2025 Theses Doctoral

Extinction on Islands: Integrating Taxonomic, Functional, and Phylogenetic Dimensions of Vulnerability in Fragmented Landscapes

Monagan, Ivan Vincent

Habitat loss and fragmentation are among the most urgent threats to global biodiversity, particularly in tropical ecosystems where high levels of endemism, ecological specialization, and small geographic ranges elevate extinction risk. While island biogeography theory has long provided a foundation for understanding species distributions in fragmented landscapes, its application to real-world conservation remains limited by an underrepresentation of trait-based ecology and phylogenetic frameworks essential for understanding extinction processes. As biodiversity declines accelerate, there is a critical need for frameworks that link ecological and evolutionary processes to predict extinction vulnerability.

This dissertation addresses this gap by developing an eco-evolutionary framework that synthesizes island biogeography, trait-based ecology, and phylogenetics to investigate the mechanisms driving species decline in Madagascar’s High Plateau herpetofauna.

Chapter 1 presents a systematic global review of the Taxon Cycle theory - an influential model in island biogeography that frames species distributions as cyclical processes of colonization, ecological specialization, and range contraction leading to extinction. Through a structured review of 50 empirical studies across a wide range of taxa and insular systems, this chapter evaluates the strength of evidence for Taxon Cycle dynamics and assesses how modern phylogenetic tools—particularly time-calibrated phylogenies and population genomics—have enabled new empirical tests of the model. The results reveal broad support for Taxon Cycle dynamics, with 84% of studies showing evidence across all stages and 34% demonstrating robust support. These findings underscore the continued relevance of the Taxon Cycle, especially when integrated with modern advances in evolutionary biogeography, as a predictive framework for biogeographic patterning, invasive species dynamics, and extinction risk in island systems.

Chapter 2 applies island biogeography theory to an extensive dataset of amphibian and reptile assemblages from continuous and fragmented tropical forests in Madagascar’s High Plateau. This chapter introduces a novel, multi-scalar species–area relationship (SAR) framework that integrates species occurrence data with ecological traits and environmental variables across the widest known range of patch sizes (0.06–30,372 ha) studied for terrestrial herpetofauna. By disaggregating SAR patterns across key ecological axes - landscape continuity, taxonomic identity, habitat specialization, and environmental heterogeneity - this analysis provides a robust framework for disentangling the ecological effects of fragmentation. The results show that patch size is the strongest predictor of species richness, particularly for forest specialists, with sharp declines below the 10-hectare threshold. Area alone explained up to 61% of the variation in specialist richness, while habitat generalists inflated richness estimates in small patches, obscuring specialist losses. These findings highlight the nonlinear, taxon-specific effects of fragmentation and underscore the value of trait-informed SAR models. Evidence of extinction debt and substantial species deficits in smaller fragments suggests that current richness levels underestimate long-term biodiversity loss, especially for endemic and range-restricted species, reinforcing the need for conservation strategies that prioritize habitat area and ecological specialization.

Chapter 3 develops a trait-based framework to assess species-specific vulnerability to fragmentation. This approach combines ecological traits, phylogenetic relationships, and species responses across three complementary metrics: frequency of occurrence, changes in abundance, and minimum patch size occupied. Results reveal a stepwise pattern of extinction risk, with life history traits - particularly reproductive mode, body size, and microhabitat use - predicting declines across stages of fragmentation. Amphibians were primarily filtered by reproductive strategies, with aquatic breeders exhibiting greater sensitivity, while reptile responses were driven by activity period and microhabitat use. Functional and phylogenetic diversity responded asymmetrically. Amphibians in large patches showed high evolutionary diversity but reduced trait diversity, suggesting ecological filtering. In contrast, reptiles displayed stable phylogenetic structure but increasing trait convergence in smaller patches. Isolation selectively filtered phylogenetically and functionally distinct species, altering community composition without significantly reducing total richness. Together, these findings demonstrate that fragmentation acts as a trait- and lineage-specific ecological filter and underscores the importance of incorporating life history and evolutionary context into conservation planning for fragmented tropical systems.

Collectively, this dissertation demonstrates that integrating ecological traits, evolutionary history, and spatial heterogeneity provides a more nuanced and predictive understanding of extinction dynamics in fragmented tropical landscapes. By developing a novel, trait-informed perspective grounded in island biogeography, this work contributes to both the refinement of biogeographic theory and the development of informed conservation strategies for biodiversity hotspots like Madagascar.