Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution

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.

Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species

“…Polymorphic STRs were also found to allow for better identification of pig breeds in comparison to SNPs. Another study in wild orangutan populations identified distinct STR length changes in genes linked to species' recent local adaptations, such as increased brain size and reproductivity (Voicu et al, 2021 ).…”

Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time

“…Microsatellites or short tandem repeats, consisting of tandem repeats of motifs up to 6 bp in length, are prevalent in both prokaryotic and eukaryotic genomes. Some microsatellites have been shown to be functionally important ( Kashi and King 2006 ; Mirkin 2007 ; Gemayel et al 2010 ), but most are assumed to evolve neutrally, and for this reason, along with their abundance and high variability, they have been used extensively in population genetics studies ( Schlötterer 2004 ; Voicu et al 2021 ; Shi et al 2023 ). While there have recently been important advances in our understanding of their genomic distribution ( Srivastava et al 2019 ) and evolutionary dynamics ( Jonika et al 2020 ; Verbiest et al 2022 ), it remains unclear whether microsatellite loci are in dynamic equilibrium with respect to the length of alleles or whether alleles experience directional drift in length.…”