Comparative and evolutionary genomics of secondarily temperate adaptation in a non-Antarctic icefish

White-blooded Antarctic icefishes are a group of highly derived vertebrates, specialized to both the chronic cold of the Southern Ocean and life without hemoglobin. Their specialized phenotypes constrain icefishes mostly to the cold, highly oxygenated Antarctic waters. Yet, despite their extreme physiology, a single icefish species, the pike icefish Champsocephalus esox, successfully colonized and likely adapted to the temperate environments off the Patagonian coast of South America. However, the genetic mechanisms that enabled this polar-to-temperate transition from highly specialized Antarctic populations were previously unknown. In this work, I describe the first genomic characterization of a secondarily temperate icefish species, comparing both the genome and population-level variation of the temperate icefish (C. esox) against its Antarctic sister species (Champsocephalus gunnari). In the first research chapter (chapter 2), I describe the RADINITIO software, a pipeline for the simulation of RADseq experiments. Using this software, I model library construction parameters and identify sources of error that can impact RADseq experiments, which I then used to optimize empirical RADseq libraries used for genotyping C. esox and C. gunnari samples. In my second research chapter, I use the data from these RADseq libraries, in addition to generating chromosome-level genome assemblies for each species, to characterize the genomic architecture of secondarily temperate variation in C. esox. I find large-scale conservation in the structure and organization of temperate and Antarctic icefish genomes. However, I find evidence of structural variation in the C. esox lineage that co-localizes with regions of elevated genetic diversity and signatures of selection, highlighting possible candidate genes underlying temperate adaptation in this system. For my last research chapter, I expand on this RADseq analysis by implementing a novel Tree Sequence-based approach, which I use to reconstruct the genealogical relationships between Antarctic and temperate icefish populations, in addition to determining the age of temperate-adapted haplotypes in C. esox. I find abundant reciprocal monophyly in the genetic variation of RAD loci between C. esox and C. gunnari, indicating near complete lineage sorting between both species, likely aided by strong differential selection. Moreover, I find that candidate haplotypes for temperate adaptation in C. esox are not older than the rest of the variation in the genome, and therefore likely originated de novo during the speciation process. Overall, these results provide a view of the history of temperate adaptation in icefish and serve as a basis for the understanding of how specialist species can evolve in response to rapidly changing environments, highly relevant for cold-adapted Antarctic species in the face of climate change.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Rivera-Colon, Angel G.

Contributors dc:contributor

• Catchen, Julian M
• Cheng, Chi-Hing C
• Fuller, Rebecca
• Roca, Alfred L

• Antarctic Notothenioids
• Icefish
• Radseq
• Genome Assembly
• Evolution
• Genomics
• Population Genetics

Statement dc:rights

• © 2022 Angel G. Rivera-Colón

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/117556

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F117556