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64 results for “Pangolin”
Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia
<p>Reducing the illegal wildlife trade requires an understanding of its origins. Here we present a genomic approach for tracing confiscated scales from the world's most trafficked mammal, the white-bellied pangolin (<em>Phataginus tricuspis</em>), to their geographic origins. Analyzing scales seized in Hong Kong SAR, China from 2012–2018 revealed intense poaching along Cameroon's southern border. Poaching pressures shifted over time from West to Central Africa. Using data from seizures representing nearly one million African pangolins, we identified Nigeria as a significant hub for trafficking, where scales are amassed and shipped to Vietnam and Hong Kong SAR, China, with final transit to markets in Guangdong and Guangxi, China. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.</p>
Analysis of pangolin metagenomic datasets reveals significant contamination, raising concerns for pangolin CoV host attribution
<p>Supplementary Figures, Information and Data to accompany:</p> <p>Analysis of pangolin metagenomic datasets reveals significant contamination, raising concerns for pangolin CoV host attribution<br> <em>Adrian Jones, Daoyu Zhang, Yuri Deigin and Steven C. Quay</em></p> <p>https://arxiv.org/abs/2108.08163</p> <p> </p> <p> </p>
Fig. 5 in Identification of Amblyomma javanense and detection of tick-borne Ehrlichia spp. in confiscated Malayan Pangolins
Fig. 5. Phylogenetic tree based on the 16S rRNA (A) and gltA (B) of pathogens found in ticks from confiscated pangolins. Analyses were conducted by using MEGA software version 6.0 with the Maximum Likelihood algorithm. Bootstrap values were calculated with 1000 replicates. The number on each branch indicates bootstrap values. Red triangles: sequences of Ehrlichia spp. obtained in this study. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Identification of Amblyomma javanense and detection of tick-borne Ehrlichia spp. in confiscated Malayan Pangolins
Fig. 1. Morphologic identification of ticks on the surface of confiscated Malayan pangolins. Tick on Malayan pangolin surface (A). Dorsa view, ventral view and typical feature details of male (B) and female (C) Amblyomma javanense ticks collected from confiscated Malayan pangolins. Black bar, 2 mm.
Fig. 4 in Identification of Amblyomma javanense and detection of tick-borne Ehrlichia spp. in confiscated Malayan Pangolins
Fig. 4. The histopathological examination of Malayan pangolins tissue slide using hematoxylin-eosin (HE) staining. A: Heart, myocardial cells were necrotic, and the myoplasm at the necrosis was dissolved into vacuoles, some of which were lipid droplet vacuoles. B: Liver, sinus hepaticus was dilatate with blood stasis. C: Spleen, splenic cord widened and lymphocytes multiplied. D: Lung, alveoli collapse, inflammatory cell infiltration and capillaries congestion. E: Kidney, the renal tubules were transparent, with capillaries congested and cystic spaces dilated in the glomeruli. F: Lymph nodes, medullary blood vessels were dilated and congested, and there were many macrophages in the medullary cord. G: Salivary glands, epithelial cells of mucosa necrosis and submucosa congestion. H: Bladder, mucosa folds inward when empty. A-E, 400 X; F–H, 200X.
