*Department of Biological Sciences, Butler University;
Laboratoire Génome Populations Interactions, CNRS UMR5000, Université Montpellier II, France
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Abstract |
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Introduction |
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Molecular studies of Abpa have been consistent with the emerging picture of its role in sexual isolation. The elevated Ka:Ks ratio between the alleles, and the alternative fixation of different alleles in each subspecies (Hwang et al. 1997
), suggest a mechanism of fixation of new variants by selective sweeps. Karn and Nachman (1999)
produced supporting evidence for such directional selection by showing that in M. musculus domesticus Abpa displayed significantly reduced intron polymorphism in comparison with two X-linked genes.
The aforementioned subspecies have been defined at the periphery of the distribution range of the species: M. musculus domesticus from the Near East to western Europe through the Mediterranean Basin, M. musculus musculus from eastern Europe to northern China, north of the Himalayas, and M. musculus castaneus in South-East Asia. However, the situation in the central part of the range (from the Caucasus to eastern India, south of the Himalayas) is more complex. Populations from the northern Indian subcontinent display much more polymorphism than the peripheral subspecies for both nuclear protein genes (Din et al. 1996
) and mtDNA (Boursot et al. 1996
), and the authors cited have proposed that this is because they are closer to the cradle of the species, from which the recent radiation leading to the peripheral subspecies started. Furthermore, some areas of central Eurasia bordering the range of the peripheral subspecies have been shown to be regions of genetic admixture, for instance between M. musculus domesticus and M. musculus musculus south of the Caucasus (Orth et al. 1996
; Mezhzherin, Kotenkova, and Mikhailenko 1998
) and between M. musculus musculus and the polymorphic central populations in northern Iran (Boursot et al. 1996
; Din et al. 1996
).
We wished to know whether the peculiar pattern of rapid Abpa evolution and absence of polymorphism seen in the peripheral subspecies also prevailed in this central and more complex part of the range of the species. To further study the extent to which selection may have been involved in the evolution of Abpa, we also studied intron polymorphism in representatives of the major protein alleles and intron phylogeny between eight species of the genus Mus.
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Materials and Methods |
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Data Analysis
Sequences were aligned with the DNASIS program (Hitachi). Program MEGA version 2.1 (S. Kumar et al., personal communication) was used to calculate numbers of synonymous and nonsynonymous substitutions as well as their rates (Ka and Ks), using the modified Nei and Gojobori (1986)
method, with Jukes-Cantor correction for multiple hits and a transition-transversion rate of 2. This program also served to generate neighbor-joining trees and the node supports by bootstrap resampling. Population genetics statistics and coalescent simulations were performed using DnaSP version 3 (Rozas and Rozas, 1999
).
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Results |
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It can be seen in figure 1
that most of the differences between the alleles are nonsynonymous. All pairs of alleles display only no, one, or two synonymous differences, with the exception of the pairs involving allele g, which all display three or four differences. Note though that the g allele was inferred from the genotype of an individual heterozygous at several nucleotide positions, by supposing that it was a c/g heterozygote, and this large number of differences may be an artifact caused by improper haplotype inference. The alleles found to segregate in Pakistan (cg, table 1
) differ from each other by one to three nonsynonymous differences. Alleles h and i, found in a southern Indian locality (Nilgiri) differ from these by four to seven nonsynonymous differences and from each other by three. The M. musculus musculus allele (b) differs from all the aforementioned alleles (ci) by one to five nonsynonymous differences, whereas the M. musculus domesticus allele (a) appears the most different from all others (from 6 to 11 nonsynonymous differences). Thus, the predominance of nonsynonymous differences previously reported for the a, b, and c alleles (Hwang et al. 1997
) also holds for the newly discovered alleles. Estimated rates of synonymous (Ks) and nonsynonymous (Ka) changes between all pairs of alleles in M. musculus are plotted in figure 2
, showing the general excess of nonsynonymous changes in intraspecific comparisons.
