* Smithsonian Tropical Research Institute, Balboa, Panama
Department of Biology, Duke University, Durham, North Carolina
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Abstract |
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Key Words: sea urchins bindin speciation gamete recognition fertilization Tripneustes.
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Introduction |
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Most sea urchins are broadcast spawners, with external fertilization. Reproductive isolation between species could result from distinct spawning times or from species-specific gamete interactions. Congeneric sympatric sea urchins often have overlapping annual (Lessios 1981, 1985; McClary and Barker 1998) or monthly (Lessios 1991) spawning periods. In such cases, reproductive isolation between closely related sea urchins is, at least in part, the product of gametic incompatibility (R. R. Strathmann 1981; M. F. Strathmann 1987 (p. 522); Lessios and Cunningham 1990; Uehara, Asakura, and Arakaki 1990; Palumbi and Metz 1991). Whereas gametic incompatibility could arise between a pair of sea urchin species at any step in the interactions between gametes (e.g., sperm activation, acrosomal reaction, sperm-egg attachment, sperm-egg fusion), it appears that in closely related species it generally emerges during sperm-egg attachment and membrane fusion (see Metz et al. [1994] for discussion). The sea urchin sperm protein bindin mediates both of these processes in sea urchins. Changes in the bindin locus can thus cause gametic incompatibility and convert populations into different species. Bindin is the major insoluble component of the acrosomal vesicle (Vacquier and Moy 1977). It functions as glue between the acrosomal process and the glycoprotein bindin receptors of the vitelline layer of the egg. Bindin and bindin receptors often interact in a species-specific manner (Glabe and Vacquier 1977; Glabe and Lennarz 1979).
The evolution of bindin has been studied in three genera of sea urchins. Metz and Palumbi (1996) studied bindin sequences of the central and western Pacific species of the cosmopolitan genus Echinometra. They found many sequence rearrangements and a higher number of nonsynonymous than synonymous substitutions, an indication of positive selection, in a region just 5' of the conserved bindin core. Biermann (1998) examined bindin in Strongylocentrotus and found evidence for positive selection in the same "hotspot" observed in Echinometra. Metz, Gomez-Gutierez, and Vacquier (1998) studied the same molecule in Arbacia. In contrast to the previous studies, they found almost no sequence rearrangements and no evidence for positive selection. Changes in bindin are correlated with prezygotic isolation: species of Echinometra and Strongylocentrotus are often gametically incompatible (R. R. Strathmann 1981; M. F. Strathmann 1987 [p. 522]; Uehara, Asakura, and Arakaki 1990; Palumbi and Metz 1991), whereas species of Arbacia are gametically compatible, at least in the single cross performed by Metz, Gomez-Gutierez, and Vacquier (1998). Patterns of bindin evolution within genera also correlate with the presence of sympatric species. Echinometra and Strongylocentrotus contain species with overlapping geographical distributions, whereas all species of Arbacia are distributed allopatrically.
Metz, Gomez-Gutierez, and Vacquier (1998) examined three hypotheses that might explain the lack of variability of bindin in Arbacia: (1) Extensive gene flow over large distances within species of Arbacia may limit the potential for rapid bindin evolution. (2) Arbacia bindins may be functionally constrained. (3) Non-overlap in geographic distributions of the species of Arbacia may have obviated the necessity for the evolution of gamete recognition. A fourth hypothesis is that differences in the mode of evolution of bindin between Arbacia, on the one hand, and Echinometra and Strongylocentrotus, on the other, are due to phylogenetically inherited differences of their genomes. Arbacia belongs to the superorder Stirodonta, whereas Echinometra and Strongylocentrotus belong to the superorder Camarodonta. These superorders last shared a common ancestor approximately 160 MYA (Smith, Lafay, and Christen 1992).
We examined bindin evolution in the genus Tripneustes, a member of the superorder Camarodonta (Smith 1988). Tripneustes is pantropical and contains three allopatrically distributed species, T. ventricosus on both sides of the Atlantic, T. depressus in the eastern Pacific, and T. gratilla in the central and western Pacific as well as the Indian Ocean. The three species are morphologically very similar, to the degree that it has been suggested that they may constitute a single species (Clark 1912). Indeed, there is no mitochondrial DNA differentiation between T. depressus and T. gratilla, which suggests that eastern and western Pacific populations of Tripneustes belong to the same species (Lessios, Kane, and Robertson, in preparation) Tripneustes mature bindin sequences were obtained from all species of the genus, and from all major regions of tropical oceans. We wanted to know whether bindin variation in this genus conformed to the pattern seen in other camarodonts, or whether it resembled that of Arbacia. Because Arbacia is more distantly related to Tripneustes but resembles this genus in containing no extant sympatric species, these comparisons offer insight into the relative roles of phylogeny (and resultant similarities in molecular structure) versus selection against hybridization in the evolution of this important gamete-recognition molecule.
