Ye Orang

[Walda Caesar]

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It is tempting to propose a correlation between reduced Alu retroposition and the greater structural stability of the orang-utan genome. More than 106 Alu elements exist within primate genomes. Because of their large copy number and high sequence identity, Alu repeats play a crucial role in multiple forms of structural variation through insertion and post-insertion recombination20. By virtue of reduced Alu retroposition, the orang-utan lineage experienced fewer new insertions and a putative decrease in the number of regions susceptible to post-insertion Alu-mediated recombination events genome-wide, limiting the overall mobile element threat to the genome.

Ancestral orang-utan species ranged broadly across southeast Asia, including the mainland, while modern species are geographically restricted to their respective islands owing to environmental forces and human population expansion. Historically, protein markers, restriction fragment length polymorphisms, and small sets of mitochondrial and nuclear markers have been used to estimate the divergence and diversity of orang-utan species. We used short read sequencing to address this question from a genome-wide perspective. We first estimated average Bornean/Sumatran nucleotide identity genome-wide (99.68%) based on the alignment of 20-fold coverage of short read data from a Bornean individual to the Sumatran reference (Supplementary Information section 16). We then called single nucleotide polymorphisms (SNPs) from the alignment of all short read data from 10 individuals (five Bornean, including the 20-fold coverage mentioned above, and five Sumatran) (Supplementary Information section 4). We analysed each species separately using a Bayesian approach with 92% power to detect SNPs (Supplementary Information section 20). Because of relatively deep sequencing, allele frequency spectra were estimated accurately, but with an overestimation of singletons compared to other allele frequency categories of approximately 7.8% based on re-sequencing a subset of SNPs (n = 108) (Supplementary Information section 20). This level of error had only a marginal effect on downstream population genetic analyses (Supplementary Information section 21). Overall, 99.0% (931/940) of genotypes were accurately called within the re-sequenced subset of SNPs.

Finally, even though we found deep diversity in both Bornean and Sumatran populations, it is not clear whether this diversity will be maintained with continued habitat loss and population fragmentation. Evidence from other species suggests fragmentation is not the death knell of diversity28, but their slow reproduction rate and arboreal lifestyle may leave orang-utan species especially vulnerable to rapid dramatic environmental change. It is our hope that the genome assembly and population variation data presented here provide a valuable resource to the community to aid the preservation of these precious species.

Whole-genome sequencing was performed as described previously12,13,14. The genome assembly was constructed with a custom computational pipeline (Supplementary Information section 1). Assembly source DNA was derived from a single Sumatran female (Susie; Studbook no. 1044; ISIS no. 71), courtesy of the Gladys Porter Zoo, Brownsville, Texas. Short fragment sequencing libraries for population studies (Supplementary Information section 4) were constructed in accordance with standard Illumina protocols and sequenced on the Illumina GAIIx platform. The resulting data were processed with Illumina base-calling software and analysed using custom computational pipelines. See Supplementary Information for additional details.

The P. abelii whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the project accession ABGA00000000. The version described in this Letter is ABGA00000000.1. Assembly-based SNPs and SNPs derived from short read sequence data have been deposited in dbSNP. All short read data have been deposited into the Short Read Archive ( ) under accessions listed in Supplementary Information.

