Table 2.

Confounding influences of inherited symbionts on the interpretation of the history of a species from mtDNA.

observation	classical explanation	alternative
low mtDNA diversity within population	bottleneck of species due to colonization or population size contraction	recent spread of a symbiont or new strain of existing symbiont
high mtDNA diversity within population	large and old population	presence of more than one symbiont strain within population maintains diversity
low mtDNA diversity between populations	exchange of genes on regular basis or recent isolation	symbiont-induced selective sweep through both populations, homogenizing mtDNA
high mtDNA diversity between populations	historical isolation of populations	presence of different symbiont strains maintaining haplotype structure despite nuclear gene flow
paraphyly of single species on mtDNA-based tree	true paraphyly or incorrect previous ascertainment of species status	transfer of symbiont via hybridization, followed by selective sweep. Good species, not paraphyletic