Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
Correspondence: E-mail: pogson{at}darwin.ucsc.edu.
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Abstract |
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Key Words: balancing selection gadid fishes maximum likelihood pantophysin positive selection S2 ribosomal protein
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Introduction |
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In a wide range of species, elevated dN/dS ratios have commonly been reported at two broad classes of genesthose involved in host-pathogen interactions (e.g., Hughes and Nei 1988; Hughes 1992; Smith, Maynard Smith, and Spratt 1995; Bishop, Dean, and Mitchell-Olds 2000; Ford 2001) and those functioning in reproduction (e.g., Lee, Ota, and Vacquier 1995; Metz and Palumbi 1996; Tsaur and Wu 1997; Wyckoff, Wang, and Wu 2000; Swanson et al. 2001; Swanson, Nielsen, and Yang 2003 [see review by Ford 2002]). Despite this emerging generality, the diversity of genes that might experience positive selection in the genome is unclear. Positive selection has been described at proteins as diverse as digestive enzymes (e.g., Messier and Stewart 1997), cytochromes (e.g., Wu et al. 1999), toxins (e.g., Nakashima et al. 1995), cytokines (Shields, Harmon, and Whitehead 1996), hormones (e.g., Wallis 1996), and antifreeze proteins (e.g., Swanson and Aquadro 2002). The growing list of positively selected genes suggests that diversifying selection may be more common than previously estimated (e.g., Endo, Ikeo, and Gojobori 1996), although details of the selective process in many cases remain unknown.
In a previous study (Pogson 2001), a signature of positive selection was detected at the vesicle trafficking protein pantophysin in the Atlantic cod Gadus morhua. Pantophysin is an integral membrane protein found in small (<100 nm) cytoplasmic microvesicles that are thought to function in a variety of intracellular shuttling pathways (Haass, Kartenbeck, and Leube 1996; Windoffer et al. 1999; Brooks et al. 2000). Although pantophysin's role in trafficking pathways remains unknown, it shares a characteristic structure of two cytoplasmic tails, four membrane-spanning domains, and two intravesicular loops in common with other physins characterized to date (Johnston, Jahn, and Sudhof 1989; Haass, Kartenbeck, and Leube 1996; Fernandez-Chacon and Südhof 1999). Examination of the nucleotide sequences of 124 pantophysin (Pan I) alleles currently segregating in northwest Atlantic populations of G. morhua by Pogson (2001) suggested a prolonged period of diversifying selection: The two common alleles differed by six fixed nonsynonymous substitutions (and no synonymous changes) that clustered in the 56 residue first intravesicular loop (IV1 domain) of the protein. A seventh polymorphic replacement mutation was also detected in the IV1 domain that exhibited clinal variation throughout the north Atlantic, suggestive of an ongoing selective sweep. It is unclear if the elevated dN/dS ratio observed at the pantophysin locus in G. morhua is related to the unusual polymorphism present in the species or whether positive selection is a more general phenomenon occurring in related species irrespective of the presence of polymorphism.
The objective of the present study was to test for positive selection at the pantophysin locus among 18 species of marine fishes belonging to the family Gadidae. Because the transmembrane structure of pantophysin and signal of selection in the IV1 domain were known before the study, maximum-likelihoodbased models of codon substitution (Yang et al. 2000) were implemented on different domains separately in addition to the entire protein. Models were also implemented that allow ratios to vary among lineages to assess the occurrence of positive selection throughout the phylogenetic tree. The 40S ribosomal S2 protein was sequenced from the same taxa to serve as a control and to provide additional phylogenetic information.
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Materials and Methods |
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Phylogenetic Analyses
For both genes, maximum-parsimony (MP), neighbor-joining (NJ), and maximum-likelihood (ML) analyses were performed using PAUP* 4.0b8 (Swofford 1998). Before the ML analyses, the hierarchical likelihood ratio tests (LRTs) implemented by the Modeltest 3.06 program of Posada and Crandall (1998) identified the General Time Reversible (GTR) model of Rodriguez et al. (1990) as the best substitution model for both genes. ML analyses were performed using empirical base frequencies, a proportion of invariable sites estimated from the data, and among-site rate heterogeneity with gamma shape parameters of 1.12 and 1.13 for the pantophysin and S2 genes, respectively. For the MP analyses, 100 replicates of random taxon addition were followed by heuristic searches with tree-bisection-reconnection (TBR) branch swapping. NJ trees were reconstructed using Kimura (1980) two-parameter (K2P) distances and allowing for rate heterogeneity as per the ML analyses. Bootstrap support values for the MP and NJ trees were obtained from 1,000 replicates. The method of Shimodaira and Hasegawa (1999) was used to test alternative tree topologies in PAUP* using the fully optimized model, 1,000 bootstrap replicates, and among-site rate variation as described above.