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Materials and Methods |
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Genomic Characterizations of Bindin
After the first Tripneustes bindin sequence was obtained from cDNA by RACE, we amplified other bindin alleles from genomic DNA. We extracted genomic DNA as described by Lessios et al. (1996) from gonad tissue preserved in ethanol, NaCl-saturated 20% dimethyl-sulfoxide solution, or in liquid nitrogen. Using Tfl DNA polymerase (Epicentre Technologies), we amplified full-length mature bindin alleles from genomic DNA with primers TvF1 (5'-CTTTATCTCGGGGCATCGTC-3') and TvR1 (5'-CTGAACTTCCAATGGCTTCC-3'). Amplification conditions were as follows: 1 min at 96°C, then 39 cycles of 45 s at 94°C, 30 s at 50°C, 150 s at 72°C and finally 5 min at 72°C. We ran the amplification products in low-melting-point agarose gels. Bands were excised and treated with Gelase (Epicentre Technologies), then cloned using a pMOSBlue blunt-ended cloning kit (Amersham). We screened positive bacterial colonies according to the same PCR protocol stated above, with either the primer pair TvF1 and TvR1 or vector primers T7 and U19. The PCR product from a single positive colony per individual was gel purified and cycle sequenced as described in Lessios et al. (1996), with primers TvF1, TvR1, MB1130+, MB1136- (5'-ARGTCAATCTTSGTSGCCC-3'), TvF3 (5'-TGATGGACCTCAGCAGTGGTGT-3'), and TvR3 (5'-CACAAAATGATGGCTCACAGTT-3'). This combination of primers sequenced both strands of the full mature bindin and its intron. Sequencing was performed on an ABI 377 automated sequencer and edited using Sequencher 3.1 (Gene Codes Corp.). Sequences have been deposited in GenBank (accession numbers AF520207-AF520222).
A total of 12 mutations unique to a single allele (singletons) were observed among 16 mature bindin sequences with a combined length of 10,200 bp. Singleton mutations may represent true differences, or they may arise from cloning and polymerase error during amplification. Thus, the upper limit of sequencing error in the study was 0.12%.
Phylogenetic Analysis
Sequences were aligned by eye with the computer program Se-Al (version 1.0, written by A. Rambaut). A bindin sequence obtained from Lytechinus variegatus was used as an outgroup to root bindin phylogenetic trees. The L. variegatus bindin cDNA sequence reported by Minor et al. (1991) was not used because it differs in sequence at four amino acids of the core region, which are identical in 30 other Lytechinus bindin sequences (unpublished data) and all of the Tripneustes bindin alleles presented here. To calculate the best-fit model for constructing a tree, we entered the bindin coding sequences (full mature bindin plus 23 codons of preprobindin sequences) of Tripneustes in Modeltest version 3.06 (Posada and Crandall 1998). Comparison of the log-likelihood ratios of nested models performed by Modeltest indicated that the simplest model with a significantly better fit to the data than other models was that of Tamura and Nei (1993). Allowing for site-specific rate categories according to codon position did not greatly improve the likelihood of the model. We used PAUP* 4.0b6 (Swofford 1998) to conduct Neighbor-Joining (Saitou and Nei 1987) phylogenetic analyses on the bindin coding sequences based on Tamura and Nei distances. Maximum parsimony and maximum likelihood (ML) trees were also constructed in PAUP. Five codons (6266 in fig. 2) that could not be unambiguously aligned between Tripneustes and Lytechinus sequences were excluded from the phylogenetic analysis. Intron sequences were not used in the final analysis because they could not be aligned between Lytechinus and Tripneustes. Analyses that included the intron but left the Tripneustes tree unrooted produced the same intrageneric topology as analyses limited to the coding sequences.
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To test for the possibility that selection might be acting at sites scattered throughout the bindin molecule and not in specific regions, we implemented a series of models in PAML version 3.0 (Yang 2000; Yang et al. 2000) based on the neighbor-joining tree of the unique bindin alleles. We calculated the likelihood of this tree under two neutral models (M1 and M7) that do not allow for positively selected sites and under three alternate models (M2, M3, and M8) that do (see Swanson, Aquadro, and Vacquier 2001). Then, we compared the log-likelihoods between the neutral and selection models. We also used PAML to test for evidence of changing dN/dS ratios along different lineages of the neighbor-joining tree by first calculating the likelihood for a model that kept the dN/dS ratio constant across the tree and then calculating the likelihood for a model that allowed each branch to have a separate dN/dS ratio. Finally, we tested for selection on bindin using the McDonald-Kreitman (1991) test to compare the dN/dS ratios within and between species.
Comparative Rates of Bindin Evolution
To ask whether bindin evolves faster in some genera than in others, we compared our data for Tripneustes bindin to all full-length mature bindin sequences of Metz and Palumbi (1996) for Echinometra, of Biermann (1998) for Strongylocentrotus, and of Metz, Gomez-Gutierez, and Vacquier (1998) for Arbacia. To calculate rates, we standardized intrageneric bindin differentiation by dividing dN and dS for the entire bindin molecule by the interspecific Kimura (1980) two-parameter (K2P) genetic distance of the mitochondrial cytochrome oxidase I (COI) gene. Average COI divergence between species of Tripneustes was calculated from all sequences included in Lessios, Kane, and Robertson (in preparation), of Echinometra from all sequences in Palumbi et al. (1997), and of Strongylocentrotus from all sequences in Kessing (1991). Because Metz, Gomez-Gutierez, and Vacquier (1998) sequenced a different region of COI, we obtained our own sequences from 102 individuals of four species of Arbacia, covering the same 640 bp that were sequenced in Tripneustes. This region completely overlaps the 450 bp sequenced by Palumbi et al. (1997) in Echinometra and most of the 440 bp sequenced by Kessing (1991) in Strongylocentrotus.
