Friesen, V. L. | Search bioRxiv

bioRxiv2026

Widespread introgression and a potential role for a neo-sex chromosome in booby diversification and speciation

Speciation in marine taxa is dynamic and complex, often occurring in the absence of absolute geographic barriers to gene flow. Boobies comprise a clade of seven highly mobile seabird species with high diversity in the eastern Pacific Ocean, where no land barriers separate extant sister species and hybridization is widespread. They exhibit striking diversity in bare-part coloration, an important signal of mate quality, and possess a novel multiple sex chromosome system (Z1Z2Z1Z2 / Z1Z2W), likely resulting from a fusion between an ancestral autosomal microchromosome and the W chromosome. To understand speciation processes in the context of gene flow, we sequenced and analyzed 29 short-read booby genomes and assembled a reference northern gannet genome to (1) test for introgression, (2) characterize genomic patterns of divergence across species, and (3) investigate the gene content and evolution of the neo-sex chromosome. We found that divergence among eastern Pacific sister taxa is temporally associated with periods of glacial maxima. Between periods of glacial maxima, two pairs of sister species (blue-footed and Peruvian boobies; masked and Nazca boobies) exhibit strong signatures of episodic introgression, indicating that speciation has occurred over multiple periods of divergence followed by gene flow. However, in the third pair of sister species, genomic signatures showed higher divergence within brown booby populations than between brown and Cocos boobies. We also identified the epidermal differentiation complex - a gene cassette involved in skin, feather, beak, and claw development - on the neo-sex region of the W chromosome, where it spans the boundary between the putatively recombining and non-recombining regions, with interspecific variation in the exact recombination suppression boundary. We inferred that this complex may contribute to diversity in feather and bare part coloration across boobies. Together, these results reveal that diversification and speciation in a clade of highly mobile seabirds emerged from a complex evolutionary history involving historical climate dynamics, introgression, and sex chromosome evolution.

evolutionary biology↗

bioRxiv2018

A complex copy number variant underlies differences in both colour plumage and cold adaptation in a dimorphic seabird.

Colour morphs associated with different physiological adaptations offer unique opportunities to study the genomic basis of otherwise elusive adaptive traits. These complex balanced polymorphisms are often controlled by groups of tightly linked genes, and understanding how these supergenes evolve and are maintained is an active area of research in evolutionary biology (Schwander et al. 2014, Thompson and Jiggins 2014). Within the Atlantic, the common murre (Uria aalge, a colonial seabird) displays a plumage colour dimorphism ( bridled and unbridled) that seems to be associated with differences in thermal adaptation (Birkhead 1984; Reiertsen et al. 2012). The genes associated with bridling and how these genes affect thermal adaptation are unknown. Using whole genome resequencing, we investigate the genomic basis of differences in colouration and thermal adaptation between the two morphs, and how the association between the two traits is maintained despite random mating. We identify a 60 kb genomic region of high differentiation laying in the intergenic area amongst three candidate genes for colouration and thermal adaptation: retinoic acid receptor beta (RARB), thyroid hormone receptor beta (THRB), and nuclear receptor subfamily 1 group D member 2 (NR1D2 or Rev-erb{beta}). Differentiation is due to a complex copy number variant (CNV) that suppresses recombination locally. We show that this CNV acts as a supergene and maintain association between regulatory elements likely affecting gene expression of one or more of the identified candidate genes. Our analyses also provide insights into the origin of the dimorphism: while copy number proliferation in the unbridled haplotype was potentially mediated by transposable elements (TEs), the bridled haplotype seems to have introgressed from the more cold-adapted sister species, the thick-billed murre (U. lomvia). Our results highlight the role of copy number variants in adaptation, especially when association among traits is maintained in the face of gene flow. They also shed light into the molecular mechanisms of adaptive thermogenesis in birds, which is poorly understood.\n\nHighlightsO_LIDifferences in plumage colour in Atlantic common murres are associated with different thermal adaptations\nC_LIO_LIA single region is highly differentiated between bridled and unbridled morphs\nC_LIO_LIA complex copy number variant in a non-coding region underlies the dimorphism\nC_LIO_LITransposable elements and adaptive introgression from the thick-billed murre seem to explain the origin of the dimorphism\nC_LI

evolutionary biology↗