Bioinformatics & Genomics Unit, Center for Genomic Regulation, Barcelona, Spain Museum of Comparative Zoology, Harvard University, MA, USA
Dating back to almost 400 My, spiders are amongst the most diverse terrestrial predators but their phylogeny and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics and lineage diversification analyses. We assembled a transcriptome-based dataset of 159 spider species to scrutinize family-level interrelationships. Moreover, we used our phylotranscriptomic backbone to constrain the analysis of a Sanger dataset for nearly 1,000 species to explore lineage diversification. Lastly, we leveraged our transcriptomic data to investigate functional novelties that putatively drove spider diversification. Our analyses, based on ca. 2,500 genes, reject a single origin of the orb-web (the “ancient orb-web hypothesis”), and suggest that orb-webs evolved multiple times since the late Triassic-Jurassic. We found no strong association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) revealed an enrichment in genes related to behavior and sensory reception, the Retrolateral Tibial Apophysis (RTA) clade—the most diverse araneomorph spider lineage—showed enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.
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