Molecular evolution of rDNA in sturgeons: features and mechanisms

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Molecular evolution of rDNA in sturgeons
features and mechanisms

• Constantine V. Rozhkovan
• Galina N. Chelomina

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Diagram of the rDNA array of eukaryotes
NTS non-transcribed spacer ETS external
transcribed spacer ITS internal transcribed
spacer. The detail of the small subunit (18S)
rRNA gene shows PCR primers (and their
orientations) used for amplification and
sequencing of the gene. Cross-hatched box
indicates the cloned and sequenced 486 bp part of
the entire gene.
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Model for concerted evolution of tandemly
repeated multi-gene families (Liao, 1999)
The coding sequences are depicted as unblackened
arrows, and the intergenic spacers are depicted
as lines. The ?anking sequences of the two arrays
are differently labeled (as either blackened or
cross-hatched boxes).
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18S rDNA diversity in sturgeon species and hybrids
Taxa n S h Hd Pi k
Acipenser fulvescens 18 31 12 0.935 0.01138 5.510
Acipenser schrenckii 22 20 11 0.714 0.00878 4.251
Huso dauricus 38 13 16 0.863 0.00979 4.649
Total 78 44 34 0.871 0.01123 5.335
Taxa n S h Hd Pi k
A. schrenckii H. dauricus 26 42 21 0.978 0.01666 8.031
A. schrenckii A. baerii 14 18 10 0.890 0.01258 6.088
Total 40 50 29 0.955 0.01530 7.373
n sample size S number of polymorphic
(segregating) sites h number of haplotypes Hd
haplotypic diversity Pi nucleotide
diversity k average number of nucleotide
differences.
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G E N E S
P S E U D O G E N E
S
Af Acipenser fulvescens As Acipenser
schrenckii Hd Huso dauricus SD A.
schrenckii H. dauricus SB A. schrenckii A.
baerii - here and further Genebank data
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Genes
Pseudogenes
A
B
C
Af A. fulvescens, As A. schrenckii, Hd H.
dauricus, A.br A. brevirostrum, A.ruth A.
ruthenus. Number of bars and numerals on
connecting lines corresponds to a number of
mutation steps, n number of clones.
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Pseudogenes
Genes
SD A. schrenckii H. dauricus, SB A.
schrenckii A. baerii. Number of bars and
numerals on connecting lines corresponds to a
number of mutation steps, n number of clones.
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Groups compared Groups compared n S h Hd Pi k
Genes Species Hybrids 31 12 9 16 6 9 0.301 0.909 0.00120 0.00578 0.581 2.803
Pseudogenes Species Hybrids 47 28 38 36 28 20 0.944 0.923 0.01117 0.01379 5.306 6.648
Groups compared Groups compared ZnS (C?T) (G?A) other substitution La-Lb Z
Species Genes Pseudogenes 0.182 0.082 1 2.5 1 1 -0.010836 2.540
Hybrids Genes Pseudogenes 0.226 0.276 1 2 1 1.5 -0.010587 2.083
n sample size S number of polymorphic
(segregating) sites h number of haplotypes Hd
haplotypic diversity Pi nucleotide
diversity k average number of nucleotide
differences.
ZnS Kellys neutrality test L relative
evolution rate La and Lb the average distances
(number of nucleotide substitutions per site)
between genes and pseudogenes clusters in
comparison with the common ancestor if Z?1.96,
than hypothesis of constant evolutionary rate is
rejected.
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Recombination events
Taxa Rg Ras 4 gt Rm S d
A. fulvescens 13.7 0.0283 10 2 31 483.22
