Using genomics to evolve our understanding of the phylogeographic history of the Galapagos giant tortoise radiation

The endemic Galapagos giant tortoises (Chelonoidis sp.) are iconic emblems of both evolutionary biology and the fight to save endangered species. This radiation of at least 15 lineages across multiple islands can be considered a "natural experiment" and is an excellent study system for evolutionary biology that has the benefit of also being of huge public and conservation interest.

Research over the last 20-years using genetic markers such as microsatellites and mitochondrial gene sequencing has revealed much about the history of divergence among lineages and patterns of colonization across the archipelago. Their phylogeographic history roughly follows the island progression rule (Poulakakis et al. 2020), with older lineages found on the older islands, and younger lineages found on younger islands within the archipelago.

However, this understanding of the radiation has recently been called into question. Current models were developed based on the mitochondrial genome phylogeny, while recent whole nuclear genome sequencing has revealed substantial mito-nuclear discordance (Jensen et al. 2022a). Additionally, several previously unknown lineages (Jensen et al. 2022b and unpublished data) have been discovered through genome sequencing of museum specimens.

Thus, there is a need to build new phylogeographic models that reconcile patterns from both nuclear and mitochondrial genomes and that incorporate all lineages.

Phylogeographic analyses in this system are complicated due to the recent divergence of the lineages (within the last 2 million years), and especially on Isabela Island. Isabela is home to 6 of the living lineages, including some of the most critically endangered, but the island is only estimated to have formed a maximum of 800,000-years ago. Species delimitation analyses have revealed mixed support for whether they should be considered distinct species (Gaughran et al. 2023).

This provides a model system for the process of lineage separation and studying the process of speciation by teasing apart incomplete lineage sorting from ongoing geneflow.

The overall goal of the project will be to use whole genome data from representatives of all living and extinct lineages of Galapagos giant tortoise to build a robust, dated phylogeny, which will be used to underpin biogeographic models to uncover the true history of divergence and colonization in this radiation. As part of this, I also aim to leverage population-level sampling from the most recently diverged lineages on Isabela Island to tease apart incomplete lineage sorting from gene-flow, which will provide evidence as to the potential species status of these lineages.