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Fig. 2. Sequences of A The two PIS of h@Zfound in the moncgoncnt r o ~ eBr @W//SRUS.
the two copies of
hsp82 found in (A) ......................................................................................................
......................................................................................................
1
...
...
102
I A
" "
A
U C TCT CAC TTT ATC OOC TAT CCG ATC AAG CTG GT- GTG GM %&Z W AGA W M G GAG ATT ACT G M
nifera. For each spe-
! .................................................... .............................................
.............F ::: ............ .............................................
291
cies, the copies are ...........-----...-..-................
...
A
..
.........
106
.A. a*. a.,.
A. . . . . . . .
............
::( ...::I^""
........................... ...
22
TFG GM OM --A CG- -TC MA G M GTG -T- %&Z MA CAT TC- C M TT- ATT GGT TAT C U A l l MA TTA TT- B f G -M M- -M CO- W- M- GM AT- TC- GAT
316
......... ............... A. .
... A
....................
.. . . . . . . . . . ,.I ::I A
....
...........
... ..I
A
....
!t?
.A
.
present in the genome of a single individual of species, prepared from a small natural isolate or Findings for bdelloid rotifers were very
each species. DNA was extracted from a popu- a single animal. For each gene, 24 to 38 ampli- different. Each of the four bdelloid genomes
lation recently propagated from a single individ- cons from two to four polymerase chain reaction examined contains two or more highly diver-
ual or, in the case of some of the nonbdelloid (PCR) amplifications were cloned in plasmids gent copies of hsp82. No copies were found
and sequenced in both directions (30). As a that are as closely similar to each other as
measure of neutral difference in coding regions, those in nonbdelloid rotifers (Tables 1 and 2).
Table 1. Divergence of hsp82 copies in sexually we used the uncorrected percentage difference Two copies were found in M. qiradricornif-
reproducing rotifen. Percent difference (%) is indi- at fourfold degenerate sites,here designated D4, era, differing at fourfold degenerate sites by
cated above the total number of differences found
(no.) in each species at all nucleotide sites (Total), a quantity that is slower to saturate and less 54% (Fig. 2B). Three copies were found in
synonymous sites (Syn.), and fourfold degenerate sensitive to transition-transversion bias than are Adineta vaga and Habrotrocha constricta
sites (D4). Average sequence differences for the D. differences at twofold and threefold degenerate and four in Philodina roseola. The highest
pseudoobscura region correspondingto D. melano- sites (31).For the genesexamined, 11to 18%of values of D4 between hsp82 copies in each of
gaster codon positions 1 to 270 (the longest length all coding sites are fourfold degenerate. these three bdelloid genomes are 30, 26, and
available) are calculated for 11 isolates reported in Sequence divergence of hsp82. We exam- 49%, respectively, and the corresponding
(28). ined hsp82 in four bdelloid species representing lowest values are 6.0,6.6, and 3.5%. All three
the three major familieswithin the class and, for copies of hsp82 in A. vaga contain a 57- to
Length Difference (%/no.)
Species examined comparison, seven species of sexually repro- 58-bp intron, and the divergence between
(bp) Total Syn. D4 ducing rotifers (30).The region examined was intron copies parallels D4 for adjacent exons.
the 843- to 888-bp segment correspondingto D. In agreement with the above results,
B. plicatilis AUS rnelanogaster codons 13 to 302, except in Ma- Southern blots of genomic DNA probed with
crotrachela quadricomifera and Brachionus hsp82 revealed restriction fragments diagnos-
B. plicatilis RUS tic for each of the four copies of hsp82 in P.
plicatilis RUS, for which the regions examined
B. calyciflorus were the 51.8-and 498-bp segments, respective- roseola and for each of the three copies in H.
ly, corresponding to D. melanogaster codons constricta and no other fragments (32). As
E. ehrenbergi 152 to 320. expected, Southern blots of the monogonont
Genomes of each of the seven sexually re- B. plicatilis AUS showed only a single frag-
S. socialis producing rotifers were found to contain either ment, corresponding to the two nearly iden-
S. nebaliae
two nearly identical hsp82 sequences,as depict- tical copies of hsp82 in this species.
ed for B. plicatilis RUS in Fig. 2A, or only a Relative rate tests show no significant dif-
M. moniliformis single sequence (Table 1). The highest D4 in ference between bdelloids and monogononts
this group of nonbdelloid rotifer genomes was in hsp82 fourfold degenerate substitution
Average 2.4% (average 1%). A similar average D4 rates, using the acanthocephalan M. monili-
D. (0.5%) may be calculatedfor the corresponding formis as an outgroup (32).There is therefore
pseudoobscura
region of hsp82 in a natural population of Dro- no indication that nucleotide mutation rates in
(SD) bdelloids differ from those in monogononts.
sophila pseudoobscura (28).
