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

Text AbstractIn 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 (FST 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 Nes before the LGM, experienced severe bottlenecks (Ne [~] 102-103), 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. Article summaryThis research examines how climate changes shaped genetic diversity of cactus wrens across North American warm deserts. Using coalescent methods, researchers tracked effective population size changes over 100,000 years, using ecological niche modeling they predicted habitat suitability across climate periods. Results showed that continental and peninsular populations experienced bottlenecks during the Last Glacial Maximum, followed by demographic recovery on warm periods. However, the sex chromosome (Z) revealed male-biased demographic patterns in peninsular populations. Future projections indicated habitat suitability reductions for peninsular populations, highlighting conservation concerns. These findings demonstrate that past climate shaped genetic diversity of cactus wrens.