Mature bindin sequences within the same genus were aligned by eye. Sequences from different genera were generally too divergent outside of the core region to be aligned with confidence. Thus, only intrageneric comparisons were feasible. In contrast to Tripneustes and Arbacia, in which alignments could be made for the whole mature bindin, the glycine-rich repeat regions in Echinometra and Strongylocentrotus bindins could not be aligned unambiguously. These regions (111 codons 3' of the core in Strongylocentrotus, 26 codons 5' of the core and 32 codons 3' of the core in Echinometra) were excluded from this analysis. Bindin intron sequences of Arbacia, Tripneustes, and Strongylocentrotus were aligned by eye for each genus. Intron sequences for Echinometra were not included, because they were unavailable in GenBank. Inversions in the bindin intron were aligned between sequences that shared them and were considered as gaps in sequences with the opposite inversion.
Strongylocentrotus polyacanthus was not included in the analysis, because COI data were not available for this species. S. franciscanus was also excluded, because its bindin sequences could not be unambiguously aligned with the sequences from the rest of the genus. T. depressus and T. gratilla sequences were treated as coming from the same species, because neither their bindin nor their COI sequences (Lessios, Kane, and Robertson, in preparation) are reciprocally monophyletic. Finally, we included Hemicentrotus pulcherrimus in the Strongylocentrotus analysis, because both COI (Kessing 1991) and bindin (Biermann 1998) data indicate that it is nested within this genus.
Codon Bias
We estimated codon bias for each full-length mature bindin allele from Arbacia, Tripneustes, Echinometra, and Strongylocentrotus with the program CODONS (Lloyd and Sharp 1992) by calculating the effective number of codons (ENC) (Wright 1990). These ENC values can range from 20 (same codon always used for an amino acid) to 61 (random use of each codon for every amino acid). A separate calculation was carried out for each allele, and then the values were averaged for each genus.
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Results |
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Tripneustes bindins have the highly conserved core observed in bindins from all other studied genera. Of 66 amino acids defined as the core in this study (98163 in fig. 2), 65 are identical to those of Lytechinus variegatus, and 64 are identical to the bindin sequences of S. purpuratus (Gao et al. 1986), S. franciscanus (Minor et al. 1991), and A. punctulata (Glabe and Clark 1991). All 18 amino acids (119136 in fig. 2) implicated in membrane fusion (Ulrich et al. 1998, 1999) are identical to those in all other known bindins.
At a point 5' of the core, Tripneustes bindins contain a glycine-rich repeat GG(Q/S/P) (V/G)GGG(G/S) (N/G) (S/M/G) reminiscent of glycine-rich motifs present in Echinometra and Strongylocentrotus but absent in Arbacia. This repeat is present in two copies in T. ventricosus, and in three copies in T. depressus and T. gratilla (fig. 2). This is the only insertion/deletion (indel) observed in Tripneustes mature bindin. Hydrophobicity plots of Tripneustes bindin are similar to those of other Camarodont sea urchins (Zigler and Lessios in preparation); they do not contain the 3' hydrophobic domain observed in Arbacia bindin (Glabe and Clark 1991).
The single intron is in the same location as in all other bindins studied to date (after amino acid 93 in fig. 2). It contains a region of approximately 75 bp just inside its 5' end that is inverted in half of the Tripneustes alleles with respect to other Tripneustes alleles. All T. ventricosus alleles, plus three alleles of T. gratilla ("Marquesas 80," "Guam 2," and "Papua New Guinea 1"), have one form of the inversion, whereas all T. depressus alleles and the rest of the T. gratilla alleles have the other form.
Genealogy of Alleles
Figure 3 depicts the genealogy of the sequenced bindin alleles, reconstructed by neighbor joining, using only coding sequences (mature bindin and preprobindin sequences). Neighbor joining, using Tamura and Nei (1993) distances, divides the genealogy into Atlantic and Pacific clades. Parsimony and ML methods place the "Guam 2," "Marquesas 80," and "Papua New Guinea 1" alleles with the Atlantic alleles. That different methods of phylogenetic reconstruction result in roots placed between different nodes of the Tripneustes bindin tree is probably due to the large number of changes between Tripneustes and Lytechinus, relative to the changes within Tripneustes. Mitochondrial DNA divides the Atlantic and Pacific haplotypes into reciprocally monophyletic clades (Lessios, Kane, and Robertson, in preparation)
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In the Pacific, bindin alleles of T. depressus, off the coast of America, and of T. gratilla from the central and Indo-West Pacific do not sort according to nominal species or collection locality. One allele from Kiritimati, which, according to collecting location should belong to T. gratilla, actually groups with T. depressus. The T. depressus alleles (plus the Kiritimati allele) is a sister group to the T. gratilla sequences from Reunion, in the Indian Ocean. The other three T. gratilla sequences are basal in the Pacific clade. The basal position of these three alleles is consistent with the observed intron inversion: each of these alleles has the T. ventricosus form of the inversion, whereas the rest of the Pacific individuals have the other form. There are no fixed nonsynonymous changes between T. gratilla and T. depressus. The close affinity of bindin from the two Pacific species mirrors a similar lack of differentiation of mtDNA sequences (Lessios, Kane, and Robertson, in preparation). Apparently, gene flow between the eastern and central Pacific is either continuing or has been very recently interrupted.