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The second major result is that wherever admixture of the subspecies appears geographically possible, we found an admixture of subspecies-specific Abpa alleles: a and b in Adjaria, a, b, and c in Armenia, b and c in northern Iran, and a and c in Tehran.
The third major result concerns the new polymorphisms encountered. Whereas the samples from Delhi appeared fixed for the c allele, consistent with the apparent monomorphism for this allele further east in M. musculus castaneus, the Pakistani samples display significant polymorphism, with four of the 11 individuals sampled heterozygous for c and one rare allele each (alleles dg, table 1 ). The sample from southern India also displays polymorphism, with two new alleles (h and i) found nowhere else.
Interspecific Coding Sequence Variation
A 998-bp fragment covering the 785-bp intron and the coding parts of the flanking exons (183 bp in the left exon and 30 in the right exon, including the stop codon) was sequenced in 12 of the 68 M. musculus mice described previously as well as in one mouse from each of six other species in the genus Mus. Considering only the coding regions, the sequences in the right exon showed no variation, and we will not consider this region further. The sequences of the left exon are shown in figure 4 . The M. musculus sequenced were homozygous for one of the three major alleles, a, b, and c, reported by Hwang et al. (1997)
. We also obtained the same coding sequences reported by Hwang et al. (1997)
for Mus spretus, M. spicilegus and Mus caroli. The additional Mus species we report here all had unique coding sequences except for M. macedonicus, which was identical to M. spicilegus. In figure 5
, we plotted Ka against Ks to show that the ratio Ka:Ks is greater than 1 in most interspecific comparisons and often even greater than 2, as already reported on a more limited set of species (Karn and Nachman 1999
). The phylogenetic information in these coding sequences is poor because of the short length of the sequence and also because of the homoplasy on several variable sites. Part of this homoplasy presumably results from convergent evolution of this protein under strong selection pressure.
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It is possible to develop an estimate of the age of the c allele using the total length of the tree relating the five intron sequences inferred, in units of numbers of mutations (m). Making the conservative assumption that n alleles sampled have evolved along n independent lineages since the appearance of the original mutation that gave birth to the c allele at time t in the past, we expect:
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Interspecific Intron Phylogeny
Figure 6
shows the variations observed in the 785-bp intron sequences among the eight species of Mus, including the previously reported sequence of M. caroli (Karn and Nachman 1999
) and the variations inside M. musculus described previously. Figure 7 shows the phylogenetic tree generated from these intron sequences, including the five c allele haplotypes inferred as described previously. The topology of the tree is unexpected because the house mouse M. musculus is not monophyletic and its subspecies stand as outgroups vis à vis the other Palearctic species (M. spretus, M. spicilegus, and M. macedonicus), whereas the reverse was expected based on previous studies (reviewed for instance in Boursot et al. 1993
). In particular, the position of M. musculus musculus outside the other Palearctic species and subspecies is supported by a very high bootstrap score (94%). The divergence of the intron of the musculus subspecies (with coding allele b), especially relative to that of the c allele introns, is striking because the b and c protein alleles show relatively few differences compared with the more divergent domesticus allele. In fact, the Ka:Ks ratio for the b/c comparison was among the lowest (0.83) in all intra- and interspecific comparisons of alleles (figs. 2 and 5
).
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Discussion |
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This is worth noting because another potential actor in sexual selection, the Y chromosome, shows a different phylogeographic pattern. Boissinot and Boursot (1997)
recognized two lineages of Y chromosome, one being shared by M. musculus musculus and M. musculus castaneus, whereas the other prevailed in M. musculus domesticus as well as in central Eurasia. On the basis of the low molecular divergence between these major Y chromosome lineages, they suggested that this might be explained by secondary sweeps after the subspeciation process. Using a different geographic scenario for the subspeciation process and not taking into account the low Y chromosome divergence, Prager, Orrego, and Sage (1998)
favored instead the hypothesis of the segregation of ancestral polymorphism.
