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Deleterious Mutations at the Mitochondrial ND3 Gene in South American Marsh Rats (Holochilus)
Patricia Kennedya and Michael W. Nachmanaa Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
Corresponding author: Patricia Kennedy, Department of Ecology and Evolutionary Biology, Biosciences West Bldg., University of Arizona, Tucson, AZ 85721., pkennedy{at}u.arizona.edu (E-mail).
Communicating editor: R. R. HUDSON
| ABSTRACT |
|---|
Statistical analyses of DNA sequences have revealed patterns of nonneutral evolution in mitochondrial DNA of mice, humans, and Drosophila. Here we report patterns of mitochondrial sequence evolution in South American marsh rats (genus Holochilus). We sequenced the complete mitochondrial ND3 gene in 82 Holochilus brasiliensis and 21 H. vulpinus to test the neutral prediction that the ratio of nonsynonymous to synonymous nucleotide changes is the same within and between species. Within H. brasiliensis we observed a greater number of amino acid polymorphisms than expected based on interspecific comparisons. This contingency table analysis suggests that many amino acid polymorphisms are mildly deleterious. Several tests of the frequency distribution also revealed departures from a neutral, equilibrium model, and these departures were observed for both nonsynonymous and synonymous sites. In general, an excess of rare sites was observed, consistent with either a recent selective sweep or with populations not at mutation-drift equilibrium.
Afundamental goal of population genetics is to understand the forces that give rise to and maintain genetic variation in natural populations. The relative ease of collecting DNA sequence data has facilitated measurement of genetic variation within species (for reviews, see ![]()
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Several statistical tests of the neutral model use data from a single locus and have been used to investigate evolutionary forces acting on mitochondrial DNA (mtDNA). For example, the neutral model predicts that the ratio of replacement to silent polymorphism within species is equal to the ratio of replacement to silent fixed differences between species (![]()
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At least three hypotheses may explain the excess of intraspecific amino acid polymorphisms seen at mitochondrial genes. First, many amino acid mutations may be slightly deleterious (![]()
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We are interested in exploring the generality of the nonneutral patterns observed in mtDNA. Here we report mtDNA sequence variation within and between two species of South American marsh rats in the genus Holochilus. Marsh rats are semi-aquatic rodents that live in marshes and along stream banks throughout wet, lowland regions of South America (![]()
| MATERIALS AND METHODS |
|---|
Samples and DNA preparation:
A total of 103 marsh rats from 8 populations of Holochilus brasiliensis (N = 82) and 2 populations of H. vulpinus (N = 21) were collected along a river drainage extending from northern Paraguay to central Argentina (Figure 1), as previously described (![]()
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DNA amplification and sequencing:
Sequencing templates were prepared using polymerase chain reaction (PCR) with primers that amplified a 488-bp fragment that included the entire ND3 gene. The primers PKND3-L9385 and PKND3-H9831 were used for both amplification and sequencing. Primer numbers refer to the position of the 3' base in the complete mouse mitochondrial sequence of ![]()
Data analysis:
Sequences were aligned by eye, and the numbers of replacement and silent polymorphisms and fixed differences were counted. The ND3 gene is 345 bp in length excluding the stop codon. Two different measures of nucleotide variation,
(![]()
(![]()
, is calculated from the average number of nucleotide differences between all pairs of sequences in a sample and
is calculated from the number of segregating sites in a sample. Thus
takes into account the frequencies at which polymorphisms are present in the sample, while
is based solely on the observed number of segregating sites. For mitochondrial sequences, both are estimators of the neutral parameter 2Neµ, where Ne is the effective population size for females and µ is the neutral mutation rate.
To test the neutral prediction that the ratio of replacement to silent nucleotide changes is the same within and between species (![]()
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) and the average number of pairwise nucleotide differences (
), while Fu and Li's D compares the distribution of mutations on internal (
i) and external branches (
e) of the gene tree. Both tests are based on the neutral prediction that these different estimators of 2Neµ will be the same; the expectation for both Tajima's D and Fu and Li's D under neutrality is zero. Simulations indicate that the power of these tests to reject the null model is not great unless sample sizes are quite large (i.e., in excess of N = 50; ![]()
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and may be more powerful for detecting population growth or hitchhiking events than Tajima's D or Fu and Li's D (![]()
| RESULTS |
|---|
Sequence variation:
The aligned ND3 nucleotide and protein sequences are shown in Figure 2. For each species, the consensus sequence is shown and polymorphic nucleotide and amino acid sites are given in lower case.
