Integrative Approaches Illuminate Evolutionary Divergence in the Bar-tailed Lark Complex ( Ammomanes cinctura)

Abstract: Ammomanes cinctura (Bar-tailed Lark) is a lark species with a wide distribution in the Palearctic. One of its subspecies, A. c. arenicolor, has a wide range across northern Africa, within which it shows very minor morphological variation but deep divergence in the mitochondrial cytochrome b locus between two geographically widely separated populations. There are two additional allopatric subspecies, A. c. cinctura (Cape Verde Islands) and A. c. zarudnyi (Iran to Pakistan), which differ slightly more in morphology. The genomic population structure, evolutionary history, and taxonomic status of the different populations within this species remain unclear. I applied an integrative approach, using genomic single nucleotide polymorphisms (SNPs), mtDNA and morphological data, to investigate the evolutionary divergence within Ammomanes cinctura. I acquired whole-genome sequence data from twelve individuals from Morocco (n=2), Saudi Arabia (n=7), and Iran (n=3), and performed phylogenetic and population structure analyses. Mitochondrial genomes were assembled and cytochrome b was extracted for phylogeny. Biometric measurements and quantified plumage analysis were conducted on museum specimens of all three subspecies. According to the mitochondrial data, the samples from Saudi Arabia and Iran form a clade that is deeply diverged (5.94 Mya, 95%HPD 3.15–8.95 Mya) from a clade comprising the samples from Morocco and Cape Verde Islands. In contrast, the nuclear SNPs recovered a very shallow divergence (0.095 Mya, 95%HPD 0.04-0.16 Mya) and weak population structure between the samples from Morocco vs. Saudi Arabia–Iran. Morphological results indicated that zarudnyi is slightly differentiated from the other two subspecies, with a larger body size, and the three subspecies are slightly divergent in plumage. The close similarity between Moroccan and Saudi Arabian birds in morphology was also confirmed, in conflict with the molecular data – highlighting the problem with trinomials in this case. The results suggest that the deep divergence in mitochondrial DNA is due to a complex evolutionary history.