Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Abstract |
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Introduction |
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Recently, a number of studies have focused on the rapid evolution of seminal proteins in Drosophila and have reported the presence of extensive directional selection (Aguadé, Miyashita, and Langley 1992
; Clark et al. 1995
; Tsaur, Ting, and Wu 1998
; Swanson et al. 2001a
). One explanation is that sperm competition between different males results in the rapid divergence of sperm-associated proteins, increasing the probability of successful fertilization. In marine invertebrates, male- and female-expressed genes involved in sperm-egg recognition and binding also have been shown to evolve rapidly (Swanson and Vacquier 1995
; Metz and Palumbi 1996
; Swanson and Vacquier 1998
; Swanson et al. 2001b
; Swanson and Vacquier 2002
), demonstrating that molecular coevolutionary processes may drive the evolution of sex- and reproduction-related traits. Similarly, positive Darwinian selection may often be the prevailing force acting on male reproductive genes in humans and primates, including several sperm genes (Rooney and Zhang 1999
; Wyckoff, Wang, and Wu 2000
). It is therefore expected that sperm-expressed genes, as a group, may show higher divergence because of intersexual selective pressures acting on these genes. Morphological evidence supports this hypothesis because sperm morphology reveals substantial diversity, even between closely related species (Eberhard 1985
; Pitnick 1996
). Yet, even with these examples, it has not been systematically tested whether sperm genes, as a general class, are rapidly evolving. In fact, an alternative explanation is that because sperm proteins perform a critical reproductive function, the vast majority of sperm-associated genes may possess significant selective constraints and thus may follow a distribution of divergence similar to other tissue-specific genes. Here, we report that proteins specifically found in mammalian sperm are rapidly evolving when compared with a large sample of tissue-specific orthologous genes from human and mouse lineages and further demonstrate that positive Darwinian selection has acted on a variety of sperm components.
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Materials and Methods |
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Sperm proteins with more than two orthologs and with characterized function were further tested for evidence of positive selection. A maximum likelihood approach was implemented using the program codeml (Yang 1997
), which uses a codon substitution model of evolutionary change. This method detects positive selection at the level of the codon (Yang 1994
) and uses a likelihood ratio test to test various models of selection against a neutral model. Orthologous sperm-specific sequences from different mammalian species were extracted from GenBank. DNA sequences producing significant matches (E < 10-6) were then aligned with ClustalX, Version 1.81 (Thompson et al. 1997
) and neighbor-joining trees (Saitou and Nei 1987
) drawn. Sequences were bootstrapped 1,000 times, and a consensus tree was drawn and examined manually to select orthologous genes and exclude paralogs. A bootstrap level of 90% was used as a cut-off value for a significant node. Bayes theorem was also used to calculate the posterior probability that each codon belongs to a certain class of
(where
= dN/dS). Codons that identify with classes of
> 1 are purported to be under positive selection. Because of the high divergence of many genes, we confirmed tests of positive selection by using a more conservative DNA sequence alignment by removing the immediate regions flanking indels until all sequences revealed identical nucleotides at one codon.
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Results and Discussion |
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The comparison of the rate of nonsynonymous substitutions with the rate of synonymous substitutions has commonly been used to measure the selective pressures on a gene (i.e., Ka/Ks). If the rate of amino acid replacement is higher than the rate of synonymous changes, the gene is typically thought to have evolved under positive selection. But there is no clear cutoff between neutral evolution, Ka/Ks = 1, and positive selection, Ka/Ks > 1. For example, a ratio of Ka/Ks = 1.1 may be interpreted as either positive or neutral selection. In our human and mouse comparison of orthologous genes, most of the values of Ka/Ks are less than 1, providing no indication of positive selection driving sperm protein evolution but rather a relaxed selective constraint. Yet on average, sperm-specific genes have a significantly higher ratio of Ka/Ks in sperm proteins than in genes from five other tissues (fig. 2
), and there is a twofold increase in the average Ka/Ks of sperm-specific genes when compared with all tissue-specific genes [mean Ka/Ks (sperm) = 0.50 (N = 35) versus mean Ka/Ks (nonsperm) = 0.19 (N = 473); P = 0.001]. Although the data may suggest prematurely that sperm genes have lower selective constraints than do other tissue-specific genes, ratios of Ka/Ks are generally not powerful predictors of positive selection because they represent an average value over all codons and cannot identify positively selected amino acid sites. A maximum likelihood approach has been more successful in detecting positively selected sites within a gene, even when the average Ka/Ks over the entire gene is less than 1 (Yang 1994
; Swanson et al. 2001b
). This method is preferred over average measures of Ka/Ks in detecting positive selection because it can test whether similar selective forces are acting over the entire length of a gene.
Using this approach, sperm-specific genes with known functions were tested for the presence of positively selected codon sites (table 2
). The first test compares an evolutionary model that estimates a single class of the parameter, = dN/dS, with the constraint, 0 <
< 1 (M0), to a model that allows for three site classes, including one that estimates
greater than unity (M3). A total of 13 out of 19 sperm-specific genes show a significantly better fit to model M3 (table 2
), suggesting heterogeneity in
across most of the sperm-specific genes. A second, more conservative test compared models that assume a beta distribution on the parameter
: one model, where 0 <
< 1 (M7), is compared with a model that contains the additional site class,
> 1 (M8). Four out of 19 sperm-specific genes show a significantly better fit to model M8 over M7 with relatively large values of
(table 2
), indicating that these genes contain positively selected amino acids. Surprisingly, these four sperm genes represent diverse functional classes, including a protein involved in chromatin condensation, protamine-1 (PRM1), a protein involved in glycolysis, sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS), and two proteins involved in sperm-egg binding, Adam 2 precursor (ADAM2) and sperm adhesion molecule 1 (SAM1).
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Acknowledgements |
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Footnotes |
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1 Present address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
Keywords: tissue-specific genes
sperm
rapid evolution
positive Darwinian selection
Address for correspondence and reprints: Dara G. Torgerson, Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1. torgerdg{at}mcmaster.ca
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References |
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