Effective Characterisation of the Complete Orang-Utan Mitochondrial DNA Control Region, in the Face of Persistent Focus in Many Taxa on Shorter Hypervariable Regions

Abstract

The hypervariable region I (HVRI) is persistently used to discern haplotypes, to distinguish geographic subpopulations, and to infer taxonomy in a range of organisms. Numerous studies have highlighted greater heterogeneity elsewhere in the mitochondrial DNA control region, however–particularly, in some species, in other understudied hypervariable regions. To assess the abundance and utility of such potential variations in orang-utans, we characterised 36 complete control-region haplotypes, of which 13 were of Sumatran and 23 of Bornean maternal ancestry, and compared polymorphisms within these and within shorter HVRI segments predominantly analysed in prior phylogenetic studies of Sumatran (~385 bp) and Bornean (~323 bp) orang-utans. We amplified the complete control region in a single PCR that proved successful even with highly degraded, non-invasive samples. By using species-specific primers to produce a single large amplicon (~1600 bp) comprising flanking coding regions, our method also serves to better avoid amplification of nuclear mitochondrial insertions (numts). We found the number, length and position of hypervariable regions is inconsistent between orang-utan species, and that prior definitions of the HVRI were haphazard. Polymorphisms occurring outside the predominantly analysed segments were phylogeographically informative in isolation, and could be used to assign haplotypes to comparable clades concordant with geographic subpopulations. The predominantly analysed segments could discern only up to 76% of all haplotypes, highlighting the forensic utility of complete control-region sequences. In the face of declining sequencing costs and our proven application to poor-quality DNA extracts, we see no reason to ever amplify only specific ‘hypervariable regions’ in any taxa, particularly as their lengths and positions are inconsistent and cannot be reliably defined–yet this strategy predominates widely. Given their greater utility and consistency, we instead advocate analysis of complete control-region sequences in future studies, where any shorter segment might otherwise have proven the region of choice.

Short Communication: Effectiveness of nuclear gene in species and subspecies determination of captive orangutans

“…Thus, the phylogenetic relationships between orangutan subspecies at BMOUI could not be defined due to the low degree of vWF gene variation in the present analysis. However, our results in genetic relationships at species level help to substantiate the phylogenetics of orangutans reported in previous mtDNA studies (Muir et al 2010;Ma et al 2013;Banes and Galdikas, 2016;Kamaluddin et al 2018). Moreover, this knowledge is a prerequisite to the development of a comprehensive and practical approach for conserving Bornean and Sumatran orangutan genetic resources in captivity.…”

Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas

“…Present-day mitochondrial diversity in the eastern gorillas is currently the lowest of all great apes: It is over 20 times lower than in Homo sapiens 72 , almost 50 times lower than in eastern chimpanzee ( Pan troglodytes schweinfurthii) and the bonobo ( Pan paniscus) 45 , and around 100 times lower than in Sumatran orangutan ( Pongo abelli) 73 , 74 . We also detected pronounced differences in mitochondrial diversity among gorilla species: western lowland gorillas harbor many highly diverse haplotypes, whereas only a few, closely related, haplotypes are found in the eastern species, particularly in mountain gorillas.…”