A Survey of Chromosomal and Nucleotide Sequence Variation in Drosophila miranda | Genetics

A Survey of Chromosomal and Nucleotide Sequence Variation in Drosophila miranda

  1. Soojin Yi*,1,
  2. Doris Bachtrog† and
  3. Brian Charlesworth†
  1. * Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637-1573
  2. † Institute of Cell, Animal and Population Biology, University of Edinburgh, King’s Buildings, Edinburgh EH9 3JT, United Kingdom
  1. 1 Corresponding author: Department of Ecology and Evolution, University of Chicago, 1101 E. 57th St., Chicago, IL 60637. E-mail: soojinyi{at}midway.uchicago.edu

Abstract

There have recently been several studies of the evolution of Y chromosome degeneration and dosage compensation using the neo-sex chromosomes of Drosophila miranda as a model system. To understand these evolutionary processes more fully, it is necessary to document the general pattern of genetic variation in this species. Here we report a survey of chromosomal variation, as well as polymorphism and divergence data, for 12 nuclear genes of D. miranda. These genes exhibit varying levels of DNA sequence polymorphism. Compared to its well-studied sibling species D. pseudoobscura, D. miranda has much less nucleotide sequence variation, and the effective population size of this species is inferred to be several-fold lower. Nevertheless, it harbors a few inversion polymorphisms, one of which involves the neo-X chromosome. There is no convincing evidence for a recent population expansion in D. miranda, in contrast to D. pseudoobscura. The pattern of population subdivision previously observed for the X-linked gene period is not seen for the other loci, suggesting that there is no general population subdivision in D. miranda. However, data on an additional region of period confirm population subdivision for this gene, suggesting that local selection is operating at or near period to promote differentiation between populations.

DROSOPHILA miranda is a sibling species of D. pseudoobscura and D. persimilis, first described by Dobzhansky (1935). Except for a few slight differences observed in the laboratory, D. miranda is phenotypically indistinguishable from its sibling species (Dobzhansky 1935). Nevertheless, it is almost completely reproductively isolated from them (Dobzhansky and Tan 1936; Dobzhansky 1937). In addition, D. miranda possesses an unusual karyotype. Dobzhansky (1935) was puzzled by the fact that males and females of D. miranda each had a different number of chromosomes at meiosis. Later it was shown that the autosome that is monosomic in females, designated X2 (or the neo-X), corresponds to chromosome 3 in D. pseudoobscura and D. persimilis (Dobzhansky and Tan 1936; Macknight 1939). The missing homolog of X2 was found to have fused to the Y chromosome and is now termed the neo-Y chromosome (Macknight 1939; Steinemann and Steinemann 1998).

Since then, a series of investigations have shown that the neo-sex chromosomes of D. miranda represent a remarkable intermediate stage in the evolution of sex chromosomes. More specifically, the neo-Y chromosome of D. miranda is partially degenerate, and parts of the counterpart neo-X chromosome have evolved dosage compensation (Steinemann and Steinemann 1998). Examination of the pattern of molecular evolution of neo-sex-linked genes in D. miranda provides a means for investigating the early phases of sex chromosome evolution. It has been proposed that Y chromosomes degenerate as a result of the greatly reduced effective population size (Ne) of the nonrecombining Y chromosome, compared with that of its freely recombining counterpart, the X chromosome (Charlesworth 1996; Charlesworth and Charlesworth 2000). Polymorphism data show that Ne for the neo-Y is ∼30-fold less than that for the neo-X (Bachtrog and Charlesworth 2000, 2002; Yi and Charlesworth 2000). On the other hand, data on variation in D. miranda from genes other than neo-sex-linked loci are scarce, and little is known about the population biology of this species. Anecdotal evidence suggests that it was relatively abundant just a few decades ago in northern California and in the Canadian province of British Columbia (J. Coyne and A. Beckenbach, personal communications). In recent years, however, many attempts to collect this species from its natural habitat have failed, and currently the last time D. miranda was caught in the wild was in 1997 in Mather, California (M. Noor, personal communication).

Some authors have suggested that there is a substantial amount of genetic heterogeneity between populations of D. miranda. Dobzhansky and Koller (1938) reported some incipient reproductive isolation between strains collected from two different locations. Goddard et al. (1990) reported that the DNA composition within the species of D. miranda, as measured by DNA-DNA hybridization, varied considerably. However, no subsequent study has followed up these observations. Recently, a survey of nucleotide polymorphism at the X-linked locus period (per) revealed an unusual pattern of sequence diversity, suggesting the existence of population subdivision (Yi and Charlesworth 2000). This is the only study of nucleotide variation to show such a pattern so far.

Another possible type of genetic variation in D. miranda is chromosomal variation. Both of its sibling species, D. pseudoobscura and D. persimilis, have numerous inversion polymorphisms, which are particularly abundant on chromosome 3 (Powell 1992, 1997). The extent of inversion polymorphism in D. miranda, however, has not been systematically documented, even though there are references to such polymorphism in the literature (Dobzhansky and Tan 1936; Macknight 1939; Dobzhansky and Powell 1975).

