu et al. 2006; Gao et al. 2010; Karol et al. 2010; Chang and Graham 2011). In this hypothesis, the three bryophyte groups, namely liverworts, mosses, and hornworts, diverged sequentially and form a paraphyletic group with the hornworts sister to the tracheophytes. This phylogeny supports an intuitively elegant evolutionary trajectory whereby plants increased in morphological complexity from single-celled algae to seed plants via bryophyte intermediates (Karol et al. 2001; McCourt et al. 2004). Specifically, it implies that the gametophyte-dominant bryophyte life-cycle was ancestral among land plants and that the complex modular growth form of the vascular plant sporophyte evolved from the simplistic bryophyte sporophyte that consists only of a single growth module (Kato and Akiyama 2005; Barthélémy and Caraglio 2007).
Data from: Gene expression levels are correlated with synonymous codon usage, amino acid composition and gene architecture in the red flour beetle, Tribolium castaneum
Gene expression levels correlate with multiple aspects of gene sequence and gene structure in phylogenetically diverse taxa suggesting an important role of gene expression levels in the evolution of protein-coding genes. Here we present results of a genome-wide study of the influence of gene expression on synonymous codon usage, amino acid composition and gene structure in the red flour beetle, Tribolium castaneum. Consistent with the action of translational selection, we find that synonymous codon usage bias increases with gene expression. However, the correspondence between tRNA gene copy number and optimal codons is weak. At the amino acid level, translational selection is suggested by the positive correlation between tRNA gene numbers and amino acid usage which is stronger for highly expressed genes. In addition, there is a clear trend for increased use of metabolically cheaper, less complex, amino acids as gene expression increases. tRNA gene numbers also correlate negatively with amino acid size/complexity score indicating the coupling between translational selection and selection to minimize the use of large/complex amino acids. Interestingly, the correlation between tRNA gene numbers and amino acid size/complexity score appears to be widespread given our analyses of 10 additional genomes and might be explained by selection against negative consequences of protein misfolding. At the level of gene structure, three major trends are detected 1) CDS length increases across low and intermediate expression levels but decreases in highly expressed genes; 2) the average intron size shows the opposite trend, first decreasing with expression, followed by a slight increase in highly expressed genes and 3) intron density remains nearly constant across all expression levels. These changes in gene architecture are only in partial agreement with selection favoring reduced cost of biosynthesis.
Data from: Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates
Synonymous codon usage (SCU) patterns are shaped by a balance between mutation, drift, and natural selection. To date, detection of translational selection in vertebrates has proven to be a challenging task, obscured by small long-term effective population sizes in larger animals and the existence of isochores in some species. The consensus is that, in such species, natural selection is either completely ineffective at overcoming mutational pressures and genetic drift or perhaps is effective but so weak that it is not detectable. The aim of this research is to understand the interplay between mutation, selection, and genetic drift in vertebrates. We observe that although variation in mutational bias is undoubtedly the dominant force influencing codon usage, translational selection acts as a weak additional factor influencing synonymous codon usage. These observations indicate that translational selection is a widespread phenomenon in vertebrates and is not limited to a few species.
Data from: Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment
Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this hypothesis. In particular, the extent of synonymous variation across genes in that experiment does not reflect the variation observed in natural isolates of E. coli. Instead, gene length alone predicts with high accuracy the prevalence of synonymous changes in the experimental populations. We hypothesize that patterns of synonymous variation in natural E. coli populations are instead caused by differences across genomic regions in their effective population size that, in turn, reflect different histories of recombination, horizontal gene transfer, selection, and population structure.
FIGURE 5 in Phyllomedusa itacolomi Caramaschi, Cruz & Feio, 2006, a junior synonym of Phyllomedusa ayeaye (B. Lutz, 1966) (Hylidae, Phyllomedusinae)
FIGURE 5. Phyllomedusa ayeaye holotype (MNRJ 3722), dorsal (A) and ventral (B) views.
FIGURE 2 in Long-legged flies (Diptera: Dolichopodidae) in the collection of the Natal Museum: A review of C. H. Curran's types, new synonyms, and new combinations
FIGURE 2. Acropsilus vorax (Curran), hypopygium, left lateral view. Scale bar: 0.1 mm
FIGURE 1 in Long-legged flies (Diptera: Dolichopodidae) in the collection of the Natal Museum: A review of C. H. Curran's types, new synonyms, and new combinations
FIGURE 1. Acropsilus vorax (Curran), wing. Scale bar: 0.5 mm.
FIGURE 11 in Apaturinae (Lepidoptera: Nymphalidae) from the Korean Peninsula: Synonymic Lists and Keys to Tribes, Genera and Species
FIGURE 11. Diagram of the distributional ranges of the Hestina persimilis species complex.
FIGURE 2 in Redescription of Lophiodes infrabrunneus Smith and Radcliffe, 1912, a senior synonym of L. abdituspinus Ni, Wu and Li, 1990 (Lophiiformes: Lophiidae)
FIGURE 2. Esca of Lophiodes infrabrunneus, MNHN 2055–3434, 258 mm SL. Bar = 1 mm.
FIGURES 33 in Two new species and two new synonyms of Systropus Wiedemann, 1820 from Palaearctic China (Diptera: Bombyliidae)
FIGURES 33. Systropus sp. (male and female), mating (Beijing, Yanqing, Sihai).
FIGURE 1 in Taxonomy of Anterastes and related genera: a new synonym and a new species of Anterastes
FIGURE 1. Map showing localities and haplotypes used in phylogenetic analyses.
FIGURE 2. Pseudonus squamiceps. USNM 227191 in Revision of the bathyal fish genus Pseudonus (Teleostei, Bythitidae); P. s q u a m i c e p s a senior synonym of P. platycephalus, new to Australian waters
FIGURE 2. Pseudonus squamiceps. USNM 227191, SL 108, male. Lateral view.
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.