Tests for Positive Selection
The CODEML program of the PAML package (Yang 1997) was used to test for the presence of positively selected sites (i.e., codons) in the S2 and Pan I genes. LRTs were performed comparing the scores obtained from models M7 and M8. Model M7 (ß) assumes that ratios follow a ß distribution constrained in the interval (0, 1). Under model M8 (ß and
), an additional class of sites is added to the M7 model that allow for a proportion to have
ratios (estimated from the data) to exceed unity. Although other models in the PAML package were also implemented (i.e., M0, M1, M2, and M3), the results presented here are restricted to the comparisons of M7 and M8 because these represent the most stringent tests of positive selection (Anisimova, Bielawski, and Yang 2001). Because of a priori knowledge of pantophysin's structure (Haass, Kartenbeck, and Leube 1996) and the signal of selection in the IV1 domain of G. morhua (Pogson 2001), analyses were also performed on the four domains of the protein separately (cytoplasmic, transmembrane, IV1, and IV2). To evaluate the presence of local optima on the likelihood surface (cf. Suzuki and Nei 2001), model M8 was rerun with starting
values of 0.5, 1.0, 1.5, and 3.0. If sites with
ratios greater than 1 were identified, the Bayesian method of Nielsen and Yang (1998) was used to calculate posterior probabilities for each site.
For genes/domains in which positive selection was inferred by LRTs, estimates of ratios along branches of the phylogeny were obtained by "free-ratios" models, which assume a different ratio for each branch. To evaluate the heterogeneity of substitution patterns among pantophysin domains, as well as between the Pan I and S2 genes, the fixed-sites models described in Yang and Swanson (2002) were also implemented on the combined data sets. These models allow for the possibility of different substitution rates (rs), base frequencies (
s), transition/transversion rate ratio (
), and
ratios among the partitioned data (i.e., the four Pan I domains and the S2 gene). Nested LRTs were then applied to evaluate the extent of heterogeneity among domains/genes. Fixed-sites models were also implemented on a subset of 12 species that overlapped with Carr et al.'s (1999) study by combining 896 bp of mtDNA (401 bp of cytochrome b and 495 bp of COI) to the Pan I and S2 sequences as a sixth partition. ML estimates of synonymous and nonsynonymous substitution rates between pantophysin and S2 sequences were obtained by the method of Yang and Nielsen (2000) using the yn00 program in the PAML package.
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Results |
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Positive Selection
Table 3 presents the results of tests for positive selection involving the comparison of models M7 and M8. For all tests, G. ogac and G. macrocephalus were collapsed into a single lineage because they were indistinguishable at the protein level. Considering the entire pantophysin sequence, model M8 fit the data significantly better than model M7 and 8.4% of the sites were identified as experiencing positive selection with a mean ratio of 4.74. Model M8 suggested the presence of 17 positively sites (12 in the IV1 domain and five in the IV2 domain), but only seven sites had posterior probabilities exceeding 0.95 (fig. 2). When models M7 and M8 were implemented on the IV1 domain separately, the same 12 positively selected sites were identified, but the mean
ratio increased to 5.35 and all had posterior probabilities greater than 0.95. An additional two sites were identified (positions 24 and 67), but posterior probabilities for both were low (<0.64). Models fit to the IV2 domain alone performed more poorly than those on the entire sequence; only three positively selected sites were identified, with only one having P > 0.95. Four sites experiencing diversifying selection were also identified in the transmembrane domains, but, because the LRT was not significant, these likely represent false positives. Different starting values of
were found to have a negligible effect on model M8 (not shown). No positively selected sites were detected in the S2 gene.
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Results from the Fixed-Sites Models
Table 4 presents the results of the fixed-sites models implemented on the combined pantophysin and S2 data sets that had been divided into five partitions (the four Pan I domains and the S2 sequences). The transmembrane topology of pantophysin confirmed by Haass, Kartenbeck, and Leube (1996) allowed the a priori division of the protein into four domains for these analyses. Allowing the substitution rate to vary among partitions (model B) fit the data significantly better than the simplest model (A) that assumes no rate heterogeneity. Rates of substitution in the IV1 and IV2 domains were both three times higher than observed in the transmembrane regions of the same protein and four times higher than observed at the S2 gene. Overall, pantophysin was evolving about 2.5 times faster than S2. Likelihood ratio tests comparing more complex models to simpler nested models were all significant. Model F (equivalent to performing separate analyses on each partition) provided a significantly better fit than model E despite using 33 x 5 branch lengths for the five partitions. Similar results were obtained for the reduced data set of 12 species (overlapping with Carr et al. [1999]) in which 896 bp of mtDNA sequence was added as a sixth partition (not shown). Here, the LRT comparing models A and B was highly significant (2 = 326.69, P < 0.0001) and indicated that the pantophysin IV1 and IV2 domains were evolving at about 80% of the rates exhibited by the two mitochondrial genes. Overall, the two mitochondrial genes were evolving at about twice the rate of the entire pantophysin sequence.