It is important to characterize the extent of genetic and chromosomal variation in D. miranda and to compare it with its sibling species. This information is essential for inferring the selective forces underlying the evolution of the neo-sex chromosomes in this species, since it provides a benchmark against which the unusual patterns of DNA sequence polymorphism and evolution on the neo-sex chromosomes (Bachtrog and Charlesworth 2000, 2002; Yi and Charlesworth 2000) can be compared. We have accordingly studied several aspects of the population genetics of D. miranda. First, we have investigated the amount of chromosomal variation in D. miranda. This is the first such documentation from this species and is important for our purposes, since inversions can distort the patterns of neutral DNA sequence variability (Andolfattoet al. 2001). Second, we have surveyed the amount of genetic diversity at 12 nuclear genes and their divergence from D. pseudoobscura. This provides estimates of the typical extent of neutral variation and the effective population size of this species, which are critical parameters for inferring the operation of various evolutionary forces. Third, using nucleotide sequence data from our additional loci, we have asked if the pattern of population subdivision observed at the per locus (Yi and Charlesworth 2000) is a general phenomenon in this species. Such subdivision would complicate the interpretation of standard tests for departure from neutrality, which assume panmixia. Finally, we have used the pattern of nucleotide diversity from many loci to examine the population history of this species, i.e., whether there has been an episode of population expansion, as proposed for its sibling species D. pseudoobscura (Kovacevic and Schaeffer 2000; Machadoet al. 2002). Again, such an effect would complicate tests of neutrality.

MATERIALS AND METHODS

Strains used and genomic DNA preparation for polymorphism analyses: The strains of D. miranda that were used in Yi and Charlesworth (2000) were also used in this work. For all genes except Adh, genomic DNA (gDNA) was extracted from a single male fly from each strain of D. miranda by means of the Puregene gDNA extraction kit (Gentra, Research Triangle Park, NC). Genomic DNA from a strain of D. pseudoobscura from Mather, California, used by Yi and Charlesworth (2000), was also extracted from single male flies using the same method and used to obtain outgroup sequences for cyp1, elav, Gapdh2, sc, and sesB (gene nomenclature according to FlyBase; see below).

The extracted gDNA from each strain was rehydrated in 50 μl TE buffer and then electrophoresed in 1% agarose gels for the estimation of quality and quantity. For one 25-μl PCR reaction, <20 ng of gDNA sufficed for successful amplification of the final product. Among the 12 loci newly amplified in this study, 10 are expected to be on the X chromosome of the obscura group of Drosophila (see below). Therefore, except for the 2 autosomal loci Adh and sry-α, use of a single male fly should ensure homozygosity of the sequencing templates.

Genomic DNA used for the amplification of Adh was obtained in the following way, which is similar to the method used by McAllister and Charlesworth (1999) for the study of Adh in D. americana. Interspecific crosses between a single D. pseudoobscura male and a female from D. miranda were performed. This was done separately for each of the 12 strains of D. miranda. Single progeny from these crosses should contain one copy of a D. pseudoobscura Adh allele and one copy of a D. miranda Adh allele. Genomic DNA was extracted from single progeny from each cross according to the same protocol as above. The Adh allele specific for D. miranda could thus be amplified by using D. miranda specific primers. For the amplification of sry-α, the PCR product from a single male of D. miranda was used for sequencing. If we found any potentially ambiguous sites from a single PCR product, we chose gDNA from another single male fly to repeat the process until we were certain of the homozygosity of the sequences.

Polytene chromosome preparation and inversion analyses: Larvae were reared at 18° in low-density banana medium cultures (Yi and Charlesworth 2000). Larvae were cleaned in Shen’s solution (Nicoletto 1959), and salivary glands of third instar larvae were dissected out in 45% acetic acid. The glands were transferred to a drop of 1 part concentrated lactic acid:2 parts water:3 parts glacial acetic acid on a siliconized coverslip and fixed for 5 min. A drop of a solution of Gurr’s orcein (Bio/medical Specialties, Santa Monica, CA), prepared according to Nicoletto (1959), was added, and the glands were stained for 2 min. A siliconized slide was gently lowered onto the coverslip and moved from side to side, to spread the glands. The slide was then examined at ×100; if the nuclei remained clustered and intact, the coverslip was tapped with the end of a mounted needle to burst them. The slide was then pressed gently between the folds of a paper towel, and the edges of the coverslip were sealed with nail varnish. Slides were examined with brightfield illumination at ×400 or ×630 (oil immersion) with a Zeiss Standard microscope.

To identify polymorphic inversions, one line (MSH 38; see Yi and Charlesworth 2000) was arbitrarily selected as a tester strain. Crosses of females from each of the other 11 strains to this tester were made, and a minimum of one female larva per strain was scored for the presence of inversion loops (means of 1.5 female and 0.67 male larvae per line were scored). The breakpoints of inversions were established with reference to the photographic and drawn polytene chromosome maps of Das et al. (1982); the standard arrangements were taken to be the band orders represented in their Figure 2. Once the inversions had been identified (see results), further characterization of the lines was carried out by examining squashes of larvae obtained directly from the lines.

Primers, PCR amplification, and sequencing for polymorphism analyses: We report new DNA sequence polymorphism data at 12 loci from D. miranda. We chose 10 genes that were expected to be located on the left arm of the X chromosome (XL), which corresponds to the ancestral X chromosome of the genus Drosophila (Muller’s element A; Powell 1997) and the right arm of the X chromosome (XR). These are: cyclophylin (cyp1), elav, an intergenic region between esterase 5C and esterase 5B (Est-5; Babcock and Anderson 1996), Gapdh2, a segment of period (per-new; see below), runt (run), scute (sc), ADP/ATP translocase (sesB), sisterless A (sisA), and swallow (swa). This selection of genes partly depended upon the availability of orthologous sequences from other species. In addition, we also chose two autosomal loci, Alcohol dehydrogenase (Adh) and serendipity alpha (sry-α). The Adh region sequenced includes the intergenic region between Adh and Adh-related (Adhr) loci and also the first exon and intron of the Adhr locus. We treat these two loci as a single unit throughout the analyses, because they are amplified as a single consecutive segment. The structure of each locus and the positions of the sequenced regions are depicted in Figure 1.