Adaptive Evolution
Relative rates of change of the different regions of the Tripneustes bindin molecule are qualitatively similar to patterns of bindin evolution in other Camarodont sea urchins. Rates of nonsynonymous change are highest in the hotspot region, lowest in the core, and intermediate in the rest of the molecule (table 1). Only nonsynonymous changes are observed in the hotspot region. However, in contrast to the pattern in Echinometra and Strongylocentrotus, the excess of nonsynonymous changes in the hotspot region is not significant in any pairwise comparison. Tripneustes bindins also lack the large number of potentially important indels (Palumbi 1999) seen in the other Camarodont genera. In addition, using the models implemented in PAML, we found no evidence for positively selected sites dispersed throughout the molecule. The likelihood of models that allowed for positively selected sites was not significantly higher than that of models that did not (table 2). Nor did we find any evidence for significant variation in dN/dS ratios between lineages. Allowing a different dN/dS ratio for each branch in the phylogeny did not produce a significantly better model than a model with a single dN/dS ratio for the entire tree (table 2). Finally, a comparison of the ratios of replacement to silent differences within and between species was not significantly different from neutral expectation (McDonald and Kreitman 1991). Four replacement substitutions and zero silent substitutions are fixed between Pacific (T. gratilla and T. depressus) and Atlantic (T. ventricosus) individuals, and there are 12 replacement polymorphisms and 12 silent polymorphisms within the two groups (Fisher's exact test P = 0.11).
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The trend seen for the silent sites of the expressed region does not extend to the intron. Intron sequences are not available for Echinometra, but a comparison between Arbacia and Tripneustes, on the one hand, and Strongylocentrotus on the other, indicates that the ratio of intron to COI divergence is not different between the two groups, which is what would be expected if both the intron and COI evolve linearly with time.
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Discussion |
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Despite the similarities in structure of Tripneustes bindin with that of other Camarodont sea urchins, its mode of evolution appears to be more like that of Arbacia. In contrast to Echinometra or Strongylocentrotus bindin, Tripneustes bindin has evolved slowly. For example, bindin of T. ventricosus from the Caribbean differs from bindin of the eastern Pacific T. depressus by only four fixed amino acid changes and a single indel. These two species were presumably separated from each other for more than 3 million years by the Isthmus of Panama (Coates and Obando 1996). There are no fixed amino acid differences or indels between T. depressus and T. gratilla from the Indo-Pacific, despite the tremendous geographical distance separating the eastern Pacific from the West Indian Ocean. This level of differentiation is almost as low as that seen in the bindin of Arbacia, in which only a single indel distinguishes species on either side of Central America (Metz, Gomez-Gutierez, and Vacquier 1998). It contrasts with differentiation in Echinometra, in which species separated for less than 1.5 MY have 7 fixed amino acid differences (Metz and Palumbi 1996) and in Strongylocentrotus in which S. purpuratus and S. droebachiensis, separated for less than 3 MY, show 21 amino acid differences (Biermann 1998). In addition, bindin of Tripneustes, like that of Arbacia, has only one indel, whereas indels are much more numerous in Echinometra and Strongylocentrotus. Such indels may be functionally important in gamete recognition (Palumbi 1999). Bindin of Tripneustes, like that of Arbacia, shows no evidence of diversifying selection that would manifest itself in significantly more replacement substitutions than silent nucleotide substitutions. Finally, Tripneustes and Arbacia show a lower ratio of bindin to COI substitutions than Echinometra or Strongylocentrotus, despite the inevitable underestimation of bindin divergence in the latter two genera, arising from the exclusion from the analysis of the most variable regions, which could not be aligned. What could account for such similarities between distantly related taxa and differences between closely related ones?
One possible explanation might be the relative age of the species in different genera. By COI and intron divergence (but not by the number of silent substitutions in bindin) the extant species of Arbacia and Tripneustes diverged earlier from each other than did the species of Echinometra and Strongylocentrotus. If, as Civetta and Singh (1995, 1998) have suggested for sex-related genes of Drosophila, the episodes of adaptive bindin evolution are concentrated to the time that new species are formed, and if positive selection on the molecule is subsequently relaxed, then older species may lose the signature of an excess of replacement substitutions relative to silent substitutions. This explanation cannot, however, be applied to bindin. A concentration of adaptive changes at the moment of speciation would decrease the ratio of replacement substitutions to silent substitutions in older species. Increased time since speciation would also decrease the ratio of bindin to COI divergence. However, longer time since speciation could not decrease the absolute number of amino acid changes fixed between species after they have been accumulated early in divergence. The low number of such replacements in Arbacia and Tripneustes must therefore indicate that they have never gone through a period of accelerated bindin divergence. This possibility is also supported by our analysis of the apportionment of replacement and silent substitutions along branches of the Tripneustes bindin tree, which failed to show a concentration of adaptive change in younger (or older) lineages.
