Ancient introgression and recent hybridization as evolutionary processes in the Galapagos giant tortoises

Overview

Background
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 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. Divergence among the lineages 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, some lineages have more complex histories, and recent analyses of whole-genome sequences (E. Jensen, in prep), have revealed that unexpected, ancient introgression has played a role in the history of some lineages.

In addition to ancient occurrences, there are cases of known recent hybridization due to direct human movement of tortoises among islands. These circumstances have led to a happy accident: there are living hybrids of otherwise extinct species (Russello et al. 2007, Poulakakis et al. 2008, Garrick et al. 2012, Edwards et al. 2013). A breeding program has been established with hybrids between the extinct species from Floreana Island (C. niger) and the extant species from Volcano Wolf, Isabela Island (C. becki), with the goal of increasing the representation of the Floreana genome in the offspring of the program, and repatriating them to Floreana as part of plans to restore the ecology of the island. This breeding program is being closely genetically monitored, to maximize Floreana ancestry in the offspring, while minimizing any negative effects of inbreeding or loss of fitness due to hybrid incompatibility (Miller et al. 2017, Miller et al. 2018).

Objectives
The PhD student will collect and analyse whole genome sequences to gain novel insights into the roles that ancient gene flow and introgression have played in the evolution of Galapagos giant tortoises. By developing in-depth reconstructions of demographic histories and phylogeographic models, the student will develop a new, deeper understanding of the history of these species.

The second goal of the studentship will be to interrogate the genomes of several C. niger/C. becki hybrids that are founders in the captive breeding program to understand the genome-level patterns of hybridization and possible fitness consequences. These results will be used to make recommendations about how the captive breeding program should be managed, providing the student the opportunity to translate their findings into applied conservation actions.

This research will integrate a comprehensive dataset of whole genomes to push forward our understanding of the role of introgression and gene flow in speciation, and genome-level consequences of hybridization. The natural experiment of the Galapagos giant tortoise radiation is the perfect avenue for such study, as it offers numerous recently diverged lineages, with complex histories that can be compared and used to provide context for point estimates among lineages. The results of these studies will be used by the Giant Tortoise Restoration Initiative to guide their captive breeding and repatriation efforts, as they are committed to having their conservation efforts guided by understanding what is most evolutionarily appropriate for these incredible creatures. Research in this system will provide insights that can be used to inform the conservation of other endangered species, particularly those where hybridization is seen as a threat to the integrity of genetically distinct lineages.

Methodology

The student will analyse whole genome sequences from the 12 extant lineages of Galapagos giant tortoise, plus 3 extinct lineages, to build phylogeographic models of the history of this radiation, taking into account our new understandings of demographic history (Jensen et al., in prep) and the well-document geological history of the archipelago (Geist et al. 2014).

The student will also generate whole-genome sequences from founders and offspring in the Floreana captive breeding program. They will use assignment tests on windows across the genome to map out specific regions of the genome with ancestry to C. niger and C. becki for each individual. Knowing which windows are descendant from each parental lineage will allow an assessment of which functional genes are descendant from C. niger in each individual. The student will develop a framework to understand and predict the fitness consequences of the mosaic of C. niger and C. becki ancestry in these hybrid individuals and breeding among them.

Project Timeline

Year 1

Training in laboratory methods, genomic analyses, high performance computing and bioinformatics. Sample acquisition, genome sequencing, literature review

Year 2

Focus on the phylogeographic history project, finalize datasets and analyses, prepare manuscript

Year 3

Focus on analysing the hybrid genomes, finalize datasets and analyses, prepare manuscripts, present at conferences and write thesis

Year 3.5

Finalize analyses, manuscripts and thesis

Training
& Skills

The student will join a highly collaborative, international network of researchers studying Galapagos giant tortoises, and benefit from having multiple mentors available to them.

The student will gain technical skills and specific training in DNA sample and library preparation, bioinformatics and genomic analyses. Over the course of the PhD the student will gain transferable skills such as creative thinking and problem solving, scientific writing, public outreach of science, networking, and technical skills in data analysis and visualization, and high-performance computing.

References & further reading

https://www.galapagos.org/conservation/our-work/tortoise-restoration/

Edwards, D. L., E. Benavides, R. C. Garrick, J. P. Gibbs, M. A. Russello, K. B. Dion, C. Hyseni, J. P. Flanagan, W. Tapia, and A. Caccone. 2013. The genetic legacy of Lonesome George survives: Giant tortoises with Pinta Island ancestry identified in Galápagos. Biological Conservation 157:225-228.
Garrick, R. C., E. Benavides, M. A. Russello, J. P. Gibbs, N. Poulakakis, K. B. Dion, C. Hyseni, B. Kajdacsi, L. Marquez, S. Bahan, C. Ciofi, W. Tapia, and A. Caccone. 2012. Genetic rediscovery of an ‘extinct’ Galapagos giant tortoise species. Current Biology 22:R10-11.
Geist, D. J., H. Snell, H. Snell, C. Goddard, and M. D. Kurz. 2014. A paleogeographic model of the Galápagos islands and biogeographical and evolutionary implications. Pages 145-166 in K. S. Harpp, E. Mittelstaedt, N. d’Ozouville, and D. W. Graham, editors. The Galápagos: a natural laboratory for the earth science. John Wiley & Sons, Inc, New Jersey.
Jensen, E. L., S. Gaughran, R. Garrick, M. A. Russello, and A. Caccone. In Prep. Demographic history and patterns of molecular evolution: surprises from whole genome sequencing in the radiation of extant Galapagos giant tortoises.
Miller, J. M., M. C. Quinzin, N. Poulakakis, J. P. Gibbs, L. B. Beheregaray, R. C. Garrick, M. A. Russello, C. Ciofi, D. L. Edwards, E. A. Hunter, W. Tapia, D. Rueda, J. Carrión, A. A. Valdivieso, and A. Caccone. 2017. Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provide Founders for Species Restoration Program. Scientific Reports 7:11471.
Miller, J. M., M. C. Quinzin, E. H. Scheibe, C. Ciofi, F. Villalva, W. Tapia, and A. Caccone. 2018. Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island. Journal of Heredity 109:620-630.
Poulakakis, N., S. Glaberman, M. Russello, L. B. Beheregaray, C. Ciofi, J. R. Powell, and A. Caccone. 2008. Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Procedings of the National Academy of Science U S A 105:15464-15469.
Poulakakis, N., J. M. Miller, E. L. Jensen, L. B. Beheregaray, M. A. Russello, S. Glaberman, J. Boore, and A. Caccone. 2020. Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. Journal of Zoological Systematics and Evolutionary Research.
Russello, M. A., L. B. Beheregaray, J. P. Gibbs, T. Fritts, N. Havill, J. R. Powell, and A. Caccone. 2007. Lonesome George is not alone among Galápagos tortoises. Current Biology 17:R317-318.

Further Information

Evelyn Jensen, evelyn.jensen@yale.edu

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