Abstract
The genus Pongo is ideal to study population genetics adaptation, given its remarkable phenotypic divergence and the highly contrasting environmental conditions it’s been exposed to. Studying its genetic variation bears the promise to reveal a motion picture of these great apes’ evolutionary and adaptive history, and also helps us expand our knowledge of the patterns of adaptation and evolution. In this work, we advance the understanding of the genetic variation among wild orangutans through a genome-wide study of short tandem repeats (STRs). Their elevated mutation rate makes STRs ideal markers for the study of recent evolution within a given population. Current technological and algorithmic advances have rendered their sequencing and discovery more accurate, therefore their potential can be finally leveraged in population genetics studies. To study patterns of population variation within the wild orangutan population, we genotyped the short tandem repeats in a population of 21 individuals spanning four Sumatran and Bornean (sub-) species and eight Southeast Asian regions. We studied the impact of sequencing depth on our ability to genotype STRs and found that the STR copy number changes function as a powerful marker, correctly capturing the demographic history of these populations, even the divergences as recent as 10 Kya. Moreover, gene ontology enrichments for genes close to STR variants are aligned with local adaptations in the two islands. Coupled with more advanced STR-compatible population models, and selection tests, genomic studies based on STRs will be able to reduce the gap caused by the missing heritability for species with recent adaptations.
Highlights
Wild orangutans inhabiting the islands of Sumatra and Borneo are the only Southeast Asian great apes (Wich et al, 2008)
After imposing highly conservative filtering criteria on the set of short tandem repeats (STRs) genotyped for each individual, our catalog of wild orangutan STR variation encompasses 70,594 STR variants and 415789 STR invariants genotyped across 137225 STR loci
We discovered that an individual from the Sumatran population has on average 1954 ± 1312 STR variants, whereas an individual from the Bornean population has on average 2,946 ± 1846 STR variants
Summary
Wild orangutans inhabiting the islands of Sumatra and Borneo are the only Southeast Asian great apes (Wich et al, 2008). They belong to the Pongo genus, diverged into three distinct species, the Sumatran Pongo abelii and P. tapanuliensis and the Bornean Pongo pygmaeus (Wich et al, 2008; Nater et al, 2017). Orangutans from southern Sumatra migrated to Borneo 1 Ma to 700 Kya (Mattle-Greminger et al, 2018), their transition being facilitated by low sea levels and elevated ice volume during the glaciation periods in the Pleistocene epoch. The bottleneck was followed by an expansion in the Bornean population 30–10 Kya, followed by the divergence of the three Bornean subspecies: Pongo pygmaeus, Pongo pygmaeus morio and Pongo pygmaeus wurmbii
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