Metz, Gomez-Gutierez, and Vacquier (1998) considered three hypotheses as possible explanations for the decelerated bindin evolution in Arbacia: (1) high gene flow, (2) functional constraint, and (3) degree of overlap of species distributions. First, they suggested that high levels of gene flow and a lack of population subdivision within species of Arbacia may limit the rate of bindin evolution. Tripneustes, like Arbacia, shows low levels of biogeographic subdivision, at least in the Pacific (Lessios, Kane, and Robertson, in preparation). However, it is not clear that these two genera are exceptional among echinoids in that respect. High gene flow over thousands of kilometers is a standard feature of all sea urchin species with planktonic larvae (Palumbi and Wilson 1990; Palumbi et al. 1997; Lessios et al. 1999; McCartney, Keller, and Lessios 2000; Lessios, Kessing, and Pearse 2001). In particular, the observations of minimal population subdivision over a range of several thousand kilometers in Indo-West Pacific Echinometra (Palumbi et al. 1997) and in eastern Pacific S. purpuratus (Palumbi and Wilson 1990) or S. franciscanus (Debenham et al. 2000) indicate that the accelerated interspecific bindin divergence relative to Arbacia and Tripneustes cannot be attributable to this factor alone.
Second, Metz, Gomez-Gutierez, and Vacquier (1998) proposed that slow bindin evolution in Arbacia might be due to functional constraints imposed by its molecular structure. They suggested that lack of repeat elements and indels, as well as the presence of a 3' hydrophobic domain, represent evolutionary constraints on Arbacia bindins that are not shared by bindins of Camarodonts. Tripneustes bindin, despite three repeats and a lack of 3' hydrophobic domain, evolves almost as slowly as Arbacia bindin. It appears, therefore, that these features of the molecule do not necessarily affect its evolutionary rate.
The third hypothesis of Metz, Gomez-Gutierez, and Vacquier (1998) was that positive selection, arising from the presence of sympatric congeners, is operating on bindin of Echinometra and Strongylocentrotus, but is absent in Arbacia. Echinometra and Strongylocentrotus contain sympatric species, which are generally gametically incompatible (R. R. Strathmann 1981; M. F. Strathmann 1987 [p. 522]; Uehara, Asakura, and Arakaki 1990; Palumbi and Metz 1991). All extant species in Tripneustes and Arbacia are allopatric. There are no data about gametic compatibility between Tripneustes species, but A. punctulata and A. incisa are gametically compatible (Metz, Gomez-Gutierez, and Vacquier 1998). Thus, it is possible that reinforcement of reproductive isolation among the sympatric species of Echinometra and Strongylocentrotus may explain the observed patterns of bindin evolution. This is a pattern of reinforcement (Noor 1997) on the genus level. However, as is also true for these patterns on the population level (Butlin 1987; Noor 1999), we do not know the process that produced them. Did the presence of congeners create selective pressures for bindin divergence in Strongylocentrotus and Echinometra, or did divergence in bindin, caused by selection arising from another cause, permit species in these genera to invade the same area and coexist without fusing or becoming extinct? This question cannot be answered with certainty, but the patterns of intraspecific and interspecific divergence can provide a clue. If selection to avoid hybridization were responsible for the reinforcement pattern, we would have expected an excess of amino acid replacements between species (particularly between sympatric species) of Echinometra and Strongylocentrotus relative to within species. This however, is not the case in either genus. In the rapidly evolving 40 codon bindin region of Echinometra, the ratio of replacement substitutions to silent substitutions between alleles is larger than unity in both intraspecific and interspecific comparisons, and McDonald-Kreitman (1991) tests are not significant (Metz and Palumbi 1996). In the same region of bindin, comparisons between S. franciscanus and either S. purpuratus or S. droebachiensis indicate that the ratio of replacement substitutions to silent substitutions is higher within than between species (Debenham, Brzezinski, and Foltz 2000). Palumbi (1999) has shown experimentally that, in Echinometra, males carrying different bindin alleles have different rates of success in fertilizing females, depending on the female bindin genotype, and that intraspecific polymorphism is thus maintained by selection. Such selection could arise from male heterozygote advantage, nontransitive female preferences (Palumbi 1999), or interlocus conflict evolution between the sexes (Rice and Holland 1997). These processes can operate within species whether or not they are sympatric with a congener (Metz, Gomez-Gutierez, and Vacquier 1998). Thus, it is possible that the selective force that accelerates bindin evolution in some genera is not avoidance of hybridization in sympatry. The pattern of reinforcement suggested by the comparison between genera with sympatric and allopatric species may be due to the ability of congeneric species with divergent bindin to coexist.
