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FIGURE 4 in The purportedly Indo-Australian gecko species Cnemaspis timoriensis (Duméril & Bibron, 1836) is actually the first named species of the neotropical genus Gonatodes Fitzinger, 1843 (Squamata: Gekkonidae)
FIGURE 4. Body views of the holotype of Gymnodactylus timoriensis Duméril & Bibron, 1836, specimen number MNHN 0810. The specimen is shown in dorsal (A), ventral (B), and lateral (C) views. A close-up of a lateral portion of the trunk (D) is shown to illustrate the faint, but recognizable patterning. Figure created by Mark O'Shea from photos by Lee Grismer (C) and Hinrich Kaiser (A, B, D).
FIGURE 2. Excerpt from the 1864 in The purportedly Indo-Australian gecko species Cnemaspis timoriensis (Duméril & Bibron, 1836) is actually the first named species of the neotropical genus Gonatodes Fitzinger, 1843 (Squamata: Gekkonidae)
FIGURE 2. Excerpt from the 1864 catalogue in the MNHN showing that the holotype of Gymnodactylus timoriensis was initially listed with the older collection number 1412, and only subsequently reassigned as 810 (column at right). The threedigit number was subsequently adjusted to a four-digit number by adding a leading zero in order to comply with regulations when the numbering system was modernized, resulting in the accepted number 0810 for the specimen. This entry also identifies Timor as the collecting locality and Gaudichaud as the collector. It is perhaps curious that the next listed specimen was also collected by Gaudichaud at Coquimbo [Chile] and originally listed under the name Gymnodactylus gaudichaudii—a generic designation later changed in handwriting to Gonatodes [though misspelled as Gonotades]. Photo by Ivan Ineich.
FIGURE 1. Historical vignettes from L in The purportedly Indo-Australian gecko species Cnemaspis timoriensis (Duméril & Bibron, 1836) is actually the first named species of the neotropical genus Gonatodes Fitzinger, 1843 (Squamata: Gekkonidae)
FIGURE 1. Historical vignettes from L'Uranie's voyage around the world (1817–1820). (A) L'Uranie at anchor near Pulau Lawak, Raja Ampat Archipelago, Indonesia in late 1818. Shown is part of a panoramic engraving by Claude Niquet (1770– 1831) made from a drawing the painter Ambroise Louis Garneray (1783–1857) created based on a sketch by Alphonse Pellion (1796–1868). Garneray and Pellion were crew members on the voyage. (B–E) Key members of the round-the-world expedition of L'Uranie and La Physicienne, during which the holotype of Gymnodactylus timoriensis was collected. (B) Charles Gaudichaud-Beaupré (undated), in a painting by an unknown artist. (C) Louis de Freycinet (ca. 1812), in an engraving by an unknown artist. (D) Jean René Constant Quoy (ca. 1850), painted by an unknown painter during his appointment as inspector general of the French Naval Bureau of Medicine and Surgery. (E) Joseph Paul Gaimard (ca. 1839) in a lithograph by the painter and lithographer Louis-Émile Lassalle (1811–1871).
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively.
Box 4 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Box 4 | Classifying SARS-CoV-2 The species demarcation threshold (also known as demarcation limit) in the family Coronaviridae is defined by viruses whose PPD(s) may cross the inter-species demarcation PPD threshold (threshold 'violators'). Due to their minute share of ~10–4 of the to- tal number of all intra- and inter-species PPDs, these violators may not even be visually recognized in a conventional diagonal plot clus- tering viruses on a species basis (panel a of the figure in Box 4). Furthermore, they do not involve any virus of the species Severe acute respiratory syndrome-related coronavirus, as is evident from the analysis of maximal intraspecies PPDs of 2,505 viruses of all 49 coronavirus species (of which 39 are established and 10 are pending or tentative) (panel b of the figure in Box 4) and PDs of 256 viruses of this species (panel c of the figure in Box 4). Thus, the genomic variation of the known viruses of the species Severe acute respiratory syndrome-related coronavirus is smaller compared to that of other comparably well-sampled species—for example, those prototyped by MERS-CoV, human coronavirus OC43 (HCoV-OC43) and in- fectious bronchitis virus (IBV) (panel b of the figure in Box 4)—and this species is well separated from other known coronavirus species in the sequence space. Both of these characteristics facilitate the un- ambiguous assignment of SARS-CoV-2 to this species. Intra-species PDs of SARS-CoV-2 belong to the top 25% of this species and also include the largest PD between SARS-CoV-2 and an African bat virus isolate (SARSr-CoV_BtKY72)56 (panel c of the figure in Box 4), representing two basal lineages within the species Severe acute respiratory syndrome-related coronavirus that