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. 2019 Oct 7;9(10):3167-3179.
doi: 10.1534/g3.119.400560.

Genome Size Evolution Differs Between Drosophila Subgenera With Striking Differences in Male and Female Genome Size in Sophophora

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Free PMC article

Genome Size Evolution Differs Between Drosophila Subgenera With Striking Differences in Male and Female Genome Size in Sophophora

Carl E Hjelmen et al. G3 (Bethesda). .
Free PMC article

Abstract

Genome size varies across the tree of life, with no clear correlation to organismal complexity or coding sequence, but with differences in non-coding regions. Phylogenetic methods have recently been incorporated to further disentangle this enigma, yet most of these studies have focused on widely diverged species. Few have compared patterns of genome size change in closely related species with known structural differences in the genome. As a consequence, the relationship between genome size and differences in chromosome number or inter-sexual differences attributed to XY systems are largely unstudied. We hypothesize that structural differences associated with chromosome number and X-Y chromosome differentiation, should result in differing rates and patterns of genome size change. In this study, we utilize the subgenera within the Drosophila to ask if patterns and rates of genome size change differ between closely related species with differences in chromosome numbers and states of the XY system. Genome sizes for males and females of 152 species are used to answer these questions (with 92 newly added or updated estimates). While we find no relationship between chromosome number and genome size or chromosome number and inter-sexual differences in genome size, we find evidence for differing patterns of genome size change between the subgenera, and increasing rates of change throughout time. Estimated shifts in rates of change in sex differences in genome size occur more often in Sophophora and correspond to known neo-sex events.

Keywords: Drosophila; Genome size; phylogenetic comparative methods; sex chromosome.

Figures

Figure 1
Figure 1
Phylogeny of Drosophila genus. The phylogeny of Drosophila was reconstructed using a supermatrix method in MrBayes. Posterior support values for each node can be found in Figure S1. Further analyses referring to Sophophora and Drosophila are based on the taxa's placement in the clades that split at the node indicated with an asterisk. The phylogeny was dated using known divergence times. Here, sex difference for all lineages is reconstructed using a simple Brownian motion model. Negative trait values correspond to species with larger genomes in males whereas positive values correspond to species with larger genomes in females.
Figure 2
Figure 2
Genome Size by Sex and Sex Difference Calculation between Sophophora and Drosophila (Left panel) Whole genome size comparisons between Drosophila (left) and Sophophora (right). Male whole genome sizes are indicated in red. Female whole genome sizes are indicated in black. (Right panel) Intersexual difference comparison between the subgenera.
Figure 3
Figure 3
Intersexual difference between documented Neo-Sex, XO, and XY species.
Figure 4
Figure 4
Rate of change in genome size and sex difference change through time. (A) The rate of female genome size change throughout time (B) The rate of male genome size change throughout time (C) The rate of sex difference change throughout time. The left panels (red) are for the entire Drosophila genus. The middle panels (blue) represent the Sophophora subgenus. The right panels (green), represent the Drosophila subgenus.

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