Fig. 3 in Identification of Amblyomma javanense and detection of tick-borne Ehrlichia spp. in confiscated Malayan Pangolins
Fig. 3. Gross pathological lesions of dead Malayan pangolins after autopsy. A: Pale, even purple, superficial mucosa around the nose and mouth. B: Congestion and hemorrhage observed in the lung. C: Myocardial edema, pericardium effusion and ventricular congestion in the heart. D: Kidney congestion. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Identification of Amblyomma javanense and detection of tick-borne Ehrlichia spp. in confiscated Malayan Pangolins
Fig. 2. Phylogenetic tree based on the 16S rRNA (A) and ITS2 (B) of ticks from confiscated Malayan pangolins. Analyses were conducted using MEGA 6.0 with the Maximum Likelihood algorithm. Bootstrap values were calculated with 1000 replicates. The number on each branch indicates bootstrap value. Red triangles and red lines: sequences of ticks obtained in this study. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins
<p><strong>Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins</strong><br> </p> <p>Rémi Allio<sup>1,2,§,</sup>*, Sophie Teullet<sup>1,§</sup>, Dave Lutgen<sup>1,3,4,§</sup>, Amandine Magdeleine<sup>1</sup>, Rachid Koual<sup>1</sup>, Marie-Ka Tilak<sup>1</sup>, Benoit de Thoisy<sup>5,6</sup>, Christopher A. Emerling<sup>1,7</sup>, Tristan Lefébure<sup>8</sup>, and Frédéric Delsuc<sup>1,</sup>*</p> <p><br><sup>1</sup>ISEM, Univ. Montpellier, CNRS, IRD, Montpellier, France</p> <p><sup>2</sup>CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France </p> <p><sup>3</sup>Institute of Ecology and Evolution, University of Bern, Bern, Switzerland</p> <p><sup>4</sup>Swiss ornithological Institute, Sempach, Switzerland</p> <p><sup>5</sup>Institut Pasteur de la Guyane, Cayenne, French Guiana, France</p> <p><sup>6</sup>Kwata NGO, Cayenne, French Guiana, France</p> <p><sup>7</sup>Biology Department, Reedley College, Reedley, CA, USA</p> <p><sup>8</sup>Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France</p> <p><sup>§</sup>Equal contribution</p> <p> </p> <p>*Correspondence</p> <p>Rémi Allio: remi.allio@inrae.fr</p> <p>Frédéric Delsuc: frederic.delsuc@umontpellier.fr</p> <p> </p> <p><strong>Abstract</strong></p> <p>Ant-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, hypertrophied salivary glands producing large amounts of saliva, and powerful claws for ripping open ant and termite nests. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase acidic gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites. While the southern tamandua (Tamandua tetradactyla) harbors four functional CHIA paralogs (CHIA1-4), Asian pangolins (Manis spp.) have only one functional paralog (CHIA5). Here, we performed a comparative transcriptomic analysis of salivary glands in 33 placental species, including 16 novel transcriptomes from ant-eating species and close relatives. Our results suggest that salivary glands play an important role in adaptation to an insect-based diet, as expression of different CHIA paralogs is observed in insectivorous species. Furthermore, convergently-evolved pangolins and anteaters express different chitinases in their digestive tracts. In the Malayan pangolin, CHIA5 is overexpressed in all major digestive organs, whereas in the southern tamandua, all four functional paralogs are expressed, at very high levels for CHIA1 and CHIA2 in the pancreas, and for CHIA3 and CHIA4 in the salivary glands, stomach, liver, and pancreas. Overall, our results demonstrate that divergent molecular mechanisms within the chitinase acidic gene family underlie convergent adaptation to the ant-eating diet in pangolins and anteaters. This study highlights the role of historical contingency and molecular tinkering of the chitin-digestive enzyme toolkit in this classic example of convergent evolution.</p> <p> </p> <p><strong><em>Figures & Tables</em></strong></p> <p><strong>Figure 1</strong>: Dated placental mammal phylogeny including representative species of the four major clades (Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria) for which CHIA gene repertoires have been previously characterized. Numbers between brackets represent percentages of invertebrates included in the diet with myrmecophagous species indicated by an ant silhouette. Ψ symbols indicate CHIA pseudogenes as determined in previous studies (Emerling et al. 2018; Janiak et al. 2018; Wang et al. 2020<a href="https://www.zotero.org/google-docs/?IVkGtZ">)</a>. Ancestral CHIA gene repertoires for Placentalia and Ferae (Pholidota + Carnivora) as inferred by Emerling et al. (2018) are presented. The chronogram was extracted from <a href="http://www.timetree.org">www.timetree.org</a> <a href="https://www.zotero.org/google-docs/?Vr0bO1">(Kumar et al. 2022)</a>. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 2</strong>: A. Mammalian chitinase-like gene family tree reconstructed using a maximum likelihood gene-tree/species-tree reconciliation approach on protein sequences. The nine chitinase paralogs are indicated on the outer circle. Scale bar represents the mean number of amino acid substitutions per site. B. Synteny analysis of the nine chitinase paralogs in humans (Homo sapiens), tarsier (Carlito syrichta), nine-banded armadillo (Dasypus novemcinctus) and the two main focal convergent ant-eating species: the southern tamandua (Tamandua tetradactyla) and the Malayan pangolin (Manis javanica). Assembly names and accession numbers are indicated below species names. Boxes represent different contigs with their most upstream and downstream BLAST hit positions to chitinase genes (colored arrows). Genes PIFO and DENND2D (grey arrows) are not chitinase paralogs but were used in the synteny analysis. Arrow direction indicates gene transcription direction as inferred in Genomicus v100.01 <a href="https://www.zotero.org/google-docs/?qjXWzo">(Nguyen et al. 2022)</a> for genes located on short contigs. Ψ symbols indicate pseudogenes as determined in <a href="https://www.zotero.org/google-docs/?IVkGtZ">Emerling et al. (2018)</a>. Genes with non significant BLAST hits were not represented and are probably not functional or absent. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 3</strong>: Comparison of predicted ancestral protein sequences of the nine mammalian chitinase paralogs. A. Conserved amino acid residues of the canonical chitinolytic domain active site (DXXDXDXE). Arrows indicate paralogs in which changes occurred in the active site. B. Summary of the evolution of chitinase paralogs functionality. C. Conserved cysteine residues of the chitin-binding domain. The arrow indicates OVGP1 in which the last four cysteines have been replaced.</p> <p><strong>Figure 4</strong>: Expression of the nine chitinase paralogs in 40 mammalian salivary gland transcriptomes. The 33 species are presented in their phylogenetic context covering the four major placental clades: Afrotheria (AFR), Xenarthra (XEN), Euarchontoglires (EUA), and Laurasiatheria (LAU). The chronogram was extracted from <a href="http://www.timetree.org">www.timetree.org</a> <a href="https://www.zotero.org/google-docs/?Vr0bO1">(Kumar et al. 2022)</a>. Non-functional pseudogenes are only indicated for the three focal species (in bold) using a Ψ symbol: nine-banded armadillo (Dasypus novemcinctus), southern tamandua (Tamandua tetradactyla) and Malayan pangolin (Manis javanica). Expression level is represented as log10 (Normalized Counts + 1). Asterisks indicate the 16 new transcriptomes produced in this study. Myrmecophagous and insectivorous species are indicated by ant and beetle silhouettes, respectively. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 5</strong>: Expression of the nine chitinase paralogs in 72 transcriptomes from different organs of the three focal species: the nine-banded armadillo (Dasypus novemcinctus), the Malayan pangolin (Manis javanica), and the southern tamandua (Tamandua tetradactyla). Non-functional pseudogenes are represented by a Ψ symbol and hatched background. Boxes indicate organs of the digestive tract. Expression level is represented as log10 (Normalized Counts + 1). Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 6</strong>: Summary figure presenting the evolution and expression of chitinase acidic (CHIA) paralogous genes in the convergently evolved Malayan pangolin (Manis javanica) and southern tamandua (Tamandua tetradactyla) in their phylogenetic context. Reconstructed CHIA gene repertoires are indicated for the two myrmecophagous species and for the most recent common ancestor (MRCA) of placentals, pangolins+carnivores (Ferae) and anteaters+sloths (Pilosa). Non-functional pseudogenes are represented by the Ψ symbol and dashed line contour. Organ icons indicate expression of the corresponding gene in different digestive organs. SG: Salivary glands; S: Stomach; T: Tongue; P: Pancreas; L: Liver; I: Intestine. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a> and <a href="https://www.vecteezy.com/">www.vecteezy.com</a>.</p> <p> </p> <p><em><strong>Supplementary Materials</strong></em></p> <p><strong>Table S1: </strong>Detailed information on the tissues sequenced or retrieved from public databases for the project.</p> <p><strong>Table S2</strong>: BUSCO v5 scores of all transcriptomes based on a dataset of 9,226 single-copy orthologs conserved in over 90% of mammalian species <a href="https://www.zotero.org/google-docs/?lrFE5h">(Manni et al. 2021)</a>. </p> <p> </p> <p><strong><em>Zenodo supplementary files</em></strong></p> <p><strong>CHIAs_OG_tree-RAxML_EPA</strong><strong>.zip </strong>contains CHIA sequences (obtained from the OrthoFinder orthogroups and the sequences used to infer the chitinase genes evolution) and the corresponding ML tree. </p> <p><strong>Chitinases_ancestral_sequences.zip </strong>contains the ancestral chitinase sequence reconstructions, the associated posterior probabilities, and the alignment of the ancestral sequences inferred by RAxML-NG. </p> <p><strong>Chitinases_gene_tree.zip</strong> contains input and output files corresponding to the chitinase gene tree presented in Figure 2: </p> <p>- mammalina_species_tree_input_Generax.newick = species tree used for the reconciliation with Generax</p> <p>- chitinase_gene_alignment_renamed_input_Generax.fasta = chitinase gene alignment with the sequence names renamed for Generax</p> <p>- chitinase_gene_alignment_not_renamed.fasta = chitinase gene alignment with the original sequence names (for information)</p> <p>- chitinases_gene_tree_sequences_renamed_input_Generax.newick = chitinase gene tree inferred with RAxML-NG and reconciled using the TreeRecs algorithm to find the optimal rooting scheme; this tree was used for Generax</p> <p>- reconciled_chitinase_genes_tree_output_Generax.newick = reconciled chitinase gene tree inferred by Generax and presented in Figure 2</p> <p><strong>Chitinases_expression.zip </strong>contains all orthogroup gene expressions plus chitinase gene expressions.</p> <p><strong>Kallisto_abundances.zip</strong> contains the abundances estimated with kallisto for each organ of each species<em>.</em></p> <p><strong>Supplementary table figure 2B - BLAST</strong> <strong>results.xlsx</strong> contains BLAST results supporting sequence inferences. </p> <p><strong>Transcriptome_assemblies.tar.gz</strong> contains the transcriptome assemblies obtained for each organ and species with Trinity.</p>
Habitat occupancy of the critically endangered Chinese pangolin (Manis pentadactyla) under human disturbance in an urban environment: Implications for conservation
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Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia
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Supp. Info. for Further analysis of metagenomic datasets containing GD and GX pangolin CoVs indicates widespread contamination, undermining pangolin host attribution
<p>Supplemanty Information for <strong>Further analysis of metagenomic datasets containing GD and GX pangolin CoVs indicates widespread contamination, undermining pangolin host attribution</strong></p> <p>Files:</p> <p>Supp_Info_1_PRJNA641544_DG14_DG18.xlsx</p> <p>Supp_Info_3_PRJNA606875_SRR11093270_reads_blast_nt_seq5_hsps1_PCT80_E0.05_hsps.txt</p> <p>Supp_Info_4_PRJNA573298_Analysis.xlsx</p>
Classification of African ground pangolin behaviour based on accelerometer readouts: validation of bio-logging methods
<p>Data and R Scripts for the manuscript titled "Classification of African ground pangolin behaviour based on accelerometer readouts: validation of bio-logging methods".</p> <p>Code is for labelling accelerometer data and running a random forest model.<br>Script01. Label the accelerometer data with behavioural labels from BORIS<br>Script02. Create summary metrics and resample frequencies. This includes code adapted from (Clark, 2019; Clark et al., 2022). https://ore.exeter.ac.uk/repository/handle/10871/120152, https://www.int-res.com/abstracts/meps/v701/p145-157/<br>Script03. Run random forest for each frequency and smoothing window.</p> <p>AccelerometerData.zip containes Files grouped by individual. For each individual there is:</p> <p>Accelerometer_data: Accelerometer data.</p> <p>ID: BORIS behaviour output</p> <p>ID_labs: Labelled accelerometer data</p>