constitute very few known viruses (Fig. 2b,c). These relationships stand in contrast to the shallow branching of the most populous lineage of this species, which includes all the human SARS-CoV isolates collected during the 2002–2003 outbreak and the closely related bat viruses of Asian origin identified in the search for the potential zoonotic source of that epidemic57. This clade structure is susceptible to homologous recombination, which is common in this species44,58,59; to formalize clade definition, it must be revisited after the sampling of viruses representing the deep branches has improved sufficiently. The current sampling defines a very small median PD for human SARS-CoVs, which is approximately 15 times smaller than the median PD determined for SARS-CoV-2 (0.16% versus 2.6%; panel c of the figure in Box 4). This small median PD of human SARS-CoVs also dominates the species- wide PD distribution (0.25%; panel c of the figure in Box 4). Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
Fig. 2 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Fig. 2 | Phylogeny of coronaviruses. a, Concatenated multiple sequence alignments (MSAs) of the protein domain combination44 used for phylogenetic and DEmARC analyses of the family Coronaviridae. Shown are the locations of the replicative domains conserved in the ordert Nidovirales in relation to several other ORF1a/b-encoded domains and other major ORFs in the SARS-CoV genome. 5d, 5 domains: nsp5A-3CLpro, two beta-barrel domains of the 3C-like protease; nsp12-NiRAN, nidovirus RdRp-associated nucleotidyltransferase; nsp12-RdRp, RNA-dependent RNA polymerase; nsp13-HEL1 core, superfamily 1 helicase with upstream Zn-binding domain (nsp13-ZBD); nt, nucleotide. b, The maximum-likelihood tree of SARS-CoV was reconstructed by IQ-TREE v.1.6.1 (ref. 45) using 83 sequences with the best fitting evolutionary model. Subsequently, the tree was purged from the most similar sequences and midpoint-rooted. Branch support was estimated using the Shimodaira–Hasegawa (SH)-like approximate likelihood ratio test with 1,000 replicates. GenBank IDs for all viruses except four are shown; SARS-CoV, AY274119.3; SARS-CoV-2, MN908947.3; SARSr-CoV_BtKY72, KY352407.1; SARS-CoV_PC4-227, AY613950.1. c, Shown is an IQ-TREE maximum-likelihood tree of single virus representatives of thirteen species and five representatives of the species Severe acute respiratory syndrome-related coronavirus of the genus Betacoronavirus. The tree is rooted with HCoV-NL63 and HCoV-229E, representing two species of the genus Alphacoronavirus. Purple text highlights zoonotic viruses with varying pathogenicity in humans; orange text highlights common respiratory viruses that circulate in humans. Asterisks indicate two coronavirus species whose demarcations and names are pending approval from the ICTV and, thus, these names are not italicized.
FIGURE 1 in A new species of Cypris (Crustacea: Ostracoda) from the Iberian Peninsula and the Balearic Islands, with comments on the first ostracod named using the Linnean system
FIGURE 1. Bottom part of page 344 and top part of p. 345 of Linnaeus' (1746) Fauna Svecica, including the description of an ostracod of the genus Monoculus with code 1185.
FIGURES 1–6 in New species, a new name, and new synonyms for Chimarra spp. (Insecta: Trichoptera: Philopotamidae) of India
FIGURES 1–6. Chimarra oliveri sp. nov., male genitalia. 1, left lateral; 2, dorsal; 3, tergum VIII dorsal; 4, right inferior appendage, ventral; 5, phallus, left lateral; 6, phallus, ventral.
Supplementary material 1 from: Parapar J, Capa M, Nygren A, Moreira J (2020) To name but a few: descriptions of five new species of Terebellides (Annelida, Trichobranchidae) from the North East Atlantic. ZooKeys 992: 1-58. https://doi.org/10.3897/zookeys.992.55977
Table S1. Locality and collecting data, museum registration numbers and references to figures of Terebellides specimens
Supplementary material 2 from: Parapar J, Capa M, Nygren A, Moreira J (2020) To name but a few: descriptions of five new species of Terebellides (Annelida, Trichobranchidae) from the North East Atlantic. ZooKeys 992: 1-58. https://doi.org/10.3897/zookeys.992.55977
Table S2. List of COI sequences considered in present study (Group A), museum vouchers and GenBank accession numbers
Figs 1–6 in Alleviating the taxonomic impediment of DNA barcoding and setting a bad precedent: names for ten species of 'Astraptes fulgerator' (Lepidoptera: Hesperiidae: Eudaminae) with DNA-based diagnoses
Figs 1–6. Intraspecific variation in final instar larval Astraptes spp. 1–3. A. fruticibus 03-SRNP-14690, 05-SRNP-45170, 03-SRNP-30304; 4–6. A. inflatio 02-SRNP-32206, 05-SRNP-96, 02-SRNP-24519; images from Janzen & Hallwachs (2009), which the authors have indicated are in the public domain (Janzen et al., 2009).
