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Figure S3 in Large-scale snake genome analyses provide insights into vertebrate development
Figure S3. Snake-specific genome structural variations (SSSVs), snake-diverged conserved non-coding elements (SD-CNEs that were diverged in snakes but were still conserved in the outgroup) (SD-CNEs), and orthologous genes used for evolutionary analysis, related to Figure 3 and STAR Methods (A) SSSVs distribution in different genome regions. (B) Genomic reads coverage of the snake-specific lost gene GHRL across four lizards (green anole [Acar], Anan's rock agama [Lsac], Komodo dragon [Vkom],and viviparous lizard [Zviv]), and 14 newly sequenced snakes. (C) Z-score cut off of SD-CNEs. (D) The enriched MGI terms that related to snake phenotypes for genes with SD-CNE (adjusted p value <0.05). SD-CNEs (dots) are located around the transcription start site of the genes enriched in eye, eyelid, ear, lung, mandible, maxillary, sternum, and tooth development-related terms. (E) Enriched GO terms (adjusted p value <0.05) for the newly evolved coding genes in snakes. Those related to dietary excess, protein digestion, and olfactory receptor activity were colored in red, blue, and brown, respectively. (F) Enriched GO terms (adjusted p value <0.05) for snake-specific coding genes that were lost. Red, blue, orange, and green were used to indicate the terms involved in vision, lens development, appetite, and bile acid biosynthetic process, respectively. (G) SSSV deletion in the potential regulatory region of RP1. (H) Counts of orthologous genes used for evolutionary analysis among 27 selected species.
Figure 3 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 3. Genetic basis of skeletal system evolution and organ adaptation in snakes PSGs, REGs, WGCNA hub genes, lost genes, SSSV-related genes, newly evolved genes, and SD-CNE-associated genes are marked in different colors and are represented by rectangles. (A) Renewal of genomic elements contributing to snake skull development and digestion. Related genes are shown in their corresponding regions. (B) The evolution of genomic elements has potentially facilitated the evolution of the elongated body plan of snakes. (C) The evolution of genes related to lung development and function. The heatmap shows the expression levels of WGCNA hub genes, PSGs, and SSSV-related genes in green anole (Acar), keeled slug snake (Pber), and many-banded krait (Bmul) (The ''_numbers'' represents the different copies of a multi-copy gene). (D) Whole-body X-ray images and relative lengths of the fourth forelimb phalanx and third hindlimb phalanx of wild and PTCH1-mutated mice (eight samples per group, the significance is indicated as *p <0.05). Mean ± SD is shown by error bar. See also Figure S4 and Table S3.
Figure S1 in Large-scale snake genome analyses provide insights into vertebrate development
Figure S1. Phylogenetic and divergent time tree of snakes, related to Figure 1 (A) Phylogenetic tree distributions of selected snake species, topology inferred from a previous study.173 (B) Maximum likelihood (ML) phylogenetic tree inferred from the 31-taxon whole-genome alignments. Ultrafast bootstraps were repeated 3,000 times, with NNI UFBoot tree optimization and SH-like approximate likelihood ratio test (SH-aLRT) performed. SH-aLRT support rate/ultrafast bootstrap support rate is indicated at each node. (C) Inferred ML phylogenetic tree using orthologous genes. 1,980 1:1 orthologous genes were concatenated to a super gene sequence for constructing the ML phylogenetic tree using IQ-TREE. 10,000 ultrafast bootstraps were carried out and the two support rates were marked at each node. (D) ML phylogenetic tree inferred from 4d sites. 4d sites were extracted from the orthologous genes and taken as input for IQ-TREE to infer the ML phylogenetic tree. The two supports were computed by 10,000 ultrafast bootstraps and SH-aLRT. (E) Inferred ML phylogenetic tree of conserved non-coding elements (CNEs). All CNEs were identified and concatenated into a single sequence for the ML phylogenetic tree inferred using 5,000 ultrafast bootstraps and SH-aLRT. (F) Coalescent phylogenetic tree inferred from 51,302 1-kb orthologous genomic segments using ASTRAL-III. (G) Coalescent phylogenetic tree inferred from 1,980 1:1 orthologous genes using ASTRAL-III. The poorly supported nodes are indicated in red. (H) DicoVista gene tree topologies frequency analysis. The frequency of three topologies (t1–t3) is shown, and the red is the main topology. The divergence time (million years ago [mya]) of the species is estimated using r8s and the incongruent clades are in red. (I) Divergence time of the 31 species. r8s estimated divergence time using the whole-genome alignments.The estimated divergence time (million years ago [mya]) is labeled on each node and 6 calibrating nodes used are marked. (J) MCMCTree estimated divergence time of the 31 species using 4d sites. Six calibrating nodes used are marked and the estimated divergence time represented in million years is labeled.