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Discussion |
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Prior knowledge of diversifying selection in the IV1 domain of G. morhua allowed random-sites models of codon substitution to be implemented on four domains of pantophysin separately. This approach was expected to provide an advantage in identifying positively selected sites because it is known that estimating ratios averaged over all amino acid positions in a protein can reduce the ability to detect positive selection (Crandall et al. 1999; Anisimova, Bielawski, and Yang 2001). However, the results obtained from the models fit to the four domains tended not to outperform those using all sites. Fitting model M8 fit to the IV1 domain did result in a dramatic improvement in the posterior probabilities of positively selected sites, but the same model fit to the IV2 domain failed to identify two sites suggested by the analysis on the entire sequence (table 3). Because the numbers of sequences analyzed was sufficient to detect positive selection with reasonable power, the small number of sites in the IV2 domain and/or low sequence divergence might explain the discrepancies between models fit to separate domains versus the entire sequence.
Implementation of the fixed-sites models that used prior knowledge of differential selection among pantophysin domains also fit the data more poorly than the random-sites models. This is likely caused by the presence of sites experiencing positive and purifying selection in the IV1 and IV2 domains, as several highly conserved features are evident in both intravesicular loops. For example, two cysteine residues are present in both regions (C23 and C52 in IV1 and C150 and C160 in IV2) similar to pantophysin and the related synaptophysin of both human and mouse (see Haass, Kartenbeck, and Leube 1996). Furthermore, in the IV1 domain, a block of five amino acids (YPFRL) is completely conserved among the 18 gadid species examined in the present study and in both human and mouse physins (Haass, Kartenbeck, and Leube 1996). The interspersion of sites experiencing positive and purifying selection in the partitioned data compromises the performance of fixed-sites models and highlights the advantages provided by the random-sites models of Nielsen and Yang (1998) and Yang et al. (2000). Yang and Swanson (2002) reached similar conclusions in their fixed-sites analyses of abalone lysins and human class I MHC alleles.
The detection of positive selection in the two intravesicular loops of pantophysin (and at specific residues within both loops) should direct researchers to explore the functional significance of these domains (and sites). Diversifying selection in the internalized loops of pantophysin could be driven by variable selection pressures related to changes in the physicochemical properties of the vesicle's cargo or to its interactions with other trafficking proteins. However, it is also possible that the positive selection observed is unrelated to pantophysin's normal function. For example, after microvesicle fusion, the intravesicular loops will be externalized on the target membrane, and if this occurs with the plasma membrane, the loops will be exposed on the cell surface. The intravesicular regions of all pantophysins characterized to date contain potential N-glycosylation sites, and Brooks et al. (2000) have recently shown that adipocyte pantophysin is glycosylated in vivo. Because many pathogens are known to target surface glycoproteins as receptors for cell invasion (Karlsson 1995), pathogen evasion might be responsible for the positive selection detected in the IV1 and IV2 domains as suggested for other cell surface proteins by Baum, Ward, and Conway (2002). The pathogen evasion hypothesis fails to explain the high divergence between the two Pan I alleles of G. morhua in a 30-bp region of the second intron in which a stem-loop structure has been disrupted by several deletions in the Pan IB allelic lineage (Pogson 2001). In this species, epistatic selection may be operating to maintain specific associations of intron and amino acid mutations in the IV1 domain that may be unrelated to pathogen evasion per se.
The diversifying selection observed in the present study was not associated with balanced polymorphism in any gadid species other than the Atlantic cod G. morhua. The divergent allelic lineages observed in the Atlantic cod could be an example of what Hughes (1999) has termed "transient polymorphism" that evolves in a single species because of a unique association of selection and opportunity. The absence of polymorphism in other gadids is somewhat surprising in that the four of the five polymorphic IV1 sites observed in G. morhua were targets of positive selection in the broader group. However, our ability to detect polymorphism in other taxa was limited by the small numbers of individuals sequenced (usually three or less) and the sampling of only a single population. It is noteworthy that the Pan I polymorphism in G. morhua would have gone undetected with a similar sampling strategy in several north Atlantic populations (i.e., Nova Scotia or the Barents Sea) because of highly skewed allele frequencies (see Pogson 2001).
