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Figure 8 from: Zhang Z, Pan D, Hao X, Sun H (2020) Two new species of freshwater crabs of the genera Eosamon Yeo & Ng, 2007 and Indochinamon Yeo & Ng, 2007 (Crustacea, Brachyura, Potamidae) from southern Yunnan, China. ZooKeys 980: 1-21. https://doi.org/10.3897/zookeys.980.52186
Figure 8 Indochinamon malipoense sp. nov. holotype, male, 53.0 × 42.7 mm, NNU 180505 A left third maxilliped B left G1 (ventral view) C left G1 (dorsal view) D left G2 E sterno-pleonal cavity with right G1 in situF left G1 terminal segment (ventral view). Scale bars: 1.0 mm.
Figure 11 from: Zhang Z, Pan D, Hao X, Sun H (2020) Two new species of freshwater crabs of the genera Eosamon Yeo & Ng, 2007 and Indochinamon Yeo & Ng, 2007 (Crustacea, Brachyura, Potamidae) from southern Yunnan, China. ZooKeys 980: 1-21. https://doi.org/10.3897/zookeys.980.52186
Figure 11 Color in life of Indochinamon malipoense sp. nov. A brownish-red male B yellowish-cyan male. Photographs by Hongying Sun, 5 April 2018, Tianbao Town, Yunnan Province, China.
Figure 10 from: Zhang Z, Pan D, Hao X, Sun H (2020) Two new species of freshwater crabs of the genera Eosamon Yeo & Ng, 2007 and Indochinamon Yeo & Ng, 2007 (Crustacea, Brachyura, Potamidae) from southern Yunnan, China. ZooKeys 980: 1-21. https://doi.org/10.3897/zookeys.980.52186
Figure 10 The ventral view of left G1 AIndochinamon malipoense sp. nov. holotype, male, 53.0 × 42.7 mm, NNU 180505 BIndochinamon tannanti male, 43.3 × 34.9 mm, NNU 180801 CIndochinamon changpoense male, 44.1 × 35.6 mm, NNU 161701. Scale bars: 1.0 mm.
Figure 4 from: Xiang C-L, Pan H-L, Min D-Z, Zhang D-G, Zhao F, Liu B, Li B (2021) Rediscovery of Mazus lanceifolius reveals a new genus and a new species in Mazaceae. PhytoKeys 171: 1-24. https://doi.org/10.3897/phytokeys.171.61926
Figure 4 Maximum Likelihood phylogram of Mazaceae as inferred from analysis of nrITS. Support values ≥ 50% BS or 0.90 PP are displayed near the branches following the order ML-BS/BI-PP.
Figure 3 from: Xiang C-L, Pan H-L, Min D-Z, Zhang D-G, Zhao F, Liu B, Li B (2021) Rediscovery of Mazus lanceifolius reveals a new genus and a new species in Mazaceae. PhytoKeys 171: 1-24. https://doi.org/10.3897/phytokeys.171.61926
Figure 3 Maximum Likelihood phylogram of Mazaceae as inferred from analysis of combined dataset of matK, rbcL, rps16 and trnL-trnF. Support values ≥ 50% BS or 0.90 PP are displayed near the branches following the order ML-BS/BI-PP.
Figure 2 from: Xiang C-L, Pan H-L, Min D-Z, Zhang D-G, Zhao F, Liu B, Li B (2021) Rediscovery of Mazus lanceifolius reveals a new genus and a new species in Mazaceae. PhytoKeys 171: 1-24. https://doi.org/10.3897/phytokeys.171.61926
Figure 2 Mazus fruticosusA voucher of "Mazus lanceifolius" sampled in Deng et al. (2019), deposited at JIU (the herbarium of Jishou University, Hu'nan, China) B habit and habitat C leaves D flower in frontal view, showing morphology of its lower lips E flower in frontal view, showing morphology of its upper lips F flowers in lateral view. Scale bars: 2 cm (C); 0.5 cm (D, E, F).
Figure 1 from: Xiang C-L, Pan H-L, Min D-Z, Zhang D-G, Zhao F, Liu B, Li B (2021) Rediscovery of Mazus lanceifolius reveals a new genus and a new species in Mazaceae. PhytoKeys 171: 1-24. https://doi.org/10.3897/phytokeys.171.61926
Figure 1 Puchiumazus lanceifolius (≡ Mazus lanceifolius) A lectotype deposited at K (A. Henry 5837, barcode K001079356) B habit C stem, showing the obtuse ribs D leaves E inflorescence F flower in lateral review G young fruits. Scale bars: 5 cm (B); 0.5 cm (C, F, G); 2 cm (D); 1 cm (E).