,o l *
loo
.;- -, , , , ,, , , , ,, , , , , , , , , , , , , < , , < , , , < , I
............................................
:., ., ., .. pr
,,,,-
i,. , ., .., Mq
M
and M ,quadricornifera,
b as are both lineages of
tbp in H, constricta.
Other nodes are at-
tributed to duplication
events (D) or to sepa-
rations of taxa (S).
Dashed lines indicate lineages that should have originated at species separations but
were not found and may have been lost or undetected. Numbers at nodes are
percentages of 1000 bootstrapped alignments (when over 50%) of fourfold and three-
fold degenerate codon positions (and, in the case of tbp, intron positions) supporting
each clade by maximum parsimony (above the line) or by neighbor-joining (below the
line) using 8.plicatilis AUS, a member of the sister class Monogononta, as an outgroup
(43).The same tree topologies are found using neighbor-joining of synonymous site
differences. The same tbp tree was also obtained with only fourfold and threefold
degenerate sites or only introns. In all analyses, fewer than 10% of bootstrapped
alignments resulted in trees that lacked an ancient a-b divergence.
Sequence divergence of tbp, rpol31, and vation of gene copies involved in such interac- As with hsp82, the six copies of tbp identi-
tpi. Two divergent copies and no closely similar tions disadvantageous. fied in bdelloids belong to one or the other of
copies of each of these three genes were found Phylogeny of hsp82 and tbp in bdelloid two ancient lineages, also designated a and b,
in individual bdelloid genomes. The region of rotifers. Relationships among the 12 copies of that began to diverge after the separation of
tbp corresponding to D. melanogaster codons hsp82 and among the 6 copies of tbp sequenced bdelloids and monogononts but before the bdel-
187 to 295 was examined in the bdelloids P. in bdelloid rotifers are depicted in Fig. 3. All loid radiation (Fig. 3B). Descendants of both
roseola, M.quadricomifera, and H. consm'cta copies of hsp82 belong to one or the other of tbp lineages are present in the genome of H.
and in the monogonont B. plicatilis AUS. D4 two ancient lineages, designated a and b, that consm'cta.
values for tbp in the bdelloid genomes are 14, began to diverge after the separation of bdel- The average fourfold degenerate differ-
16, and 44%, respectively. Each copy contains loids and monogononts but before the separa- ence between the a and b lineages of tbp
two introns of about 60 bp, and the average tion of the bdelloid families we examined (Fig. (53%, SD 5.5) is not significantly different
difference between intron copies is about equal 3A). Representatives of both lineages are from that between the a and b lineages of
to D4 for the surrounding exons (Table 3). Only present in individual genomes of P. roseola and hsp82 (49%, SD 4.2), consistent with the
a single tbp sequence, without introns, was M.quadricomifera. In addition, apparent dupli- indication from phylogenetic analysis that the
found in B. plicatilis. cations and losses of hsp82 occurred occasion- a and b lineages of both genes began to
The tpi and rpol31 genes were examined ally during the bdelloid radiation. diverge during the same interval. For com-
only in the bdelloid P. roseola, giving D4
values of 73 and 12%, respectively. Both
Table 2. Divergence (D4) of hsp82 copies in bdelloid rotifers. Each copy is designated by the first letters
"pies of tpi have three introns of about 60 of the genus and species followed by a number. Divergences between copies within the same genome are
b ~and, the average difference between intrOn shown in boldface. The A. vaga intron is located after 0. melanogaster codon position 88; the total
copies is 36% (Table 4). divergence between copies Avl and Av2, Avl and Av3, and Av2 and Av3 in the intron is 47,49, and 5.3%,
Nucleotide differences between gene copies respectively. A 58-bp intron is present after 0. melanogaster codon position 241 in Hcl. Neither intron
in coding regions ofall four genes examined in is present in any other rotifer examined, indicating that they appeared late in bdelloid evolution. No
bdelloid genomes are mainly at codon third h5p82 introns were found in any nonbdelloid rotifer.
