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

Rivera-Colon, Angel G.

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

Description

Title

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

Author(s)

Rivera-Colon, Angel G.

Issue Date

2022-11-17

Director of Research (if dissertation) or Advisor (if thesis)

Catchen, Julian M

Doctoral Committee Chair(s)

Catchen, Julian M

Committee Member(s)

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

Department of Study

Evolution Ecology Behavior

Discipline

Biology

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• antarctic notothenioids
• icefish
• RADseq
• genome assembly
• evolution
• genomics
• population genetics

Abstract

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.

Graduation Semester

2022-12

Type of Resource

Thesis

Copyright and License Information

© 2022 Angel G. Rivera-Colón

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