Genome Biology & Evolution 

We are combining genome sequencing, comparative genomics, phylogenetics and gene expression profiling to explore the role of genome duplication in fish evolution, to reconstruct the evolution of gene families, and to infer patterns of genome evolution

Representative papers:
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Bertolotti AC, Layer RM, Gundappa MK, Gallagher MD, Pehlivanoglu E, Nome T, Robledo D, Kent MP, Røsæg LL, Holen MH, Mulugeta TD, Ashton TJ, Hindar K, Sægrov H, Florø-Larsen B, Erkinaro J, Primmer CR, Bernatchez L, Martin SAM, Johnston IA, Sandve SR, Lien S, Macqueen DJ. 2020. The structural variation landscape in 492 Atlantic salmon genomes. Nature Commun. 11: 5176.  https://doi.org/10.1038/s41467-020-18972-x
 
Redmond AK, Zou J, Secombes CJ, Macqueen DJ, Dooley H. 2019. Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons: Front. Immunol. 10:1558.
 
Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien, S. Martin SAM, Holland PW, Sandve SR, Macqueen DJ. 2017. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 18:111. DOI: 10.1186/s13059-017-1241-z
 
Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ. 2015. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc. Natl. Acad. Sci. USA. 30:  9370–9375. DOI10.1073/pnas.1419329112
 
Macqueen DJ, Johnston, IA. 2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc. Soc. Biol. B. 281: 20132881. DOI: 10.1098/rspb.2013.2881
From Redmond et al. Clock rooting reveals that complement-like immunity existed in the first animals. In Prep.