Divergent selection, recombination variability, and noncoding introgression drive speciation and adaptation in...

Area of Science:

• Genomics
• Evolutionary Biology
• Ichthyology

Background:

• The fourfinger threadfin (Eleutheronema rhadinum) is a valuable fisheries resource in China, but its genomic characteristics and evolutionary history are not well understood.
• Understanding its genome is crucial for appreciating its evolutionary adaptations and for conservation efforts.

Purpose of the Study:

• To assemble the first chromosome-level genome of Eleutheronema rhadinum.
• To conduct a comparative genomics analysis with its sister species, Eleutheronema tetradactylum.
• To investigate the genomic basis of speciation, adaptation, and gene flow in Eleutheronema.

Main Methods:

• Chromosome-level genome assembly of E. rhadinum (~591 Mb).
• Comparative genomics analysis with E. tetradactylum.
• Analysis of olfactory receptors across 48 fish lineages.
• Genome resequencing and identification of highly differentiated regions.
• Investigation of noncoding variations and introgression footprints.

Main Results:

• Identified significant gene family expansions in innate immunity, olfaction, and opsin.
• Demonstrated habitat-specific evolutionary pressures shaping olfactory system diversification.
• Revealed widespread, heterogeneous genomic differentiation driven by natural selection, including linked selection.
• Highlighted the role of noncoding variations in Eleutheronema speciation.
• Observed introgression across the genome, influenced by recombination rates and noncoding regions.

Conclusions:

• The study provides crucial genomic resources for E. rhadinum.
• Genomic divergence is influenced by natural selection, noncoding variations, and recombination rates.
• Recombination rates play a key role in maintaining species boundaries despite gene flow, offering insights into Eleutheronema evolution and conservation.