Whichever hypothesis is correct, it remains true that, given the presently available data, the distribution of Abpa alleles appears more compatible with that of mtDNA than with that of the Y chromosome. The unique feature of Abpa, on the other hand, is that it is an autosomal gene that is monomorphic in the peripheral subspecies, and our new data substantially increases the resolution of its peripheral distributions.
Secondary Admixture of Peripheral Fixed Abpa Variants
In the case of mtDNA, because the phylogeny of alleles was precisely reconstructed, the occurrence of domesticus and musculus variants in Transcaucasia as well as in northern Iran could be interpreted with confidence as resulting from secondary admixture of the well-differentiated subspecies-specific lineages (Boursot et al. 1996
; Orth et al. 1996
; Boissinot and Boursot 1997
; Prager, Orrego, and Sage 1998
). Such conclusions were harder to reach in the case of allozymes because the phylogenies of the alleles were unknown (Din et al. 1996
; Orth et al. 1996
). In the case of Abpa, our intron sequence data clearly show that the a, b, and c alleles sampled in regions where they co-occur have not coexisted for a long time in the same homogeneous gene pool because they each belong to one of three well-differentiated lineages with no polymorphism (a and b alleles) or little polymorphism compared with the divergence between alleles (the c allele). Thus, it seems natural to consider that their co-occurrence south of the Caucasus and in northern Iran resulted from secondary introgression of the subspecies-specific a, b, and c alleles.
Apparently, whatever selective pressure led to the monomorphism of Abpa in the peripheral subspecies did not prevent secondary admixture there. We can contrast these results with those of the Y chromosome: in neither of the two regions of secondary admixture of mtDNA and Abpa (Transcaucasia and northern Iran) has any evidence of Y chromosome lineage admixture yet been found (Boursot et al. 1996
; Orth et al. 1996
; Boissinot and Boursot 1997
; Prager, Orrego, and Sage 1998
). Rather, only the musculus-like Y chromosome type has been found, up to now, in these regions. The absence of Y chromosome admixture could result from the sterility of hybrid males, a phenomenon that has been reported in some intersubspecific crosses (Forejt 1996
). However, the generality of this phenomenon is far from established. The hybrid zone between domesticus and musculus has been studied in detail in Europe and has given evidence of very strong counterselection against Y chromosome introgression (Vanlerberghe et al. 1986
; Tucker et al. 1992
; Dod et al. 1993
; Prager, Boursot, and Sage 1997
). Similar data on Abpa will allow further comparison of the consequences of selection on these two parts of the genome and their relative role in species isolation.
Directional Selection on Abpa?
As summarized in the introduction, there are various arguments (absence of polymorphism, elevated Ka:Ks ratio, behavioral data) to support the idea that Abpa, at least in the peripheral subspecies, is evolving under some form of selection pressure that might have to do with recognition and mate choice. Karn and Nachman (1999)
suggested that allelic sweeps could account for the significantly reduced intron polymorphism in Abpaa. This picture is reinforced by our observation of a single 998-bp Abpab sequence, very different from that of Abpaa, in five samples of the M. musculus musculus populations. Although we could not test for selection, having fixed the b allele in M. musculus musculus populations because no other region of the genome was available for comparison, the monomorphism we observed for this allele is at least consistent with the idea that selective sweeps can fix Abpa alleles in the M. musculus peripheral subspecies. Whether the apparent fixation of the c allele in the South-East Asian subspecies M. musculus castaneus is also accompanied by an absence of intron polymorphism should be the subject of future investigation.
