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Fig. 4 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?

Fig. 4. Cluster analysis based on karyotypes and genome sizes. The vertical bars on the right-hand side of the figure illustrate the closeness of samples found in different rivers and appearing in the same branch of the cluster (cf. Fig. 3). Letters A-E indicate cytotypes described in Fig. 2.

Fig. 3 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?

Fig. 3. Nuclear DNA content per individual (pg, + 95% confidence interval) among the sampled fishes. Rectangles include individuals with the same karyotype and dotted lines within rectangles subdivide samples into groupings of individuals with similar nuclear DNA contents.

Fig. 2 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?

Fig. 2. Five different cytotypes found among the samples of Synbranchus marmoratus analyzed. A – from the samples coded as PR, PR, and MS; B – from the samples coded as 2 3 2 SP and SP; C – from the sample coded as PR; D – karyotype 2 3 1

Fig. 1 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?

Fig. 1. South America map showing the major river drainages. The detail show the collecting locations. The bold dashed line in the detail indicates the limit of the last great marine incursion into South America (from the south) at approximately five million years ago (modified from Frailey, 2002). The lighter dashed lines indicate the state-specific boundaries hosting the collecting locations. MS 1,2 = rio Miranda (state of Mato Grosso do Sul; 2n=46 and 2n=42); SP 1 = rio Mogi-Guaçu (state of São Paulo; 2n=44); SP 2 = rio Tietê (state of São Paulo; 2n=42); SP 3 = rio Paraná (state of São Paulo; 2n=42); PR 1 = ribeirão Água do Caixão (state of Paraná; 2n=46); PR = rio Tibagi (state of Paraná; 2n=42); PR = rio Paraná (state of Paraná; 2n=42).

opencc-zeroNov 2022View details →

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Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analyzed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future work should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.

opencc-by-4.0Sep 2022View details →

Additional files of scTensor paper "scTensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data"

Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand-receptor (L-R) gene co-expression. However, the analytical methods are still not mature; such methods cannot detect CCIs and the related L-R pairs simultaneously or also are not appropriate to detect many-to-many CCIs. In this work, we propose scTensor, a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L-R pairs. Through extensive studies with simulated and empirical datasets, we have shown that scTensor could detect some hypergraphs, which cannot be detected by conventional methods, especially when those CCIs are many-to-many relationships.

opencc-by-4.0Dec 2022View details →

Text-fig. 2. Light micrographs of Pinus spp. cuticles prepared with the modified, gentle bleaching procedure. a: Cuticle 1, Pinus sp. 1. Nearly the entire width of the leaf has been preserved. Five parallel rows of stomata are visible. b: Cuticle 1, close-up of (a). Two guard cells are visible around each stoma. c: Cuticle 1, close-up of eight stomata. Two guard cells and eight subsidiary cells are visible around each stoma. d: Cuticle 2, Pinus sp. 2. Some folding of the cuticle occurred during preparation, but many parallel rows of stomata on both sides of a thin, central midvein are evident. e: Cuticle 2, close-up of (d). Pairs of guard cells surround each stoma. f: Cuticle 2, close-up of (e). Subsidiary and epithelial cells can be observed around the stomata. in A Modified, Step-By-Step Procedure For The Gentle Bleaching Of Delicate Fossil Leaf Cuticles

Text-fig. 2. Light micrographs of Pinus spp. cuticles prepared with the modified, gentle bleaching procedure. a: Cuticle 1, Pinus sp. 1. Nearly the entire width of the leaf has been preserved. Five parallel rows of stomata are visible. b: Cuticle 1, close-up of (a). Two guard cells are visible around each stoma. c: Cuticle 1, close-up of eight stomata. Two guard cells and eight subsidiary cells are visible around each stoma. d: Cuticle 2, Pinus sp. 2. Some folding of the cuticle occurred during preparation, but many parallel rows of stomata on both sides of a thin, central midvein are evident. e: Cuticle 2, close-up of (d). Pairs of guard cells surround each stoma. f: Cuticle 2, close-up of (e). Subsidiary and epithelial cells can be observed around the stomata.

opencc-by-4.0Dec 2022View details →

Data of publication: "Many-Body Radiative Decay in Strongly Interacting Rydberg Ensembles"

The uploaded files contain the data of the simulations presented in the figures in <a href="https://doi.org/10.1103/PhysRevLett.129.243202">https://doi.org/10.1103/PhysRevLett.129.243202</a>.

opencc-by-4.0Feb 2023View details →

Companion data of Summarizing task-based applications behavior over many nodes through progression clustering

This is the companion data for the paper *Summarizing task-based applications behavior over many nodes through progression clustering* by Lucas Leandro Nesi, Vinícius Garcia Pinto, Lucas Mello Schnorr, and Arnaud Legrand accept for publication in 31st Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (<a href="https://www.pdp2023.org/">PDP 2023</a>). The remaining of the companion is at: https://gitlab.com/lnesi/companion-pdp-2023.