Supplementary material 1 from: Xiang C-L, Pan H-L, Min D-Z, Zhang D-G, Zhao F, Liu B, Li B (2021) Rediscovery of Mazus lanceifolius reveals a new genus and a new species in Mazaceae. PhytoKeys 171: 1-24. https://doi.org/10.3897/phytokeys.171.61926
Figures S1, S2
Figure 5 from: Xiang C-L, Pan H-L, Min D-Z, Zhang D-G, Zhao F, Liu B, Li B (2021) Rediscovery of Mazus lanceifolius reveals a new genus and a new species in Mazaceae. PhytoKeys 171: 1-24. https://doi.org/10.3897/phytokeys.171.61926
Figure 5 Morphological comparisons of the four genera of MazaceaeAPuchiumazus lanceifoliusBDodartia orientalisCLancea tibeticaDMazus stachydifoliusA1, B1, C1, D1 habits A2, B2, C2, D2 flowers A3, B3, C3, D3 fruits.
Data from: Delay of gratification is associated with white matter connectivity in the dorsal prefrontal cortex: a diffusion tensor imaging study in chimpanzees (Pan troglodytes)
Individual variability in delay of gratification (DG) is associated with a number of important outcomes in both non-human and human primates. Using diffusion tensor imaging (DTI), this study describes the relationship between probabilistic estimates of white matter tracts projecting from the caudate to the prefrontal cortex (PFC) and DG abilities in a sample of 49 captive chimpanzees (Pan troglodytes). After accounting for time between collection of DTI scans and DG measurement, age and sex, higher white matter connectivity between the caudate and right dorsal PFC was found to be significantly associated with the acquisition (i.e. training phase) but not the maintenance of DG abilities. No other associations were found to be significant. The integrity of white matter connectivity between regions of the striatum and the PFC appear to be associated with inhibitory control in chimpanzees, with perturbations on this circuit potentially leading to a variety of maladaptive outcomes. Additionally, results have potential translational implications for understanding the pathophysiology of a number of psychiatric and clinical outcomes in humans.
Data from: Conspicuousness, color resemblance, and toxicity in geographically diverging mimicry: the pan-Amazonian frog Allobates femoralis
Predation risk is allegedly reduced in Batesian and Müllerian mimics, because their coloration resembles the conspicuous coloration of unpalatable prey. The efficacy of mimicry is thought to be affected by variation in the unpalatability of prey, the conspicuousness of the signals, and the visual system of predators that see them. Many frog species exhibit small colorful patches contrasting against an otherwise dark body. By measuring toxicity and color reflectance in a geographically variable frog species and the syntopic toxic species, we tested whether unpalatability was correlated with between-species color resemblance and whether resemblance was highest for the most conspicuous components of coloration pattern. Heterospecific resemblance in colorful patches was highest between species at the same locality but unrelated to concomitant variation in toxicity. Surprisingly, resemblance was lower for the conspicuous femoral patches compared to the inconspicuous dorsum. By building visual models, we further tested whether resemblance was affected by the visual system of model predators. As predicted, mimic-model resemblance was higher under the visual system of simulated predators compared to no visual system at all. Our results indicate that femoral patches are aposematic signals and support a role of mimicry in driving phenotypic divergence or mimetic radiation between localities.
Data from: Insights into the maize pan-genome and pan-transcriptome
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
Data from: The early history of Annonaceae (Magnoliales) in Southeast Asia suggests floristic exchange between India and Pan-Indochina by the late Oligocene
The collision between India and Eurasia in the mid‐Palaeogene facilitated terrestrial floristic exchange. However, due to the complexity of this geological event and scarcity of fossil record, the plant migration patterns between the two plates are still highly debated. In this study, we focus on the Oligocene floristic exchange between India and Pan‐Indochina mainly based on a carpological study of Annonaceae, an emblematic family unique in its pantropical distribution and frugivore‐based dispersal strategy. A new seed species, Anonaspermum orientalis sp. nov., is described from the upper Oligocene Yongning Formation of Guangxi, southern China. The species represents the earliest known occurrence of this family in Pan‐Indochina. The specimens are characterized by ovate–elliptic seed shape, thicker seed testa, two‐lobed organization, lamelliform rumination and an obvious cone‐like plug. The palaeobiogeographical reconstruction of Annonaceae indicates that the most parsimonious dispersal scenario for the annonaceous taxon from the late Oligocene of China is the Out‐of‐India route, in parallel with other plant genera inferred to have migrated between India and Pan‐Indochina during that period.
