Comparative and demographic analysis of orang-utan genomes

Abstract

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

Figure 1. Divergence among great apes, a small ape, and an Old World monkey with respect to humans.

We estimated nucleotide divergence in unique gap-free sequence, indicated at each node, from the alignment of rhesus macaque (yellow), gibbon (purple), orang-utan (orange), gorilla (aqua), chimpanzee (green) and human (blue) whole genome shotgun reads to the human reference (Hs.35; Supplementary Information section 3). Note that the Bornean (P. pygmaeus) and Sumatran (P. abelii) orang-utan species showed nucleotide identity comparable to that of bonobo (Pan paniscus) and chimpanzee (Pan troglodytes). Estimates of divergence time based on sequence identity are indicated at each node, ∼1 Myr implies approximately 1 Myr or less. Values taken from refs and where indicated. PowerPoint slide

Figure 2. The neocentromere of orang-utan chromosome 12.

Note the identical order of four sequentially arranged BAC-derived FISH probes indicated in yellow, blue, green and red (given in Supplementary Information section 8) between the normal (a) and neocentromere-bearing (b) configurations of orang-utan chromosome 12, despite discordant centromere positions. The left image of a and the right image of b are DAPI-only images that show the primary constriction of both chromosomal forms, indicated by the arrows. The neocentromere recruits centromeric proteins CENP-A and CENP-C and lies within a ∼225 kb gene-free and α satellite-free region. The neocentromere-bearing variant is polymorphic in both Bornean and Sumatran populations, suggesting the neocentromere arose before the Bornean/Sumatran split, yet has not been fixed in either species. PowerPoint slide

Figure 3. Alu quiescence in the orang-utan lineage.

We identified only ∼250 lineage-specific Alu retroposition events in the orang-utan genome, a dramatically lower number than that of other sequenced primates, including humans. The total number of lineage-specific L1, SVA and Alu insertions is shown (pie chart) at the terminus of each branch of the phylogeny of sequenced great apes shown in grey at left, along with the rate of insertion events per element type (bar graph). Reduced Alu retroposition potentially limited the effect of a wide variety of repeat-driven mutational mechanisms in the orang-utan lineage that played a major role in restructuring other primate genomes. PowerPoint slide

Figure 4. Enrichment for positive selection in the cerebroside-sulphatid metabolism pathway.

We identified six genes (indicated in yellow) under moderate to strong positive selection in primates (P < 0.05) that fall within the cerebroside-sulphatid region of the sphingolipid metabolism pathway (adapted from human KEGG pathway 00600). This pathway is associated with several human lysosomal storage disorders, such as Gaucher’s disease, Sandhoff’s disease, Tay-Sachs disease and metachromatic leukodystrophy. Abbreviations, annotations and connections are presented in accordance with KEGG standards: solid lines represent direct relationships between enzymes (boxes) and metabolites (circular nodes), dashed lines represent indirect relationships, arrowheads denote directionality (see http://www.genome.jp/kegg-bin/show_pathway?map00600 for further details). PowerPoint slide

Figure 5. Orang-utan population genetics and demographics.

a, Site-frequency spectra for 13.2 × 10⁶ Bornean (red) and Sumatran (blue) SNPs are shown based on the ascertainment of 10 chromosomes per species; note the enrichment of low-frequency SNPs among Sumatran individuals. b, The majority of SNPs were restricted to their respective island populations as the ‘heat’ of the two-dimensional site-frequency spectra, representing high allele counts, lay along the axes. c, Our demographic model estimated that the ancestral orang-utan population (N_e = 17,900) split approximately 400,000 years ago, followed by exponential expansion of Sumatran N_e and a decline of Bornean N_e, culminating in higher diversity among modern Sumatran orang-utans despite a lower census population size. The model also supported low-level gene flow (<1 individual per generation), indicated by arrows. PowerPoint slide