Genome wide SNP data in Maderian wolf spiders
Genomic data provides useful information regarding population history and species divergence. However, interpreting complex evolutionary processes remains challenging, particularly in cases of recent divergence and ancestral polymorphism. This study addresses the taxonomic and evolutionary complexities of two endemic Hogna wolf spiders from Madeira, H. maderiana from Porto Santo and H. insularum from Madeira, Desertas, Bugio, and Porto Santo, which exhibit mitochondrial gene tree discordance and ambiguous morphological boundaries. Using ddRADseq genomic data, population, and coalescent-based demographic analyses, we aim to determine whether these two nominal species represent a case of early divergence with unsorted molecular markers due to incomplete lineage sorting (ILS). Moreover, we want to determine if they are hybridising within the island of Porto Santo, where they co-occur, or if they represent a single species exhibiting extreme morphological polymorphism. Our genetic structure analyses revealed two genetic clusters, one for each nominal species, but individuals identified as H. insularum from Porto Santo exhibited signs of admixture. However, the demographic modelling and D-statistics rejected gene flow and instead suggest the existence of a third lineage in Porto Santo. This lack of genetic separation between these lineages likely reflects short recent divergence and unsorted ancestral polymorphisms. Overall, our findings highlight the challenges of inferring hybridisation solely based on population structure analyses, which may lead to an overestimation of gene flow. This study shows the importance of integrating demographic modelling and genetic data to resolve complex evolutionary histories and emphasizes the need for careful interpretation of genomic data to avoid misattributing gene flow.