PCR primers were designed for each gene using conserved sequences inferred from the alignments of available orthologous sequences (Table 1). All sequenced regions except for Est-5 include coding regions. Usually one 25-μl PCR reaction was enough to provide templates for the subsequent sequencing reactions. For 7 of the 10 X-linked genes (excluding Est-5, run, and swa loci), the same male genomic DNA was used to generate the polymorphism data. We used Taq polymerase from Roche Molecular and Biochemicals (Indianapolis) for PCR and the BIG Dye-termination cycle sequencing kit from Perkin Elmer (Foster City, CA) for sequencing reactions. All sequences were run on an ABI 377 sequencer for both strands, using overlapping internal primers when necessary. All sequences are stored under GenBank accession nos. AY238758-AY238879.

Localization of gene probes to D. miranda chromosomes: PCR products from genomic DNA were extracted from 1% agarose gel using the QIAquick gel extraction kit (QIAGEN, Chatsworth, CA) and then labeled with Biotin High Prime (Roche Molecular Biochemicals) for use as a probe. Salivary glands from third instar larvae were dissected and hybridized with each probe. The hybridization procedure largely followed the protocol of Maside et al. (2001). Sites of hybridization were detected by staining with diaminobenzidine and peroxidase (Vector Laboratories, Burlingame, CA). Slides were examined under a ×40 phase-contrast objective and stained with 5% pH 7.1 Giemsa solution (Gurr) when chromosome bands were faint or when there was a lot of background. The banding patterns of polytene chromosomes of D. miranda reported by Das et al. (1982) were used as the reference point when determining the sites of hybridization.

Polymorphism and divergence data analyses: DNA sequences were aligned using the Clustal option in the MegAlign program (part of the DNA STAR package). The highly variable region from the 3′ region of the sisA gene was manually aligned using the interface of the SeqEd program, minimizing the number of insertion/deletions. Further editing was performed as appropriate for various analyses. For most of the within-population variation studies, the SITES program (Hey and Wakeley 1997) and DnaSP program v. 3.50 (Rozas and Rozas 1999) were used. A coalescent simulation to investigate the variance of FST measures was obtained from Molly Przeworski and Eli Stahl. Multilocus Hudson-Kreitman-Aguadé (HKA) tests were performed using J. Hey’s program using coalescent simulations (Machadoet al. 2002).

Figure 1.

—Structure of gene segments surveyed in this study. Exons are shown as solid boxes, drawn to approximate scales. The double-headed arrows indicate the segments of DNA sequenced for each locus.

RESULTS

Locations of genes surveyed in this study: The chromosomal locations of the 12 genes whose polymorphism pattern have been reported here are shown in Figure 2. All genes were found on the chromosomes expected from the conserved chromosome arm homologies within the genus Drosophila (Table 9.4, p. 307 of Powell 1997). All the genes that are X linked in D. melanogaster are on XL in D. miranda. Est-5 (on chromosome arm 3L of D. melanogaster) was found to be on XR, as expected from the fact that, in the pseudoobscura and affinis subgroups of the subgenus Sophophora of Drosophila, a fusion between elements A and D created a new X chromosome arm, XR (p. 309 of Powell 1997). Adh, which is on 2L in D. melanogaster, is found on the homologous chromosome, chromosome 4 of D. miranda. The location of sry-α also follows the expected chromosomal homologies (chromosome 2, homologous to 3R of D. melanogaster).

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TABLE 1

Primer sequences used for PCR amplification

The chromosomal assignments all correspond to those in the closely related species, D. pseudoobscura (Babcock and Anderson 1996; Segarraet al. 1996; Kovacevic and Schaeffer 2000), where these have been determined. However, the physical locations of the genes within the chromosomes are likely to differ. One significant difference when compared to the genetic map of XL of D. pseudoobscura (Kovacevic and Schaeffer 2000) is that the positions of sisA and run are inverted in D. miranda. This probably corresponds to the major medial inversion distinguishing the XL chromosome arms of these two species (Dobzhansky and Tan 1936; Andersonet al. 1977).

Polymorphic inversions: Table 2 shows the lines for which inversion loops were detected in crosses with MSH38 (see materials and methods). A total of four inversions were detected, on chromosome arms XR, X2, and 2, respectively; no inversions were found on XL or chromosome 4 (Figure 2). The large inversion 2-2 was found only in association with the included inversion 2-1. Further examination of the lines themselves showed that MSH38 is segregating for inversion XR-1; out of six female larvae examined, four were heterozygous for this inversion. In good preparations, it was possible to identify the inversions XR-1, X2-1, and 2-2 in homo- or hemizygotes, using the orders of certain landmarks (prominent banding patterns and puffs). No lines other than MSH38 showed any signs of the presence of XR-1, so that it is apparently a low-frequency inversion. All six MSH38 female larvae examined for X2-1 were found to be homozygous for the standard arrangement. Similar examinations of the other strains suggests that this inversion is probably fixed in the seven lines that had been found to contain it in the test crosses with MSH38 (Table 2). This indicates that it has a frequency of ∼50% in the D. miranda population. Inversion 2-1 was found to segregate in the cross of line 0101.3 with MSH38, but all five larvae examined from 0101.7 (from both the testcross and the line itself) carried the inversion. It is interesting to note that Macknight (1939) described an inversion that was almost certainly X2-1; he found it in a stock that had been treated with X rays and inferred that it had been induced by this treatment. Line 0101.4 showed segregation for the compound inversion 2-1 + 2-2 in the testcrosses with MSH38; neither inversion was seen in any of the other lines. Both 2-1 and 2-1 + 2-2 are therefore low-frequency inversions.

