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.
Highlights
High levels of mitochondrial sequence divergence can be misconstrued as indicating the presence of more than one species2017 The Authors
We confirmed that the population sample of tree wetafrom Rangiwahia contains high mtDNA diversity, resulting from the presence of individuals at the same location with very different haplotypes
Using a combination of morphological characters and nuclear markers, we observed no concordance among clusters inferred from different datasets
Summary
High levels of mitochondrial sequence divergence can be misconstrued as indicating the presence of more than one species2017 The Authors. The acquisition of mitochondrial sequence 2 data has been promoted as a tool for identification of specimens [1,2], the application of mtDNA data frequently raises questions rather than discriminating among hypotheses [3]. 15 years since its introduction the fundamental flaws of DNA barcoding as an approach for taxonomic discovery [9,10,11] are still often ignored. The presence within a single interbreeding population of multiple mtDNA lineages or haplogroups that differ by more than 3% sequence divergence is, for example, likely if populations have been large for many generations. We demonstrate how hypotheses that explain this pattern can be distinguished by using a New Zealand orthopteran as a case study
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