Fig. 2 in One Or Two: How Many Species Of The Genus Pyrrhocorax (Passeriformes, Corvidae) Inhabited The Crimea During The Late Pleistocene?

Fig. 2. Locations of bone sites in the Emine-Bair-Khosar Сave on the section (Vremir & Ridush, 2005 modified).

Fig. 3 in One Or Two: How Many Species Of The Genus Pyrrhocorax (Passeriformes, Corvidae) Inhabited The Crimea During The Late Pleistocene?

Fig. 3. Minimal and maximal values, arithmetic mean and standard deviation (SD) for the total length of coracoideum, humerus, ulna, carpometacarpus, femur, tibiotarsus and tarsometatarsus: PP — extant Pyrrhocorax pyrrhocorax (after Tomek & Bochenski, 2000); PGg — extant Pyrrhocorax graculus graculus (after Tomek & Bochenski, 2000); PGv — Pyrrhocorax graculus vetus from the Emine-Bair-Khosar Cave (our data); n — number of specimens.

Fig. 1 in One Or Two: How Many Species Of The Genus Pyrrhocorax (Passeriformes, Corvidae) Inhabited The Crimea During The Late Pleistocene?

Fig. 1. Map showing the Late Pleistocene and Early Holocene cave sites in the Crimean Peninsula yielding the remains of choughs (Pyrrhocorax): 1 — Emine-Bair-Khosar; 2 — Kiik-Koba; 3 — Kosh-Koba; 4 — AdzhiKoba; 5 — Sjuren 1; 6 — Alymivskyi Navis; 7 — Karani-Koba; 8 — Murzak-Koba; 9 — Fat'ma-Koba.

Fig. 5 in One Or Two: How Many Species Of The Genus Pyrrhocorax (Passeriformes, Corvidae) Inhabited The Crimea During The Late Pleistocene?

Fig. 5. Humerus (A) and coracoideum (C) of Pyrrhocorax graculus vetus from Emine-Bair-Khosar compared to respective bones (B, D) of Pyrrhocorax graculus. Arrows indicate a clear edge of the impressio musculus pectoralis (1) and a large tuberculum brachiale (2).

Fig. 4 in One Or Two: How Many Species Of The Genus Pyrrhocorax (Passeriformes, Corvidae) Inhabited The Crimea During The Late Pleistocene?

Fig. 4. Differences in the length of tubular bones of Pyrrhocorax graculus vetus and extant Pyrrhocorax graculus. Data on the remains from France and extant birds follow Mourer-Chauviré (1975). Measurements are presented according to the scheme in Mourer-Chauviré (1975).

Fig. 6 in One Or Two: How Many Species Of The Genus Pyrrhocorax (Passeriformes, Corvidae) Inhabited The Crimea During The Late Pleistocene?

Fig. 6. Measurements of humerus (А) and tarsometatarsus (В) of Pyrrhocorax graculus vetus from the EmineBair-Khosar Cave (Late Pleistocene, Ukraine), Pyrrhocorax graculus from Llonin Cave (Late Pleistocene, Spain) and extant Pyrrhocorax graculus.

Figure 6 in How many metazoan species live in the world's largest mineral exploration region?

Figure 6. UpSet plot of all CCZ species (named and unnamed species combined) at regional scales (A and B) Top bars show total species shared or independent, intersecting with region in the lower panel (species independent per region correlate to a ''dot'' or shared between region to a ''dash'' connecting the regions). Side bars show total species per region. (A): all species by region, (B), all species in contract areas and reserved areas pooled versus those in APEIs pooled. See also Data S3 and S4.

Figure 5 in How many metazoan species live in the world's largest mineral exploration region?

Figure 5. Species and family diversity in the Clarion-Clipperton (A–D) Diversity estimators (solid line, rarefaction; dashed line, extrapolation): (A) Chao1 species diversity 6,233 (+/¯82 SE); N = 112,428 ind., S(obs) = 4,716; extrapolation maximum sample size: 224,858 ind; (B) Chao2 species diversity 7,620 (+/¯132 SE); N = 1,668 samples; S(obs) = 4,779, extrapolation maximum sample size, 3,336 samples. Family diversity estimators: (C) Chao1 family diversity 469 (+/¯18 SE); N = 70,597 ind., F(obs) = 406; extrapolation maximum. N: 141,194 ind.; (D) Chao2 family diversity 544 (+/¯24 SE); N = 2,179 samples; F(obs) = 423; extrapolation maximum N: 4,358 samples. See also Table 1, Figures S1–S3, and Data S3 and S4.