High Abpa Intron and Exon Polymorphism in the Central Region
The co-occurrence in the central region of new Abpa variants not found at the periphery (alleles dg in Pakistan and h and i in southern India) and the observation of substantial intron polymorphism are two major differences with previous observations on Abpa. As was the case for the three major alleles, the new ones were derived essentially by nonsynonymous substitutions, which is usually taken as evidence for selection. However, the protein polymorphism encountered in the Pakistani and southern Indian samples as well as the intron polymorphism of the c allele from Pakistan and northern India is not compatible with the hypothesis of directional selection having driven the evolution of the Abpa gene in these populations. The intron nucleotide diversity encountered in our sample of five individuals with c alleles ( = 0.27%) contrasts with the absence of polymorphism among seven M. musculus domesticus (Karn and Nachman 1999
; this study) and five M. musculus musculus (this study). It is greater than the diversity encountered in M. musculus domesticus at the two X gene introns used by Karn and Nachman (1999)
to reject neutrality at Abpa (0.135% and 0.16%). Estimates of effective population sizes from nucleotide diversity in the c introns (N
106, see Results) appear quite high for a vertebrate.
In fact, our observations on Abpa variation in the central region would better fit a hypothesis of diversifying selection maintaining this polymorphism. However, to retain this hypothesis, we would have to eliminate the alternative explanation that the observed polymorphism is because of secondary admixture of differentiated populations. Clearly, a better understanding of the genetic makeup of this complex central region will be critical to properly understand the type of selection underlying the generation and maintenance of this polymorphism.
Is Selection on Abpa in Peripheral Subspecies Linked to Commensalism?
It seems that the recent extension of the three subspecies to their peripheral range in Eurasia is linked to the advent of commensalism with humans (reviewed in Boursot et al. 1993
; Sage, Atchley, and Capanna 1993
). Perhaps selection on Abpa alleles in the peripheral populations relative to the central ones changed as the result of this recent and rapid expansion. Mus musculus evolved for at least half a million years before it became commensal with humans and before it had radiated very extensively outside the region shown in figure 3B
. It could be that during the peripheral expansion in relation to commensalism, ABP-mediated sexual selection became more important in the ecology of mouse populations.
Clearly, the c allele could not have been fixed by selection in relationship to commensalism because we estimate its origin to be far older (at least 40,000 years old) than commensalism (10,000 years; Auffray, Vanlerberghe, and Britton-Davidian 1990
). However, it may be that the protein polymorphism observed in the center results from the secondary admixture of previously differentiated and monomorphic populations and that the c intron polymorphism results from recent recombination with the other divergent alleles. This would be another consequence of commensalism, that presumably promoted gene flow.
The suggestion that gene flow is responsible for Abpa polymorphism in the central region does not fit well with the proposed role for ABP as a recognition signal. However, it could be that this salivary protein has some other function, implying a variable role for selection depending on the environment (for example, Laukaitis, Critser, and Karn [1997
] suggested that ABP's original function may have involved conditioning the mouse's pelt). Its role in sexual selection would be a side effect only emphasized under certain conditions when the pressure for sexual selection becomes predominant compared with that exerted by environmental factors. The changes of condition that presumably accompanied the rapid expansion of the peripheral subspecies to the whole continent could have created such a change in the selection regime. In the case of one of the best studied polymorphisms at the DNA level, the Drosophila melanogaster ADH locus, evidence is accumulating that the kinds of selection pressures operating on the gene have changed in space and time, especially since the recent worldwide spread of this commensal species (Veuille et al. 1998
; Begun et al. 1999
). A search for possible alternative functions of ABP should contribute to resolving the issue of the kinds of selection pressures influencing its evolution.
The Peculiar Phylogenetic History of Abpa
The phylogeny of the Abpa introns that we obtained shows several unexpected aspects, given what is known of the speciation and subspeciation history in the genus Mus (reviewed in Boursot et al. 1993
; Sage, Atchley, and Capanna 1993
). Considering only the topology of the tree in figure 7
, it is striking that the house mouse sequences lie outside the other Palearctic species sequences. This external position is strongly supported in the case of M. musculus musculus. If we interpreted the result in this way, we would have to suppose that the M. musculus alleles (or at least the Abpab allele) are of alien origin and were captured by an interspecific transfer from an unknown species (we have sampled all species known to date). Setting aside this hypothesis, we can ask whether we sequenced orthologous copies of Abpa in all species. If a gene duplication produced two copies of Abpa (say copies I and II), it must have happened before the divergence of the Palearctic species to account for the position of the house mouse sequences (and especially the b allele) outside this group. It must also be hypothesized that our primers amplified, say, copy I but not copy II in all taxa except M. musculus, whereas the reverse pattern of amplification success occurred for copy II. This appears quite improbable. Supposing then that the primers picked orthologous exons in all species, we have to explain that the transfer of information between copies concerned only the intron. This could have happened by ectopic conversion of one copy by the other. Although ectopic conversion has been found to occur in mice (e.g., Murti, Bumbulis, and Schimenti 1994
), it was also shown to be improbable for sequences this short (Cooper, Schimenti, and Schimenti, 1998
). Observations of its effects remain anecdotal, so that its likelihood appears hard to assess at present.
