Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus)

Cruz-López, Medardo; Fernández, Guillermo; Hipperson, Helen; Palacios, Eduardo; Cavitt, John; Galindo-Espinosa, Daniel; Gómez del Angel, Salvador; Pruner, Raya; Gonzalez, Oscar; Burke, Terry; Küpper, Clemens

doi:10.1186/s12862-020-01676-7

Table 1 Diversity at MHC class I exon 3 in the Snowy Plover (Charadrius nivosus). Segregating sites of amino acids (S_aa), average nucleotide diversity (π), evolutionary distance of nucleotide sequences (d_nt) and amino acid sequences (d_aa). The measures of diversity, and the synonymous and non-synonymous substitution rates, were calculated for the complete sequence (All), and separately for the PBR and non-PBR sites within each population. The number of genotyped individuals per population (N) and the number of samples that passed the quality filters (n) are shown. To have comparable measures of diversity we randomly selected 15 allele sequences for each population, with the exception of Nayarit and Puerto Rico, where we found only 13 and 9 alleles, respectively

From: Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus)

Population	Lat	Long	N (n)		dN ± S.E	dS ± S.E	dN /dS	S_aa	π	d_nt ± S.E	d_aa ± S.E
C. n. nivosus (UTA)	40.9	−112.13	40 (40)	All	0.05 ± 0.01	0.08 ± 0.02	0.62	21	0.06	0.07 ± 0.01	0.09 ± 0.02
				PBR	0.33 ± 0.13	0.12 ± 0.07	2.75	8	0.21	0.35 ± 0.15	0.34 ± 0.09
				Non-PBR	0.02 ± 0.01	0.08 ± 0.02	0.25	13	0.04	0.04 ± 0.01	0.05 ± 0.01
C. n. nivosus (SAQ)	30.4	− 115.97	47 (35)	All	0.05 ± 0.01	0.08 ± 0.02	0.62	20	0.05	0.06 ± 0.01	0.08 ± 0.02
				PBR	0.34 ± 0.12	0.11 ± 0.07	3.10	8	0.21	0.36 ± 0.21	0.34 ± 0.08
				Non-PBR	0.02 ± 0.01	0.07 ± 0.02	0.28	12	0.03	0.03 ± 0.01	0.04 ± 0.01
C. n. nivosus (CEU)	23.91	− 106.95	49 (49)	All	0.05 ± 0.01	0.07 ± 0.02	0.71	20	0.05	0.06 ± 0.01	0.08 ± 0.02
				PBR	0.33 ± 0.12	0.11 ± 0.07	3.00	8	0.21	0.35 ± 0.16	0.35 ± 0.08
				Non-PBR	0.02 ± 0.01	0.07 ± 0.02	0.28	12	0.03	0.03 ± 0.01	0.04 ± 0.01
C. n. nivosus (NAY)	22.41	−105.62	13 (10)	All	0.06 ± 0.01	0.13 ± 0.03	0.46	19	0.07	0.07 ± 0.01	0.09 ± 0.02
				PBR	0.38 ± 0.14	0.18 ± 0.11	2.11	8	0.25	0.46 ± 0.29	0.37 ± 0.08
				Non-PBR	0.02 ± 0.01	0.12 ± 0.03	0.17	11	0.05	0.05 ± 0.01	0.05 ± 0.02
C. n. nivosus (TEX)	19.46	−98.97	23 (14)	All	0.06 ± 0.01	0.09 ± 0.02	0.67	19	0.06	0.07 ± 0.01	0.09 ± 0.02
				PBR	0.39 ± 0.14	0.14 ± 0.09	2.80	8	0.23	0.42 ± 0.21	0.37 ± 0.08
				Non-PBR	0.02 ± 0.01	0.09 ± 0.02	0.22	11	0.03	0.04 ± 0.01	0.05 ± 0.01
C. n. nivosus (FLO)	30.02	−85.57	40 (36)	All	0.05 ± 0.01	0.10 ± 0.02	0.50	19	0.06	0.07 ± 0.01	0.08 ± 0.02
				PBR	0.35 ± 0.12	0.13 ± 0.08	2.70	8	0.22	0.38 ± 0.19	0.36 ± 0.08
				Non-PBR	0.02 ± 0.01	0.09 ± 0.02	0.22	11	0.04	0.04 ± 0.01	0.05 ± 0.01
C. n. occidentalis (PER)	−13.84	−76.24	21 (21)	All	0.06 ± 0.01	0.09 ± 0.02	0.70	20	0.06	0.07 ± 0.01	0.09 ± 0.02
				PBR	0.36 ± 0.13	0.14 ± 0.08	2.60	8	0.23	0.41 ± 0.19	0.37 ± 0.09
				Non-PBR	0.02 ± 0.01	0.09 ± 0.02	0.22	12	0.03	0.04 ± 0.01	0.05 ± 0.01
C. n. tenuirostris (PUR)	17.93	−67.18	17 (13)	All	0.06 ± 0.01	0.15 ± 0.04	0.40	18	0.07	0.07 ± 0.01	0.09 ± 0.02
				PBR	0.36 ± 0.15	0.22 ± 0.13	1.64	8	0.24	0.49 ± 0.36	0.34 ± 0.07
				Non-PBR	0.03 ± 0.01	0.14 ± 0.04	0.21	10	0.05	0.05 ± 0.01	0.06 ± 0.02

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