D.P.L. led the project and manuscript preparation. D.P.L., A.S., T.M.-B., C.P.P., M.A.B., A.N., E.E.E., M.W.H., C.L.-O., C.D.B., J.M. and M.H.S. led the analyses. Sanger data production, assembly construction, testing and submission: L.W.H, W.C.W., S.-P.Y., Z.W., A.T.C., P.M., M.M., L.A.F., R.A.F., J.O.N., C.P., K.C.W, L.V.N., D.M.M., A.C., H.H.D., J.H., C.L.K., G.R.F. and J.R. BAC sequencing: T.A.G. 454 cDNA sequencing: V.M. and C.M. Illumina sequencing: L.C., K.D.D. and C.F. SNP validation: H.S. Indel assessment: G.L., S.M., A.H. and C.P.P. Segmental duplication, divergence and structural variation studies: T.M.-B., C.A., L.C., Z.C., J.M.K. and E.E.E. Gene models: S.W., S.S. and A.J.V. Assembly-based SNPs: Y.C. and P.F. Ancestral reconstruction and rearrangement analyses: J.M., B.R., B.S., R.B., J.H., D.H., R.S.H. and W.M. Regional variation in nucleotide divergence analyses: R.F., O.F., F.D., D.F., E.G., M.O. and A.N. Cytogenetics and neocentromere characterization: R.R., O.C., N.A., G.D.V., S.P and M.R. Repeat analyses: M.K.K., J.A.W., B.U., M.A.B., A.F.A.S. and R.H. Gene family evolution analyses: C.C., D.R.S. and M.W.H. Protease gene family studies: V.Q., X.S.P., G.R.O. and C.L.-O. Orthologue and defensin analyses: T.V., B.B., A.R. and W.M. Positive selection analyses: C.K., T.V., H.A.L., V.T., A.L.M. and A.S. Short read alignments, SNP calling and population genetics: A.R., X.M., J.D. and C.D.B. Demographic analyses: R.N.G. Coalescent-HMM analyses: T.M., J.Y.D., A.H. and M.H.S. Orang-utan samples for diversity sequencing: O.A.R. BAC library construction: Y.Y. and P.J.d.J. Principal investigators: G.M.W., E.R.M., R.A.G. and R.K.W.

This file contains Supplementary Information, Sections 1-22 (see Table of Contents), which include Supplementary Figures with legends, Supplementary Tables, Supplementary Methods and additional references. (PDF 11307 kb)

This spreadsheet provides a general description of each cDNA data set generated for this project, as well as an internal experiment ID, flow cell ID, submission date and a Short Read Archive accession number. (XLS 24 kb)

This spreadsheet provides a general description of each short read genomic DNA data set generated for this project, including species (Bornean/Sumatran), individual identification number, sex, flow cell ID, a description of the data type (read length and whether paired end or fragment data), and a Short Read Archive accession number for each lane of data. (XLS 31 kb)

This file contains data with regard to variation in dS in relation to genomic position and distance from structural elements of the genome (centromeres and telomeres) and rearranged regions of the genome, referenced in Supplemental information section S7. (XLS 161 kb)

This file contains data with regard to variation in dS along the orangutan branch and hominid branch on a chromosome-by-chromosome basis, referenced in Supplemental Information section S7. (XLS 93 kb)

This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence ( -nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.

Animals self-medicate using a variety of plant and arthropod secondary metabolites by either ingesting them or anointing them to their fur or skin apparently to repel ectoparasites and treat skin diseases. In this respect, much attention has been focused on primates. Direct evidence for self-medication among the great apes has been limited to Africa. Here we document self-medication in the only Asian great ape, orang-utans (Pongo pygmaeus), and for the first time, to our knowledge, the external application of an anti-inflammatory agent in animals. The use of leaf extracts from Dracaena cantleyi by orang-utan has been observed on several occasions; rubbing a foamy mixture of saliva and leaf onto specific parts of the body. Interestingly, the local indigenous human population also use a poultice of these leaves for the relief of body pains. We present pharmacological analyses of the leaf extracts from this species, showing that they inhibit TNFα-induced inflammatory cytokine production (E-selectin, ICAM-1, VCAM-1 and IL-6). This validates the topical anti-inflammatory properties of this plant and provides a possible function for its use by orang-utans. This is the first evidence for the deliberate external application of substances with demonstrated bioactive potential for self-medication in great apes.

Since our first observations of fur-rubbing with D. cantleyi by Bornean orang-utans in the Sabangau Peat-swamp forest in Central Kalimantan province, Indonesia in 2003, we have documented a total of ten cases up to September 2015. This is a very rare behaviour. To our knowledge, this is the only place in the range of either Pongo species where this behaviour has been witnessed. Chemical analyses of the properties of this plant are consistent with the hypothesis that fur-rubbing is a form of self-medication used to treat joint and muscle inflammation19. It is also important to note that local indigenous human inhabitants use this plant for the same purpose. This is also the case for use of Vernonia amygdalina by chimpanzees in Western Tanzania, where the indigenous human population also uses this plant for the treatment of parasites and stomach upset; recovering from similar symptoms in roughly the same amount of time10,12.

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