Within H. brasiliensis (N = 82), 24 segregating sites and 25 different haplotypes were detected at the ND3 gene (Table 1). Within H. vulpinus (N = 21), 2 polymorphic sites and 3 haplotypes were observed (Table 2). No insertion-deletion variation was observed within or between either species, and the length of the ND3 gene in Holochilus (348 bp) is the same as in humans (![]()
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Within H. brasiliensis, there is evidence for multiple mutations at the same site (violations of the infinite sites model). When parsimony trees are constructed using all the data, there are 617 equally parsimonious networks linking the 25 haplotypes; these trees have a consistency index of 0.8 (![]()
There is some evidence of geographic structuring to the distribution of variation within H. brasiliensis (Table 1 and Table 3). The most common protein variant was present in every population. However, of the eight rare variants, four were restricted to single populations, three were observed in two populations, and one was observed in three populations (Figure 3). Nucleotide diversity among the eight H. brasiliensis populations ranged from a low of
= 0.39% to a high of
= 0.89% (Table 4). Average FST calculated among all H. brasiliensis populations was 0.178 and FST calculated between the two H. vulpinus populations was 0.386 (Table 5). To test for population subdivision, we performed a
2 test of haplotype frequencies in the different localities with rare haplotypes lumped such that the expected number of each haplotype in each locality was at least two (![]()
2 = 22.9, d.f. = 7, P = 0.0018). We also performed permutation tests of subdivision (![]()
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The average uncorrected sequence divergence between H. brasiliensis and H. vulpinus was 18.9% for the entire ND3 gene. Divergence for the entire gene, corrected for multiple hits using Kimura's two-parameter model (![]()
Tests of neutrality:
We observed 9 replacement and 17 silent polymorphisms within species (both species together), and 7 replacement and 49 silent fixed differences between species (Table 6). These ratios are significantly different from each other using a G log-likelihood ratio test (P < 0.05). The ratios are also significantly different from each other when polymorphism data from only H. brasiliensis are compared to fixed differences between the species (P < 0.05). There were too few segregating sites within H. vulpinus to construct a test with polymorphism data from that species alone. These comparisons are based on uncorrected levels of sequence divergence and do not account for multiple mutations at the same site, either within or between species. Corrected values do not represent independent observations and thus are inappropriate for use in a contingency table analysis (![]()
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We investigated departures from a neutral frequency distribution by looking at the total number of segregating sites, the number of singletons, and the average number of pairwise differences within H. brasiliensis (Table 7). There is clear evidence for an excess of rare sites. Tajima's D, Fu and Li's D, and Fu's Fs are negative when all sites are considered together as well as when replacement or silent sites are considered alone. Tajima's D is significantly negative only for replacement sites, while Fu and Li's D is significantly negative for the entire data set and for silent sites alone. Fu's Fs is significantly negative for both replacement and silent sites. The frequency distribution of polymorphic sites is shown in Figure 4; 14 of 24 polymorphisms were present in just one or two individuals.
|
| DISCUSSION |
|---|
Excess amino acid polymorphism in natural populations:
As in previous studies (![]()
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In principle, deviations from neutral expectations in a 2 x 2 contingency table analysis may be due to forces affecting the numbers in any or several of the four cells. For example, it is possible that the deviation we observe is due to the accumulation of adaptive synonymous substitutions between species. There is mounting evidence that selection on silent sites may play an important role in Drosophila (e.g., ![]()
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One possibility is that selection pressures have changed recently, allowing an accumulation of formerly deleterious, but currently neutral, amino acid polymorphisms (Figure 5). For example, ![]()
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Another possibility is that multiple amino acid polymorphisms are being maintained in populations by some form of balancing selection. Although the uniparental inheritance of mtDNA precludes heterosis, it is possible that selection acting upon nuclear-cytoplasmic interactions is maintaining mitochondrial variants. Many of the mitochondrial genes for which excess amino acid variation has been documented (ATPase, cytochrome b, cytochrome oxidase, and NADH dehydrogenase complex) have subunits encoded by both the nucleus and mitochondrion. However, theoretical studies suggest that it is difficult to maintain multiple mitochondrial variants via cyto-nuclear interactions (![]()
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A third explanation for these data is that many amino acid mutations are weakly deleterious. First proposed by ![]()
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and, as such, are expected to contribute differentially to heterozygosity and to substitution (![]()
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1, evolution will stop (![]()
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There are, however, other lines of evidence that support the view that deleterious mutations may be common in mtDNA. First, a number of mitochondrial missense mutations are known to cause disease in humans, and some disease phenotypes appear to be due to multiple mutations, each of small effect (![]()
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The hypothesis that mitochondrial amino acid mutations are mildly deleterious makes at least one testable prediction. ![]()
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Frequency distribution of polymorphisms in H. brasiliensis:
Tests of the frequency distribution were consistent in revealing an excess of rare sites (Table 7). These departures from neutral expectations were observed for both nonsynonymous and synonymous sites. These results could be due to a population expansion or a selective sweep on the mitochondrial genome (![]()
Generality and implications of nonneutral mtDNA evolution:
The results presented here show that the nonneutral patterns first documented for humans, house mice, and fruit flies are not unique to those species. This study, in conjunction with a recent analysis of published mtDNA datasets (![]()
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Another question raised by these observations is whether excess intraspecific amino acid polymorphisms are specific to mtDNA, or whether these observations may also extend to nuclear loci. Few data exist with which to address this issue, and most polymorphism and divergence data from nuclear genes come from Drosophila. In D. melanogaster, while some genes show an excess of intraspecific replacement polymorphism, most do not (e.g., ![]()
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| ACKNOWLEDGMENTS |
|---|
We thank A. S. KONDRASHOV for discussion, S. L. CROWELL for help in the lab, and P. ANDOLFATTO, R. R. HUDSON, and one anonymous reviewer for comments on the manuscript. This work was supported by a National Science Foundation (NSF) Research Training Grant to P.K. and NSF grants to M.W.N.
Manuscript received October 31, 1997; Accepted for publication June 12, 1998.
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