Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts

By G. Hurst, F. Jiggins. Proceedings of the Royal Society of London. Biological Sciences, 2005

896 citations recorded by the source corpus.

Mitochondrial DNA (mtDNA) has been a marker of choice for reconstructing historical patterns of population demography, admixture, biogeography and speciation. However, it has recently been suggested that the pervasive nature of direct and indirect selection on this molecule renders any conclusion derived from it ambiguous. We review here the evidence for indirect selection on mtDNA in arthropods arising from linkage disequilibrium with maternally inherited symbionts. We note first that these symbionts are very common in arthropods and then review studies that reveal the extent to which they shape mtDNA evolution. mtDNA diversity patterns are compatible with neutral expectations for an uninfected population in only 2 of 19 cases. The remaining 17 studies revealed cases of symbiont-driven reduction in mtDNA diversity, symbiont-driven increases in diversity, symbiont-driven changes in mtDNA variation over space and symbiont-associated paraphyly of mtDNA. We therefore conclude that these elements often confound the inference of an organism's evolutionary history from mtDNA data and that mtDNA on its own is an unsuitable marker for the study of recent historical events in arthropods. We also discuss the impact of these studies on the current programme of taxonomy based on DNA bar-coding.

Subfields: Ecology, Evolution, Behavior and Systematics, Insect Science

View Paper: https://www.semanticscholar.org/paper/02690c394dc344e7359c610ef1fde379d8eb7d50

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In Ecology, Evolution, Behavior and Systematics

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Citations in the corpus

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DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep‐sea environments (2007, background): “…1996; Avise & Johns 1999; Hebert et al. 2003b; Moritz & Cicero 2004; Meyer & Paulay 2005) including problems associated with inherited symbionts (Hurst & Jiggins 2005), with introgression/ hybridization (e.g. Masta et al. 2002; Babik et al. 2005) or with very recent speciation (e.g. Johnson &…”
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified (2008, background): “Maternally inherited symbionts, such as Wolbachia, can cause linkage disequilibrium with mtDNA and, whether a population becomes infected with such symbionts, the mtDNA associated with the initial infection will spread throughout the population and result in the homogenization of mtDNA haplotypes (6”
On the instability and evolutionary age of deep-sea chemosynthetic communities (2013, background): “Mutations in the host (and particularly in mitochondrial genomes) could hitchhike to fixation with beneficial new mutations in cytoplasmically co-transmitted symbiont genomes that experience selective sweeps (Hurst and Jiggins, 2005).”
Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding (2012, background): “Another important reason is the ease of PCR amplification and sequencing of chloroplast genes, despite some intrinsic problems similar to those encountered when using animal mitochondrial DNA [1].”
Mitochondrial DNA as a marker of molecular diversity: a reappraisal (2009, background): “Issues regarding the general utility (and use) of mtDNA barcodes are under constant debate and research (e.g. Moritz & Cicero 2004; Hurst & Jiggins 2005; Meyer & Paulay 2005; Hickerson et al. 2006; Elias et al. 2007; Roe & Sperling 2007; Whitworth et al. 2007; Wiemers & Fiedler 2007; Rach et al.…”
Revealing secret liaisons: DNA barcoding changes our understanding of food webs (2010, background): “Since clades in a mitochondrial gene tree may not always represent independently evolving species (Funk & Omland, 2003; Hurst & Jiggins, 2005; Knowles & Carstens, 2007; Lohse, 2009), we confirmed any patterns emerging from the COI material by sequencing a subset of members of all mitochondrial…”