Crack the ‘Blackbox’: A Response to “The Dangers of Data Blackboxing: A Comment on Elias et al., Journal of Biogeography (2024)”

Aim This is in response to the criticism raised in JBI‐24‐0467.R1 against our paper, Elias et al. (2024, Journal of Biogeography, 51, 1049–1063). Location Southwestern Pacific Islands. Taxon Argyrodes bonadea. Methods Contrary to claims of specimen misidentification, we demonstrated the limitations of morphology‐based taxonomy in our targeted cryptic species, Argyrodes bonadea complexes, and emphasised that RAD‐seq data were our primary data that supported our result, while CO1 served as Supporting Information. Results Host specificity patterns—Amami‐Okinawa Lineage (AOL) specialising in Cyrtophora (Amami) and Nephila (Okinawa), versus the generalist Austral‐Asia Lineage (AAL)‐were robustly supported through rarefaction analyses of field data using current data. Re‐analyses of both raw and polished CO1 datasets confirm consistent haplotype networks, effectively refuting concerns about sequence quality and result replicability in Elias et al. (2024). While mitochondrial CO1 alone offers limited resolution, the genome‐wide SNPs provide clear evidence that ecological divergence is driven by host shifts, rather than geographic barriers such as the Kerama Gap, which underlies genetic differentiation. Conclusions We maintain our confidence in our conclusions while recognising methodological differences in interpreting between traditional (morphological and CO1) and complex genomic data. The challenges raised reflect broader methodological challenges in reconciling traditional biological concepts with emerging modern bioinformatics tools.