Figure 2.
Figure 2.

—Gene locations and the newly discovered inversions from this study. Drawn on the polytene chromosome map of D. miranda from Figure 2 of Das et al. (1982). The proximal region for each chromosome arm is on the right.

Summary of data on DNA sequence polymorphisms, divergence, and functional constraints: The loci surveyed in this study showed a wide range of levels of genetic diversity at the DNA sequence level (Table 3; see supplementary material at http://www.genetics.org/supplemental/ for full details of haplotypes). Both indel variants and single nucleotide polymorphisms (SNPs) were present. There are a total of 23 indel variants from seven loci, all from introns or untranscribed regions. Five loci, elav, Gapdh2, sesB, sry-α, and swa, did not show any indels. The 3′ noncoding region of sisA had a region that was highly variable for complex indel variants. This corresponds to the position 1091-1157 of the alignment. At the run locus, all the indel variants occurred in a region surrounding a core indel of 12 nucleotides. Note that the indels are determined using the most parsimonious alignments, so that the real numbers may slightly differ from our estimates.

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TABLE 2

Polymorphic inversions detected in D. miranda

We observed more than five times as many SNPs as indels. In three cases two or three adjacent SNPs were in complete linkage disequilibrium (two cases at the run locus, one at the per-new locus: see supplementary material at http://www.genetics.org/supplemental/). The mutation events that created these clusters of SNPs are unlikely to be independent events. This is inconsistent with the infinite sites model (Kimura 1971), which is the basis of the methods used to analyze the pattern of SNPs. Therefore, in these three cases we counted each cluster as one SNP. This is reflected in all the SNP analyses described below.

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TABLE 3

Summary of polymorphism and divergence statistics

Summary statistics on SNPs at each locus are presented in Table 3, together with the estimated numbers of nucleotide substitutions per site from D. pseudoobscura for silent sites (KS). Previous data from the per locus (Yi and Charlesworth 2000) are also compiled in Table 3 for the purpose of comparison. These are denoted as “per-ori.” Newly obtained results from another region of the per locus (see materials and methods) are shown as “per-new.” A simple average of the silent site pairwise nucleotide diversity from Table 3 is 0.43%. The mean KS (weighted by the numbers of synonymous sites per gene) is 3.4%; a contingency χ2 test shows highly significant variation in KS among loci (χ2 = 36.4, P < 0.0003). The variance in observed KS values is 1.75 × 10-4, ∼1.78 times that expected purely on the basis of sampling variation with a constant underlying KS.

We observed reasonable correlations between nucleotide site diversities and the presumed functional roles of the corresponding region. For example, the 3′ noncoding region of Adh is a short intergenic region between the Adh and the Adhr locus (see Figure 1), which may include several motifs related to the expression of both Adh and Adhr (Marfany and Gonzales-Duarte 1992) and/or sequences required for appropriate splicing. This is consistent with its low level of variation (one variant from 282 sites surveyed). The sequenced 3′ noncoding region of sc is highly conserved between D. melanogaster and D. subobscura and known to contain the polyadenylation signal and a conserved region with an unknown function, as well as putative Sxl-binding sites (Botellaet al. 1996). We found that the 3′ region of sc harbors very little variation. Divergence from D. pseudoobscura is also very low (K3′ = 1.79%). The 5′ flanking region of the sisA locus showed a much lower level of nucleotide diversity (π= 0.07%) than the 3′ region (π= 0.76%). When compared with the homolog from D. pseudoobscura, the 5′ region was much more conserved than the 3′ region, indicating either that the two regions have very different mutation rates or that the 5′ region is under strong selective constraint in both D. pseudoobscura and D. miranda. The 5′ region of the sisA gene surveyed in this study encodes two putative numerator sequences for the X chromosome/autosome counting mechanism (Erickson and Cline 1998) as well as a TATA box. In contrast to this, the 3′ region of this gene is not known to include any highly conserved regions when compared with those of D. melanogaster, D. pseudoobscura, and D. virilis (Erickson and Cline 1998).

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TABLE 4

The distribution of the Tajima’s D statistic and the estimated recombination parameter

The most polymorphic locus was run, with a value of silent site pairwise diversity (π) of 1.52%, more than twice as much as the next most variable locus, sisA. This is mainly due to its very polymorphic intron, which harbored 14 polymorphic sites within 261 bp. The pattern of SNPs within the introns of the run locus shows tight associations between many closely linked variants (see supplementary material at http://www.genetics.org/supplemental/), although the level of recombination estimated from the SNPs is fairly large (Table 4). Fu’s F-statistic (Fu 1997) suggests that the number of haplotypes is smaller than expected under the neutral model (F =-4.28, P < 0.05). It is possible that a site under balancing selection is closely linked to these variants. Interestingly, the synonymous sites at the run locus showed a much lower level of divergence from D. pseudoobcura than that of the intron sites (KS = 1.13%, compared to KI for the intron = 6.32%). The numbers of conserved and substituted synonymous and intronic sites show a significantly heterogeneous pattern (two-tailed Fisher’s exact test, P < 0.05).

