Weak Nuclear Divergence Despite Pronounced Mitochondrial Divergence Within a Widespread Desert‐Inhabiting Palearctic Lark (Aves: Alaudidae)

ABSTRACT The Bar‐tailed Lark Ammomanes cinctura is a polytypic bird species with a wide distribution. One of its three subspecies, A. c. arenicolor , has previously been found to show deep mitochondrial divergence between its geographically most distant populations, from Morocco and Saudi Arabia, respectively. We applied an integrative approach using genome‐wide single nucleotide polymorphisms (SNPs), mitochondrial DNA (mtDNA), morphological and bioacoustic data to investigate the evolutionary divergence within A. cinctura . We confirmed the existence of two distinct mitochondrial clades: one including samples from Morocco and Cape Verde Islands and the other including samples from Saudi Arabia and Iran. We estimated that these lineages diverged 2.14 million years ago (Mya). In contrast, we recovered shallow divergence in the nuclear SNPs (estimated split time: 0.08 Mya) between the samples from Cape Verde–Morocco versus Saudi Arabia–Iran, and population structure analyses favored a single genetic cluster. Analyses of museum specimens confirmed earlier statements that the eastern subspecies, A. c. zarudnyi , has slightly longer wing and tail than the two others, and that the three subspecies are slightly divergent in plumage. Finally, our analyses of vocalisations suggested that some geographical differences might exist, but the commonest song type is found across the range. The reasons for the considerably deeper divergence in mitochondrial DNA relative to that of nuclear SNPs are unresolved and will require more comprehensive sampling to elucidate.