Because Echinometra was the first genus in which evolution of bindin was studied, and because its rapid evolution under positive selection fit patterns found in other genes related to sexual reproduction (Civetta and Singh 1995, 1998; Lee, Ota, and Vacquier 1995; Vacquier, Swanson, and Lee 1997; Ferris et al. 1997; Tsaur and Wu 1997; Aguadé 1999; Hellberg and Vacquier 1999; Wyckoff, Wang, and Wu 2000; Swanson et al. 2001), it has been tacitly assumed that the patterns of positive selection and rapid allele divergence exemplify the mode of evolution of this locus (e.g., Palumbi 1998; Wyckoff, Wang, and Wu 2000; Van Doorn, Luttikhuizen, and Weissing 2001). Biermann's (1998) evidence from Strongylocentrotus reinforced this view. However, the information from Tripneustes now indicates that what Metz, Gomez-Gutierez, and Vacquier (1998) found in Arbacia was not an isolated exception, and not a characteristic of stirodont versus camarodont sea urchins. Why bindin should evolve faster in certain genera of sea urchins and not others remains unclear, but the addition of data from more sea urchin taxa will help determine the factors that promote or retard evolution in this molecule.
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Acknowledgements |
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Footnotes |
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Stephen Palumbi, Associate Editor
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Literature Cited |
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Aguadé, M. 1999. Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila. Genetics 152:543-551.
Akashi, H. 1995. Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139:1067-1076.
Akashi, H. 1997. Codon bias evolution in Drosophilapopulation genetics of mutation-selection drift. Gene 205:269-278.[CrossRef][ISI][Medline]
Alvarez-Valin, F., K. Jabbari, and G. Bernardi. 1998. Synonymous and nonsynonymous substitutions in mammalian genes: intragenic correlations. J. Mol. Evol. 46:37-44.[ISI][Medline]
Biermann, C. H. 1998. The molecular evolution of sperm bindin in six species of sea urchins (Echinoida: Strongylocentrotidae). Mol. Biol. Evol. 15:1761-1771.
Butlin, R. 1987. Speciation by reinforcement. Trends Ecol. Evol. 2:8-13.[CrossRef][ISI]
Civetta, A., and R. S. Singh. 1995. High divergence of reproductive tract proteins and their association with postzygotic reproductive isolation in Drosophila melanogaster and Drosophila virilis group species. J. Mol. Evol. 41:1085-1095.[ISI][Medline]
Civetta, A., and R. S. Singh. 1998. Sex-related genes, directional sexual selection, and speciation. Mol. Biol. Evol. 15:901-909.[Abstract]
Clark, H. L. 1912. Hawaiian and other Pacific Echini. Memoirs Museum Comp. Zool. Harvard Coll. 34:209-383.
Coates, A. G., and J. A. Obando. 1996. The geologic evolution of the Central American Isthmus. Pp. 2156 in J. B. C. Jackson, A. G. Coates, and A. Budd, eds. Evolution and environment in tropical America. University of Chicago Press, Chicago.
Comeron, J. M., and M. Aguadé. 1996. Synonymous substitutions in the XDH gene of Drosophila: heterogeneous distribution along the coding region. Genetics 144:1053-1062.
Comeron, J. M., and M. Kreitman. 1998. The correlation between synonymous and nonsynonymous substitutions in Drosophila: mutation, selection or relaxed constraints? Genetics 150:767-775.
Debenham, P., M. A. Brzezinski, and K. R. Foltz. 2000. Evaluation of sequence variation and selection in the bindin locus of the red sea urchin, Strongylocentrotus franciscanus. J. Mol. Evol. 51:481-490.[ISI][Medline]
Debenham, P., M. Brzezinski, K. Foltz, and S. Gaines. 2000. Genetic structure of populations of the red sea urchin, Strongylocentrotus franciscanus. J. Exp. Mar. Biol. Ecol. 253: 49-62.[CrossRef][ISI][Medline]
Dunn, K. A., J. P. Bielawski, and Z. Yang. 2001. Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics 157:295-305.
Ferris, P. J., C. Pavlovic, S. Fabry, and U. W. Goodenough. 1997. Rapid evolution of sex-related genes in Chlamydomonas. Proc. Natl. Acad. Sci. USA 94:8634-8639.
Frohman, M. A., M. K. Dush, and G. R. Martin. 1988. Rapid production of full-length cDNAs from rare transcripts by amplification using a single gene specific oligonucleotide primer. Proc. Natl. Acad. Sci. USA 85:8998-9002.[Abstract]
Gao, B., L. E. Klein, R. J. Britten, and E. H. Davidson. 1986. Sequence of mRNA coding for bindin, a species-specific sperm protein required for fertilization. Proc. Natl. Acad. Sci. USA 83:8634-8638.[Abstract]
Glabe, C. G., and D. Clark. 1991. The sequence of the Arbacia punctulata bindin cDNA and implications for the structural basis of species-specific sperm adhesion and fertilization. Dev. Biol. 143:282-288.[CrossRef][ISI][Medline]
Glabe, C. G., and W. J. Lennarz. 1979. Species-specific sperm adhesion in sea urchins. J. Cell Biol. 83:595-604.
Glabe, C. G., and V. D. Vacquier. 1977. Species specific agglutination of eggs by bindin isolated from sea urchin sperm. Nature 267:836-838.[ISI][Medline]
Hellberg, M. E., and V. D. Vacquier. 1999. Rapid evolution of fertilization selectivity and lysin cDNA sequences in teguline gastropods. Mol. Biol. Evol. 16:839-848.[Abstract]
Kessing, B. D. 1991. Strongylocentrotid sea urchin mitochondrial DNA: phylogenetic relationships and patterns of molecular evolution. Masters thesis, University of Hawaii, Honolulu.
