Arthropod mtDNA paraphyly: a case study of introgressive origin

Mitochondrial paraphyly between arthropod species is not uncommon, and has
been speculated to 
largely be the result of incomplete lineage sorting
(ILS) of ancestral variation within the common 
ancestor of both species,
with hybridisation playing only a minor role. However, in the absence of

comparable nuclear genetic data, the relative roles of ILS and
hybridisation in explaining 
mitochondrial DNA (mtDNA) paraphyly remain
unclear. Hybridisation itself is a multifaceted 
gateway to paraphyly,
which may lead to paraphyly across both the nuclear and mitochondrial

genomes, or paraphyly that is largely restricted to the mitochondrial
genome. These different 
outcomes will depend upon the frequency of
hybridisation, its demographic context, and the extent 
to which mtDNA is
subject to direct selection, indirect selection, or neutral processes.
Here we 
describe extensive mtDNA paraphyly between two species of
iron-clad beetle (Zopheridae) and 
evaluate competing explanations for its
origin. We first test between hypotheses of ILS and 
hybridisation,
revealing strong nuclear genetic differentiation between species, but with
the 
complete replacement of Tarphius simplex mtDNA through the
introgression of at least five mtDNA 
haplotypes from T. canariensis. We
then contrast explanations of direct selection, indirect selection, 
or
genetic drift for observed patterns of mtDNA introgression. Our results
highlight how 
introgression can lead to complex patterns of mtDNA
paraphyly across arthropod species, while
simultaneously revealing the
challenges for understanding the selective or neutral drivers that
underpin such patterns.