Application of High-Throughput Sequencing Methods to Spider Phylogenomics and Speciation with a Focus on the Mygalomorph Genus Aptostichus

Abstract

Spiders are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve higher level spider evolutionary relationships, I assembled a transcriptome-based data set comprising 70 ingroup spider taxa and executed phylogenomic analyses of a core ortholog supermatrix (Chapter I). To address questions at the species/population level, I employed a combination of two genomic sequencing approaches – targeted enrichment (anchored hybrid enrichment) and restriction enzyme based (genotyping-by-sequencing) – to evaluate relationships within the Aptostichus atomarius species complex (Chapter II). Finally, to understand the genomic basis of species diversity at the level of transcription, I compared transcriptomes of eight closely related species including ingroup A. atomarius complex members and outgroup taxa. Within the transcribed genes I detected gene families under selection and recovered sequences potentially associated with dune endemic lineages (Chapter III). All three chapters are designed with a single overarching goal: to move spider evolutionary biology and systematics forward by generating and utilizing next-generation sequence data and resources.