Figure 5 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 5. Evolution of blind and infrared-sensitive snakes (A) Specialized traits of blind snakes. (B) Gene regression underlies eye degeneration in blind snakes. Lost genes are shown in green. Heatmap showing the significant down-regulation of the expression of genes in blind snake eyes (QN, quantile normalized). (C) BSD-CNE-associated genes enriched in odontogenesis and bone-development-related GO terms. (D) Amino acids sequences alignment (left) and enzymatic activity (right) of CHIA. The amino acids in red are positively selected sites in blind snakes. The error bar represents mean ± SD of enzymatic activity. The enzymatic activity is significantly higher in Diard's blind snake (Student's t-test p value = 8.78e-09). (E) Infrared sensing-related genes in infrared-sensitive snakes. PSGs, REGs, and variation-shared genes are indicated in purple, blue, and red, respectively. Average expression levels (represented by FPKM) of these genes in seven tissues of the brown-spotted pitviper are shown. See also Figure S5 and Tables S4 and S5.
Figure 4 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 4. Genome features associated with snake-specific sense organ evolution, highlighting PSGs, REGs, newly evolved genes, SD-CNEassociated genes, lost genes, and SSSV-associated genes (A) Lost and highly expressed genes in snake eyes. Diagram of the snake eye showing lost genes in blue. Heatmap of highly expressed genes (QN, quantile normalized). (B) Diagram of the snake inner ear. Twelve SD-CNE-associated genes and four SSSV-associated genes are involved in ear development. Expression levels (scaled fragments per kilobase per million mapped reads [FPKM]) of sound perception-related PSGs and REGs in 10 keeled slug snake (Pber) tissues are shown in circles. Circle size is positively correlated to the expression level. (C) Diagram of the taste transduction process. Solid lines indicate direct interactions, and dotted lines indicate indirect interactions. See also Table S3.
Figure 1 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 1. Phylogeny of snakes Maximum-likelihood phylogenetic tree inferred from whole-genome sequences of 31 species. Divergence times of all nodes were estimated by r8s with whole-genome sequences using six calibration points (Figures S1I and S1J). All genomes generated in this study are in red. Maps were taken from those in a previous study.24
Figure S5 in Large-scale snake genome analyses provide insights into vertebrate development
Figure S5. Genome evolution of snake sensory system, related to Figures 4 and 5 (A) Expression patterns of genes associated with eye development in human embryos at different embryonic stages (4.7–8 weeks post conception [wpc]) and red cornsnake embryos at 10, 30, and 50 days post oviposition (dpo). (B) KMT2C specific amino acids residue lost in snakes and its associated snakes divergent CNE (SD-CNE). The black line portrays gene structure with blue blocks representing CDSs and the numbers indicate the exact positions on the European glass lizard reference genome. Three segments of snake-specific amino acid residue loss are manifested by internal numbers ''4002–4004,'' ''2110–2112,'' and ''1983–1987.'' One SD-CNE located at 30 regulate region of KMT2C is marked by a red block. (C) Alignment of SSSV that inserted into the 5 kb upstream of PDZD7 transcription start site. This SSSV conveys a new EBF1 binding site with a regulatory potential (RP) score: 0.78. (D) Taste transduction involved genes were expressed in tongue and brain of three snakes (plumbeous water snake [Hplu], keeled slug snake [Pber], and Asian vine snake [Apra]). The numbers in cells indicate the scaled FPKM values. (E) Comparison of eye structures between Diard's blind snake and Asian vine snake, keeled slug snake. The magnifications were marked as ''*×'' at the bottomright corner of each histological sections. (F) GOChord plot (produced by GOplot package) of blind snake divergent CNEs involved coding gene-enriched GO terms (p value <0.05). Left half of GOChord displayed genes of different GO terms and the right showed the GO term descriptions. Each gene was linked to a GO term by the colored bands. (G) REVIGO clusters of significantly overrepresented (p value <0.01) GO terms for blind snake REGs. (H) Expression levels of TRPV4 and TRPA1 in seven tissues of brown spotted pitviper. (I) Genome locations of pitviper diverged conserved non-coding elements (PVD-CNEs), and the infrared-sensitive python and boa divergent conserved non-coding elements (ISPBD-CNEs) in PMP22 and NFIB.
