*Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of Sciences;
Departments of Ecology and Evolutionary Biology and Molecular, Cellular, and Developmental Biology, University of Michigan
SRY, a Y-chromosomal gene that is pivotal in initiating the development of testis and a determinant of male sex in mammals (Goodfellow and Lovell-Badge 1993
), has been subject to intense evolutionary study in the past decade (Foster et al. 1992
; Tucker and Lundrigan 1993
; Whitfield, Lovell-Badge, and Goodfellow 1993
; Pamilo and O'Neill 1997
; Nagai 2001
). SRY protein is a transcription factor containing the conserved DNA-binding HMG domain (
78 amino acids) in the middle of the sequence and highly variable N- and C-terminal sequences (Whitfield, Lovell-Badge, and Goodfellow 1993
). A higher rate of nonsynonymous nucleotide substitution than that of synonymous substitution in the terminal regions of SRY has been reported in primates and rodents, with suggestions that these regions may be subject to positive Darwinian selection (Tucker and Lundrigan 1993
; Whitfield, Lovell-Badge, and Goodfellow 1993
). Here, we sequence the SRY genes of nine Old World (OW) monkeys and show that the evolution of the SRY has been significantly decelerated in these species. Thus, the SRY shows a complex pattern of erratic evolution among different groups of primates, raising an intriguing possibility of varied selective pressures on this fundamentally important gene in evolution.
Using PCR and DNA sequencing, we determined the SRY gene sequences of nine OW monkeys (see fig. 1
). The SRY sequences of six hominoids, one OW monkey, and one New World (NW) monkey were available in the GenBank at the time of this study. Thus, a total of 17 sequences are analyzed here (fig. 1
). Because the HMG domain of SRY is conserved throughout mammalian evolution, we only analyze the N- and C-terminal regions, which have 120 codons after the indels are removed. We first computed the numbers of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions between pairs of the six hominoid sequences, using the modified Nei-Gojobori method (Zhang, Rosenberg, and Nei 1998
). We found that dN is greater than dS for 13 of the 15 pairwise comparisons (fig. 2
), suggesting possible actions of positive selection. We then conducted the same analysis for the 10 OW monkeys and found that dN is smaller than dS for most of these comparisons (fig. 2
). Only among closely related OW monkeys did we find greater dN than dS. In such cases, however, the numbers of substitutions are too few to draw any solid conclusion of the possible action of positive selection. Regardless, the contrasting patterns of high dN/dS ratios in hominoids and low ratios in OW monkeys are clear (fig. 2
). Use of Li's (1993)
method gave similar results.
|
|
With the estimates of the potential numbers of synonymous (S) and nonsynonymous (N) sites in SRY sequences, one may test the hypothesis of neutral evolution (Zhang, Kumar, and Nei 1997
). In the present case, we estimated that S = 108 and N = 252. Thus, for hominoids, the n/s ratio (3.86) is not significantly greater than N/S (252/108 = 2.33) (P = 0.14, Fisher's test). For the reference branch, n/s (3.15) and N/S are not significantly different either (P = 0.21). For OW monkeys, however, n/s (1.2) is significantly lower than N/S (P = 0.04), suggesting the action of purifying selection.
To sum up, our analysis revealed reduced rate of nonsynonymous substitution and action of purifying selection in the terminal regions of SRY in OW monkeys. Although confirming earlier results of high nonsynonymous substitution rates of SRY in hominoids (Whitfield, Lovell-Badge, and Goodfellow 1993
), we were not able to reject the neutral evolution hypothesis. As such, whether the rapid evolution of hominoid SRY is caused by positive selection or relaxed functional constraints remains an open question. Assuming that positive selection did occur in SRY, Hurst (1994)
proposed that the selection is associated with a promiscuous mating system and predicated that there will be more nonsynonymous substitutes in polygamous than monogamous taxa. Our data, however, are not consistent with his prediction, as polygamous primates (such as langurs, macaques, and chimpanzees) do not show higher dN/dS ratio than the monogamous gibbon. The SRY gene is located in the nonrecombining region of the Y chromosome, which means that it may be subject to certain evolutionary forces that are nonexistent or relatively unimportant in the case of autosomal genes. These evolutionary forces and phenomena include the Hill-Roberson effect, Muller's ratchet, genetic hitchhiking, background selection, male-driven evolution, hemizygosity, and reduced effective population size (Tucker and Lundrigan 1995
; Charlesworth and Charlesworth 2000
). However, the relative contributions of these confounding effects on the rate of nucleotide substitution are still unclear, and it is unknown whether natural selection is more likely or less likely to be detected on Y-linked genes. To understand the unexpected evolutionary pattern of SRY, we turn to the structural and functional data of the protein. It is interesting to note that all clinical mutations in human SRY resulting in phenotypic sex reversal are found in the HMG domain, except for one case of a nonsense mutation in the C-terminal region (Hawkins et al. 1992
; Goodfellow and Lovell-Badge 1993
; Tajima et al. 1994
; Werner et al. 1995
). This suggests that the non-HMG regions are under relatively relaxed selective pressures. Computational analysis on the variation of substitution rate among sites also led to this conclusion (Zhang and Gu 1998
). These notions, however, do not exclude the possibility that the non-HMG regions may be under weak positive or purifying selection. In fact, the action of purifying selection is detected in OW monkeys. The variation of dN/dS ratio among primate lineages also suggests to us that these non-HMG regions are not functionless. Rather, our findings suggest that they may play varied roles in SRY functioning among different lineages. Structure-function analysis of several primate SRY proteins may thus shed light on the functions of these non-HMG regions and help resolve the evolutionary mysteries of this fundamentally important protein.
Acknowledgements
We thank Dr. Priscilla Tucker for valuable comments. This work was supported by Natural Science Foundation of China and Chinese Academy of Sciences grants (KSCX2-1-05) to Y-p.Z. and a start-up fund of the University of Michigan to J.Z.
Footnotes
Rodney Honeycutt, Reviewing Editor
Keywords: SRY
evolution
hominoids
Old World monkeys
natural selection
Address for correspondence and reprints: Ya-ping Zhang, Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China. zhangyp{at}public.km.yn.cn
.
Address for correspondence and reprints: Jianzhi Zhang, Departments of Ecology and Evolutionary Biology and Molecular, Cellular, and Developmental Biology, University of Michigan, 3003 Natural Science Building, 830 North University Avenue, Ann Arbor, Michigan 48109. jianzhi{at}umich.edu
.
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