Inversions maintain differences between migratory phenotypes of a songbird

Area of Science:

• Evolutionary genetics
• Genomics
• Speciation research

Background:

• Structural rearrangements are crucial for adaptation and speciation.
• Identifying these in non-model organisms is challenging.
• Willow warblers (Phylloscopus trochilus) offer a unique system to study these processes.

Purpose of the Study:

• To characterize structural rearrangements in divergent genomic regions of the willow warbler.
• To investigate the role of these rearrangements in local adaptation, migration, and environmental gradients.
• To identify candidate genes associated with these adaptive traits.

Main Methods:

• Utilized a combination of long reads, linked reads, and optical mapping for high-resolution genome assembly.
• Analyzed three divergent chromosome regions in Phylloscopus trochilus.
• Dated divergence times between inverted and non-inverted haplotypes.

Main Results:

• Identified large inversions (0.4–13 Mb) in all three studied divergent regions.
• Found similar divergence times (~1.2 Myrs) for inverted and non-inverted haplotypes across regions.
• Detected additional functional differences and identified candidate genes for migration and environmental adaptation.

Conclusions:

• Genomic inversions play a significant role in local adaptation and potentially speciation in the willow warbler.
• The findings support a model of secondary contact and hybridization between allopatric populations where inversions originated.
• Advanced genomic techniques enable the discovery of genes underlying complex adaptive traits.