Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus

Table 2 Levels of polymorphism in GOT paralogs in T. californicus

Pop.	Paralog	# Hap.	π_syn	S_syn	π_nonsyn	S_nonsyn	π_syn+nc	S_syn+nc	Taj. D	Indels in coding region
SD	GOT1p1	6	0.06674	3	0	0	NA	NA	1.09
	GOT1p2	10	0.04501	34	0.00675*	15	0.04359	34	0.21	70 bp insert (one haplotype)
	GOT1Sr	4	0	0	0	0	0.00076	5	0.372
	GOT1Sd	10	0	0	0.00538*	5	0.00466	12	1.144	1bp fixed
	GOT1_6a	10	0.00742	4	0.00119	2	0.0057	4	1.06	1bp poly.
LJS	GOT1p1	6	0.02401	13	0.00195	4	NA	NA	0.74
	GOT1p2	10	0.02296	29	0.00495	15	0.02223	29	−1.48
	GOT1Sr	4	0.00186	1	0.00136	5	0.0008	5	−0.446
	GOT1Sd	8	0.0163	6	0.00494*	5	0.00977	23	0.23	1bp poly.
	GOT1_6a	10	0.00211	1	0.00044	1	0.00092	0	0.12
AB	GOT1p1	6	0.00111	1	0.0004	1	NA	NA	−1.13
	GOT1p2	6	0.00412	3	0.00087	1	0.00399	3	0.56
	GOT1Sr	4	0.00479	2	0.0023*	3	0.00102	4	1.06	(stop codon poly.)
	GOT1Sd	4	0	0	0.00287	2	0.00045	1	−0.754
	GOT1_6a	10	0.00214	1	0.00043	1	0.00304	4	1.5
SCN	GOT1p1	6	0.01356	8	0	0	NA	NA	0.27
	GOT1p2	10	0.01774	14	0.00155	4	0.01747	14	−0.05
	GOT1Sr	2	0	0	0	0	0.00122	6	NA
	GOT1Sd	9	0.036	8	0.0123*	9	0.00632	9	0.672	4bp poly., 1bp poly., 4bp fixed
	GOT1_6a	8	0.016	11	0.0023	5	0.0165	14	−0.21

# Hap. indicates the number of haplotypes sequenced for each gene. S indicates the number of segregating sites for each type of polymorphism (syn-synonymous, non-syn-nonsynonymous, syn+nc-noncoding and synonymous). π gives the average pairwise sequence divergence for each of the same three catergories of sites. Taj. D is the value of Tajima’s D. Poly. indicates that site is polymorphic.
*Note calculations of non-synonymous polymorphism correct reading frame caused by indels in coding region for comparison to other sequences.

ISSN: 2730-7182