*2.4. Multiple Functional Transfers of Mitochondrial rps1 in Papilionoideae*

A phylogenetic analysis of nuclear and mitochondrial copies of *rps1* for papilionoid legumes was conducted (Figure 5). Nuclear genomes of two *Trifolium* species (*T. pratense* and *T. repens*) (Table S1) included multiple *rps1* copies. Nuclear copies of *rps1* were placed in two separate positions, one that included *Lotus* sister to the taxa in the tribes Fabeae and Trifolieae and the second with four genera of the tribe Trifolieae (*Trigonella*, *Melilotus*, *Medicago* and *Trifolium*). Branch lengths for the nuclear copies of *rps1* were substantially longer than mitochondrial copies indicating accelerated substitution rates. The Trifolieae was monophyletic but the branch leading to the tribe was very short and the bootstrap value (BS = 43%) was low. In Trifolieae, the mitochondrial *rps1* sequences formed a paraphyletic grade sister to a monophyletic group of nuclear *rps1* (BS = 96%).

**Figure 5.** Maximum likelihood phylogeny of *rps1* gene. Bootstrap values are indicated at nodes. Sequences from mitogenome are indicated in brown. Sequences from nuclear genome are indicated as black and chromosome (Chr) numbers are specified in the parentheses when available.