Patterns of SNP variation, neutrality tests, and the effect of recombination: Using several different methods, we tested whether the observed patterns of SNP variation and divergence from all loci are compatible with the simple neutral model. First, we performed the HKA test (Hudsonet al. 1987). This was done for silent sites only, to avoid the effects of purifying selection on replacement sites (see the previous section). We excluded the per-ori and per-new region from the following analyses, to avoid the possible confounding effect of local selection suggested by their high FST values (see below). We used the multilocus form of the HKA test, using 10,000 coalescent simulations to test the significance of the deviation (see Machadoet al. 2002).

When all the loci in Table 3 (excluding per-ori and per-new) were considered, the sum of the deviations was 17.03 (d.f. = 10, P < 0.03). The largest deviation came from the lower-than-expected number of segregating sites for the swa locus (1 observed and 5.56 expected) and to a lesser degree the higher-than-expected divergence (15.04 observed and 11.65 expected). When we excluded the swa locus from the multilocus HKA test, the sum of the deviations decreased to 12.96 and was not significant (d.f. = 9, P < 0.09). This strongly suggests that the observed deviation from the neutral model was caused mostly by the low polymorphism relative to divergence of the swa locus. The same conclusion was reached using a likelihood-ratio alternative to the HKA test (S. Wright and B. Charlesworth, unpublished results).

The McDonald-Kreitman test (McDonald and Kreitman 1991) examines the pattern of polymorphism and divergence between two different types of sites along the same sequence. Under the neutral model, the ratio of replacement to silent variation should be similar to the ratio of replacement to silent divergence. Only the combined data from per-ori and per-new showed a significant deviation (see discussion). However, the numbers of polymorphic sites within D. miranda and the fixed differences between the D. miranda and D. pseudoobscura in the exons are small in all the comparisons, due to both the small effective population size of D. miranda (see discussion) and the short divergence time between these two species. The power of this test is thus likely to be low.

Another class of neutrality tests focuses on the frequency distribution of mutations. We will describe the results from the Tajima’s D statistic (Tajima 1989). Other tests yielded similar conclusions (results not shown). A significantly negative value of Tajima’s D suggests that more low-frequency variants than expected are under the equilibrium neutral model of molecular variation. A significantly positive Tajima’s D indicates a higher-than-expected fraction of high-frequency variants.

Table 4 shows the Tajima’s D statistics for each locus for all types of sites combined and for silent sites alone. Est-5 had the most negatively skewed value, with 10 singletons out of 13 SNPs. In contrast, Adh had mostly high-frequency variants, giving the most positive Tajima’s D. We assessed whether the observed frequency distributions of SNPs were compatible with neutral expectation by examining the distributions of the Tajima’s D statistics on the null hypothesis of neutrality and equilibrium. The variance of Tajima’s D decreases with increasing recombination level among the sites in the sample (Wall 1999). The significance of Tajima’s D should therefore be assessed using the recombination rates for the sampled genes. There are, however, no independent estimates of recombination rates for D. miranda. We employed the information from the SNP data to infer the recombination parameters for each locus (Table 4). We used ρ, obtained by the composite likelihood method of Hudson (2001) as an estimate of the population recombination rate C = 4Ner (where Ne is the effective population size; r is the evolutionarily effective recombination rate, which is one-half or two-thirds the recombination rate in females for autosomal and X-linked loci, respectively).

In Table 4, we show the 95% confidence intervals (C.I.s) of Tajima’s D for the two most extreme cases, no recombination vs. free recombination. The estimated population recombination estimate per nucleotide site for each locus and its value relative to the estimate of θ from the number of segregating sites, θ^w (Watterson 1975), are also shown. Under the neutral model, this ratio reflects the ratio of recombination rate to mutation. Tajima’s D for all but one locus, Est-5, in Table 4 falls within the observed 95% C.I., assuming free recombination. To investigate Est-5 further, we performed coalescent simulations to find the critical values of C for which the model cannot explain the observed pattern. The observed negative Tajima’s D for Est-5 falls outside the lower bound of the 95% C.I. when the recombination parameter becomes >12 for the whole gene. The estimated recombination parameter for the gene was 16.0. The probability of a Tajima’s D less than -1.42, conditioned upon the estimated level of recombination, was 0.013. Other test statistics for the frequency distribution (Fu and Li 1993) also showed a significant departure from neutrality for Est-5 when the estimated recombination rate was used (Fu and Li’s D* =-1.68, P < 0.008; Fu and Li’s F* =-1.83, P < 0.015). However, this is not significant after a sequential Bonferroni correction (Rice 1989), so that further data are required to determine whether there really is a departure from neutrality at Est-5.

In the sibling species to D. miranda, D. pseudoobscura, and D. persimilis, most of the genes surveyed exhibit a negative Tajima’s D, which has been attributed to a recent population expansion in these species (Machadoet al. 2002). We also tested, using coalescent simulations, whether the prevalence of negative Tajima’s D values in D. miranda provides any evidence for such an expansion. When we used only X-linked genes, the observed mean Tajima’s D (-0.64) was significantly lower than the simulated mean value (-0.58, P = 0.03). However, this result was not robust: when we included the two autosomal loci, the deviation from neutrality was not significant (P < 0.1). There is thus no firm evidence for a recent genome-wide population expansion in D. miranda.

