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 405

non-PBR, as well as the overall domain are shown in Table 2. Of the 13 sites predicted to be
involved in the PBR (Brown et al., 1993), nine (69.2%) were variable whereas 12 out of 36
(33.3%) in the non-PBR were polymorphic. The relative frequency of d N was higher than that
of d S especially in the PBR (Table 2).

Phylogenetic Reconstruction

The phylogenetic reconstruction based on the NJ algorithm showed that sequences of the
baiji at three loci did not form a monophyletic clade but grouped with those of the finless
porpoise (Figure 2). For example, in the NJ tree of MHC-I gene, three alleles of the baiji
( Live-I*01 , 02 , 04 ), respectively, grouped with three alleles of the finless porpoise ( Neph-
I*19 , 33 , 14 ) (Figure. 2c). In addition, some alleles from different species of the family
Phocoenidae were within a same lineage. For instance, Neph-I*04 clustered with five alleles
of the vaquita ( Phocoena sinus ) with 94% bootstrap support (Figure 2c), whereas two alleles,
respectively, from the vaquita ( Phsi-DQB*01 ) and harbor porpoise P. phocoena ( Phph-a )
were included in a lineage constituted mainly by the finless porpoise alleles (Figure 2b).

Boja-DRA*01
Bibo-DRA*01
BoLA-DRA
Boga-DRA*01
Syna-DRA*01
Syca-DRA*01
Bula-DRA*01
Ande-DRA*01
Bula-DRA*02
Ande-DRA*02
Ovar-DRA
Cahi-DRA
Ovmo-DRA

53

74

58

68

71

63

97

87

63

Live-DRA*02
Live-DRA*01
Neph-DRA*01
Neph-DRA*03
Neph-DRA*02
Neph-DRA*04
Neph-DRA*05
ELA-DRA*JBH45
ELA-DRA*JBZ185
ELA-DRA*JBD17

100

90

100

76

0.01

Figure 2 . Neighbor-joining phylogenetic trees reconstructed based on nucleotide sequences of the DRA
(a), DQB (b) and MHC-I (c), from a matrix of Kimura 2-parameter nucleotide distances. Numbers at
branch-points represent bootstrap support values and only bootstrap values P ≥ 50% (1000 replicates)
were shown. Identical alleles between the baiji and finless porpoise were marked with frame. Other
allelic sequences downloaded from GenBank were included in the analyses, they are: (a)DRA: B.
javanicus (Boja-DRA*01: AF385487), Bison bonasus (Bibo-DRA*01: AF385485), B. gaurus (Boga-
DRA*01: AF385486), Syncerus caffer nanus (Syna-DRA*01: AF385491), S. c. caffer (Syca-DRA*01: