Larks (Alaudidae) have enlarged neo-sex chromosomes, which are formed by the ancestral avian sex-chromosomes and additional fusions of autosomal regions from chromosome 4A, 3, and 5. The ancestral avian sex chromosomes are known in all today living bird species and are in passerines formed by four evolutionary strata which have ceased recombining at separate times. Within the genus Alauda, additional neo-strata are present that have formed before the divergence of the genus. One additional, large stratum is evident on chromosome 3 within the Skylark and the Rasolark (stratum 3-c), which is not evident in the Oriental lark. Neither is this stratum evident in eastern populations of the Skylark. This observation is in conflict with the autosomal phylogenetic tree of Alauda, but is in agreement with the mitchondrial tree, indicating that the true species history of the genus might be complex, and vary across genomic regions. This observed pattern can be explained in three ways. Multiple observations of independent and parallel events of recombination cessation across the sex chromosomes within the lark family makes two independent events of recombination cessation in the Skylark and the Raso lark plausible. However, the extent of recombination cessation in both species is remarkably similar, suggesting the there was one single event of recombination cessation. Alternatively, stratum 3-c could be a longstanding polymorphism. While W-polymorphisms surviving for an extended amount of evolutionary time is considered unlikely due to inefficient selection on the W, the modern Skylark effective population size is large for being a bird species. If the population has been large for long enough, a polymorphism could potentially have been sustained over long evolutionary time scales, with diffferent haplotypes fixing in the Raso lark and Oriental lark. Finally, this observation could be explained by introgression, most likely from the large Skylark population into the much smaller Raso lark population. Introgression of a W chromosome might be considered unlikely under Haldane’s rule, especially in the context the unusual size of these sex-chromosomes, which provide a large target for the accumulation of incompatibilities. However, there might be other processes acting that provide a net fitness benefit for females, an introgression event could potentially have re-introduced previously lost genes, mask deleterious variation segregating on Z and the 3-c homologous PAR and inflate female functional heterozygosity. Here, I will use whole genome re-sequenced females and males to investigate evolutionary histories across the genome in contrast the autosomal species tree of the genus Alauda. In addition of the autosomal regions, I will extract and analyse sequences from the Z and W chromosomes, as well as the mitochondrion. I will perform various phylogenetic, population genomic and demographic analyses along these genomic regions to elucidate the evolutionary history and timing of events of these regions in the Alauda lark genus. With this study, I aim to provide insight into how neo-sex chromosomes can experience dynamic evolution and highlight their role and potential in species evolution.