Genome evolution across temporal scales, from synteny and evolution spanning >200 million years to genomic divergence and mito-nuclear discordance among congeners since the Miocene
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Authors
Chen, Ying
Date
2025-03-26
Type
thesis
Language
eng
Keyword
Mito-nuclear discordance , Speciation , Sex system , Genome assembly , Genome annotation , Genome evolution , Hybridization , Synteny , Frog
Alternative Title
Abstract
Our understanding of evolution and speciation has deepened tremendously due to advances in assessing whole-genome variation and analyzing vast quantities of genomic and transcriptomic datasets. In this thesis, I use genomic tools to examine frog and toad genomic evolution across 220 million years, as well as to conduct a case study on within-genus evolution involving hybridization between non-sister species. I first assembled and annotated the first chromosome-level reference genome for the western chorus frog (Pseudacris triseriata), a temperate North American treefrog (Hylidae), and compared it to 28 other anuran genomes. Using additional double digest restriction-site associated DNA sequencing (ddRADseq) data, I deduced the XY sex system in P. triseriata, finding a candidate sex-determining region being an ~1Mb indel variant on the largest chromosome pair. My comparative genomic analyses revealed exceptionally conserved chromosomal evolution along with gene orders in frogs and toads over their 220 million years of evolution. I found that some BUSCO genes were not syntenic among lineages and may have influenced anuran trait evolution and lineage diversification. In the second part of my thesis, I leveraged this annotated genome to examine a mito-nuclear discordance case involving two non-sister chorus frog lineages, P. triseriata and the boreal chorus frog (P. maculata), which began diverging about 10 million years ago. I sampled across the range of these two species in Eastern North America and assessed genetic variation using both mitochondrial and nuclear markers. Phylogeographic analyses revealed that chorus frog populations occupying northern Michigan, Ontario, Québec and New York possessed mitochondrial genomes that were most closely related to P. maculata overlying a nuclear genome that was more related to P. triseriata, a result of hybridization between the two species beginning in the late Pleistocene. While gene flow between this hybrid lineage and P. triseriata continued, I found some evidence of reproductive isolation, with steep geographic clines in both mtDNA and nuDNA in a narrow contact zone in Ontario and well-structured geographic diversity. My research shows that species can remain compatible and hybridize after long periods of divergence and that hybridization may be an important evolutionary force in lineage diversification and evolution.
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ProQuest PhD and Master's Theses International Dissemination Agreement
Intellectual Property Guidelines at Queen's University
Copying and Preserving Your Thesis
This publication is made available by the authority of the copyright owner solely for the purpose of private study and research and may not be copied or reproduced except as permitted by the copyright laws without written authority from the copyright owner.