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.[ISI][Medline]
Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA 2: molecular evolutionary genetics analysis software. Arizona State University, Tempe.
Lee, Y. H., T. Ota, and V. D. Vacquier. 1995. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12:231-238.[Abstract]
Lessios, H. A. 1981. Reproductive periodicity of the echinoids Diadema and Echinometra on the two coasts of Panama. J. Exp. Mar. Biol. Ecol. 50:47-61.[CrossRef][ISI]
Lessios, H. A. 1984. Possible prezygotic reproductive isolation in sea urchins separated by the Isthmus of Panama. Evolution 38:1144-1148.[ISI]
Lessios, H. A. 1985. Annual reproductive periodicity in eight echinoid species on the Caribbean coast of Panama. Pp. 303312 in B. F. Keegan and B. D. S. O'Connor, eds. Echinodermata. Proceedings, 5th International Echinoderm Conference. A. A. Balkema, Rotterdam.
Lessios, H. A. 1991. Presence and absence of monthly reproductive rhythms among eight Caribbean echinoids off the coast of Panama. J. Exp. Mar. Biol. Ecol. 153:27-47.[ISI]
Lessios, H. A., and C. W. Cunningham. 1990. Gametic incompatibility between species of the sea urchin Echinometra on the two sides of the Isthmus of Panama. Evolution 44:933-941.[ISI]
Lessios, H. A., B. D. Kessing, and J. S. Pearse. 2001. Population structure and speciation in tropical seas: phylogeography of the sea urchin Diadema. Evolution 55:955-975.[ISI][Medline]
Lessios, H. A., B. D. Kessing, D. R. Robertson, and G. Paulay. 1999. Phylogeography of the pantropical sea urchin Eucidaris in relation to land barriers and ocean currents. Evolution 53:806-817.[ISI]
Lessios, H. A., B. D. Kessing, G. M. Wellington, and A. Graybeal. 1996. Indo-Pacific echinoids in the tropical east Pacific. Coral Reefs 15:133-142.[CrossRef][ISI]
Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.[ISI][Medline]
Littlewood, D. T. J., and A. B. Smith. 1995. A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata). Phil. Trans. R. Soc. Lond. Ser. B 347:213-234.[ISI][Medline]
Lloyd, A. T., and P. M. Sharp. 1992. CODONS: a microcomputer program for codon usage analysis. J. Hered. 83:239-240.[ISI][Medline]
Mayr, E. 1954. Geographic speciation in echinoids. Evolution 8:1-18.[ISI]
McCartney, M. A., G. Keller, and H. A. Lessios. 2000. Dispersal barriers in tropical oceans and speciation in Atlantic and eastern Pacific sea urchins of the genus Echinometra. Mol. Ecol. 9:1391-1400.[CrossRef][ISI][Medline]
McClary, D., and M. Barker. 1998. Reproductive isolation? Interannual variability in the timing of reproduction in sympatric sea urchins, genus Pseudechinus. Invert. Biol. 117:75-93.[ISI]
McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.[CrossRef][ISI][Medline]
Metz, E. C., G. Gomez-Gutierez, and V. D. Vacquier. 1998. Mitochondrial DNA and bindin gene sequence evolution among allopatric species of the sea urchin genus Arbacia. Mol. Biol. Evol. 15:185-195.[Abstract]
Metz, E. C., R. E. Kane, H. Yanagimachi, and S. R. Palumbi. 1994. Fertilization between closely related sea urchins is blocked by incompatibilities during sperm-egg attachment and early stages of fusion. Biol. Bull. 187:23-34.
Metz, E. C., and S. R. Palumbi. 1996. Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin. Mol. Biol. Evol. 13:397-406.[Abstract]
Minor, J. E., D. R. Fromson, R. J. Britten, and E. H. Davidson. 1991. Comparison of the bindin proteins of Strongylocentrotus franciscanus, S. purpuratus, and Lytechinus variegatus: sequences involved in the species specificity of fertilization. Mol. Biol. Evol. 8:781-795.[Abstract]
Mortensen, T. 19281951. A monograph of the Echinoidea. C. A. Reitzel, Copenhagen.
Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.[Abstract]
Noor, M. A. F. 1997. How often does sympatry affect sexual isolation in Drosophila? Am. Nat. 149:1156-1163.[CrossRef][ISI]
Noor, M. A. F. 1999. Reinforcement and other consequences of sympatry. Heredity 83:503-508.[CrossRef][ISI][Medline]
Palumbi, S. R. 1998. Species formation and the evolution of gamete recognition loci. Pp. 271278 in D. J. Howard and S. H. Berlocher, eds. Endless forms: species and speciation. Oxford University Press, Oxford.
Palumbi, S. R. 1999. All males are not created equal: fertility differences depend on gamete recognition polymorphisms in sea urchins. Proc. Natl. Acad. Sci. USA 96:12632-12637.