Dataset for large-scale self-organisation in dry turbulent atmospheres
<p>Datasets for all figures in "Large-scale self-organisation in dry turbulent atmospheres". The data comes from a simulation of the Boussinesq equations in a triply periodic domain of vertical height H and horizontal dimension L = 32H, in the presence of gravity, a stable mean density gradient, and solid body rotation in the vertical direction. Datasets are in TXT format except for two dimensional spectra, which are stored in NetCDF format.</p>
Accounting for behaviour in fine-scale habitat selection: a case study highlighting methodological intricacies
<p>Data for the article “Accounting for behaviour in fine-scale habitat selection: a case study highlighting methodological intricacies”</p> <p>By LT Beumer, NMS Schmidt, J Pohle, J Signer, M Chimienti, JP Desforges, LH Hansen, SH Pedersen, DA Rudd, M Stelvig, FM van Beest</p> <p>The data set includes five files: A readme file describing the data files, and four data files accompanying the above publication.</p> <p>For further queries please contact Larissa T. Beumer: ltbeumer@gmail.com</p> <p> </p>
Summer litter decomposition is moderated by scale-dependent microenvironmental variation in tundra ecosystems
<p>Tundra soils are one of the world's largest organic carbon stores, yet this carbon is vulnerable to accelerated decomposition as climate warming progresses. The landscape-scale controls of litter decomposition are poorly understood in tundra ecosystems, which hinders our understanding of the global carbon cycle. We examined the extent to which the thermal sum of surface air temperature, soil moisture and permafrost thaw depth influenced litter mass loss and decomposition rates (<em>k</em>), and at which spatial thresholds an environmental variable becomes a reliable predictor of decomposition, using the Tea Bag Index protocol across a heterogeneous tundra landscape on Qikiqtaruk - Herschel Island, Yukon, Canada. We found greater green tea litter mass loss and faster decomposition rates (<em>k</em>) in wetter areas within the landscape, and to a lesser extent in areas with deeper permafrost active layer thickness and higher surface thermal sums. We also found higher decomposition rates (<em>k</em>) on north-facing relative to south-facing aspects at microsites that were wetter rather than warmer. Spatially heterogeneous belowground conditions (soil moisture and active layer depth) explained variation in decomposition metrics at local scales (< 50 m<sup>2</sup>) better than thermal sum. Surprisingly, there was no strong control of elevation or slope on litter decomposition. Our results reveal that there is considerable scale dependency in the environmental controls of tundra litter decomposition, with moisture playing a greater role than the thermal sum at < 50 m<sup>2</sup> scales. Our findings highlight the importance and complexity of microenvironmental controls on litter decomposition in estimates of carbon cycling in a rapidly warming tundra biome.</p>
A pilot-scale partial nitritation-anammox process for treatment of anaerobic sludge digester effluent
<p>In most of the wastewater treatment operational practices with anaerobic sludge digestion, the ammonia rich centrate (>100mg/L) is recycled back to the main treatment line which increases the NH<sub>4</sub><sup>+</sup>-N loading to the treatment by as much as 10–30% (Fan 2020). The partial nitritation-anammox (PN/A) process is a biological process that provides an environmentally, economically, and technically sound solution to treat anaerobic sludge digester effluent.</p> <p>The application of the anammox process in the wastewater system could result in higher nitrogen removal in the digester effluent as there have been related research conducted at lab-scale using synthetic wastewater (Awolusi et al., 2020). However, due to the process sensitivity to operating conditions, there is a need to optimize at pilot scale to emerge as an efficient process, especially in the South African environment as this technology has a possibility to be promoted as an alternative and/or additional bioprocess to be applied in full scale throughout the country.</p>
D. viride occupancy in Compiegne forest at two spatial scales with temporal survey at fine scale, used in Percel et al. study
