Explaining large mitochondrial sequence differences within a population sample

Abstract

Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an exemplar to distinguish among competing hypotheses. Within our sample of tree wētā (Hemideina crassidens; Orthoptera), we found multiple mtDNA haplotypes for a protein-coding region (cytb/ND1) that differed by a maximum of 7.9%. From sequencing the whole mitochondrial genome of two representative individuals, we found evidence of constraining selection. Heterozygotes were as common as expected under random mating at five nuclear loci. Morphological traits and nuclear markers did not resolve the mtDNA groupings of individuals. We concluded that the large differences found among our sample of mtDNA sequences were simply owing to a large population size over an extended period of time allowing an equilibrium between mutation and drift to retain a great deal of genetic diversity within a single species.

Anthropogenic cause of range shifts and gene flow between two grasshopper species revealed by environmental modelling, geometric morphometrics and population genetics

“…Tavares & Baker, ), simulation studies show that large stable populations are expected to have multimodal distributions because the history of coalescent events imposes a substantial correlation on this non‐recombining DNA sequence (Slatkin & Hudson, ). Similar intra‐specific diversity of mtDNA has been demonstrated in other Orthoptera (Morgan‐Richards et al ., ).…”

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

“…Consequently, the delimitation of cryptic taxa has extensively relied on mitochondrial DNA (mtDNA) divergences (Krishnamurthy & Francis, 2012). However, it is now well established that deep mtDNA lineages do not always represent significant population divergences (Collins & Cruickshank, 2012;Morgan-Richards et al, 2017;Zink & Barrowclough, 2008), and even when they do, whether these kept diverging independently or faded away by recurrent episodes of admixture often remains an open question (Garrick, Banusiewicz, Burgess, Hyseni, & Symula, 2019).…”

Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or Phenotype

“…However, in cases when species are polyphyletic with respect to their mtDNA, this method may identify species groups, but will be unreliable to identify species. Funk and Omland [29] determined that species-level polyphyly was relatively common, and that reliance on mtDNA alone would misidentify species approximately 30% of the time; similar criticisms have been put forth on theoretical and empirical grounds [67][68][69][70]. In our group of tiger beetles, mtDNA would misidentify species 24.5% of the time (Figure 3).…”