Box 1 The mitochondrial bottleneck
The paradox of dramatic shifts in frequency of mtDNA genotypes across few generations, despite vast numbers of mtDNA molecules in mature oocytes (Hauswirth & Laipis 1982; Ashley et al. 1989), can be explained, in part, by a mitochondrial bottleneck that occurs during early developmental stages (Bergstrom & Pritchard 1998). Although not the only factor likely at work (Birky 2001; Cao et al. 2007), this bottleneck may prevent an accumulation of deleterious mutations and ‘mutational meltdown’, that would otherwise occur in a clonally inherited molecule via Muller's ratchet (Bergstrom & Pritchard 1998; Shoubridge & Wai 2007).
While there is little contention about their existence, what remains debated is whether it is at embryogenesis, or oogenesis, that the strongest effects of mitochondrial bottlenecks are felt (Jenuth et al. 1996; Smith et al. 2002; Cao et al. 2007; Cree et al. 2008; Khrapko 2008). During mammalian embryogenesis, total embryonic mtDNA content remains constant during early stages of the cleaving embryo (Cao et al. 2007; Cree et al. 2008), with mitochondria being equally apportioned to daughter cells. Most of the blastocyst forms extra-embryonic tissues; thus, only a subset of all cells (the inner cell mass, ICM) will contribute to the developing embryo (Hogan et al. 1986; Fleming et al. 1992). The apportionment of mitochondria to the ICM constitutes a numerical bottleneck, during which rare mtDNA haplotypes are prone to loss (Bergstrom & Pritchard 1998). During mammalian oogenesis, the vast number of germ cells at maturity originates from a limited number of progenitor germ cells (PGCs), each of which contains approximately 10–100 mitochondria (Shoubridge & Wai 2007). There is then an enormous expansion in cell number (to ~25 000 and ~107 primary oocytes in mice and human, respectively), and increase in mitochondria number. The number of mtDNA molecules increases dramatically to around 200 000 mtDNA copies in mature oocytes (Jansen & de Boer 1998; Shoubridge & Wai 2007).
This large decrease in mtDNA per cell during embryogenesis, and dramatic increase in oogenesis, means only a subset of maternal mtDNAs will re-populate successive generations. For a heteroplasmic individual this often means a return to homoplasmy, but can lead to strong founder effects (Bergstrom & Pritchard 1998).
Box 2 Detecting recombination
It is now widely accepted that intermolecular recombination can occur in animal mtDNA (Rokas et al. 2003; Piganeau et al. 2004; Tsaousis et al. 2005), although whether it occurs frequently enough to cause concern is contentious (Elson & Lightowlers 2006). Empirical evidence is required to determine the frequency of intermolecular recombination in animals. However, many factors exist which may not only prevent recombination, but also its detection when it does occur.
Several events are required to occur simultaneously for mtDNA recombination to be detectable. First, there is the necessity for two mtDNA molecules to be present within a cell that differ at two or more nucleotide sites. If individuals are homoplasmic, or heteroplasmic but differ at only one site, recombination will be undetectable (Fig. 2). Second, molecules need to be in close enough physical proximity to allow a crossover event which, unlike nuclear chromosomes, is not part of the life cycle of mtDNA. This may require aggregation of nucleoids, or fusion of organelles (reviewed by Yaffe 1999). Third, essential nuclear-encoded enzymes, such as those for fusion and genome exchange and repair need to be available (Thyagarajan et al. 1996; Lakshmipathy & Campbell 1999b; Yaffe 1999; Santel & Fuller 2001). To complicate matters, alignment of homologous regions may be hindered by its circular nature and, for a recombinant molecule to remain intact, two crossovers events are needed.
[ Detectable recombination in mtDNA. ]
Even if recombination has occurred between heterologous mtDNA molecules, detection is not guaranteed. The low frequency of recombinant mtDNA molecules, compared to the vast majority of intact molecules, means that they are particularly prone to loss by drift during the stochastic processes of vegetative segregation and the genetic bottleneck. Without proliferation, frequencies will likely be too low for the detection limits of standard technologies (Loeb 2001; Kmiec et al. 2006), and the likelihood of proliferation is reduced with low initial frequencies.
One way to circumvent the cost and time of direct analyses is to employ indirect tests, which, through statistical frameworks, estimate the likelihood that patterns of polymorphism distribution can be explained by recombination (Posada & Crandall 2001; Bruen et al. 2006), and many tests are currently available. A useful collection of some methods can be accessed via the RDP3 (http://darwin.uvigo.es/rdp/rdp.html, Martin et al. 2005), and RecombiTEST (http://www.lifesci.sussex.ac.uk/CSE/test/index.php, Piganeau et al. 2004) websites. It should be noted that, as well as levels of recombination, the effectiveness of indirect tests is associated with other parameters, including recombinant frequency and sequence diversity (Posada & Crandall 2001; Wiuf et al. 2001; Bruen et al. 2006). This means that detection of a recombination event is not guaranteed by any one indirect test, particularly at low levels of recombination (Bruen et al. 2006). Further, the power of indirect tests is often determined using sequences simulated under a set of general parameters (Posada & Crandall 2001; Bruen et al. 2006). When they are tested using sequence simulated under mitochondrial parameters, overall they do less well (D. J. White & N. J. Gemmell, unpublished). A consensus view is that wherever indirect tests are required, multiple tests should be used.
A final consideration is that, even if statistical support is given for recombination, true recombination may not be detected. Instead, the signal may derive from a molecular artefact that resembles a recombinant molecule, resulting from polymerase infidelity during the amplification reaction (termed ‘jump PCR’). In the study of Kraytsberg and colleagues, where definitive evidence for intermolecular recombination in humans was revealed, they incorporated single-molecule PCR to control for this phenomenon (Kraytsberg et al. 2004).