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41 results for “Orangutan”
Figure S2 in Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
Figure S2. Kernel density mirror plot of Euclidean D2 analyses of six principal components calculated from 26 cranio-mandibular morphological variables. Related to Figure 1C. The between-species distribution (blue line) was calculated as the distances of all P. abelii samples to the P. pygmaeus centroid plus all of the P. pygmaeus samples to the P. abelii centroid, whereas the within-species distribution (red line) was calculated as the distances of all P. abelii samples to the P. abelii centroid plus all of the P. pygmaeus samples to the P. pygmaeus centroid. The dotted line represents the distance of the P. tapanuliensis sample to the P. abelii centroid (exact permutation test; within-species distribution: p-value<0.001; between-species: p-value<0.001), whereas solid line represents the distance of the P. tapanuliensis samples to the P. pygmaeus centroid (within-species: p-value<0.001; between-species: p-value<0.001).
Figure 4 in Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
Figure 4. Sex-Specific Evolutionary History of Orangutans Bayesian phylogenetic trees for (A) mitochondrial genomes and (B) Y chromosomes. The mitochondrial tree is rooted with a human and a central chimpanzee sequence and the Y chromosome tree with a human sequence (not shown). **Posterior probability = 1.00. (C) Genotype-sharing matrix for mitogenomes (above the diagonal) and Y chromosomes (below the diagonal) for all analyzed male orangutans. A value of 1 indicates that two males have identical genotypes at all polymorphic sites; a value of 0 means that they have different genotypes at all variable positions.
Figure S1 in Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
Figure S1. Comparisons of five dental variables across P. abelii (red), P. pygmaeus (blue), P. tapanuliensis (black horizontal line), and P. p. palaeosumatrensis (green). Related to Figure 1B. Variables include upper canine breadth (A), lower canine breadth (B), lower M1 length (C), lower M1 breadth (D), and lower M1 area (E). For each boxplot, the middle line is the median value of the distribution, with the box representing the first (lower extreme) and third (upper extreme) quartile values (i.e., the interquartile range [IQR]), and the whiskers representing the lower and upper extreme values that are within 1.5 x IQR of the first and third quartile values. Exact permutation analyses suggested that P. tapanuliensis could be differentiated statistically from the P. abelii mean for both the upper (p-value<0.001) and lower canine breadths (p-value<0.001) and from the P. 'pygmaeus' palaeosumatrensis mean for lower M1 length (p-value<0.001), breadth (p-value<0.001), and area (p-value<0.001). P. tapanuliensis could not be differentiated statistically from the P. pygmaeus mean for any of the five dental measures.
Figure 2 in Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1A. n indicates the number of sequenced individuals. See also Table S4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1-Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections).
Figure 1. Morphological Evidence Supporting a in Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S1 and Tables S1 and S2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S2.
Figure 4 in The type specimens and type localities of the orangutans, genus Pongo Lacépède, 1799 (Primates: Hominidae)
Figure 4. Two significant orangutan specimens. (A) Facial view of a (Bornean ex-captive) juvenile orangutan skull (the holotype of Simia wallichii Gervais 1838), sent to Paris before 1818 by Nathaniel Wallich. MNHN-ZM-AC-A517 © MNHN – Cécile CALLOU – 2016, published with permission. (B) Mounted adult male orangutan skin, NHMUK 1856.11.8.1, collected in Sarawak, Malaysia by A.R. Wallace; probably the male from Semabang whose lack of cheek flanges convinced Wallace there are two species. © Trustees of the Natural History Museum, London, published with permission.
Figure 3 in The type specimens and type localities of the orangutans, genus Pongo Lacépède, 1799 (Primates: Hominidae)
Figure 3. Map of locations in west Borneo, with inset map locating Borneo in Southeast Asia. 8: Rejang; 9: Binatang; 10: Darau, Narasit and Ilang; 11: Sarebas; 12: Lanjak-Entimau Wildlife Sanctuary; 13: Batang Lupar; 14: Batang Undup; 15: Marup; 16: Batang Ai National Park; 17: Danau Sentarum; 18: Batangtu, Ketungau River; 19: Sangi, Sadong River; 20: Simunjang; 21: Semabang; 22: Kundah hill (= Bukit Punda); 23: Sabal Forest Reserve; 24: Balai Ringin Protected Forest; 25: Bako; 26: Singhi; 27: Gunung Paku; 28: Semongok Forest Reserve (= Semonggok or Semenggoh); 29: Gunong Bungo; 30: Sambas; 31: Mempawah; 32: Landak (= Ngabang); 33: Landak River; 34: Pontianak; 35: Sungai Sama; 36: Sanggau; 37: Kapuas Valley; 38: Succadana (= Sukadana); 39: Gunung Palung National Park.
