Limestone karst formations are unique ecosystems that harbor many species found nowhere else in the world. Unfortunately, these ecosystems are severely threatened due to their importance in the cement industry. This is especially notable in Southeast Asia where extensive tracts of karst outcrops are being quarried to the ground, resulting in the inevitable extinction of numerous species of plants and animals. Consequently, conservation efforts have been geared towards the discovery and description of new species to highlight the importance of this ecosystem as imperiled arks of biodiversity. However, relatively little research has focused on understanding the mechanisms that have generated this biodiversity. This project aims to elucidate the genetic mechanisms responsible for the evolution of karst-adapted organisms by investigating how genes interact with the environment to drive the formation of new species. Results from this study will not only aid in informing conservation measures in threatened karst habitats worldwide, but will also contribute towards the understanding of how species adapt to an ever changing environment.
Bent-toed Geckos of the genus Cyrtodactylus exhibit a wide array of specialized ecotypes that are associated with different habitats. Among these, karst-adapted species have evolved independently six times in three distantly related clades in Malaysia, indicating that the diversification of karst lineages may be ecologically driven (ecological speciation). The replicated evolution of karst adaptation in Bent-toed Geckos represents a unique and compelling natural system to determine whether geckos transitioning to karsts are subjected to ecologically-based divergent selection that ultimately leads to speciation. Because karst ecosystems are characterized by unique geomorphological features and physiochemical conditions that set them apart from non-calcareous environments, divergent selection is expected to act on independently evolving karst lineages that occur in separate but similar karst environments. This study will use genome-wide SNP data obtained using a double-digest restriction-site associated DNA (ddRADseq) protocol due to the availability of large numbers of independent loci across the genome, which enable the detection of departure from neutrality and signatures of selection. A hybridization capture using RAD probes method (hyRAD) will then be used to obtain comparable and orthologous loci among more distantly related groups. Signatures of ecologically-based divergent selection can then be detected by identifying genetic polymorphisms that exhibit high correlation with environmental variables using a latent factor mixed model (LFMM) method. Additionally, karst and non-karst lineages are expected to be in different stages of reproductive isolation, with older lineages showing less (or a complete lack of) gene flow among populations compared to lineages that have diverged more recently, in which gene flow may be common.