positions and are distributed throughout the se-
quenced regions, as illustrated in Fig. 2B. No Coding sequence
in-frame stop codons are present in any copy, Length Mql Mq2 Prl Pr2 Pr3 Pr4 Hcl Hc2 Hc3 Avl Av2 Av3
synonymous substitutions consistently outnum- (bp) 516 519 873 873 879 879 873 873 873 870 870 870
ber replacement substitutions, and amino acid
sequences closely match those of the corre- Mql
sponding genes in other organisms. Evidently, Mq2
Prl
all copies are functional. It may be that non- Pr2
functional copies are deleterious even in the Pr3
presence of functional copies and are eliminat- Pr4
ed by selection, consistent with the partial dom- Hcl
inance of deleterious recessives observed in Hc2
heterozygotes of diverse species (33-35). Also, Hc3
Av 1
in the absence of segregation, strong heterotic Av2
interactions may evolve ( I ) , making the inacti-
Table 3. Divergence of tbp copies in bdelloid rotifers. Divergences between melanogaster codon position 271 and intron 2 after the second nucleotide of
copies within the same genome are shown in boldface. Values are D4 except codon 295, a conserved intron-exon boundary (39).
for introns, for which total difference is given. lntron 1 is located after D.
Length Prl Pr2 Mql Mq2 Hcl Hc2 Prl Pr2 Mql Mq2 Hcl Hc2 Prl Pr2 Mql Mq2 Hcl Hc2
(bp) 327 327 327 327 327 327 70 70 70 70 53 60 63 67 63 67 46 46
parison, the average D4 values between bdel- reproducing species that have an evanescent ever, consistent with the failure to find males,
loids and the monogonont B. plicatilis AUS or unrecognized diploid form. The failure to hermaphrodites, or meiosis, it appears more
for hsp82 and tbp are 75% (SD 6) and 79% observe male bdelloids and the lack of hap- plausible to interpret our findings as further
(SD 3), respectively. loid females in any metazoan life cycle make evidence that the Class Bdelloidea has evolved
Discussion. We find that genomes of ro- this possibility remote. for tens of millions of years without sexual
tifers of the Class Bdelloidea are strikingly A second remarkable feature of bdelloid reproduction or genetic exchange between
different from genomes of rotifers belonging genomes is the consistent presence in individual former alleles.
to the other three classes of the phylum, in genomes of divergent copies of each of the four
which reproduction is known to be obligately genes examined, a condition not encountered in References and Notes
1. M. J. D. White. Modes of Speciation (Freeman, San
or facultatively sexual, and from genomes of any of the nonbdelloid rotifers (Tables 1 to 4) or Francisco. 1978).
sexually reproducing species generally. in reported sequences of any other invertebrate. 2. G. Bell. The Masterpiece of Nature: The Evolution and
First, nearly identical pairs of genes were Although several all-female lines in diverse Genetics of Sexuality (Univ. of California Press, Berke-
animal taxa are known to have arisen as allo- ley, CA. 1982).
found in nonbdelloid rotifers, as expected in 3. A. J. Richards, Plant Breeding Systems (Allen and
sexually reproducing diploids, but were not ploids (1, 2), the consistent finding of highly Unwin, Boston, 1986).
found in bdelloids. Even the most similar cop- divergent gene copies in bdelloids cannot be 4. E. Mayr. Animal Species and Evolution (Harvard Univ.
ies found in any bdelloid genome are more attributed to recent species hybridization, for Press, Cambridge, MA, 1963).
5. J. Maynard Smith. Nature 324, 300 (1986).
divergent than the most divergent pair found in this would require a multitude of separate hy- 6. R. L. Wallace and T. W . Snell, in Ecology and Classi-
any other rotifer (Tables 1 to 4). Although not bridizations between highly divergent parents fication of North American Freshwater Invertebrates,
conclusive, a firther suggestion that bdelloid and the disappearance of or failure to recognize J. H. Thorp and A. P. Covich. Eds. (Academic Press, San
Diego. CA. 1991), pp.187-248.
genomes are not composed of allelic pairs of the parental sexual species. Moreover, phyloge- 7. J. R. Garey, T. J. Near, M. R. Nonnemacher, S. A.
haplotypes comes from the observation that at netic analysis of hsp82 and tbp, the two genes Nadler, j. Mol. Evol. 43. 287 (1996).
least 3 of the 13 chromosomes in the karyotype examined in more than one bdelloid species, 8. J. R. Garey, A. Schmidt-Rhaesa, T. J. Near, S. A. Nadler,
Hydrobiologia 387/388, 83 (1998).
of P. roseola and 2 of the 13 chromosomes in reveals that each copy of hsp82 and each copy 9. G. Melone, C. Ricci, H. Segers, R. L. Wallace, Hydro-
the karyotype of Habrotrocha rosa have no of tbp belongs to one or the other of two biologia 3871388, 101 (1998).
morphological homologs (18, 36). lineages that began to diverge before the bdel- 10. D. B. Mark Welch, Invert. Biol. 119. 17 (2000).
