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Mismatch Distributions and Intragenic Recombination Analyses
Mismatch distribution analyses supported a pattern of demographic expansion or high
mutation rate leading to sequence convergence in the finless porpoise at three MHC loci. The
goodness-of-fit tests were not significant ( P > 0.05) (Figure 3), while the analyses for the baiji
differed significantly from expectations under the sudden-expansion model ( P < 0.05) (Figure
3). This suggested that the baiji did not undergo a historical population expansion, or total
recombination at sequences of three loci.
The GENECONV analysis showed that intragenic recombination (or homologous gene
conversion) events in the baiji and finless porpoise have occurred at the DQB locus, but not at
the MHC-I and DRA loci (Table 5). Intragenic recombination events were not only detected
within segmental variants of the baiji but also between alleles of the two species. As a whole,
three Neph-DQB and nine Live-DQB alleles were found to be involved in intragenic
recombination events (P < 0.05, Table 5). Further, some sequence blocks (i.e. DNA block 30-
152 and DNA block 30-172, see Table 5) were repeatedly involved in recombination events
and may have served as recombination hot spots.
Figure 3. The observed pairwise difference (bars), and the expected mismatch distributions under the
sudden expansion model (solid line) of the MHC-I, DQB , and DRA alleles in the baiji and finless
porpoise.
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