The Evolution of Pholcidae (Araneae) Spiders

Abstract

The roles of trait evolution, introgression, and mitochondrial genome (mitogenome) evolution in shaping heterogeneous biodiversity within the tree of life are not yet fully understood. This thesis examines these factors in the diverse spider family Pholcidae (Araneae), which comprises five subfamilies (rough number of described species): Ninetinae (80), Arteminae (100), Modisiminae (500), Smeringopinae (130), and Pholcinae (900). We applied target capture sequencing (TCS) of ultra-conserved elements (UCE) and low-coverage whole genome sequencing (lcWGS) to 193 pholcid samples, sequencing new genetic markers and recovering them from TCS and lcWGS data to create the largest Pholcidae phylogeny with 956 species. Phylogenetic inference was conducted using different data matrices and methods (concatenation vs. coalescence; Maximum Likelihood vs. Bayesian), alongside the reconstruction of speciation/extinction dynamics and the measurement of evolutionary flexibility of body size and leg length, testing their correlations with speciation/extinction and species richness. We also investigated introgression using D, f₄−ratio, fbranch, and fdM statistics, and assembled and characterized mitogenomes from TCS and lcWGS data. We redefined Arteminae as two subfamilies: Arteminae (including only Artema and Priscula) and Phy***inae [1] (for 'other Arteminae') and identified two new species [1] from northeastern Brazil, forming a new genus [1] and a new subfamily Cai***inae [1]. Our results proposed a new Pholcidae phylogeny: (Pholcinae + Smeringopinae) + (Cai***inae + ((Arteminae + Ninetinae) + (Phy***inae + Modisiminae))). We also assembled 193 pholcid mitogenomes, with 98 being complete or near-complete, representing an 18% increase in spider mitogenomes. Some mtPCGs and tRNA genes were difficult to annotate with existing methods. The gene order of mitochondrial protein-coding genes (mtPCGs) within Pholcidae is highly conserved. We found significant purifying selection and strong codon usage bias in mtPCGs, and the latter was likely driven by selection rather than mutation bias. We observed large mitochondrial genetic distances. We detected multiple introgressions within Pholcidae, both inter-subfamily and inter-genus. Introgression and rapid mitogenome evolution may contribute to discordance in Pholcidae phylogenies. We identified positive correlations between evolutionary flexibility and speciation rate, trait evolution rate, and species richness. We noted a near-isometric relationship between body size and leg length in species-rich lineages, while species-poor lineages showed positive allometry; the former indicates stabilizing selection, the latter suggests directional selection. We observed a positive correlation between trait evolution rate and microhabitat shift rate, indicating that environmental heterogeneity and frequent microhabitat shifts enhance evolutionary flexibility, allowing exploitation of new resources and habitats. We argue that a lack of evolutionary flexibility, such as seen in dwarfism or gigantism, might lead to evolutionary dead ends. Organisms may not evolve according to Cope's rule. We call for improved spider mitogenome annotation and consider the impact of introgression on phylogenetic discordance in phylogenomics. Our analyses provide new insights into Pholcidae evolution and mechanisms underlying uneven biodiversity distribution. (Note [1]: The taxonomic names will be made available in a journal publication, and I will not apply the formal taxonomic names in this thesis in order to avoid any possible confusion about validity and availability; for the same reason, new subfamily names below are written in a way that clearly shows that they are not made available by this thesis.)