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 410

Table 5. Gene conversion events between MHC DQB sequences from the baiji and
finless porpoise, identified using GENECONV. Sim P = Simulated P values based on
10,000 permutations; Begin = first nucleotide of the converted region; End = last
nucleotide of the converted region; Length = length of the converted region; MisM Pen
indicates the mismatch penalty

MisM
Pen

Sequence 1 Sequence 2 Sim P Begin End Length

Neph-DQB*03 Live-DQB*8 0.0406 30 152 123 None

Neph-DQB*03 Live-DQB*11 0.0406 30 152 123 None

Neph-DQB*03 Live-DQB*13 0.0406 30 172 143 None

Live-DQB*16 Live-DQB*8 0.0406 30 152 123 None

Live-DQB*16 Live-DQB*11 0.0406 30 152 123 None

Live-DQB*16 Live-DQB*13 0.0406 30 172 143 None

C ONCLUSION

Gene Duplication and Genetic Variation of the MHC Genes

Many mammalian species have one single DRA locus (Chu et al., 1994; Takada et al.,
1998), which is further approved by the present chapter. All the baiji and finless porpoise
individuals examined in this study had no more than two alleles of the DRA gene, strongly
suggesting that the DRA primers used in this study had amplified a single locus in this study.
However, some examples of strong gene duplication evidence were found for the DQB and
MHC-I loci. For example, as shown in the Results section, three, four, or five distinct
sequences were detected separately in eight individuals of the finless porpoise and 10
individuals of the baiji, suggesting at least three copies of DQB gene existed in both species.
In contrast, at least three copies were also found for the MHC-I gene considering that three to
five distinct sequences were detected in most samples examined in both species. Gene
duplication was corroborated in humpback whales ( Megaptera novaeangliae ), southern right
whales ( Eubalaena australis ) and grey whales ( Eschrichtius robustus ) (Baker et al., 2006;
Flores-Ramirez et al., 2000). These duplications could be analogous or homologous with
cattle, which are also known to have two or three transcribed DQB and MHC-I loci (Ellis et
al., 1999a, b). However, there were no significant groupings of sequences that would indicate
divergence of the duplicate genes, and so it was unable to attribute each sequence to specific
loci. Further, although Baker et al. (2006) suggested that DQB duplication in the baleen whale
(suborder Mysticeti) and baiji (suborder Odonotoceti), an early divergence of the toothed
whales (suborder Odonotoceti; Cassens et al., 2000), is consistent with retention of an
ancestral condition shared with the ruminants and loss in the more derived cetaceans such as
the beluga, the narwhal (family Monodontidae) and the true dolphins ( Delphinus delphis
included in family Delphinidae), this was not supported by the finless porpoise (family
Phocoenidae) examined in this chapter.
Although populations have dramatically declined in numbers, the baiji (which may now
be extinct) and the finless porpoise still retain considerable MHC genetic diversity, which is
supported by the large number of unique sequences examined in this chapter. For the baiji, a