Climate cycles drive demographic history and genomic divergence in cactus wrens ( Campylorhynchus brunneicapillus ) across North American warm deserts

In this study, we characterized the genetic structure and reconstructed the demographic history of cactus wrens ( Campylorhynchus brunneicapillus), an endemic species of desert regions of North America, that shows a clear phenotypic and genotypic variation. We evaluated the effects of historical climate change on the structure and population dynamics of desert species using genomic data through genotyping by sequencing (GBS) and applied a population structure analysis ( F _ST and ADMIXTURE), revealing two genetically differentiated groups: one continental and another peninsular in Baja California. Subsequently, we implemented the MSMC2 coalescent model on data divided into autosomal regions and the Z sex chromosome to estimate changes in effective population size ( Ne ) through evolutionary time. Additionally, we developed ecological niche models (ENMs) projected to the Last Glacial Maximum (LGM), Last Interglacial (LIG), Present times, and Future (2060 - 2080). Results indicate that both populations maintained moderated Ne ’s before the LGM, experienced severe bottlenecks ( Ne ∼ 10 ² -10 ³ ), followed by a sustained expansion. However, recovery was limited to the Z chromosome of the peninsular population. These findings reveal how glaciations and interglacials shaped the evolutionary history of desert species and provide genomic evidence of the splitting of C. affinis from C. brunneicapillus .