Figure 2 in The type specimens and type localities of the orangutans, genus Pongo Lacépède, 1799 (Primates: Hominidae)
Figure 2. Map of localities in north, central and south Borneo, with inset map locating Borneo in Southeast Asia. 1: Mt Kinabalu; 2: Crocker Range National Park; 3: Padas River (Sungai Padas); 4: Brunei Town (= Bandar Seri Begawan); 5: Niah; 6: Sungai Silat; 7: Balui; 10: Darau, Narasit and Ilang; 12: Lanjak-Entimau Wildlife Sanctuary; 16: Batang Ai National Park. Kalimantan: 17: Danau Sentarum; 18: Batangtu, Ketungau River; 40: Kotaringin (= Kotawaringin); 41: Tanjung Puting National Park; 42: Sampit; 43: Sabangau National Park; 44: Kahajan (= Kahayan) River; 45: Sungai Lading; 46: Teweh River; 47: Tanjung-Jawa; 48: Doeson or Dusun (= Barito River); 49: Banjarmasin; 50: Klumpang Bay; 51: Pemukan Bay; 52: Passeer (= Tanahgrogot); 53: Balikpapan Bay; 54: Samarinda; 55: Mahakam River; 56: Kutai National Park; 57: Sangatta (= Sengata); 58: Sungai Menganne; 59: Sembakung River; 60: Danum Valley; 61: Abai, Kinabatangan River; 62: Elapura, Sandakan Bay; 63: Sepilok Orangutan Sanctuary.
Data from: Orangutans (Pongo pygmaeus) recognize their own past actions
The ability to recognize oneself in a mirror is known as self-recognition, whereas delayed self-recognition is the ability to recognize the relationship between current self and past actions. While 3-year-old human children have self-recognition without the ability for delayed self-recognition, 4-year-old human children demonstrate the capability for both. Chimpanzees, the most closely related species to humans, have displayed the ability for delayed self-recognition. However, little is known about whether this ability is shared amongst all hominid species. In this study, we examined whether orangutans, the most distantly related species to humans within the hominid group, could recognize their own past actions using the preferential-looking paradigm. Our results demonstrated that orangutans were able to discriminate between a delayed video of themselves presented after a 2-second delay, and a recorded video of the day prior. This suggests that orangutans have the ability to relate their own past actions to current actions, although we found no evidence of self-directed behavior. We believe these findings will contribute to our growing understanding of hominid self-recognition.
Figure 3 in Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland.The ABC analyses are based on the comparison of 3,000 non-coding 2-kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model's posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S3.
Data from: Orangutans (Pongo pygmaeus) recognize their own past actions
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Generation of induced pluripotent stem cells from Bornean orangutans
GEO Series GSE235790. Pongo pygmaeus. 4 samples. Type: Expression profiling by high throughput sequencing.
Human embryonic stem cell, chimpanzee induced pluripotent stem cell, orangutan induced pluripotent stem cell, rhesus embryonic stem cell, and their derived cortical organoid RNA-seq
GEO Series GSE106245. Pongo abelii; Macaca mulatta; Homo sapiens; Pan troglodytes. 55 samples. Type: Expression profiling by high throughput sequencing.
ChIP-chip from four orangutan cells with CENP-A
GEO Series GSE81003. Pongo pygmaeus; Pongo abelii; Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Genome wide expression patterns of 19 human urinary cells as well as 6 primary urinary cells and 17 corresponding iPSCs of human, gorilla and orangutan
GEO Series GSE155889. Gorilla gorilla; Homo sapiens; Pongo abelii. 42 samples. Type: Expression profiling by high throughput sequencing.
Figure 1 in The type specimens and type localities of the orangutans, genus Pongo Lacépède, 1799 (Primates: Hominidae)
Figure 1. Map of South Asia, showing places mentioned in the text.
Figure 5 in The type specimens and type localities of the orangutans, genus Pongo Lacépède, 1799 (Primates: Hominidae)
Figure 5. (Continued)
Dataset: Vocal complexity in the long calls of Bornean orangutans
<div> <p>Data and code used for PeerJ article titled, "Vocal complexity in the long calls of Bornean orangutans"</p> <p> </p> <p><strong>Abstract</strong></p> <p>Vocal complexity is central to many evolutionary hypotheses about animal communication. Yet, quantifying and comparing complexity remains a challenge, particularly when vocal types are highly graded. Male Bornean orangutans (Pongo pygmaeus wurmbii) produce complex and variable “long call” vocalizations comprising multiple sound types that vary within and among individuals. Previous studies described six distinct call (or pulse) types within these complex vocalizations, but none quantified their discreteness or the ability of human observers to reliably classify them. We studied the long calls of 13 individuals to: 1) evaluate and quantify the reliability of audio-visual classification by three well-trained observers, 2) distinguish among call types using supervised classification and unsupervised clustering, and 3) compare the performance of different feature sets. Using 46 acoustic features, we used machine learning (i.e., support vector machines, affinity propagation, and fuzzy c-means) to identify call types and assess their discreteness. We also additionally used Uniform Manifold Approximation and Projection (UMAP) to visualize the separation of pulses using both extracted features and spectrogram representations. We found low inter-observer reliability and poor classification accuracy using Ssupervised approaches, showed low inter-observer reliability and poor classification accuracy, indicating that pulse types were not discrete. We propose an updated pulse type classification scheme approach that is highly reproducible across observers and exhibits high strong classification accuracy using support vector machines. Although the low number of call types suggests long calls are fairly simple, the continuous gradation of sounds seems to greatly boost the complexity of this system. This work responds to calls for more quantitative research to define call types and measure quantifythe gradedness of in animal vocal systems and highlights the need for a more comprehensive framework for studying vocal complexity vis-à-vis graded repertoires. </p> </div>
Gene expression profiles of induced pluripotent stem cells (iPSCs) and skin fibroblasts from orangutans
GEO Series GSE69603. Pongo abelii; Homo sapiens. 8 samples. Type: Expression profiling by array.
orangutan_true_vs_predicted_lymphoblastoid_expression
<p>True expression based on three metrics versus predicted expression values for an orangutan lymphoblastoid cell line. </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.