Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations

Rianti, Puji; Perwitasari-Farajallah, Dyah; Sajuthi, Dondin; Pamungkas, Joko; Nater, Alexander; Krützen, Michael

doi:10.1016/j.hjb.2015.09.002

Cited by 4 publications

(7 citation statements)

References 53 publications

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“…Of all prior studies considered, only three amplified the complete hypervariable region I as defined herein [47–49]. However, the authors of two of these studies [47,49] elected not to submit their sequences for publication ( e .…”

Section: Resultsmentioning

confidence: 99%

“…However, the authors of two of these studies [47,49] elected not to submit their sequences for publication ( e . g .…”

Section: Resultsmentioning

confidence: 99%

“…To demonstrate the forensic utility of progressively longer sequences, we cut our alignment to the various lengths of those published and analysed in six prior studies: 244 positions [41]; 325 positions [45,46]; 387 positions [48]; 409 positions [47] and 422 positions [49] (for nucleotide positions, see Table 1). In the case of the latter two studies, for which the authors chose not to release their sequences, we cut the alignment based on the length of the analysed sequences specified in each manuscript.…”

Section: Methodsmentioning

confidence: 99%

“…Nonetheless, the segment amplified by Warren et al . (2001) continues to be the predominant mitochondrial marker used in orang-utan phylogenetic studies, though most have produced sequences of varying lengths that may not encompass the full stretch of hypervariability [45–49] (Table 1). While many studies report amplifying the ‘hypervariable region I’, the length and position of such a stretch is unknown in either species, and thus is presumably considered similar to those reported in closely related taxa.…”

Section: Introductionmentioning

confidence: 99%

“…We first determine the length and position of the purported hypervariable region I within the complete control region, and assess the extent to which this section was sequenced and analysed in six major published orang-utan phylogenetic studies [41,45–49] (Table 1). Rather than arbitrarily defining further hypervariable regions, we then compare the extent and utility of polymorphisms present in the remainder of the control region–all of which have been ignored to date in all prior studies of intra-island phylogeography–to those occurring in the aforementioned predominantly analysed segments ( i .…”

Section: Introductionmentioning

confidence: 99%

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

Banes

Galdikas

2016

PLoS ONE

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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.

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Section: Resultsmentioning

confidence: 99%

“…However, the authors of two of these studies [47,49] elected not to submit their sequences for publication ( e . g .…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Banes

Galdikas

2016

PLoS ONE

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Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

Vasiljevic

Morf

Senn

et al. 2022

Ecology and Evolution

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In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.

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Assessment of genetic diversity, detection of strain-specific single nucleotide polymorphisms and identification of the Bangladesh and Vietnam strain of Channa striata by PCR-RFLP analysis of the mitochondrial COI gene fragment

Alam

Projna

Zafrin

et al. 2022

Aquaculture and Fisheries

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Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations

Cited by 4 publications

References 53 publications

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

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

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

Assessment of genetic diversity, detection of strain-specific single nucleotide polymorphisms and identification of the Bangladesh and Vietnam strain of Channa striata by PCR-RFLP analysis of the mitochondrial COI gene fragment

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