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. Author manuscript; available in PMC: 2019 Jan 2.
Published in final edited form as: Nat Genet. 2018 Jul 2;50(8):1102–1111. doi: 10.1038/s41588-018-0153-5

Figure 3. Inference of koala population demographic history and analysis of contemporary koala populations using genome mapped markers.

Figure 3

a Phylogenetic tree of the CYP2 gene family in the koala (31 members of CYP2), as compared with marsupials: tammar wallaby, Tasmanian devil, gray short-tailed opossum; and eutherian mammals: human, rat, mouse, dog, platypus; and outgroup chicken. Two independent monophyletic expansions are seen in koala, in the CYP2C subfamily (highlighted by red sectors).

b CYP synteny map showing expansion of CYP2C genes in koala and mouse suggesting that this adaptive characteristic has arisen via tandem duplication.

c-h Selection analysis of CYP gene expansion: c, Normalised dN-dS (SLAC method) across 152 CYP sequences (sites with data koala and ≥ 1 other species). Points at the end of bars indicate statistically significant (α = 0.1) evidence for selection across the tree: four sites show positive selection (SLAC method; green circular points); 70 sites episodic selection (MEME method; blue diamonds). d, Episodic selection across koala CYPs (n = 31 sequences); x-axis shows codons under selection anywhere on the tree (identified in c). e, Comparison of mean episodic selection among koala CYP sequences (n = 70 codons). f, g, h, Mean EBF (natural log transformed, zeroes excluded) for koala tree tips (n = 31; red) relative to all others (n = 121; nine species; blue). Points show mean; error bars ± 95% CI; codon positions as in a. A “+” or “-” indicates that the koala mean value falls above/below the 95% CI for all other species (i.e. a two-tailed test at α = 0.05). Statistics are unadjusted for multiple comparisons.