mtDNA and nuclear discordance
Culicoides albertensis , C. sonorensis , and C.
variipennis have a considerable amount of genome-wide differentiation
(Fig. 1); however, there was no clear differentiation of the COI gene
(Fig. 5). In fact, several individuals of C. albertensis andC. variipennis shared identical haplotypes. Multiple studies have
shown a high degree of genetic similarity in mtDNA between C.
sonorensis and C. variipennis (Hopken, 2016; Jewiss-Gaines,
Barelli, & Hunter, 2017; Shults, 2015), though it was proposed that
this was due to misidentifications. As all of the individuals included
in our mitochondrial haplotype analysis from the current study were
identified to species using the SNP data, this lack of mitochondrial
separation has an underlying biological source. Ongoing hybridization
with “leaky” pre-zygotic isolation, or a semipermeable species
boundaries, has been shown to produce mitochondrial introgression
without detectable nuclear DNA introgression (Chan & Levin, 2005;
Harrison, 1990). This is likely due to the fact the mitochondrial genome
is independent of the nuclear genome and thus unlinked to the genes
contributing to reproductive isolation (Harrison, 1989). This does not
appear to be the case throughout the entire complex though as
hybridization was also found between C. sonorensis and C.
occidentalis and the mtDNA from these two species was highly divergent.
In addition to the convergence of a single haplogroup by three species,C. occidentalis was found to have two distinct haplogroups based
on geography (Fig. 5). The mean percent divergence between C.
occidentalis from California (CABL) and C. occidentalis from the
other collection sites (BC-NV-UT) was equal to the divergence between
the other species in the complex (Table 3). This high level of
differentiation within C. occidentalis could be due to geographic
isolation alone; however, endosymbionts have also been shown to
significantly increase mitochondrial diversity in the presence of
geographic structure (Ballard, Chernoff, & James, 2002; Behura, Sahu,
Mohan, & Nair, 2001). Naturally occurring endosymbionts have been found
in Culicoides midges, including C. sonorensis (Covey et
al., 2020; Pagès, Muñoz-Muñoz, Verdún, Pujol, & Talavera, 2017), and
recently, a Cardinium sp. was linked to mitochondrial divergence
of C . imicola (Pilgrim et al., 2021). Further screening is
needed to determine the diversity and abundance of endosymbionts
infecting Culicoides midges, though the possibility remains that
these could be playing a role in the phylogeographical structure ofC. occidentalis .