Figure 3 in How many metazoan species live in the world's largest mineral exploration region?

Figure 3. Fauna from the CCZ (A–J) All fauna are species described from the region and illustrating a range of phyla and size classes, (A) the sea cucumber, Psychropotes dyscrita (Clark, 1920),32 commonly known as the ''gummy squirrel'' (scale bar: 5 cm); (B) the primnoid coral Abyssoprimnoa gemina Cairns, 201539 (scale bar: 5 mm, note the rights to this image are owned by Springer Nature who have granted permission for reuse); (C) the antipatharian coral, Abyssopathes anomala Molodtsova & Opresko, 201731 (scale bar: 2 cm); and (D) the hexactinellid sponge, Sympagella clippertonae Herzog, Amon, Smith & Janussen, 2018.40 (scale bar: 1 cm). Row 2, (E) the cyclostomatid bryozoan, Pandanipora helix Grischenko, Gordon & Melnik, 201830 (scale bar: 500 Mm); (F) the isopod, Macrostylis metallicola Riehl & De Smet, 20207 (scale bar: 0.2 mm); (G) the polychaete, Neanthes goodayi Drennan, Wiklund, Rabone,Georgieva,Dahlgren & Glover, 202127; and (H) the mollusc, Ledella knudseni J. D. Taylor & Wiklund, 201735 (scale bar: 0.5 mm). Row 3, (I) the nematode, Odetenema gesarae Bezerra, Pape, Hauquier & Vanreusel, 202136 (scale bar: 100 Mm); (J) the kinorhynch, Meristoderes taro Sánchez, Pardos & Martínez Arbizu, 201933 (scale bar: 10 Mm); the loriciferan, Fafnirloricus polymetallicus Fujimoto, 202034 (scale bar: 100 Mm), and the copepod, Siphonis aurreus Mercado-Salas, Khodami & Martínez Arbizu, 201928 (scale bar: 100 Mm). All authors provided permission for reuse of plates (please see Acknowledgments).

Figure 2 in How many metazoan species live in the world's largest mineral exploration region?

Figure 2. Rates of species descriptions in the CCZ; proportion of species diversity in the CCZ that is undescribed (A) Rates of new descriptions and publications in the CCZ. Cumulative totals of new taxa (families, genera, and species combined) and new species described from the CCZ and taxonomic publications per year, over the period 1980–2022. Yearly totals of new descriptions also shown. (B) Proportion of recorded benthic metazoan diversity from the CCZ that is undescribed: named species recorded in red (both those described from the CCZ and elsewhere), unnamed species shown in blue (''unassigned'' are records not identified to phyla). Depictions of some of the new CCZ species by phyla: Annelida, Neanthes goodayi Drennan, Wiklund, Rabone, Georgieva, Dahlgren & Glover, 202127; Arthropoda, Siphonis aurreus Mercado-Salas, Khodami & Martínez Arbizu, 201928; Brachiopoda, Oceanithyris juveniformis Bitner & Zezina, 201329; Bryozoa, Pandanipora helix Grischenko, Gordon & Melnik, 201830; Cnidaria, Abyssopathes anomala Molodtsova & Opresko, 201731; Echinodermata, Psychropotes dyscrita (Clark, 1920)32; Kinorhyncha, Meristoderes taro Sánchez, Pardos & Martínez Arbizu, 201933; Loricifera, Fafnirloricus polymetallicus Fujimoto, 202034; Mollusca, Ledella knudseni J. D. Taylor & Wiklund, 201735; Nematoda, Odetenema gesarae Bezerra, Pape, Hauquier & Vanreusel, 202136; Porifera, Chaunoplectella megapora Wang, Zhang, Lu & Wang, 201837; and Tardigrada, Moebjergarctus clarionclippertonensis Bai, Wang, Zhou, Lin, Meng & Fontoura, 2020.38 See also Data S1 and S2 and Table S1.

Figure 1 in How many metazoan species live in the world's largest mineral exploration region?

Figure 1. All geolocated published records of benthic metazoa from the literature and databases Areas of Particular Environmental Interest (APEIs) and exploration mining contract areas, both active and reserved, are shown in outline. The type localities of all species described from the CCZ to date are also shown (185 in total). Background layer: the GEBCO Grid, 2022. See also Figures S4–S6, the key resources table, and supplemental information.