Mitochondrial genome duplications, particularly within the control region, can influence evolutionary trajectories and population structure, yet their prevalence and dynamics in birds remain insufficiently understood. The rey‐headed lapwing Vanellus cinereus has recently undergone a rapid range expansion in Japan, providing a unique opportunity to study genome evolution under demographic change. We combined nanopore long‐read sequencing and Sanger validation to characterize complete mitogenomes of 44 V. cinereus individuals from historical and newly established populations across Japan, along with partial sequences from a congener, the northern lapwing V. vanellus . We analyzed structural variations, gene conversion events, and phylogenetic relationships to elucidate the evolutionary history of these populations. All V. cinereus individuals harbored a conserved ~ 2.5 kb tandem duplication spanning cytochrome b to the control region. The duplicated copies exhibited high similarity within individuals (mean 99.05%) with evidence of ongoing concerted evolution. We identified a ‘chimeric' individual displaying discordant phylogenetic positions between copies within single long‐reads, capturing a snapshot of the incomplete homogenization process via gene conversion, rather than heteroplasmy. Phylogenomic analysis revealed a specific lineage (‘Akita–Okayama' clade) that became predominant in the recently established Okayama population (62.5%), likely due to a founder effect. This study demonstrates the utility of long‐read sequencing for resolving complex mitochondrial structures. The results reveal that the mitochondrial genome of V. cinereus is shaped by the interplay of structural instability (duplication), concerted evolution, and demographic history (founder effects) during range expansion.
Nagai et al. (Sun,) studied this question.