11. J. J. Gilbert, in Reproductive Biology of the inverte-
A formal possibility that could account for loid radiation and after the separation of bdel- brates, K. G. Adiyodi and R. G. Adiyodi, Eds. (Wiley.
a lack of allele pairs in individual genomes is loids from monogononts (Fig. 3). These ancient New York, 1989), vol. 4, pp. 179-199.
that bdelloids are haploid females of sexually divergences cannot be attributed to speciation 12. J. Donner, Ordnung Bdelloidea (Akademie-Verlag,
Berlin. 1965).
because both hsp82 lineages are still present in
13. E. W . Holman, Syst. Zool. 36, 381 (1987).
Table 4. Divergence of rpol31 and tpi copies in P.
individual genomes of P. roseola and M.quad- 14. C. Ricci. Hydrobiologia 147. 117 (1987).
roseola. lntrons are located in both copies of tpi a t ricomifera and both tbp lineages are still 15. C. T. Hudson and P. H. Gosse, The Rotifera or Wheel-
present in H constricts. Such stable association animalcules (Longmans, Green, London. 1886).
three conserved positions, numbered after (40).
16. 0. P. Judson and B. B. Normark, Trends Ecol. Evol. 11,
Copy 1 of tpi contains t w o additional introns, 61 could result, however, if the two lineages de- 41 (1996).
and 59 bp in length, at conserved positions 3 and scend from ancient duplications or from an 17. W . S. Hsu, Cellule 57, 283 (1956).
9, respectively. N o introns were found in rpol31. ancient polyploid ancestor or if they descend 18. . Biol. Bull. 111. 364 (1956).
~,
For both tpi and hsp82, the differences in the 19. B. M. Waggoner and G. 0. Poinar Jr., Experientia 49,
number of introns between gene copies in individ-
from former allele pairs that neither recombined 354 (1993).
ual bdelloid genomes are comparable t o those nor segregated throughout bdelloid evolution. 20. M. Pagani, C. Ricci, C. A. Redi, Hydrobiologia 2551
between species with similarly high levels of syn- In addition, apparent duplications and losses 256, 225 (1993).
21. D. B. Mark Welch and M. Meselson, Hydrobiologia
onymous sequence difference in surrounding ex- have occurred occasionally during the bdelloid 3871388, 395 (1998).
ons (47, 42). radiation as may have resulted, for example, 22. A. Kondrashov, 1. Hered. 84, 372 (1993).
from nondisjunction. 23. J. F. Crow. Dev. Genet. 15, 205 (1994).
Length examined 24. M. Kimura and J. F. Crow, Genetics 49, 725 (1964).
D4 or Our results exclude the possibility that 25. W.-H. Li and L. A. Sadler, Genetics 129. 513 (1991).
(bp) Diff. bdelloid rotifers are ordinary diploids that 26. S. R. Palumbi and E. C. Metz, Mol. Biol. Evol. 8. 227
Copy 1 Copy 2 (%I engage in rare or cryptic sex. It remains (1991).
27. E. N. Moriyama and J. R. Powell, Mol. Biol. Evol. 13,
possible that, unlike any other metazoan that 261 (1996).
rpol3l 654 654 12 has been examined, bdelloids are ancient 28. R. L. Wang, J. Wakely, J. Hey, Genetics 147, 1091
tpi coding 510 510 73 polyploids or diploids with ancient duplica- (1997).
tpi intron 4 64 69 42 tions of every gene we studied and that they 29. W.-H. Li, Molecular Evolution (Sinauer Associates.
tpi intron 6 53 69 37 Sunderland, MA, 1997).
tpi intron 10 54 55 29
engage in some elusive form of sexual repro- 30. The rotifers examined were as follows. Bdelloidea:
duction but are unusually homozygous. How- Philodina roseola, Macrotrachela quadricornifera
www.sciencemag.org/feature/data/10500644shl. Bdel-
loids, B. calyciflorus, and both strains of B. plicatilis
were kept in large ( l o 4 t o l o 5 ) cultures grown from
Malaita, Southwest Pacific
single eggs or single individuals after 10 serial Kenneth D. Collerson,'* Sarath Hapugoda,' Balz S. Kamber,'