A comparative approach to discover the genomic determinants of natural adaptations to a sugar-rich diet in nectarivorous birds

• Applicant: Professor Dr. Michael Hiller
• Subject Area: Evolution, Anthropology ; Bioinformatics and Theoretical Biology
• Term: from 2019 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 418083601

• Final Report Year: 2023

Final Report Abstract

Excessive consumption of glucose- and fructose-sweetened soft drinks is a major risk factor for type 2 diabetes in humans. While a sugar-rich diet has adverse consequences on human health, several bird species that consume predominantly nectar are well-adapted to such a sugar-rich diet. This raises a fundamental question: What are the genes that are important for natural adaptations to a sugar-rich diet in these nectarivorous birds? To address this question, we sequenced, assembled and annotated new reference-quality genomes of six bird species, covering nectarivores and close outgroups. We performed comprehensive comparative genomic screens for mutational gain and loss of function signatures that occurred specifically in nectarivores, and analyzed shifts in gene expression patterns. We discovered that FBP2, a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved in ancestral hummingbirds. FBP2 knockdown in an avian muscle cell line upregulated glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization had upregulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss in ancestral hummingbirds was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight. Additionally, we found positive selection and expression upregulation in key glycolytic enzymes in hummingbirds, revealing genomic changes that contribute to dietary adaptation in hummingbirds. To investigate the extent of convergent molecular evolution we compared four independent nectarivorous bird lineages. Our genome-wide screens considering both changes in the gene sequences and in gene expression, and changes in conserved non-coding regions, identified important enzymes and transcriptional regulators that likely contribute to sugar diet adaptations. Furthermore, our experiments revealed functional differences between genes in nectarivorous birds and their non-nectar outgroups. Our analyses show that both convergent and lineage-specific solutions contributed to nectar feeding adaptations. While individual genes are rarely targeted in all four lineages, molecular convergence patterns in both protein-coding and non-coding regions are more prevalent at the level of similar functions and pathways, revealing that similar dietary adaptations often evolve by targeting functionally-similar but distinct genes.

Publications

• RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements. GigaScience, 8(11).
  Osipova, Ekaterina; Hecker, Nikolai & Hiller, Michael
  
• Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737-746.
  Rhie, Arang; McCarthy, Shane A.; Fedrigo, Olivier; Damas, Joana; Formenti, Giulio; Koren, Sergey; Uliano-Silva, Marcela; Chow, William; Fungtammasan, Arkarachai; Kim, Juwan; Lee, Chul; Ko, Byung June; Chaisson, Mark; Gedman, Gregory L.; Cantin, Lindsey J.; Thibaud-Nissen, Francoise; Haggerty, Leanne; Bista, Iliana; Smith, Michelle ... & Jarvis, Erich D.
  
• Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater. GigaScience, 11.
  Robledo-Ruiz, Diana A.; Gan, Han Ming; Kaur, Parwinder; Dudchenko, Olga; Weisz, David; Khan, Ruqayya; LiebermanAiden, Erez; Osipova, Ekaterina; Hiller, Michael; Morales, Hernán E.; Magrath, Michael J. L.; Clarke, Rohan H.; Sunnucks, Paul & Pavlova, Alexandra
  
• Integrating gene annotation with orthology inference at scale. Science, 380(6643).
  Kirilenko, Bogdan M.; Munegowda, Chetan; Osipova, Ekaterina; Jebb, David; Sharma, Virag; Blumer, Moritz; Morales, Ariadna E.; Ahmed, Alexis-Walid; Kontopoulos, Dimitrios-Georgios; Hilgers, Leon; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Hiller, Michael; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R. ... & Zhang, Xiaomeng
  
• Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science, 379(6628), 185-190.
  Osipova, Ekaterina; Barsacchi, Rico; Brown, Tom; Sadanandan, Keren; Gaede, Andrea H.; Monte, Amanda; Jarrells, Julia; Moebius, Claudia; Pippel, Martin; Altshuler, Douglas L.; Winkler, Sylke; Bickle, Marc; Baldwin, Maude W. & Hiller, Michael