mtDNA
Galtier N, Nabholz B, Glémin S & Hurst GDD 2009 Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol, in press.
doi:10.1111/j.1365-294X.2009.04380.x
- mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like
- questioning its relevance as a witness of recent species and population history
- ironically enough, we now know that the three human studies which motivated this fruitful search for mtDNA recombination were actually questionable
- the decay of linkage disequilibrium with physical distance (Awadalla et al. 1999) was found sensitive to methodological settings, and to the analysed data set (Ingman et al. 2000; Innan & Nordborg 2002; Piganeau & Eyre-Walker 2004)
- the excess of within-species homoplasy (Eyre-Walker et al. 1999), finally, was most probably created by short-lived, uneasy to detect mutations hotspots (Galtier et al. 2006)
- one lesson to be drawn from this interesting debate is that peculiarities of the mitochondrial mutation process can generate recombination-like patterns of sequence variation
- the prevalence of mitochondrial recombination across animals is currently difficult to assess
- a large fraction of the within-species mtDNA homoplasy is caused by mutation hot-spots
- the existence of strong within-species homoplasy is an obvious practical problem when analysing mtDNA population data
- whether it is caused by true recombination or mutation-induced convergences
- Neutrality?
- Constant mutation rate?
- The worst marker?
- the use of mtDNA has, in fact, become recently resurgent
- in particular associated with DNA barcoding for taxonomic identification and investigation of biodiversity
- in favour of mtDNA barcoding is the existence of fairly common selective sweeps in mtDNA
- whilst selective sweeps are the enemy of 'classic' interpretations of genomic diversity and population history from mtDNA diversity, these sweeps make attempts to barcode species more robust
- they reduce intraspecific variation in mtDNA, and make the 'gap' between inter- and intra-specific diversity more pronounced
- various evolutionary processes (related earlier) may either homogenize distinct species for mtDNA through hybrid introgression (making inter-specific mtDNA diversity very low), or produce balancing selection (that maintains high intraspecific diversity)
- Balancing selection on haploids? (Frequency dependence? Heterogeneous environment?)
- such effects can seriously erode the distinction between intra- and inter-specific diversity, creating errors in mtDNA driven systematics, and leading to problems in using barcodes in specimen identification
- the evolutionary rate of mtDNA is heterogeneous
- the consequence of this is that universal distance-based 'thresholds' for delineation of taxa into species do not exist
- no mtDNA based barcoding system for taxonomy and systematics will be completely accurate
- examination of variation at multiple genetic loci in a phylogenetic context, combined with careful morphological, behavioural and ecological analysis, is required to establish accurate species boundaries