<p>This repository contains two datasets in text format, to be imported in codes related to Percel et al. study of D. viride colonization process within Compiegne forest. The dataset "Data_Dviride.2017_AVCHESS_d14.txt" contains the data regarding the occupancy turnover between two surveys in three stands of the forest. The dataset "Data_Dviride.2018_foret.txt" contains the data regarding the coarse grained spatial distribution of D. viride at the forest scale.</p> <p>This repository also contains a basic script used to compute statistics reported in Table 1 of Percel et al. article.</p>
DNA metabarcoding captures different macroinvertebrate biodiversity than morphological identification approaches across a continental scale
<p><span>DNA-based aquatic biomonitoring methods show promise to provide rapid, standardized, and efficient biodiversity assessment to supplement and in some cases replace current morphology-based approaches that are often less efficient and can produce inconsistent results. Despite this potential, broad-scale adoption of DNA-based approaches by end-users remains limited, and studies on how these two approaches differ in detecting aquatic biodiversity across large spatial scales are lacking. Here, we present a comparison of DNA metabarcoding and morphological identification, leveraging national-scale, open-source, ecological datasets from the National Ecological Observatory Network (NEON). Across 24 wadeable streams in North America with 179 paired sample comparisons, we found that DNA metabarcoding detected twice as many unique taxa than morphological identification overall. The two approaches showed poor congruence in detecting the same taxa, averaging 59%, 35%, and 23% of shared taxa detected at the order, family, and genus levels, respectively. Importantly, the two approaches detected different proportions of indicator taxa like %EPT and %Chironomidae. DNA metabarcoding detected far fewer Chironomid and Trichopteran taxa than morphological identification, but more Ephemeropteran and Plecopteran taxa, a result likely due to primer choice. Overall, our results showed that DNA metabarcoding and morphological identification detected different benthic macroinvertebrate communities. Despite these differences, our results relating watershed-scale and local-scale abiotic variables to invertebrate community structure from both methods produced similar results. This suggests that DNA and morphological approaches are both suitable for use in basic and applied ecological research. Further refinement of DNA metabarcoding protocols, primers, and reference libraries–as well as more standardized, large-scale comparative studies–may improve our understanding of taxonomic agreement and data linkages between DNA metabarcoding and morphological approaches. </span></p>
Fig. 2. A in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran
Fig. 2. A GIS map of IgM seroprevalence of Toxoplasma gondii (Nicolle et Manceaux, 1908) in different provinces of Iran, during 2015–2020 (ND – no data).
Fig. 3. A in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran
Fig. 3. A GIS map of IgG seroprevalence of Toxoplasma gondii (Nicolle et Manceaux, 1908) in different provinces of Iran, during 2015–2020.
Fig. 1 in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran
Fig. 1. The seroprevalence plot of Toxoplasma gondii (Nicolle et Manceaux, 1908) in Iran in different age groups (m-month; y-year).
Рис. 6–11. ГенитаΛьные структуры самцов роΔа Celypha. 6 – C. laminaria sp. n.; 7 – C. capreolana; 8 – C. rurestrana; 9 – C. anatoliana; 10 – C. confictana; 11 – C. striana. 6 – генитаΛии (Λевая ваΛьва не изображена); 7–11 – ваΛьвы. Масштабная Λинейка 1 мм. Figs 6–11. Male genital structure of the genus Celypha. 6 – C. laminaria sp. n.; 7 – C. capreolana; 8 – C. rurestrana; 9 – C. anatoliana; 10 – C. confictana; 11 – C. striana. 6 – genitalia (left valve is not shown); 7–11 – valves. Scale bar 1 mm. in Two new species of leaf-rollers (Lepidoptera: Tortricidae) from the East Caucasus
Рис. 6–11. ГенитаΛьные структуры самцов роΔа Celypha. 6 – C. laminaria sp. n.; 7 – C. capreolana; 8 – C. rurestrana; 9 – C. anatoliana; 10 – C. confictana; 11 – C. striana. 6 – генитаΛии (Λевая ваΛьва не изображена); 7–11 – ваΛьвы. Масштабная Λинейка 1 мм. Figs 6–11. Male genital structure of the genus Celypha. 6 – C. laminaria sp. n.; 7 – C. capreolana; 8 – C. rurestrana; 9 – C. anatoliana; 10 – C. confictana; 11 – C. striana. 6 – genitalia (left valve is not shown); 7–11 – valves. Scale bar 1 mm.
