3. Origin of Euteleostean Biodiversity
39
Table 2. Primers used for PCR amplification and sequencing
Name
Sequence (5' to 3')
PCR and sequencing primers
lA157m
CGTCGGGGATCCTACCCACGATICCGNTA YGA YCA
lA296
ACGTAGGGATCACTTTGATAG
H5635
H5934m
L14724m
H15915
H15990
AGGTCTIAGCTIAATIAAAG
CCCGACGCTGCAGGGTGCCAATGTCTTTRTGRTI
TGACTIGAAAAACCAYCGTIG
ACCTCCGATCTYCGGATIACAAGAC
AGTTTAATTTAGAATCYTGGCTTTGG
Internal sequencing primers
lA437
AAGCTATCGGGCCCATACC
H5540
CCGCTGAGGGCTTTGAAGGC
fND2-1
GCCCACCTAGGVTGAATAAT
fND2-2
ATIATICASCCYAGGTGGGC
fND2-3
TCMACCTGACARAAACT
fND2-4
ATIATICAKCCWAGGTG
fcytb-1
CGATICTTYGCMTICCA
fcytb-2
GAKCCKGTTTCGTGNAGGAA
fcytb-3
TMGTMCAATGAATCTGAGG
fcytb-4
TIKGAKCCRGTTTCGTG
Primers lA157m and H5934m were modified, respectively, from IA160m
and H5937m (Kumazawa and Nishida 1993), and L14724m and H15915
were modified, respectively, from L14724 and H15915 (Irwin et al. 1991).
2.2 Phylogenetic Analyses
The determined nucleotide sequences for ND2 and cytb genes were converted to
amino acid sequences and aligned by eye with the corresponding sequences for
trout (Zardoya et al. 1995), cod (Johansen and Bakke 1996), carp (Chang et al.
1994), loach (Tzeng et al. 1992), bichir (Noack et al. 1996), coelacanth (Zardoya
and Meyer 1997), and sharks (Martin et al. 1992; Naylor et al. 1997). The alignment is obtainable from Y.K. upon request. Phylogenetic analyses were conducted
using concatenated amino acid sequences of ND2 and cytb after unalignable parts
in the C-terminus of each gene, as well as gap sites, were removed (719 sites in
total). The neighbor-joining (NJ) tree (Saitou and Nei 1987) was obtained with the
njboot program included in Lintre package (Takezaki et al. 1995) with the option
of amino Poisson-gamma distance and a gamma-parameter estimated from the data