DISCUSSION

Inversion polymorphism in D. miranda: The data reported here apparently represent the first systematic survey of chromosomal polymorphism in D. miranda. However, the dearth of wild-caught strains of D. miranda has limited the scope of this survey. The pattern of inversion polymorphism is different from that of the sibling species of D. miranda, D. pseudoobscura, and D. persimilis, in which autosomal inversion polymorphisms are largely confined to the highly polymorphic chromosome 3 (Powell 1992). This is homologous to X2 of D. miranda, which we have found to carry only a single small distal inversion at intermediate frequency. Owing to the difficulty in aligning the banding patterns of D. miranda and its sibling species for this arm (Dobzhansky and Tan 1936), it is not possible to be sure whether there is any homology between the D. miranda arrangements on X2 and the arrangements in its siblings.

In both D. pseudoobscura and D. persimilis, chromosome arm XR shows inversion polymorphisms associated with the SR meiotic drive system; we have found only a single medium-size, proximal inversion at low frequency on this chromosome arm in D. miranda. The standard arrangement of XR in D. miranda, however, shows high homology to the standard XR arrangement in D. pseudoobscura, except for a distal inversion (Dobzhansky and Tan 1936), as we have confirmed in our own preparations of hybrids between D. miranda and D. pseudoobscura. Together with the fact that XL of D. miranda is more similar to XL of D. pseudoobscura than is XL of D. persimilis, this suggests that the ancestor of D. persimilis split from that of D. pseudoobscura after their common ancestor split from the ancestor of D. miranda.

In contrast to the situation for D. pseudoobscura and D. persimilis, D. miranda has inversion polymorphisms on chromosome 2. As is often found in the obscura group (Krimbas and Powell 1992), the two inversions we have found (Table 2) share a common breakpoint at 54D/E, and the larger inversion includes the smaller one. The chromosome 2 inversions provide yet another example of inversions that are specific to a given species (Krimbas and Powell 1992), indicating that the lifetime of inversion polymorphism is usually less than that of a species.

The presence of these inversion polymorphisms raises the question of what effect they might have in distorting the pattern of nucleotide sequence polymorphism at loci that are either inside the region covered by the breakpoints or sufficiently close to the breakpoints to experience suppressed recombination in heterokaryotypes (Andolfattoet al. 2001). This is a serious issue only for chromosome X2, the neo-X chromosome, since there are either no inversions or only low-frequency inversions on the other chromosomes. The locations of genes reported by Steinemann and Steinemann (1990) and Bachtrog and Charlesworth (2002) indicate that, among X2 genes for which DNA sequence polymorphism data have so far been obtained, eve is the closest to the breakpoints of X2-1. Its position at 23A is just over one polytene chromosome division from the distal breakpoint of the inversion. In D. pseudoobscura, heterozygosity for a single inversion can reduce the frequency of recombination in the distal section of the chromosome by 50-fold but has a much smaller effect on recombination in the proximal section of the chromosome (Dobzhansky and Epling 1948). There could thus be a very low frequency of recombination between eve and the distal breakpoint of the inversion, but reduced recombination is less likely for the other loci.

Indeed, some effects of the X2-1 inversion on patterns of nucleotide sequence polymorphism at eve can be detected. Silent site diversity π at eve is about twice as high for individuals carrying the inverted chromosome compared to the standard arrangement (π= 1.39% vs. π= 0.68%). Of the 27 segregating sites at eve, 1 is in significant linkage disequilibrium with the inversion by Fisher’s exact test, and 3 by a χ2 test at the 5% significance level (none of these associations, however, remains significant after a sequential Bonferroni correction). Nevertheless, there are no fixed differences between the inverted and the standard class at eve, and the polymorphism data show evidence for recombination between the standard and the inverted chromosomes. Tests of population subdivision indicate some differentiation between the standard and inverted arrangement (significance levels were assessed using a permutation test as implemented in the DNAsp program). Hudson’s Snn statistic (Hudson 2000), which estimates the proportion of nearest neighbors in sequence space that are found in the same population, indicates a highly significant differentiation between the two classes of chromosomes (P < 0.01). But other statistics, which measure the ratio of the mean pairwise differences within populations to the mean total pairwise differences, are not significant: for KST or KST∗ (Hudson 1992a), P < 0.1. No other loci studied so far are likely to be seriously affected by the inversion polymorphisms we have described.

The effective population size of D. miranda compared to other Drosophila species: The level of silent site diversity based upon the number of segregating sites (θ^w ) is an unbiased estimator of 4Neμ under the infinite sites neutral model (Watterson 1975). If we assume that the mutation rate (μ) is constant across the genome, the effective population size (Ne) can be inferred from the θ^w values, given an estimate of μ. This is of importance, since some models of the degeneration of the neo-Y chromosome are very sensitive to the value of Ne (Gordo and Charlesworth 2001). The arithmetic average of θ^w for silent sites for the set of X-linked genes in Table 3 is 0.51%. Wright et al. (2003) have developed an alternative maximum-likelihood method for obtaining a multilocus estimate of θ, using Equation 12 of Hudson (1990) for the probability of observing S segregating sites in a sample of n chromosomes, conditioned on θ. Using this method (which assumes the same value of θ for all loci), we obtained a maximum-likelihood estimate (MLE) of θ for silent sites of 0.53% for the 11 X-linked genes that we have investigated (95% C.I. 0.38-0.74%); this agrees closely with the other estimate.

