Supplemental Material for Hjelmen et al., 2019

Figure S1: Bayesian Phylogeny reconstruction of Drosophila genus. Drosophila phylogeny was reconstructed using the supermatrix method in MrBayes. Posterior probability values are at each node. Sophophora are found in A. Drosophila are found in B.


Figure S2: Genome Size distribution by chromosome number. Distribution of genome sizes for species with 3, 4, 5, or 6 chromosomes.


Figure S3: Credible shift set for Female Genome size. BAMM analysis estimated the most likely number of rate shifts and their locations for female genome size. Here are the top nine credible shift sets. The most likely set predicts zero shifts. Dots represent the locations of the shifts, f is the probability of that shift set given the data.


Figure S4: Marginal shift tree for female genome size. Branches are extended where rate shifts of female genome size are mostly likely to occur across the phylogeny. Longer branches indicate larger rate shifts. More shifts are located in the Drosophila subgenus, supporting a difference in patterns of genome size change between the subgenera.


Figure S5: Credible shift set for Male Genome size. BAMM analysis estimated the most likely number of rate shifts and their locations for male genome size. Here are the top nine credible shift sets. The most likely set predicts zero shifts. Dots represent the locations of the shifts, f is the probability of that shift set given the data.


Figure S6: Marginal shift tree for male genome size. Branches are extended where rate shifts of male genome size are mostly likely to occur across the phylogeny. Longer branches indicate larger rate shifts. More shifts are located in the Drosophila subgenus, supporting a difference in patterns of genome size change between the subgenera.


Figure S7: Credible shift set for Sex Difference. BAMM analysis estimated the most likely number of rate shifts and their locations for sex difference in genome size. Here are the top nine credible shift sets. Dots represent the locations of the shifts, f is the probability of that shift set given the data. The most likely set predicts zero shifts.


Figure S8: Marginal shift tree for sex difference. Branches are extended where rate shifts of sex difference in genome size are mostly likely to occur across the phylogeny. Longer branches indicate larger rate shifts. More shifts are located in the Sophophora subgenus, supporting a difference in patterns of sex difference between the subgenera.


Figure S9: Female genome size mapped on colorized phylogeny. Female genome size was plotted onto a colorized phylogeny to visualize genome size change across time. Darker colors indicate smaller genomes and lighter colors indicate larger genomes.


Figure S10: Male genome size mapped on colorized phylogeny. Female genome size was plotted onto a colorized phylogeny to visualize genome size change across time. Darker colors indicate smaller genomes and lighter colors indicate larger genomes.


Table S1: Table of Accession numbers for sequences used to reconstruct phylogeny


Table S2: Table of genome size estimates.


Table S3: AICc Results from Phylogenetic Model Testing: Evolutionary model testing using fitContinous estimated the likelihood of each model (Ornstein-Uhlenbeck (OU), Brownian motion (BM), and the white noise model (White). According to AICc values, the mostly likely model for trait evolution for female and male genome size and sex difference was OU across the entire Drosophila genus and the two subgenera.


Table S4: Ornstein Uhlenbeck α and σ2 values for Female GS, Male GS, and Sex difference across the Drosophila genus and its subgenera. Parameter estimates (α and σ2) for male and female genome size were remarkably similar across the entire genus, within the Drosophila subgenus, and within the Sophophora subgenus, suggesting whole genome size evolution for each sex is similar. While female and males are similar within each group, there is a higher σ2 value in the Drosophila subgenus than in the Sophophora subgenus, suggesting a higher rate of genome size change. Parameter estimates for sex difference were found to be different between the subgenera, with larger values in the Sophophora subgenus, suggesting higher rates of change in sex differences in Sophophora than Drosophila.