Find research datasets worth reusing

FIGURE 26 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 26. Diagnostic characters of Tylenchorhynchus leviterminalis from Iran. Female (A–E, H–M) and male (F, G). A: Lateral field; B–E: Part of reproductive system; F, G, I–M: Posterior end; H: Phasmid and lateral field. (a: anus; p: phasmid; s: spermatheca) (Scale-bars: A–M = 10 µm).

FIGURE 22 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 22. Diagnostic characters of Tylenchorhynchus brassicae from Iran. Female (A–O). A, B: Phasmid and lateral field; C–O: Posterior end. (a: anus; p: phasmid) (Scale-bars: A–O = 10 µm).

FIGURE 18 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 18. Diagnostic characters of Tylenchorhynchus annulatus from Iran. Female (A–L). A: Anterior end and pharyngeal region; B–D: Pharyngeal basal bulb; E–L: Head and stylet. (Scale-bars: A = 30 µm; B–L = 10 µm).

FIGURE 17 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 17. Diagnostic characters of Trophurus ussuriensis from Iran. Female (A–H, J–N) and male (I). A–D: Cross section; E–H: Part of reproductive system; I–N: Posterior end. (s: spermatheca) (Scale-bars: A–N = 10 µm).

FIGURE 13 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 13. Diagnostic characters of Paratrophurus kenanae from Iran. Female (A–C, E–H, J–M) and male (D, I). A: Anterior end and pharyngeal region; B–D: Head and stylet; E: Lateral field; F, G: Pharyngeal basal bulb; H: Vulval region; I, K–M: Posterior end; J: Phasmid and lateral field. (a: anus) (Scale-bars: A = 30 µm; B–M = 10 µm).

FIGURE 5 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 5. Diagnostic characters of Bitylenchus parvus from Iran. Female (A–K) and male (L). A: Anterior end and pharyngeal region; B: Lateral field; C–L: Head and stylet. (Scale-bars: A = 30 µm; B–L = 10 µm).

FIGURE 14 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 14. Diagnostic characters of Trophurus impar from Iran. Female (A–C, E–K) and male (D). A: Anterior end and pharyngeal region; B–D: Head and stylet; E–K: Pharyngeal basal bulb. (c: pharyngo-intestinal valve or cardia) (Scale-bars: A = 30 µm; B–K = 10 µm).

FIGURE 3 in Morphological characterization of Trichotylenchus gorganiensis n. sp. (Nematoda: Dolichodoridae) and photomicrographs of several other species of the subfamily Telotylenchinae Siddiqi, 1960

FIGURE 3. Diagnostic characters of Bitylenchus brevilineatus from Iran. Female (A–H) and male (I–L). A: Anterior end and pharyngeal region; B, C: Longitudinal ridges apart from lateral incisures at anterior end; D: Pharyngeal basal bulb; E–I: Head and stylet; J–L: Posterior end. (Scale-bars: A = 30 µm; B–L = 10 µm).

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.

opennotspecifiedOct 2019View details →

Subspecies and Distribution. P. t. trinitatis G. S. Miller, 1899 - recorded in most of Venezuela, the Guianas, and N, NE & Brazil, also on several Caribbean Is (Aruba, Margarita, Trinidad, and Tobago). P. t. phaea G. M. Allen, 1911 — restricted to Grenada I. in Emballonuridae

Subspecies and Distribution. P. t. trinitatis G. S. Miller, 1899 - recorded in most of Venezuela, the Guianas, and N, NE & Brazil, also on several Caribbean Is (Aruba, Margarita, Trinidad, and Tobago). P. t. phaea G. M. Allen, 1911 — restricted to Grenada I.

FIGURE 29 in Five new species of Coeliccia Kirby, 1890 from Vietnam (Odonata: Platycnemididae), and information on several other species of the genus

FIGURE 29. Habitus of male Coeliccia spp. [a,b] C. uenoi, [c,d] C. curua. (a) Xuan Son NP, Phu Tho Prov., 9 vii 2018; (b) Cuc Phuong NP, Ninh Binh Prov., 15 vi 2018; (c) paratype, Ba Be NP, Bac Kan Prov., 2 vii 2017; (d) Xuan Son NP, Phu Tho Prov., 23 vii 2018, photo courtesy of Mr. Denis Matthey.

FIGURE 24 in Five new species of Coeliccia Kirby, 1890 from Vietnam (Odonata: Platycnemididae), and information on several other species of the genus

FIGURE 24. Thorax and head alive in hand of Coeliccia spp. [a,b] C. caerulea, [c,d] C. coronata, [e,f] C. diomedea, [a,c,e] male, [b,d,f] female. (a) holotype in lateral view; (b) female used for description in dorsolateral view; (c) paratype in dorsolateral view, Da Lat, Lam Dong Prov., 16 iv 2016; (d) female used for description in lateral view; (e) dorsolateral view, Quang Nam Prov., along QL14, 26 ix 2015; (f) female used for description in dorsolateral view.

FIGURE 23 in Five new species of Coeliccia Kirby, 1890 from Vietnam (Odonata: Platycnemididae), and information on several other species of the genus

FIGURE 23. Holotype of Coeliccia montana Fraser, 1932. Photos courtesy of Dr. Ben Price, Natural History Museum, London. (a) thorax and head in lateral view; (b) abdomen tip and caudal appendages in lateral view; (c) thorax in dorsal view; (d) type on card with labels.

FIGURE 22 in Five new species of Coeliccia Kirby, 1890 from Vietnam (Odonata: Platycnemididae), and information on several other species of the genus

FIGURE 22. Abdomen tip of female Coeliccia spp. used for description in lateral view. (a) C. coronata; (b) C. diomedea; (c) C. hayashii; (d) C. suoitia, covered in dirt; (e) C. galbina; (f) C. caerulea, alive in hand.

FIGURE 21 in Five new species of Coeliccia Kirby, 1890 from Vietnam (Odonata: Platycnemididae), and information on several other species of the genus

FIGURE 21. Posterior pronotal lobe of Coeliccia spp. used for description in oblique dorsal view. (a) C. suoitia; (b) C. pulchella; (c) C. galbina; (d) C. caerulea.

FIGURE 19 in Five new species of Coeliccia Kirby, 1890 from Vietnam (Odonata: Platycnemididae), and information on several other species of the genus

FIGURE 19. Thorax of female Coeliccia spp. used for description in lateral view. (a) C. coronata; (b) C. diomedea; (c) C. hayashii; (d) C. galbina; (e) C. pulchella; (f) C. suoitia.

FIGURE 18 in Five new species of Coeliccia Kirby, 1890 from Vietnam (Odonata: Platycnemididae), and information on several other species of the genus

FIGURE 18. Posterior pronotal lobe of female Coeliccia spp. [a,c,e] frontal view, [b,d,f] oblique dorsal view. (a,b) C. hayashii; (c,d) C. diomedea; (e,f) C. coronata.