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Abstract The search for the genetic basis of phenotypes has primarily focused on single nucleotide polymorphisms, often overlooking structural variants (SVs). SVs can significantly affect gene function, but detecting and characterizing them is challenging, even with long-read sequencing. Moreover, traditional single-reference methods can fail to capture many genetic variants. Using long reads, we generated a Capuchino Seedeater (Sporophila) pangenome, including 16 individuals from 7 species, to investigate how SVs contribute to species and coloration differences. Leveraging this pangenome, we mapped short-read data from 127 individuals, genotyped variants identified in the pangenome graph, and subsequently performed FST scans and genome-wide association studies. Species divergence primarily arises from SNPs and indels (< 50 bp) in non-coding regions of melanin-related genes, as larger SVs rarely overlap with divergence peaks. One exception was a 55 bp deletion near the OCA2 and HERC2 genes, associated with feather pheomelanin content. These findings support the hypothesis that the reshuffling of small regulatory alleles, rather than larger species-specific mutations, accelerated plumage evolution leading to prezygotic isolation in Capuchinos.
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Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters
Abstract Incomplete speciation can be leveraged to associate phenotypes with genotypes, thus providing insights into the traits relevant to the reproductive isolation of diverging taxa. We investigate the genetic underpinnings of the phenotypic differences between Sporophila plumbea and Sporophila beltoni. Sporophila beltoni has only recently been described based, most notably, based on differences in bill coloration (yellow vs. black in S. plumbea). Both species are indistinguishable through mtDNA or reduced-representation genomic data, and even whole-genome sequencing revealed low genetic differentiation. Demographic reconstructions attribute this genetic homogeneity to gene flow, despite divergence in the order of millions of generations. We found a narrow hybrid zone in southern Brazil where genetically, yet not phenotypically, admixed individuals appear to be prevalent. Despite the overall low genetic differentiation, we identified 3 narrow peaks along the genome with highly differentiated SNPs. These regions harbor 6 genes, one of which is involved in pigmentation (EDN3) and is a candidate for controlling bill color. Within the outlier peaks, we found signatures of resistance to gene flow, as expected for islands of speciation. Our study shows how genes related to coloration traits are likely involved in generating prezygotic isolation and establishing species boundaries early in speciation.
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- Award ID(s):
- 2232929
- PAR ID:
- 10579676
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Evolution
- Volume:
- 78
- Issue:
- 6
- ISSN:
- 0014-3820
- Format(s):
- Medium: X Size: p. 1161-1173
- Size(s):
- p. 1161-1173
- Sponsoring Org:
- National Science Foundation
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