A. schrenckii 0.50 0.0010 12 2 20 483.77
H. dauricus 5.80 0.0120 30 4 13 483.39
A. schrenckii H. dauricus 12.50 0.0285 20 2 18 483.57
A. schrenckii A. baerii 23.60 0.0488 22 5 42 483.69
Taxa Rg (genes/?genes) Ras (genes/?genes) 4 gt (genes/?genes) Rm (genes/?genes)
A. fulvescens A. schrenckii H. dauricus Species 0.000/7.9 0.001/76.4 0.001/10.5 0.001/23.7 0/0.0164 0/0.1580 0/0.0217 0/0.0491 0/2 0/12 0/30 0/24 0/1 0/2 0/4 0/5
A. schrenckii H. dauricus A. schrenckii A. baerii Hybrids 81.4/31.0 gt10 000/6.6 160/23.9 0.1682/0.0641 0/0.0137 0.3306/0.0494 0/22 0/16 0/26 0/5 0/2 0/5
R recombination parameters Rg estimate of R
per gene, Ras estimate of R, between adjacent
sites 4 gt number of pairs of sites with four
gametic types Rm minimum number of
recombination events S number of polymorphic
(segregating) sites d average nucleotide
distance between the most distant sites.
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Gene conversion
Taxa Ngc Psi Nis Conversion tracts
A. fulvescens 2 0.00723 7 391-451 Af-05 235-259 Af-11
A. schrenckii 2 0.00826 11 259-274 As-12 68-274 As-14
H. dauricus 8 0.01174 9 235-274 Hd-02 68-371 Hd-06 371-391 Hd-13 235-274 Hd-14 235-274 Hd-23 434-435 Hd-28 434-451 Hd-35 235-371 Hd-36
A. schrenckii H. dauricus 3 0.01676 11 236-275 SH-05 435-436 SH-07 68-236 SH-16
A. schrenckii A. baerii 3 0.01609 9 68-275 SB-01 435-436 SB-07 435-452 SB-11
Ngc number of gene conversion tracts
identified Psi average number of informative
nucleotide sites per site Nis number of sites
with information. First nucleotide of 486 bp
fragment corresponds to 960 nucleotide of entire
gene sequence
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Linkage disequilibrium
Species and hybrids
Taxa Sites with linkage disequilibrium
Af As Hd SD SB 68 236 260 367 381 392 396 435 436 452 68 236 260 372 392 435 436 452 68 236 260 275 372 392 435 436 452 35 68 236 260 295 333 392 435 436 452 68 236 260 275 372 392 435 436 452
Af A. fulvescens, As A. schrenckii, Hd H.
dauricus, SD A. schrenckii H. dauricus, SB
A. schrenckii A. baerii Light grey rectangle
0.01ltPlt0.05 dark grey rectangle 0.001ltPlt0.01
black rectangle Plt0.001 F sites, significant
by Fishers exact test, B sites, significant
with Bonferroni correction procedure. First
nucleotide of 486 bp fragment corresponds to 960
nucleotide of entire gene sequence
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Linkage disequilibrium
Pseudogenes
Taxa Sites with linkage disequilibrium
Af As Hd SD SB 68 366 380 395 435 68 235 259 371 391 434 435 451 68 235 259 274 371 391 434 465 451 35 68 236 260 295 333 372 392 435 452 68 236 260 275 392 435 436 452
Af A. fulvescens, As A. schrenckii, Hd H.
dauricus, SD A. schrenckii H. dauricus, SB
A. schrenckii A. baerii Light grey rectangle
0.01ltPlt0.05 dark grey rectangle 0.001ltPlt0.01
black rectangle Plt0.001 F sites, significant
by Fishers exact test, B sites, significant
with Bonferroni correction procedure. First
position of 486 bp fragment corresponds to 960
position of entire gene sequence
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Linkage disequilibrium
D
D
Acipenser schrenckii
Huso dauricus
0.4
0.4
0.2
0.2
0.0
0.0
-0.1
-0.1
-0.2
-0.2
400
0
100
200
300
0
100
200
300
400
Nucleotide distance
Nucleotide distance
D
D
Acipenser schrenckii Huso dauricus
Acipenser schrenckii Acipenser baerii
0.4
0.4
0.2
0.2
0.0
0.0
-0.1
-0.1
-0.2
-0.2
100
0
100
300
400
0
200
300
200
400
Nucleotide distance
Nucleotide distance