PLATE 7. Species not from New Zealand. Neocyclotidae. A. Cyclotus charmian Hutton, 1883 in Catalogue of New Zealand land, freshwater and estuarine molluscan taxa named by Frederick Wollaston Hutton between 1879 and 1904
PLATE 7. Species not from New Zealand. Neocyclotidae. A. Cyclotus charmian Hutton, 1883, lectotype, CMNZ M48. Rhytididae. B. Amphidoxa lavinia Hutton, 1883, syntype, NMNZ M.1754; C. Helix sinclairi Pfeiffer, 1846, Tasmania, lectotype, NHMUK 1842.11.2.23. Microcystinae. D. Trochomorpha hermia Hutton, 1883, lectotype, CMNZ M353; E. Helix campbellii Gray, 1834, Philip Island, syntype, NHMUK 1982239. Scale bars 5 mm.
Data from: The importance of naming cryptic species and the conservation of endemic subterranean amphipods
Molecular taxonomy often uncovers cryptic species, reminding us that taxonomic incompleteness is even more severe than previous thought. The importance of cryptic species for conservation is poorly understood. Although some cryptic species may be seriously threatened or otherwise important, they are rarely included in conservation programs as most of them remain undescribed. We analysed the importance of cryptic species in conservation by scrutinizing the South European cryptic complex of the subterranean amphipod Niphargus stygius sensu lato. Using uni- and multilocus delineation methods we show that it consists of 15 parapatric and sympatric species, which we describe using molecular diagnoses. The new species are not mere "taxonomic inflation" as they originate from several distinct branches within the genus and coexist with no evidence of lineage sharing. They are as evolutionarily distinct as average nominal species of the same genus. Ignoring these cryptic species will underestimate the number of subterranean endemics in Slovenia by 12 and in Croatia by four species, although alpha diversity of single caves remains unchanged. The new taxonomy renders national Red Lists largely obsolete, as they list mostly large-ranged species but omit critically endangered single-site endemics. Formal naming of cryptic species is critical for them to be included in conservation policies and faunal listings.
FIGURES 30–35 in Descriptions of three larvae of Osmylus species from Japan (Neuroptera: Osmylidae), with a proposed naming system for the larval sclerites
FIGURES 30–35. Ninth abdominal segment of Osmylus spp., dorsal (30, 32, 34) and ventral (31, 33, 35) views. 30–31) O. (O.) hyalinatus; 32–33) O. (O.) pryeri; 34–35) O. (P.) tessellatus.
FIGURES 15–17 in Descriptions of three larvae of Osmylus species from Japan (Neuroptera: Osmylidae), with a proposed naming system for the larval sclerites
FIGURES 15–17. Head of Osmylus spp., dorsal view. 15) O. (O.) hyalinatus; 16) O. (O.) pryeri; 17) O. (P.) tessellatus.
FIGURES 9–10 in Descriptions of three larvae of Osmylus species from Japan (Neuroptera: Osmylidae), with a proposed naming system for the larval sclerites
FIGURES 9–10. Cervix and thorax of Osmylus (O.) hyalinatus, showing the sclerites. 9) Left in dorsal view, right in ventral view; 10) lateral view.
FIGURES 27–29 in Descriptions of three larvae of Osmylus species from Japan (Neuroptera: Osmylidae), with a proposed naming system for the larval sclerites
FIGURES 27–29. Seventh abdominal segments of Osmylus spp., ventral view. 27) O. (O.) hyalinatus; 28) O. (O.) pryeri; 29) O. (P.) tessellatus.
FIGURES 39–44 in Descriptions of three larvae of Osmylus species from Japan (Neuroptera: Osmylidae), with a proposed naming system for the larval sclerites
FIGURES 39–44. Habitats of larvae of Osmylus spp. 39) Small stream; 40) O. (O.) hyalinatus in wooden pocket; 41) small stream; 42) O. (O.) pryeri in wooden pocket; 43) canyon stream; 44) O. (P.) tessellatus in moss on rock. Locality: 39) Takaosan, Tokyo; 40) Komeno-machi, Ehime Pref.; 41–42) Saragamine, Ehime Pref.; 43–44) Omogokei, Ehime Pref. Photo by S. Matsuno.
FIGURES 24–26 in Descriptions of three larvae of Osmylus species from Japan (Neuroptera: Osmylidae), with a proposed naming system for the larval sclerites
FIGURES 24–26. First to 8th abdominal segments of Osmylus spp., dorsal view. 24) O. (O.) hyalinatus; 25) O. (O.) pryeri; 26) O. (P.) tessellatus.
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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
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.