Population-specific signatures of intra-individual mitochondrial DNA heteroplasmy and their potential evolutionary advantages

Abstract

Heteroplasmy is the existence of more than one mitochondrial DNA (mtDNA) variant within a cell. The evolutionary mechanisms of heteroplasmy are not fully understood, despite being a very common phenomenon. Here we combined heteroplasmy measurements using high throughput sequencing on green turtles (Chelonia mydas) with simulations to understand how heteroplasmy modulates population diversity across generations and under different demographic scenarios. We found heteroplasmy to be widespread in all individuals analysed, with consistent signal in individuals across time and tissue. Significant shifts in haplotype composition were found from mother to offspring, signalling the effect of the cellular bottleneck during oogenesis as included in the model. Our model of mtDNA inheritance indicated that heteroplasmy favoured the increase of population diversity through time and buffered against population bottlenecks, thus indicating the importance of this phenomenon in species with reduced population sizes and frequent population bottlenecks like marine turtles. Individuals with recent haplotypes showed higher levels of heteroplasmy than the individuals with ancient haplotypes, suggesting a potential advantage of maintaining established copies when new mutations arise. We recommend using heteroplasmy through high throughput sequencing in marine turtles, as well as other wildlife populations, for diversity assessment, population genetics, and mixed stock analysis.

Genetic Relationships Between Commercially Produced and Natural Populations of Bombus Terrestris Dalmatinus in Terms of Mitochondrial COI and CytB

“…1). As mentioned in previous similar studies (Wernick et al, 2016;Williams et al, 2019;Pizzirani et al, 2020;Ricardo et al, 2020;Tikochinski et al, 2020) double peaks on sequence traces with both alleles from one individual were identified as mitochondrial heteroplasmy and a single individual with two haplotypes. At least one heteroplasmy was detected in 93 of 157 individuals for COI and at least 105 of 170 individuals for CytB in the current study.…”

Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators

“…Out of the various approaches for enriching mtDNA before mitogenome sequencing, this study favoured the use of back-to-back amplification primers considering its simplicity, throughput, universality, as well as flexibility and amount of template source. The assay for mitogenome amplification applicable for fresh or well-preserved blood and tissue samples can be helpful to assess issues of mitogenomics such as point and length heteroplasmy of clinical and forensic samples ( Cagnin et al, 2009 ), evolutionary mechanisms of heteroplasmy ( Tikochinski et al, 2020 ) or intraspecific phylogeography ( Avise et al, 1987 ). Our assay holds promise for tissue samples preserved in ethylenediaminetetraacetic acid (EDTA) ( Sharpe et al, 2020 ), or choline-based ionic liquids ( Oosting et al, 2020 ) as well as for certain applications based on aquatic eDNA ( Deiner et al, 2017 ; Ding et al, 2020 ).…”

Genetic polymorphism between and within Mediterranean and Red Sea populations of the green turtle (Chelonia mydas) as revealed by sequence-related amplified polymorphism (SRAP)

“…Hence, PCR-based SRAP marker will help in identifying more polymorphism as discovered in this study. From this study, we could consider that the SRAP markers as an additive tool along with other techniques using a) mtDNA such as highly polymorphic haplotyping method (Tikochinski et al, 2018;Tolve et al, 2018;Tikochinski et al, 2020); and b) nDNA to reveal variation/polymorphism between marine turtle populations and then we would have a clear genetic structure of the green turtle population in Egypt.…”