Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

Marmesat, Elena; Schmidt, Krzysztof; Saveljev, Alexander P.; Seryodkin, Ivan V.; Godoy, José A.

doi:10.1186/s12862-017-1006-z

BMC Ecology and Evolution

Table 2 Genetic diversity in MHCI and MHCII-DRB in the Lynx genus. Diversity at the nucleotide, amino acid and supertype levels are estimated as the number of observed alleles (allelic richness, AR), number (S) and proportion of segregating sites [S(%)], mean number (± standard error) of differences among alleles (K). The latter is calculated for all sites, ABS and non-ABS

From: Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

Indice	Total	L. pardinus	L. lynx	L. canadensis	L. rufus
MHC Class
Diversity level
MHC Class I
DNA (299)
AR	30	10	17	13	10
Private		0	3	4	9
S	86	72	73	76	76
S (%)	37.55	31.44	31.88	33.19	33.19
K	19.77 ± 0.52	24.11 ± 1.74	20.07 ± 1	21.51 ± 1.42	25.8 ± 1.64
Gen. dist. All	0.094 ± 0.003	0.116 ± 0.009	0.096 ± 0.005	0.103 ± 0.007	0.125 ± 0.009
Gen. dist. ABS	0.23 ± 0.01	0.27 ± 0.02	0.23 ± 0.01	0.24 ± 0.02	0.29 ± 0.02
Gen. dist. Non-ABS	0.06 ± 0	0.08 ± 0.01	0.06 ± 0	0.07 ± 0.01	0.08 ± 0.01
Protein (76)
AR	26	10	15	10	10
Private		0	3	3	8
S	45	38	39	39	40
S (%)	59.21	50	51.32	51.32	52.63
K	16.68 ± 0.4	19.97 ± 1.36	16.78 ± 0.79	17.27 ± 1.16	21.93 ± 1.28
Gen. dist. All	0.189 ± 0.005	0.231 ± 0.018	0.191 ± 0.01	0.199 ± 0.015	0.256 ± 0.017
Gen. dist. ABS	0.53 ± 0.01	0.58 ± 0.04	0.5 ± 0.02	0.54 ± 0.04	0.68 ± 0.04
Gen. dist. Non-ABS	0.11 ± 0	0.15 ± 0.01	0.12 ± 0.01	0.13 ± 0.01	0.17 ± 0.01
Supertypes
Number	11	7	8	7	8
Private		0	1	0	3
MHC Class II-DRB
DNA (247)
AR	13	7	8	3	5
Private		2	2	0	3
S	61	47	49	41	56
S (%)	24.7	19.03	19.84	16.6	22.67
K	23.71 ± 1.01	22.33 ± 1.81	23.39 ± 1.76	27.67 ± 4.37	29.1 ± 2.13
Gen. dist. All	0.104 ± 0.005	0.097 ± 0.008	0.103 ± 0.008	0.122 ± 0.021	0.129 ± 0.01
Gen. dist. ABS	0.19 ± 0.01	0.15 ± 0.01	0.16 ± 0.01	0.2 ± 0.04	0.26 ± 0.03
Gen. dist. Non-ABS	0.07 ± 0	0.07 ± 0.01	0.08 ± 0.01	0.09 ± 0.01	0.08 ± 0.01
Protein (82)
AR	12	7	7	3	5
Private		2	1	0	3
S	28	23	23	23	27
S (%)	34.15	28.05	28.05	28.05	32.93
K	16.17 ± 0.7	14.63 ± 1.23	15.72 ± 1.25	19.51 ± 3.73	20 ± 1.51
Gen. dist. All	0.18 ± 0.008	0.161 ± 0.014	0.175 ± 0.015	0.221 ± 0.046	0.226 ± 0.018
Gen. dist. ABS	0.38 ± 0.02	0.31 ± 0.03	0.36 ± 0.04	0.46 ± 0.15	0.5 ± 0.06
Gen. dist. Non-ABS	0.11 ± 0.01	0.11 ± 0.01	0.11 ± 0.01	0.14 ± 0.02	0.14 ± 0.01
Supertypes
Number	7	5	5	3	4
Private		1	0	0	1

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ISSN: 2730-7182

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