HIGH LEVEL OF MHCPOLYMORPHISM IN THE BAIJI AND FINLESS PORPOISE, WITH SPECIAL REFERENCE TO POSSIBLE CONVERGENT ADAPTATION TO THE FRESHWATER YANGTZE RIVER - Biology, Evolution and Conservation of River Dolphins Within South America and Asia - page 404

Neph-I*27 .......... .K......M. .E.....V.E .Q.S...... ..VN.....

Neph-I*28 .....G.... .K......M. .E.......E .Q.S...... ..VN.....

Neph-I*29 .......... .E......I. .E........ ...S..T..L .........

Neph-I*30 .......... .......... .........E .Q.S...... ..VN.....

Neph-I*31 .......... .......... .......... .........I ...D..T..

Neph-I*32 .......... .M........ .E.....EEQ ..GC.....I ..VD..T..

Neph-I*33 .......... .K........ .E.....EEE ...S.....I ..VN..I..

Neph-I*34 .......... .M......I. .E.......E ...C..T..L ...N..I..

Live-I*01 .......... .......... .E........ ...F.....I ..VN.ST..

Live-I*02 .......... .K........ .E.....EEE ...S.....I ..VN..I..

Live-I*03 .......... .......... .ER....EEE ...L.....I ..VN.ST..

Live-I*04 L...G..... .M.LW..... .K........ P....HH..T F.VN..T.C

Live-I*05 L......... .......... .E.....EEE ..KL.G...I ..VN.ST..

Live-I*06 .....G.... .M..W..... .Q........ P....HH..T F.VN..T.C

Figure 1. Alignment of predicted amino acid sequences of MHC-DRA (a), DQB (b) and MHC-I (c)
exon 2 from the baiji. Dots (.) indicate residues identical to the reference sequences. Putative peptide
binding sites (Brown et al. 1993, Bjorkman et al., 1987) are marked with asterisks (*).

Table 2. The estimated rates (± standard error) of nonsynonymous ( d N ) and synonymous
( d S ) substitutions for overall domain, peptide (PBR) and non-peptide (non-PBR) binding
region and the results of the Z- test of positive selection for exon 2 of MHC-I, DQB , and
DRA sequences in the baiji and finless porpoise. d S and d N values are given as
percentages per site

Loci

Sites d N d S d N /d S P

Finless
porpoise

DRA PBR 0 (0) 3.8 (4.5) 0 1.000

Non-PBR 1.2 (0.7) 0 (0) - 0.038

All 0.9 (0.5) 0.8 (0.9) 1.1 0.476

DQB PBR 10.0 (3.5) 2.3 (3.0) 4.3 0.071

Non-PBR 3.7 (1.7) 1.8 (1.0) 2.1 0.148

All 5.2 (1.5) 2.0 (0.9) 2.6 0.037

MHC-I PBR 26.9 (8.0) 1.7 (1.3) 15.8 0.002

Non-PBR 4.8 (1.5) 3.0 (1.4) 1.6 0.188

All 10.7 (2.5) 3.5 (1.4) 3.1 0.003

Baiji DRA PBR 0.0 (0.0) 0.0 (0.0) - -

Non-PBR 2.0 (1.4) 0.0 (0.0) - 0.075

All 1.4 (1.0) 0.0 (0.0) - 0.073

DQB PBR 17.7 (8.7) 2.2 (2.4) 8.0 0.033

Non-PBR 1.5 (0.9) 6.5 (3.3) 0.2 0.136

All 5.0 (1.9) 5.4 (2.7) 0.9 0.886

MHC-I PBR 42.8 (17.3) 16.9 (8.9) 2.5 0.105

Non-PBR 8.5 (2.3) 4.8 (2.9) 1.8 0.178

All 15.7 (3.6) 7.8 (3.1) 2.0 0.065

The baiji amino acid sequences correspond to sites 34-82 of the human leukocyte antigen
(HLA) and owl monkeys ( Aotus nancymaae ) MHC class I sequences (Cardenas et al., 2005).
The rates of synonymous ( d S ) and nonsynonymous ( d N ) substitutions separately for the PBR,