Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects

Table 1 Pearson correlation of substitution rates between neighboring fungal genes, for 26 species pairs among 27 fungi.

Pair #	Species 1	Species 2	Avg. divergence	# orthologs	Pearson Correlation	p-value
*1	S_cerevisiae	S_paradoxus	0.2592	4434	0.0234	0.1188
*2	S_cerevisiae	S_bayanus	0.4709	3781	0.0305	0.0606
3	S_castellii	S_mikatae	0.6585	3247	0.0029	0.8649
4	K_lactis	C_glabrata	0.6545	4077	-0.0135	0.3887
5	D_hansenii	C_lusitaniae	0.6926	3425	0.0417	0.0144
6	D_hansenii	C_guilliermondii	0.6842	3538	0.0221	0.1883
7	D_hansenii	L_elongisporus	0.6628	3345	0.0083	0.6275
8	D_hansenii	C_parapsilosis	0.6561	3324	0.0257	0.1378
9	D_hansenii	C_tropicalis	0.6104	3358	0.0073	0.6685
10	E_gossypii	S_pombe	0.7616	1536	0.0837	0.001
11	E_gossypii	Y_lipolytica	0.7114	2441	0.0297	0.1414
12	Y_lipolytica	M_grisea	0.6751	2464	0.041	0.0418
13	Y_lipolytica	A_nidulans	0.7072	2515	0.0162	0.4156
14	Y_lipolytica	C_immitis	0.7109	2584	0.0021	0.9117
15	Y_lipolytica	S_pombe	0.7271	1270	0.0404	0.1495
16	S_pombe	S_japonicus	0.6551	1461	0.0549	0.0358
*17	*C_dubliniensis*	*C_albicans*	*0.2893*	*3796*	*0.2176*	*6.30E-42*
*18	*C_dubliniensis*	*C_tropicalis*	*0.5522*	*3514*	*0.1029*	*9.80E-10*
19	C_tropicalis	C_parapsilosis	0.6059	3390	0.0426	0.013
20	C_tropicalis	L_elongisporus	0.6257	3442	-0.0227	0.1818
*21	N_crassa	C_globosum	0.5842	2369	-0.0085	0.6757
*22	U_reesii	C_immitis	0.5293	917	-0.0513	0.1201
*23	A_nidulans	A_terreus	0.6364	1121	0.037	0.2147
24	H_capsulatum	C_immitis	0.6839	847	0.0356	0.2999
*25	H_capsulatum	U_reesii	0.6655	393	0.0034	0.9459
*26	L_elongisporus	C_parapsilosis	0.6363	3152	0.0265	0.1366

The only species pairs with a significant Pearson correlation (<0.001) are those among C. dubliniensis, C. albicans, and C. tropicalis (shown in bold). This indicates that virtually all fungal genomes have uniform mutation rates. Average divergence is the fraction of all aligned 4-fold sites which differ between the two species. Species pairs in italics and marked with a * have at least 10% fewer substitutions than would be expected at mutational saturation.

ISSN: 2730-7182