Data from: Group and kin recognition via olfactory cues in chimpanzees (Pan troglodytes)
Primates were traditionally thought to have a reduced sense of smell. Although there is now evidence that olfaction plays a greater role in primate social life than previously assumed, research on the sense of smell in non-human apes is scarce. Chimpanzees sniff the ground and vegetation on boundary patrols, but the function of this behaviour is unclear. Since chimpanzees are highly territorial and can kill individuals that do not belong to their own community, sniffing might function to gather information about conspecifics, particularly concerning group membership and kinship. To investigate whether chimpanzees recognize group members and kin via olfactory cues, we conducted behavioural bioassays on two groups of chimpanzees at Leipzig Zoo. In a pilot study, we found that chimpanzees responded more strongly to urine than to faeces or body odour. We then presented urine from group members, outgroup individuals and an unscented control in aerated boxes using a simultaneous discrimination task. The first behaviour after a chimpanzee first approached a box was related to olfaction (sniffing, nose within 20 cm, licking) in 83% of cases, highlighting the importance of olfaction as a general investigation mechanism in this species. Chimpanzees sniffed significantly longer at urine stimuli than the control and significantly longer at odours from outgroup individuals than those from group members. Furthermore, the duration of sniffing was positively correlated with relatedness. Our results suggest that chimpanzees use olfactory cues to obtain information about social relationships and fill a gap in our understanding of primate chemical communication.
Data from: Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite
Background: Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient. Results: Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil). Conclusions: Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.
Data from: Genetic basis in motor skill and hand preference for tool use in chimpanzees (Pan troglodytes)
Chimpanzees are well known for their tool using abilities. Numerous studies have documented variability in tool use among chimpanzees and the role that social learning and other factors play in their development. There are also findings on hand use in both captive and wild chimpanzees; however, less understood are the potential roles of genetic and non-genetic mechanisms in determining individual differences in tool use skill and laterality. Here, we examined heritability in tool use skill and handedness for a probing task in a sample of 243 captive chimpanzees. Quantitative genetic analysis, based on the extant pedigrees, showed that overall both tool use skill and handedness were significantly heritable. Significant heritability in motor skill was evident in two genetically distinct populations of apes, and between two cohorts that received different early social rearing experiences. We further found that motor skill decreased with age and that males were more commonly left-handed than females. Collectively, these data suggest that though non-genetic factors do influence tool use performance and handedness in chimpanzees, genetic factors also play a significant role, as has been reported in humans.
FIGURES 20–21 in Paroster baylyi sp. n., P. ursulae sp. n. (Col. Dytiscidae, Hydroporinae) and the water beetle diversity of pan-gnammas on isolated granite outcrops in the Mallee of south-western Australia
FIGURES 20–21. Paroster baylyi sp. n., ventral side of 20) protarsus and 21) mesotarsus.
Analysis of extensively tested pan assay interference compounds
<p>A set of 270 PAINS (Pan Assay Interference Compounds) were detected as substructures in extensively assayed PubChem compounds. For each PAINS substructure, the total number of compounds are reported that were tested in at least 100 primary assays or at least 50 confirmatory assays. In addition, the number of active compounds, mean hit rates, and number of consistently inactive compounds are reported separately for primary and confirmatory assays.</p>
Supplementary material 1 from: Ács É, Bíró T, Boros E, Dobosy P, Duleba M, Földi A, Kiss KT, Levkov Z, Orgoványi P, Szén OP, Trábert Z, Vadkerti E, Grigorszky I (2023) Halamphora taxa in Hungarian soda pans and shallow soda lakes detected via metabarcoding and microscopic analyses. Metabarcoding and Metagenomics 7: e111679. https://doi.org/10.3897/mbmg.7.111679
Relative abundances of Halamphora species based on microscopy and metabarcodin
Supplementary material 3 from: Ács É, Bíró T, Boros E, Dobosy P, Duleba M, Földi A, Kiss KT, Levkov Z, Orgoványi P, Szén OP, Trábert Z, Vadkerti E, Grigorszky I (2023) Halamphora taxa in Hungarian soda pans and shallow soda lakes detected via metabarcoding and microscopic analyses. Metabarcoding and Metagenomics 7: e111679. https://doi.org/10.3897/mbmg.7.111679
Supplementary Alignment 1
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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)
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.