Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

Abstract

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

phylogatR: Phylogeographic data aggregation and repurposing

“…While single-locus data has its limitations in making inferences about historical demography (Matumba et al 2020), DNA barcoding, or the use of other single-locus DNA markers has provided tremendous insight into identifying evolutionary significant units and providing information on species in further need of exploration (Sholihah et al 2020;Wang et al 2020;Nneji et al 2020;Bousjein et al 2021;León-Tapia 2021). These data are particularly helpful when aiming to explore broad-scale patterns such as those on a continental scale (Dinça et al 2021) or across species (Doorenweerd et al 2020), especially for a large number of taxonomic groups, as demonstrated here.…”

phylogatR: Phylogeographic data aggregation and repurposing

“…While single-locus data has its limitations in making inferences about historical demography (Matumba et al, 2020), DNA barcoding, or the use of other single-locus DNA markers, has provided tremendous insight into identifying evolutionary significant units and providing information on species in further need of exploration (Bousjein et al, 2021;León-Tapia, 2021;Nneji et al, 2020;Sholihah et al, 2020;Wang et al, 2020). These data are particularly helpful when aiming to explore broad-scale patterns such as those on a continental scale (Dincă et al, 2021) or across species (Doorenweerd et al, 2020), especially for a large number of taxonomic groups, as demonstrated here.…”

A critically endangered estuarine limpet’s only two populations are genomically and morphologically distinct

“…Mitochondrial DNA tends to be under strong selection pressure (Ballard & Kreitman, 1995; Matumba et al, 2020), thus violating the assumption of the neutral theory of evolution (Kimura, 1983) and affecting divergence time estimation (Stewart et al, 2008; Matumba et al, 2020). No mitogenome sequence is yet available for S. compressa .…”