The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
<p>A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019, with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.</p>
Adapting camera-trap placement based on animal behaviour for rapid detection: a focus on the Endangered, white-bellied pangolin (Phataginus tricuspis)
<p>Table containing detection data of species using two camera trap placement strategies (log vs non-log)</p>
Chinese pangolins distribution sites in China from 2010 to 2022
<p>We collected Chinese pangolins' location data for burrows, infrared camera images, and live encounters obtained in China between 2010 and October 2022 by field investigations, published papers, survey reports, and online records. Given that the Chinese pangolin is still at high risk of poaching in China, these locations were only disclosed at the municipal level, and the coordinates are provided at 0.5 degree (about 50km). Therefore, we kindly remind relevant researchers to carefully use these coordinates to study the distribution of Chinese pangolin.</p>
The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
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Data from: Uncovering new lineages in the Sunda Pangolin (<em>Manis javanica</em>) with museum mitogenomics
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Estimating occupancy of Chinese pangolin (Manis pentadactyla) in a protected and non-protected area of Nepal
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Fig. 1 in Identifying SARS-CoV-2related coronaviruses in Malayan pangolins
Fig. 1 | Evolutionary relationships among human SARS-CoV-2,the pangolin coronavirus sequences obtained in this study,and the other reference coronaviruses.(A) Genome organization of coronaviruses including the pangolin coronaviruses,with the predicted ORFs shown in different colors (ORF1a is omitted for clarity).(B) Phylogeny of the subgenus Sarbecovirus (genus Betacoronavirus; n=53) estimated from the concatenated ORF1ab-S-E- M-N genes.Red circles indicate the pangolin coronavirus sequences generated in this study (Extended Data Table 1). Note that GD/P1L is the consensus sequence re-assembled from the raw data previously published7. Phylogenies were estimated using a maximum likelihood approach employing the GTRGAMMA nucleotide substitution model and 1,000 bootstrap replicates.
Data from: Historical data for conservation: reconstructing range changes of Chinese pangolin (Manis pentadactyla) in eastern China (1970-2016)
The Chinese pangolin (Manis pentadactyla) has long suffered from intense exploitation driven by consumer demand for medicinal use and food. Effective conservation management is hampered by insufficient data on pangolin status and distribution. We integrated ecological niche modeling with long-term ecological records at the local scale (e.g. from local historical documents, grey and published literature and interviews) to estimate the magnitude of potential distribution change of the Chinese pangolin in eastern China (Fujian, Jiangxi and Zhejiang provinces) over time. Our results suggest that the range of the species decreased by 52.20% between the 1970s and early 2000s, and that the population is now mainly confined to the Wuyi Mountains. This reduction in potential distribution range is attributable to anthropogenic pressures. According to our conservation prioritization analysis, the priority conservation area for the Chinese pangolin in eastern China is 51,268.4 km2, 5.62% of which is covered by nature reserves. There are 18 nature reserves and 46 prefectures which are priority areas for conservation in China. The priority-level nature reserves and prefectures in eastern China are mainly located in the center of the Wuyi Mountains, and areas declared important tend to be around the Wuyi Mountains. We propose several actions to improve the conservation status of this species: establish or enlarge nature reserves, ensure local governments at the prefecture level prioritizes conservation management, and encourage local communities to participate in pangolin conservation.
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