Table 5.

Single-copy Orthologous Quintets Partitioned by Functional Category in Six Allotetraploid Species.

Species	Functional Category	Number of Quintets	dS a	dN b	ω c	ω PAT (95% CI)d	ω MAT (95% CI)e
Quinoa	Non-organelle-targeted	6,885	0.499	0.096	0.193	0.290 (0.28–0.30)	0.332 (0.32–0.34)
	Mitochondria-targeted noninteracting	615	0.444	0.079	0.179	0.278 (0.25–0.31)	0.319 (0.29–0.35)
	Mitochondria-targeted interactingf	213	0.477	0.105	0.220	0.352 (0.29–0.42)	0.369 (0.31–0.43)
	Mitochondria enzyme complexes	69	0.465	0.084	0.180	0.279 (0.19–0.40)	0.350 (0.26–0.45)
	Plastid-targeted noninteracting	900	0.449	0.081	0.180	0.279 (0.25–0.30)	0.322 (0.30–0.35)
	Plastid-targeted interacting	212	0.463	0.091	0.197	0.290 (0.24–0.34)	0.356 (0.29–0.43)
	Plastid enzyme complexes	74	0.483	0.081	0.168	0.305 (0.15–0.40)	0.361 (0.21–0.47)
Wheat	Non-organelle-targeted	3,507	0.1882	0.035	0.187	0.444 (0.41–0.48)	0.201 (0.19–0.21)
	Mitochondria-targeted noninteracting	476	0.179	0.030	0.169	0.466 (0.38–0.55)	0.241 (0.20–0.28)
	Mitochondria-targeted interacting	67	0.162	0.033	0.206	0.651 (0.30–0.82)	0.215 (0.12–0.31)
	Mitochondria enzyme complexesg	38	0.191	0.039	0.206	0.661 (0.27–0.81)	0.077 (0.05–0.13)
	Plastid-targeted noninteracting	561	0.179	0.031	0.171	0.469 (0.39–0.54)	0.237 (0.20–0.28)
	Plastid-targeted interacting	86	0.171	0.030	0.175	0.353 (0.19–0.49)	0.278 ( 0.17–0.36)
	Plastid enzyme complexes	38	0.228	0.030	0.131	0.310 (0.09–0.53)	0.159 (0.06–0.27)
Cotton	Non-organelle-targeted	14,957	0.108	0.038	0.348	0.422 (0.41–0.43)	0.535 (0.52–0.55)
	Mitochondria-targeted noninteracting	1,076	0.106	0.033	0.309	0.391 (0.35–0.43)	0.480 (0.44–0.52)
	Mitochondria-targeted interacting	375	0.103	0.034	0.332	0.392 (0.35–0.44)	0.564 (0.48–0.65)
	Mitochondria enzyme complexes	100	0.119	0.037	0.310	0.376 (0.28–0.53)	0.568 (0.42–0.72)
	Plastid-targeted noninteracting	1,502	0.106	0.033	0.309	0.392 (0.36–0.43)	0.514 (0.48–0.56)
	Plastid-targeted interacting	270	0.102	0.031	0.303	0.352 (0.31–0.40)	0.525 (0.45–0.60)
	Plastid enzyme complexes	94	0.100	0.029	0.289	0.322 (0.23–0.46)	0.516 (0.38–0.68)
Coffee	Non-organelle-targeted	3,397	0.181	0.055	0.306	0.486 (0.45–0.52)	0.429 (0.40–0.46)
	Mitochondria-targeted noninteracting	306	0.181	0.051	0.281	0.533 (0.44–0.61)	0.548 (0.40–0.66)
	Mitochondria-targeted interacting	121	0.170	0.052	0.306	0.513 (0.39–0.65)	0.426 (0.33–0.55)
	Mitochondria enzyme complexes	31	0.187	0.057	0.307	0.597 (0.25–0.92)	0.482 (0.39–0.96)
	Plastid-targeted noninteracting	420	0.180	0.051	0.285	0.510 (0.42–0.57)	0.514 (0.39–0.61)
	Plastid-targeted interacting	88	0.163	0.049	0.300	0.438 (0.29–0.66)	0.537 (0.36–0.76)
	Plastid enzyme complexes	25	0.159	0.043	0.273	1.182 (0.23–5.17)	0.363 (0.08–1.44)
Tobacco	Non-organelle-targeted	7,323	0.438	0.090	0.205	0.522 (0.38–0.54)	0.631 (0.40–0.65)
	Mitochondria-targeted noninteracting	675	0.375	0.071	0.190	0.466 (0.40–0.53)	0.654 (0.58–0.73)
	Mitochondria-targeted interacting	209	0.374	0.082	0.220	0.490 (0.42–0.57)	0.628 (0.53–0.74)
	Mitochondria enzyme complexes	59	0.392	0.070	0.178	0.490 (0.37–0.61)	0.770 (0.50–1.37)
	Plastid-targeted noninteracting	952	0.380	0.072	0.191	0.470 (0.42–0.52)	0.628 (0.57–0.69)
	Plastid-targeted interacting	183	0.370	0.074	0.200	0.541 (0.41–0.71)	0.591 (0.47–0.73)
	Plastid enzyme complexes	72	0.406	0.070	0.173	0.736 (0.35–1.21)	0.604 (0.37–0.99)
Brachypodium	Non-organelle-targeted	11,886	0.449	0.105	0.234	0.328 (0.31–0.45)	0.347 (0.33–0.47)
	Mitochondria-targeted noninteracting	1,310	0.388	0.0759	0.196	0.318 (0.30–0.47)	0.327 (0.27–0.40)
	Mitochondria-targeted interacting	367	0.398	0.086	0.216	0.386 (0.27–0.38)	0.405 (0.30–0.49)
	Mitochondria enzyme complexes	116	0.399	0.0645	0.162	0.222 (0.14–0.34)	0.126 (0.36–0.24)
	Plastid-targeted noninteracting	1,497	0.389	0.0763	0.196	0.305 (0.26–0.37)	0.312 (0.26–0.38)
	Plastid-targeted interacting	256	0.396	0.0829	0.209	0.385 (0.24–0.49)	0.284 (0.20–0.39)
	Plastid enzyme complexes	83	0.485	0.0626	0.129	0.123 (0.06–0.22)	0.276 (0.08–0.50)

^a d_S here reflects the ML estimates of the total synonymous branch length of the entire tree from 1,000 gene-level bootstrap replicates (5 replicate runs per bootstrap replicate).

^b d_N here reflects the ML estimates of the total nonsynonymous branch length of the entire tree from 1,000 gene-level bootstrap replicates (5 replicate runs per bootstrap replicate).

^c ω here reflects the ML estimates of quintet-wide d_N relative to quintet-wide d_S.

^d ω _PAT refers to the ML estimate of the ω value for the paternal subgenome branch, with 95% CIs obtained from 1,000 gene-level bootstrap replicates (5 replicate runs per bootstrap replicate).

^e ω _MAT refers to the ML estimate of the ω value for the maternal subgenome branch, with 95% CIs obtained from 1,000 gene-level bootstrap replicates (5 replicate runs per bootstrap replicate).

^fInteracting genes are defined as those nuclear-encoded genes whose products interact with the mitochondrial/plastid genomes or gene products according to the CyMIRA classifications scheme (Forsythe et al. 2019).

^gSignificant result is likely due to poor alignment. See supplementary fig. S4, Supplementary Material online for more details.