Paralog analyses reveal gene duplication events and genes under positive selection in Ixodes scapularis and other ixodid ticks

Table 2 Number of paralogs identified from gene models (GM) and tentative consensus (TC) sequences analyzed by PAML. Paralogs were identified by Vmatch using low, medium and high stringency parameters followed by PAML analysis. Paralog pairs are reported as either GM or TC pairs

Species	Total number of GMs/TCs analyzed	Vmatch stringency level
Species	Total number of GMs/TCs analyzed	Low^a	Medium^b	High^c
Ixodes scapularis	24,925	160 GM pairs	115 GM pairs	91 GM pairs
Ixodes scapularis	20,901	1128 TC pairs	774 TC pairs	503 TC pairs
Rhipicephalus microplus	9403	178 TC pairs	132 TC pairs	104 TC pairs
Rhipicephalus appendiculatus	2766	55 TC pairs	35 TC pairs	25 TC pairs
Amblyomma variegatum	478	9 TC pairs	8 TC pairs	6 TC pairs

^aLow stringency: 75 % of the smaller TC must match ≥ 50 % of the larger TC of a paralog pair; ^bmedium stringency: 85 % of the smaller TC must match ≥ 70 % of 4 the larger TC of a paralog pair; ^chigh stringency: 95 % of the smaller TC must match ≥ 80 % of the larger TC of a paralog pair

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