Genomic Insights into Population Divergence, Evolutionary History, and Ecological Adaptation in the Fourfinger Threadfin Eleutheronema

Abstract

The four-finger threadfin Eleutheronema, comprising of Eleutheronema tetradactylum and Eleutheronema rhadinum, mostly known for its cultural significance and high nutritional value, is a commercially important fish species in China's coastal waters, but their genomic diversity and evolutionary history remain mostly unknown. This thesis offers a comprehensive investigation into the population diversity, genomic divergence, evolutionary history, and ecological adaptation of Eleutheronema species.

This thesis generated the first high-quality chromosome-level genome for E. tetradactylum (~582 Mb) and E. rhadinum (~591 Mb), respectively, serving as fundamental genomic resources for understanding the evolutionary history and distinct biological characteristics of Eleutheronema species. Resequencing the genomes of E. tetradactylum revealed that thermal and salinity might be the driving factors for geographical divergence between populations in China and Thailand. Selective sweeps analysis identified multiple genes associated with fatty acids and immunity that were under strong selection, likely contributing to adaptation through selective breeding. Additionally, resequencing data from E. rhadinum populations in China and Thailand revealed that geographical divergence shaped the different demographic trajectories and regional patterns of deleterious mutations. Purifying selection incurred fitness costs associated with inbreeding and played a role in reducing the genetic burden of homozygous deleterious mutations in the Thailand's E. rhadinum.

Furthermore, comparative genomics analysis revealed significant expansions of gene families associated with innate immunity, olfaction, and opsin in Eleutheronema species, likely facilitating adaptation to their benthic lifestyle. This thesis supported the role of natural selection, particularly long-term linked selection, in shaping the genomic landscape of divergence between E. tetradactylum and E. rhadinum. It also highlighted the impact of recombination variation and introgression in the sympatric speciation of Eleutheronema species. Moreover, the elongation of the very long-chain fatty acids (Elovl) gene family was identified to understand the molecular basis of fatty acid biosynthesis in Eleutheronema. This thesis also addressed the importance of interindividual variation at the HIF-pathway, which may impact hypoxia fitness in Eleutheronema.

This thesis not only provides crucial genomic resources for the future studies on Eleutheronema, but also offers significant insights into the divergence, evolutionary history, adaptation, and speciation of Eleutheronema species, with implications for other fish species.

Date of Award	26 Jul 2024
Original language	English
Awarding Institution	City University of Hong Kong
Supervisor	Wenxiong WANG (Supervisor)