Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Though among the most controversial topics in systematic and evolutionary biology, species are a fundamental unit in biology, and are utilized by and critical to a wide variety of studies in the life sciences. Despite this importance, little work has focused on developing and examining objective methods for species delimitation until recently. Further, New Guinea and the surrounding regions are among the most diverse and geologically complex regions globally, yet the region remains poorly explored biologically, and little work has examined the evolutionary history of the fauna in the region. To investigate the influence of factors such as sampling intensity, species richness, and phylogenetic structure on discovery methods for species delimitation, I combine simulated and empirical data. In Chapter 1, I use simulated data to examine the accuracy of three discovery methods for species delimitation under a variety of different sampling strategies. I find that genetic clustering algorithms, such as Structurama, can be highly accurate in identifying even recent divergences with limited sampling of individuals and of loci, and that Gaussian clustering can be similarly accurate, though somewhat less sensitive to detecting recent divergences. However, my results show that nonparametric delimitation is highly sensitive to errors in gene genealogy estimation, and generally fails to delimit species accurately when true coalescent gene genealogies are unknown, as in empirical applications. In Chapters 3 and 4, I apply these methods empirically to examine the species boundaries, as well as the phylogeny and other aspects of the evolutionary history of, scincid lizards of the C. bicarinata and C. fusca groups, respectively. My results in Chapter 3 indicate that species delimitation analyses may be prone to underestimating the number of species by identifying only higher levels of clustering in systems with deep phylogenetic structure. I additionally find evidence for several cryptic species in the group, including deep, species-level divergence among the populations of C. storri from Australia, the Aru Islands, and New Guinea, despite their recent connectivity via Sahul Shelf emergence during Pleistocene glaciations. Through also examining niche evolution in the group, I find evidence for niche conservatism among most species in the group, but two species, C. bicarinata and C. sp. Amau from eastern Papua New Guinea, show evidence for environmental niche divergence. Analyses of the C. fusca group in Chapter 4 provide further evidence for a tendency of discovery methods for species delimitation to under-detect species in groups with high diversity or deep phylogenetic structure. Genetic clustering algorithms based on the complete dataset only identify a small number of clusters that correspond largely to deep phylogenetic clades, but when restricted to within these clades, this method identifies clusters that correspond well to finer, putative species-level structure. I also find evidence for extensive cryptic diversity in this group, identifying 28 distinct species among my sampling of 16 currently recognized species, as well as other incongruence with current taxonomy, including synonymous species and mis-assigned populations, supporting previous evidence of the need for extensive taxonomic revision in the C. fusca group. My biogeographic analyses also providence evidence that the C. fusca group likely evolved in Australia or Australia and New Guinea before diversifying in New Guinea, dispersing at least twice across Lydekker’s line into Wallacea, and possibly also recolonizing Australia. Finally, in Chapter 5, I take a more comprehensive approach, and combine genomic and morphological data to test the validity of and examine the demographic history of two putative species of Tribolonotus from the islands of Buka and Bougainville in the northwestern Solomon Archipelogo. I use next-generation sequencing to collect a genomic dataset of several thousand loci, and apply species discovery (genetic clustering algorithms) and species validation (Bayes factor delimitations) to test for speciation between these populations. My results support this speciation event, despite the recent connectivity between these islands. I also collect a suite of morphological characters for this group and provide evidence for morphological divergence and diagnosibility. Demographic analyses applied using approximate Bayesian computation and diffusion analysis further provide evidence for a complex demographic scenario in which migration between these populations continued for some time following their initial divergence, but subsequently decreased in rate or ceased entirely. Combined, these results yield extensive insight into the utility of several methods for species delimitation, the taxonomy and systematics of Carlia and Tribolonotus in New Guinea and the surrounding regions, and the complex processes responsible for driving the generation and maintenance of the phenomenal diversity in the Sahul shelf region.



Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Austin, Christopher C.