Pangenomes reveal extensive structural variation in a suboscine passerine bird, the Pearly-vented Tody-Tyrant (Hemitriccus margaritaceiventer)

Structural variants (SV) are major drivers of evolutionary processes such as adaptation and speciation, yet their complexity and dynamics in wild populations remain largely unexplored. Avian diversity is highest in the Neotropics, primarily due to the suboscine passerine radiation; however, despite this diversity, genomic resources and studies of SVs in suboscines are scarce compared to their sister clade, the oscine passerines ('songbirds'). Here, we used long-read and chromatin conformation capture sequencing to assemble a high-quality scaffolded reference genome and construct a population-scale pangenome from 10 de novo haplotype assemblies of the Pearly-vented Tody-Tyrant (Hemitriccus margaritaceiventer), a suboscine bird with plumage variation across its distribution in South American dry forests. Our pangenome graph reveals extensive structural variation, with the chromosomal distribution of SVs strongly predicted by simple and low-complexity repeats - highlighting how specific repeat architecture may influence genome evolution. We discovered intraspecific copy number variation in multigene families including beta-keratin genes, which may contribute to ongoing integument diversification. We also found presence-absence variation in protocadherin genes, which may be associated with loss of constraint on genes underlying neurological processes such as synaptic plasticity and potentially vocal learning - consistent with the innate, rather than learned, song production of suboscines compared to oscines. Additionally, we identified a 306 kb inversion spanning several melanin pigmentation-associated genes (e.g. MREG, MLPH, RAB17), making it a candidate SV underlying known intraspecific plumage variation. Our study establishes a population-scale pangenome resource for a suboscine, enabling characterization of the genome-wide abundance, diversity, and distribution of SVs within this species.