Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life

Abstract

Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, 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 find no significant 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) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows 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.

Phylogenomics and genital morphology of cave raptor spiders (Araneae, Trogloraptoridae) reveal an independent origin of a flow‐through female genital system

“…Sections were examined using a JEOL JEM 1011 electron microscope equipped with an Olympus Megaview III digital camera. Both analytical treatments of the dataset resulted in the same topology (Figure 1a, Figures S1-S3 Supporting Information), which is congruent with the more widely sampled phylogenomic analyses of Fernández et al (2018). In analyses of concatenated loci, all the clades were recovered with strong support (bootstrap proportions > 95%) for the 50% matrix, and all but one were highly supported for the 75% matrix (Dysdera + Orsolobidae bootstrap proportion = 92%).…”

“…Total RNA extraction and postprocessing until transcriptome assembly follow Fernández et al (2018) and Kallal, Fernández, Giribet, and Hormiga (2018). Orthology assessment was conducted on amino acid sequences using UPhO (Ballesteros & Hormiga, 2016).…”

“…A total of 28 taxa, including the newly sequenced taxon T. marchingtoni, were analyzed (Table 1). We combined the new transcriptomic data from T. marchingtoni with a sample of previous transcriptomic data of species from the study of Fernández et al (2018), covering the main groups of true spiders (Araneomorphae), its sister group (Mygalomorphae), and a denser coverage of the clade Synspermiata.…”

Cytogenetics of entelegyne spiders (Arachnida, Araneae) from southern Africa

“…The superfamily Araneoidea comprises more than 15 families of ecribellate orb-weavers (Wheeler et al 2016, Dimitrov et al 2017, Fernández et al 2018. We analysed members of two families of this highly diversified group, which presents the first insights into the cytogenetics of African araneoids.…”

“…Alongside the families Uloboridae and Deinopidae, the superfamily Oecobioidea (comprising families Hersiliidae and Oecobiidae) forms the so-called "UDOH grade" (Fernández et al 2018), which is consistently recovered by molecular data in proximity to the RTA clade (Garrison et al 2016, Wheeler et al 2016, Fernández et al 2018. The superfamily Oecobioidea historically formed part of Eresoidea; however, this grouping was never supported by molecular analyses (Miller et al 2010, Wheeler et al 2016, Fernández et al 2018. Theridiidae (E-L).…”