Furthermore, this explanation based on multiple gene copies fits poorly within the time frame inferred for the phylogeny of the Abpa introns in comparison with that of the average scnDNA, depicted in figure 8 . Taking the divergence times into account, the phylogeny points to an unexpected resemblance between the Palearctic species (M. musculus musculus excluded), rather than to an abnormal divergence of M. musculus musculus from the other Palearctic species (spretus, spicilegus, and macedonicus). An explanation for this pattern would be that secondary genetic exchanges have occurred along the lineages leading to the Palearctic species.
This possibility must be taken seriously because there is evidence of a transfer of LINE-1 copies from M. spretus and M. spicilegus into laboratory strains of mice (Rikke et al. 1995
; Zhao, Green-Till, and Hardies 1998
; Hardies et al. 2000
) as well as of sporadic reciprocal exchanges of mtDNA and other genes between M. musculus domesticus and M. spretus in the wild (Orth et al. in press). Thus, interspecific genetic exchanges apparently occur between these species at a rate sufficient to be detected by limited sampling of the genome. In addition, their effects could have been emphasized at some genes for which selection favored the fixation of new alleles, and there is evidence for this in the case of Abpa. A similar case has been reported by Wang, Wakely, and Hey (1997)
, who have shown extensive introgression at the Adh locus between closely related species of the Drosophila pseudoobscura group.
Although secondary exchanges account for the abnormal Abpa resemblance of the Palearctic species, they do not explain how M. musculus musculus has retained an Abpa lineage, the divergence of which apparently predates the subspeciation of the house mouse, because the coalescence of Abpa in M. musculus occurs at 0.32, compared with only 0.15 for the average scnDNA (fig. 8
). The variance of the coalescence times of different portions of the nuclear genome among these mouse subspecies should be studied before any sound conclusion can be drawn from this observation. In a recent paper, Ting, Tsaur, and Wu (2000)
have shown that different genes can display very different coalescence patterns between closely related Drosophila species, presumably because of a combination of secondary introgression and segregation of ancestral polymorphism. They have also shown that a gene of hybrid sterility reflects much more clearly than other genes the events of reproductive divergence between these species. Although the initial picture of the evolution of the Abpa gene in the house mouse was suggestive of this kind of hypothesis, with one allele fixed in each subspecies, the picture that now emerges is more complex. On one hand, there is evidence that this gene plays a role in recognition and has evolved under strong positive Darwinian selection. On the other hand, it is difficult to rectify the notion of a ubiquitous role for it in sexual isolation, given the extensive polymorphism in some regions and the secondary interspecific exchanges that have apparently occurred. This does not necessarily rule out a role of ABP in recognition, but some other (or additional) function should be sought that would help account for the peculiar evolutionary history of this gene.
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Supplementary Material |
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Acknowledgements |
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Footnotes |
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Keywords: androgen-binding protein
Mus musculus
interspecific hybridization
sexual isolation
selection
Abbreviations: ABP, androgen-binding protein; Abpa, the gene for the alpha subunit of mouse salivary androgenbinding protein.
Address for correspondence and reprints: Robert C. Karn, Department of Biological Sciences, Butler University, 4600 Sunset Avenue, Indianapolis, Indiana 46208. rkarn{at}butler.edu
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