Рис. 1–5. Новые виΔы Λистоверток, самцы, общий виΔ и генитаΛии. 1, 3–5 – Phtheochroa tabasarana sp. n.; 2 – Celypha laminaria sp. n. 1–2 – гоΛотип, габитус; 3–5 – генитаΛии: 3 – эΔеагус, 4 – генитаΛии, эΔеагус извΛечен, 5 – генитаΛии, ΛатераΛьно. Масштабная Λинейка ΔΛя рисунков 3–5 – 1 мм. Figs 1–5. New species of leaf-rollers, males, general view and genitalia. 1, 3–5 – Phtheochroa tabasarana sp. n.; 2 – Celypha laminaria sp. n. 1–2 – holotype, habitus; 3–5 – genitalia: 3 – aedeagus, 4 – genitalia, aedeagus extracted, 5 – genitalia laterally. Scale bar for Figs 3–5 – 1 mm. in Two new species of leaf-rollers (Lepidoptera: Tortricidae) from the East Caucasus
Рис. 1–5. Новые виΔы Λистоверток, самцы, общий виΔ и генитаΛии. 1, 3–5 – Phtheochroa tabasarana sp. n.; 2 – Celypha laminaria sp. n. 1–2 – гоΛотип, габитус; 3–5 – генитаΛии: 3 – эΔеагус, 4 – генитаΛии, эΔеагус извΛечен, 5 – генитаΛии, ΛатераΛьно. Масштабная Λинейка ΔΛя рисунков 3–5 – 1 мм. Figs 1–5. New species of leaf-rollers, males, general view and genitalia. 1, 3–5 – Phtheochroa tabasarana sp. n.; 2 – Celypha laminaria sp. n. 1–2 – holotype, habitus; 3–5 – genitalia: 3 – aedeagus, 4 – genitalia, aedeagus extracted, 5 – genitalia laterally. Scale bar for Figs 3–5 – 1 mm.
Рис. 11–16. Эпигина Haplodrassus alexeevi sp. n. (11–12) и H. umbratilis (13–14 – из БеΛгороΔской обΛасти; 15–16 – из Ростовской обΛасти). Масштабные Λинейки 0.2 мм. 11, 13, 15 – вентраΛьно; 12, 14, 16 – ΔорсаΛьно. Figs 11–16. Epigyne of Haplodrassus alexeevi sp. n. (11–12) and H. umbratilis (13–14 – from Belgorod Region; 15–16 – from Rostov Region). Scale bar 0.2 mm. 11, 13, 15 – ventral view; 12, 14, 16 – dorsal view. in A new species of spiders of the genus Haplodrassus Chamberlin, 1922 (Aranei: Gnaphosidae) from the Northern Pre-Caspian area
Рис. 11–16. Эпигина Haplodrassus alexeevi sp. n. (11–12) и H. umbratilis (13–14 – из БеΛгороΔской обΛасти; 15–16 – из Ростовской обΛасти). Масштабные Λинейки 0.2 мм. 11, 13, 15 – вентраΛьно; 12, 14, 16 – ΔорсаΛьно. Figs 11–16. Epigyne of Haplodrassus alexeevi sp. n. (11–12) and H. umbratilis (13–14 – from Belgorod Region; 15–16 – from Rostov Region). Scale bar 0.2 mm. 11, 13, 15 – ventral view; 12, 14, 16 – dorsal view.
Рис. 2–6. ÀетаΛи строения пауков семейства Gnaphosidae. 2 – Gnaphosa cumensis; 3 – G. cf.cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – паΛьпа самца, вентраΛьно; 5 – эпигина, вентраΛьно; 6 – эпигина, ΑорсаΛьно. Масштабные Λинейки 0.2 мм. Figs 2–6. Family Gnaphosidae, details of structure. 2 – Gnaphosa cumensis; 3 – G. cf. cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – male palp, ventral view; 5 – epigyne, ventral view; 6 – epigyne, dorsal view. Scale bars 0.2 mm. in New data on spiders (Aranei) of the Naurzum State Natural Reserve (Kostanay Region, Kazakhstan)
Рис. 2–6. ÀетаΛи строения пауков семейства Gnaphosidae. 2 – Gnaphosa cumensis; 3 – G. cf.cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – паΛьпа самца, вентраΛьно; 5 – эпигина, вентраΛьно; 6 – эпигина, ΑорсаΛьно. Масштабные Λинейки 0.2 мм. Figs 2–6. Family Gnaphosidae, details of structure. 2 – Gnaphosa cumensis; 3 – G. cf. cumensis; 4 – Haplodrassus rugosus; 5–6 – Zelotes fuscus. 2–4 – male palp, ventral view; 5 – epigyne, ventral view; 6 – epigyne, dorsal view. Scale bars 0.2 mm.
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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.