How, then, does the Ne of D. miranda compare to that for other Drosophila species? If we assume a constant rate of neutral mutation across the genus (although this is rather questionable), the relative values of θ^w for silent sites from different species indicate the corresponding relative Ne values. Table 5 summarizes the results for several Drosophila species. Clearly, the overall level of genetic variation in D. miranda is much lower than that of its sibling species D. pseudoobscura. On the basis of relative θ^w values, we conclude that there is a four- to sixfold reduction of Ne in D. miranda compared to D. pseudoobscura. The difficulty in collecting wild D. miranda (see Introduction) is consistent with a low population size for D. miranda. Genetic diversity is also lower in D. miranda than in D. melanogaster and D. simulans (synonymous diversity in D. pseudoobscura is similar to that of African D. simulans; Table 5). When we compared the genetic diversity of X-linked genes, for which a fair amount of data is from D. miranda, Ne seems to be approximately one-half that of non-African D. melanogaster, while it is several-fold lower than that of D. simulans. Considering that Ne for D. simulans is estimated to be in the millions (Wallet al. 2002), Ne for D. miranda is likely to be in the vicinity of 1 million or less.

View this table:
TABLE 5

Comparison of estimates of θW for silent sites from different Drosophila species

Interestingly, Table 5 shows little difference in variability levels between X-linked and autosomal loci in both D. miranda and D. pseudobscura, as is also the case for African populations of D. simulans and D. melanogaster (Andolfatto 2001). Application of the likelihood version of the HKA test mentioned above indicates that the X-linked loci in D. miranda depart significantly from the level of diversity expected on the basis of their having three-quarters the Ne of the autosomal loci, the value for a Poisson offspring number distribution (S. Wright and B. Charlesworth, unpublished results). These findings suggest that sexual selection may be inflating the value of Ne for X-linked loci over the Poisson expectation in all of these species (Charlesworth 2001).

The effective population size of the neo-X chromosome and its implications for the evolution of dosage compensation: Interestingly, the MLE of θ for six neo-X-linked loci (Yi and Charlesworth 2000; Bachtrog and Charlesworth 2002) is similar (MLE 0.55%, 95% C.I. 0.35-0.84%) to the above estimates of θ for X-linked loci. Microsatellite data also show very similar levels of variability on the X chromosome and the neo-X chromosome (Bachtrog and Charlesworth 2000). The neo-X chromosome has evolved from an autosome homologous to chromosome 3 in the sibling species of D. miranda, following the fusion of the neo-Y chromosome to the true Y chromosome. The current level of genetic diversity on this chromosome is dependent upon several factors, including the level of genetic diversity before its differentiation as a sex chromosome, the time since the formation of the neo-sex chromosomes, the number of “founder” neo-X chromosomes, and the intensity and nature of selection on the genes on the neo-X chromosome. The lack of a general reduction in variability on the neo-X chromosome compared with other chromosomes suggests that the last two factors have not had a significant effect.

This is particularly relevant to the fact that many loci on the neo-Y chromosome are degenerating (Steinemann and Steinemann 1998); in response, the neo-X chromosome has been shown to have evolved dosage compensation in some regions (Bone and Kuroda 1996; Marínet al. 1996; Steinemannet al. 1996). The exact nature of the molecular mechanism of dosage compensation is not known but it is believed that cis-acting initiation sites on the X chromosome allow the spread of chromatin-modifying activities along the X (Park and Kuroda 2001). Thus, one might expect to see the signature of selective sweeps for cis-acting sites required for dosage compensation on the neo-X chromosome, i.e., reduced variation compared to the X chromosome. However, the observed mean value of θ^w on the neo-X chromosome is not smaller, nor is the variance of θ^w among loci on the neo-X larger, than that on the X. This does not support multiple selective sweeps on the neo-X chromosome. Indeed, recent evidence suggests that dosage compensation in Drosophila does not evolve on a gene-by-gene basis, as previously believed, but rather involves relatively large blocks of genes (Park and Kuroda 2001). Only few cis-acting binding sites may thus be necessary to evolve chromosome-wide dosage compensation.

Population subdivision in D. miranda and the behavior of FST statistics: Data from a 1480-bp region from the per locus provided the first DNA sequence variation data for D. miranda (Yi and Charlesworth 2000). The authors noted a pattern that suggested the existence of population subdivision, namely a distinction between the British Columbia sample and the U.S. samples. The authors also noted that, as the PER protein functions as an essential component of the biological clock in many different Drosophila species and shows evidence of geographic variation in D. melanogaster that is probably due to selection (Rosato and Kyriacou 2001), the observed differentiation between alleles from two different geographic localities might correspond to adaptation to different light cycles. However, various tests did not detect a departure from neutrality (Yi and Charlesworth 2000). Here, we revisit this issue with more sequence data from other loci and additional data from the per locus.