Palumbi, S. R., G. Grabowsky, T. Duda, L. Geyer, and N. Tachino. 1997. Speciation and population genetic structure in tropical Pacific sea urchins. Evolution 51:1506-1517.[ISI]
Palumbi, S. R., and E. C. Metz. 1991. Strong reproductive isolation between closely related tropical sea urchins (genus Echinometra). Mol. Biol. Evol. 8:227-239.[Abstract]
Palumbi, S. R., and A. C. Wilson. 1990. Mitochondrial DNA diversity in the sea urchins Strongylocentrotus purpuratus and S. droebachiensis. Evolution 44:403-415.[ISI]
Pamilo, P., and N. O. Bianchi. 1993. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281.[Abstract]
Posada, D., and Crandall, K. A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.[Abstract]
Rice, W. R., and B. Holland. 1997. The enemies within: intergenomic conflict, interlocus contest evolution (ICE) and the intraspecific red queen. Behav. Ecol. Sociobiol. 41:1-10.[CrossRef][ISI]
Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.[Abstract]
Smith, A. B. 1988. Phylogenetic relationship, divergence times, and rates of molecular evolution for Camarodont sea urchins. Mol. Biol. Evol. 5:345-365.
Smith, A. B. 1989. RNA sequence data in phylogenetic reconstruction: testing the limits of its resolution. Cladistics 5:321-344.[ISI]
Smith, A. B., B. Lafay, and R. Christen. 1992. Comparative variation of morphological and molecular evolution through geologic time: 28s ribosomal RNA versus morphology in echinoids. Philos. Trans. R. Soc. Lond. Ser. B 338: 365-382.[ISI][Medline]
Strathmann, M. F. 1987. Reproduction and development of marine invertebrates of the northern Pacific coast. University of Washington Press, Seattle.
Strathmann, R. R. 1981. On barriers to hybridization between Strongylocentrotus droebachiensis (O. F. Muller) and S. pallidus (G. O. Sars). J. Exp. Mar. Biol. Ecol. 55:39-47.[CrossRef][ISI]
Swanson, W. J., C. F. Aquadro, and V. D. Vacquier. 2001. Polymorphism in abalone fertilization proteins is consistent with the neutral evolution of the egg's receptor for lysin (VERL) and positive Darwinian selection of sperm lysin. Mol. Biol. Evol. 18:376-383.
Swanson, W. J., Z. Yang, M. F. Wolfner, and C. F. Aquadro. 2001. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc. Natl. Acad. Sci. USA 98:2509-2514.
Swofford, D. L. 1998. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
Tamura, K., and M. Nei. 1993. Estimating the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.[Abstract]
Tsaur, S.-C., and C.-I. Wu. 1997. Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila. Mol. Biol. Evol. 14:544-549.[Abstract]
Uehara, T., H. Asakura, and Y. Arakaki. 1990. Fertilization blockage and hybridization among species of sea urchins. Pp. 305310 in M. Hoshi and O. Yamashita, eds. Advances in invertebrate reproduction. Elsevier, Amsterdam.
Ulrich, A. S., M. Otter, C. G. Glabe, and D. Hoekstra. 1998. Membrane fusion is induced by a distinct peptide sequence of the sea urchin fertilization protein bindin. J. Biol. Chem. 273:16748-16755.
Ulrich, A. S., W. Tichelaar, G. Forster, O. Zschornig, S. Weinkauf, and H. W. Meyer. 1999. Ultrastructural characterization of peptide-induced membrane fusion and peptide self-assembly in the lipid bilayer. Biophys. J. 77:829-841.
Vacquier, V. D., and G. W. Moy. 1977. Isolation of bindin: the protein responsible for adhesion of sperm to sea urchin eggs. Proc. Natl. Acad. Sci. USA 74:2456-2460.[Abstract]
Vacquier, V. D., W. J. Swanson, and M. E. Hellberg. 1995. What have we learned about sea urchin sperm bindin? Dev. Growth Differ. 37:1-10.[ISI]
Vacquier, V. D., W. J. Swanson, and Y. H. Lee. 1997. Positive Darwinian selection on two homologous fertilization proteins: what is the selective pressure driving their divergence? J. Mol. Evol. 44:S15-S22.[ISI][Medline]
Van Doorn, G. S., P. C. Luttikhuizen, and F. J. Weissing. 2001. Sexual selection at the protein level drives the extraordinary divergence of sex-related genes during sympatric speciation. Proc. R. Soc. Lond. Ser. B. 268:1-7.[CrossRef][ISI][Medline]
Wolfe, K. H., and P. M. Sharp. 1993. Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J. Mol. Evol. 37:441-456.[ISI][Medline]
Wright, F. 1990. The "effective number of codons" used in a gene. Gene 87:23-29.[CrossRef][ISI][Medline]
Wyckoff, G. J., W. Wang, and C. I. Wu. 2000. Rapid evolution of male reproductive genes in the descent of man. Nature 403:304-308.[CrossRef][ISI][Medline]
Yang, Z. 2000. Phylogenetic analysis by maximum likelihood (PAML). Version 3.0. University College London, London.
Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000. Codon substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
Zhang, J., S. Kumar, and M. Nei. 1997. Small-sample tests of episodic evolution: a case study of primate lysosymes. Mol. Biol. Evol. 14:1335-1338.
Zhang, Y., and M. A. Frohman. 1997. Using rapid amplification of cDNA ends (RACE) to obtain full-length cDNAs. Pp. 6187 in I. G. Cowell and C. A. Austin, eds. Methods in molecular biology, Vol. 69. cDNA library protocols. Humana Press, Totowa, N.J.