Systematics and Biogeography
Monophyly of the subfamily Gadinae was strongly supported by both nuclear genes analyzed in the present study. The branching order of taxa differs sharply from Svetovidov (1948) and Dunn (1989), notably in the position of Micromesistius, which both authors concluded was the most-derived taxon. The pantophysin and S2 genes clearly place M. poutassou as a sister taxon to Trisopterus as the most primitive genera in the group. Unlike the mtDNA sequences analyzed by Carr et al. (1999), the pantophysin tree provided clear separation of Boreogadus/Arctogadus, Gadus spp. and Theragra, and Shimodaira-Hasegawa (1999) tests provided clear rejections of the assumption of monophyly for two genera (Gadus and Microgadus). The increased resolution provided by pantophysin does not appear to have resulted from a faster rate of evolution driven by positive selection. Removing positively selected sites identified by model M8 from the data was found to have no effect on the phylogeny, apart from collapsing the two G. morhua alleles and T. chalcogramma into an unresolved polytomy (not shown). Furthermore, fixed-sites models fit to the combined pantophysin, S2, cytochrome b, and COI sequences of 12 taxa in common with Carr et al.'s (1999) study showed that the two IV domains were evolving 80% as rapidly as the two mitochondrial genes. The inability of the mtDNA to resolve species relationships thus appears to result primarily from a higher level of homoplasy in the data.
All phylogenetic analyses implemented in the study grouped the Pan IA allele of Atlantic cod G. morhua with the Pacific Alaska pollock T. chalcogramma, rather than with the conspecific Pan IB allele. This suggests that the polymorphism characterized by Pogson (2001) may have evolved before the speciation event separating G. morhua and T. chalcogramma. This interpretation should be viewed with caution because the sequence divergence between Theragra and the two G. morhua alleles are very similar (see table 2), and only a single phylogenetically informative mutation at a positively selected site in the IV1 domain (position 51) clusters the G. morhua Pan IA allele with Theragra. Because parallel evolution is evident at many of the positively selected IV1 sites (see figure 2), it is possible that the NT mutation shared by G. morhua and T. chalcogramma is homoplasious. An extensive survey of T. chalcogramma populations throughout the Pacific has failed to uncover the pollock equivalent of the G. morhua Pan IB allele (M. Canino, personal communication). However, if a transpolymorphism did exist after the separation of G. morhua and T. chalcogramma, it is also possible that the Pan IB allele has been lost in the latter by selection or even drift (Clark 1997). Irrespective of this uncertainty, the mtDNA divergence between G. morhua and T. chalcogramma of 4.3% observed by Carr et al. (1999) can be used to provide a rough estimate of the age of the Pan I polymorphism in the Atlantic cod: assuming a standard molecular clock of 2% per Myr, the two G. morhua alleles appear to be at least 2 Myr old.
The pantophysin gene tree also raises questions about the accepted biogeographic origins of several gadid species in the north temperate oceans. The family Gadidae originated in the ArcticNorth Atlantic Basin in the early Tertiary (Svetovidov 1948) and could not have invaded the north Pacific until the opening of the Bering Strait in the mid-Pliocene about 3.0 to 3.5 MYA (Herman and Hopkins 1980). Earlier work based on allozymes (Grant 1987; Grant and Ståhl 1988) and mtDNA (Carr et al. 1999) had concluded that two Pacific species, G. macrocephalus and T. chalcogramma, represented independent invasions of the north Pacific from a presumed G. morhua ancestor. Grant and Ståhl (1988) also observed that G. macrocephalus possessed greatly reduced levels of allozyme polymorphism (and a highly skewed allele frequency spectra) compared with its presumed Atlantic ancestor and suggested it was caused by a bottleneck associated with speciation. However, the Pan I phylogeny strongly suggests that G. macrocephalus first colonized the north Pacific from an ancestor related to Boreogadus/Arctogadus and that G. morhua subsequently reinvaded the north Atlantic. The Greenland cod G. ogac represents another extremely recent recolonization of the Atlantic from a G. macrocephalus origin. A second independent colonization of the Pacific apparently occurred by the ancestor of E. gracilis/M. tomcod. These results suggest that major movements between the north temperate oceans can occur more commonly in this group than previously believed, and the low allozyme variation in G. macrocephalus cannot be attributed to a speciation bottleneck.
In summary, strong positive selection was observed at two intravesicular loops of the vesicle trafficking protein pantophysin in marine gadid fishes. The selection pressures favoring substitutions in pantophysin's IV domains appear to have been operating throughout the diversification of the subfamily Gadinae as well as the polymorphic allelic lineages detected in G. morhua. Similar to the Lyb-2 gene in the mouse studied by Hughes (1993), pantophysin may represent another example of a gene known to experience positive Darwinian selection before its function is fully understood. It is hoped that future work can take advantage of this signal of positive selection to elucidate pantophysin's role in cellular trafficking pathways.
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Acknowledgements |
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Footnotes |
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