View this table:
TABLE 6

The degree of population subdivision estimated from each locus

First, to determine whether the observed differentiation between the British Columbian population and the other Northern American populations is a pattern common to all loci, we estimated the FST statistics for the difference between these samples for all the loci with available SNP data (using the method of Hudsonet al. 1992b), including data from the originally sequenced per-ori region and the newly sequenced per-new; region. The results are shown in Table 6. The two per regions show by far the highest values of FST. If we use the concatenated SNP data set for the whole per sequence, FST = 0.36. Including this value, the arithmetic mean of the FST statistics from the 10 loci studied here is 0.10. If we exclude per, the mean FST is 0.07. A permutation test (Hudsonet al. 1992a) and the Snn test (Hudson 2000) did not yield any significant values for measures of population differentiation except for the two regions from the per locus (P < 0.05 for per-ori and per-new; P < 0.01 for the concatenated per sequences). When the samples were divided into within-British Columbia and within-U.S. populations, no significant differentiation was detected (results not shown). Microsatellite loci from D. miranda do not show any pattern of population subdivision (Bachtrog and Charlesworth 2000). We conclude that there is no genome-wide pattern of population subdivision in D. miranda.

This raises the question of whether the pattern of between-population differentiation for the per locus reflects the effects of local selection at per on sites linked to the targets of selection (Charlesworthet al. 1997) or is simply a stochastic result of neutral evolution. We emphasize that the newly sequenced per-new region is 468 bp upstream of the original region, on the basis of the annotation of per in D. pseudoobscura (Figure 1), but shows a pattern that is very similar to that for the downstream sequence (see above). Any effect of local selection must therefore extend over a region of several kilobases, given the size of per. This is compatible with the predictions of models of the effects of local selection, if the intensity of selection is comparable in size with the amount of recombination over the region in question (Charlesworthet al. 1997).

The per region seems to be experiencing a considerable amount of recombination. The scaled recombination parameters for the two regions differ by threefold (Table 4) when estimated by Hudson’s composite-likelihood method (Hudson 2001). If we take these differences literally, this suggests either a gradient of recombination frequencies increasing toward the 3′ direction or a stronger selective force causing higher linkage disequilibrium in the 5′ region of per. However, as the confidence intervals for this measure of recombination tend to be large (Hudson 2001) and there are no independent data on recombination or selection at the per locus, these remain speculations.

For simplicity, we used the concatenated data set to obtain an approximate estimate of the recombination parameter for the whole region, which encompasses 2888 nucleotides, excluding gaps in the alignment [note that the composite-likelihood method (Hudson 2001) does not assume contiguity in the sampled region]. When the whole region was used, the estimated scaled recombination rate, C, for the per region was 41.6 (0.014 per nucleotide site). If there is selection inducing linkage disequilibrium among polymorphic sites in this region, this will be an underestimate. The recombination parameter is thus likely to be at least 20-100.

To investigate the behavior of FST in relation to the per data, we first took the average FST value of 0.07 for loci excluding per (see above) and computed an estimator of Nm = 3.22 from the formula for FST for a pair of populations of size N exchanging genes at rate m (Hudsonet al. 1992b). This is a reasonable proxy for the scaled migration parameter for exchange between the British Columbia population and the other populations for D. miranda, given the limited amount of data. We then used coalescent simulations to generate samples under this two-population model, conditioning on the estimated migration parameter, assuming sample sizes of 4 and 8 for the two populations, with 31 segregating sites in 2888 bp (Hudson 2002). The 95% C.I. for FST from 1000 simulated genealogies, assuming no recombination, is [-0.27, 0.48]. The observed FST for the per region, 0.36, is within this interval. However, the distribution of FST changes with increasing recombination: with increasing recombination, the variance of the FST statistic decreases (Hudsonet al. 1992b). When we incorporated a moderate amount of recombination, the distribution of FST shrank. For example, with a scaled recombination parameter of C = 10, the 95% C.I. was [-0.21, 0.35]. With C = 50, the 95% C.I. was [-0.15, 0.28]. Therefore, with the proposed recombination rate parameter for the per locus, the observed FST falls outside the 95% C.I. expected under the neutral model (this was also found when we used the estimate of Nm from the set of loci including per).

The above results suggest that the per locus is under some form of selection, probably involving selection in different directions in the two localities (see above). Tests of neutrality such as Tajima’s D, however, did not detect such selection. Given that the extent of recombination at this locus is not completely understood, this does not reject the presence of selection. One relevant piece of information is the result of the McDonald-Kreitman test (McDonald and Kreitman 1991). When we use the combined data set for per, the McDonald-Kreitman test yields a marginally significant result (P < 0.05, one-tailed Fisher’s exact test), due to either increased divergence at the silent sites or larger-than-expected nonsynonymous within-species polymorphism. The latter possibility is consistent with the action of diversifying selection on the PER protein. Together with the incompatibility of the observed large FST statistics with the neutral model, this suggests that the peculiar pattern of polymorphism at the per locus is likely to be the result of local selective effects that differ between the two populations.

Acknowledgments

We thank Molly Przeworski and Eli Stahl for providing the codes to compute the FST from a simulated data set, Stephen Wright for running the likelihood-ratio tests, and Dick Hudson for discussions. S.Y. was funded by the National Science Foundation Doctoral Dissertation Improvement grant DEB-9701098 during the course of this research. B.C. is supported by the Royal Society and D.B. by a European Molecular Biology Organization postdoctoral fellowship.

Footnotes

  • Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under the accession nos. AY238758-AY238879.

  • Communicating editor: S. W. Schaeffer

  • Received December 31, 2002.
  • Accepted March 5, 2003.

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