Several hypotheses have been proposed to   explain such high mtDNA variation (Webb et al. 2011). First, sympatric intraspecific divergences   in mtDNA may be an artifact caused by nuclear mitochondrial pseudogenes, or numts. This is genetic   material that has been translocated from the mitochondrial to the nuclear   genome. These copies are assumed to be nonfunctional (Bensasson et al. 2001),   evolve fast, accumulate frame shifts and stop codons, and show double peaks   when sequenced (Bertheau   et al. 2011; Triant and Hayes 2011). Second, as stated above, the   divergent lineages may in fact reflect cryptic species, implying that the   taxonomy is incorrect. Recent avian examples include thrushes (Turdus spp.)   in western Amazonas (O'Neill et al. 2011), the winter wren (Troglodytes   troglodytes) in North America (Toews and Irwin 2008), and seven nonpasserine   migratory birds from the Philippines (Lohman et al. 2010).

解释线粒体DNA的这种种内高变异有几种假设（Webb et al. 2011）。首先，线粒体DNA的同域内mtDNA差异可能是由核-线粒体假基因（numts）引起的假象。这种假基因是已经从线粒体转移到核基因组的遗传物质。这些假设不起作用的拷贝（Bensasson et al. 2001），进化迅速，积累了开放阅读框的移位和终止密码子，并在测序时表现出双峰现象（Bertheau et al. 2011; Triant and Hayes 2011）。第二，如上所述，不同的谱系实际上可能反映了隐存种的存在，这意味着之前分类是不正确的。最近的鸟类例子包括亚马逊西部的画眉（Turdus spp.）（O'Neill et al.   2011），北美的冬季鹪鹩（Toews and Irwin 2008），以及七只来自菲律宾的非游牧候鸟（Lohman   et al. 2010）。