Table 1. Effective genome size (G_e), indel events per site per generation (u_id), base-substitution mutation rate per generation (u_bs), θ_s (or π_s, denoted by *) measurements for population mutation rate (Watterson 1975; Tajima 1989; Fu 1995), and estimated effective population size (N_e) for seven prokaryotic and eight eukaryotic organisms (see File S1 for details).

Species	Label	Ge (× 107 Sites)	Gc + Gnc (× 107 Sites)	uid (× 10−10 per Site per Generation)	ubs (× 10−10 Events per Site per Generation)	θs or πs	Ne (× 106)
Prokaryotes
Agrobacterium tumefaciens	Agt	0.50	0.57	0.30	2.92	0.200*	342.47
Bacillus subtilis	Bs	0.36	0.43	1.20d	3.35d	0.041	61.19
Escherichia coli	Ec	0.39	0.46	0.37e	2.00e	0.071	179.60
Mesoplasma florum	Mf	0.07	0.08	23.10f	97.80f	0.021	1.07
Pseudomonas aeruginosa	Pa	0.59	0.67	0.14g	0.79g	0.033*	210.70
Staphlyococcus epidermidis	Se	0.21	0.26	1.13	7.40	0.052	35.14
Vibrio cholerae	Vc	0.34	0.39	0.18	1.15	0.110	478.26
Eukaryotes
Arabidopsis thaliana	At	4.21	5.55a	11.20h	69.50h,p	0.008	0.29
Caenorhabditis elegans	Ce	2.50	6.37b	6.69i	14.50q	0.003	0.54
Chlamydomonas reinhardtii	Cr	3.92	5.51	0.44j	3.80j	0.032	43.31
Drosophila melanogaster	Dm	2.32	8.86c	4.61k	51.65k	0.018	0.86
Homo sapiens	Hs	3.65	21.75b	18.20l	135.13l	0.001	0.02
Mus musculus	Mm	3.55	27.17b	3.10m	54.00m	0.004*	1.77
Paramecium tetraurelia	Pt	5.68	7.28	0.04n	0.19n	0.008	101.80
Saccharomyces cerevisiae	Sc	0.87	1.02b	0.92o	2.63o	0.004	7.78

G_c + G_nc is the effective genome size when including the total amount of coding (G_c) and noncoding DNA (G_nc) that is estimated to be under purifying selection. Footnotes in u_id and u_bs indicate data sources (rates pooled when multiple data sources are available), and, when absent, indicate data generated in this study (see Materials and Methods).

^aHaudry et al. (2013).

^bSiepel et al. (2005).

^cHalligan et al .(2004).

^dSung et al. (2015).

^eLee et al. (2012).

^fSung et al. (2012a).

^gSung et al. (2012b).

^hOssowski et al. (2010).

ⁱLipinski et al. (2011).

^jSung et al. (2012a); Ness et al. (2015).

^kSchrider et al. (2013).

^lConrad et al. (2011); O’Roak et al. (2011, 2012); Kong et al. (2012); Campbell and Eichler (2013); Wang and Zhu (2014); The 1000 Genomes Project Consortium (2015).

^mUchimura et al. (2015).

ⁿSung et al. (2012b).

^oLynch et al. 2008); (Zhu et al. 2014).

^pOssowski et al. (2010); (Yang et al. 2015).

^qLipinski et al. (2011).