A Fine Scale Analysis of a Tropical Suture Zone
In my dissertation, I use a comparative approach to exploit an outstanding natural experiment, a suture zone in the rainforest of northeast Australia, to answer questions about speciation and hybridization. The suture zone consists of twenty identified contacts between phylogeographic lineages, mostly within morphologically defined species. Although the contacts in the zone likely formed concurrently in response to Holocene expansion from glacial refugia, the lineage-pairs meeting in the contacts exhibit a wide range of genetic divergences. This natural variation enables analysis of the outcomes of secondary contact at different stages of the divergence process. Importantly, although most studies of speciation focus on lineages that show marked phenotypic divergence, I focus on morphologically cryptic lineages, which, though common in nature, have been understudied in this regard. Through my dissertation, I consider contact zones between six lineage-pairs within four morphologically-defined skink species, Carlia rubrigularis, Lampropholis coggeri, Saproscincus basiliscus, and S. lewisi.
Through this work, I find support for the reality of cryptic species and argue that the presence of cryptic species can suggest a wider plurality of speciation models than we typically consider (Chapter 1). Indeed, by combining multilocus methods and dense sampling, I find that reproductive isolation between phylogeographic lineages scales tightly with divergence (Chapter 2). These results support the widespread, yet previously unsubstantiated, notion that phylogeographic structure of increasing depth represents a continuum towards complete speciation, even in the absence of overt ecologically-driven divergent selection. I extend these results by looking at introgression across the genome, finding that genome-wide selection, driven by selection against hybrids, structures introgression patterns much more strongly than locus-specific selection histories (Chapter 3). By analyzing the sole lineage-pair in this system that exhibits genealogical discordance, I suggest that geographic stability across time is key to driving divergence (Chapter 4). Further, through combining a fine-scale investigation of a single contact zone with simulations and a meta-analysis, I argue that selection against hybrids, in the form of intrinsic genetic incompatibilities, maintains species boundaries at these contact zones (Chapter 5). Finally, as my work is enabled by emerging genomic technologies for non-model organisms, I summarize my genomics approach, and its associated benefits and challenges, as applied to transcriptome data from these lineages (Chapter 6).