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Cytonuclear Disequilibrium and Genetic Drift in a Natural Population of Ponderosa Pine
Robert G. Lattaa, Yan B. Linharta, and Jeffry B. Mittonaa Department of Environmental, Population and Organismic Biology, University of Colorado, Boulder, Colorado 80309-0334
Corresponding author: Robert G. Latta, Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia B3H 4J1, Canada. E-mail robert.latta@dal.ca
Communicating editor: A. H. D. BROWN
| ABSTRACT |
|---|
We measured the cytonuclear disequilibrium between 11 nuclear allozyme loci and both mitochondrial and chloroplast DNA haplotypes in a natural population of ponderosa pine (Pinus ponderosa, Laws). Three allozyme loci showed significant associations with mtDNA variation, while two other loci showed significant association with cpDNA. However, the absolute number of individuals involved in any of the associations was small, such that in none of the nuclear-organellar combinations was the difference between observed and expected numbers >11 individuals. Patterns of association were not consistent across loci or organellar genomes, suggesting that they are not the result of mating patterns, which would act uniformly on all loci. This pattern of disequilibria is consistent with the action of genetic drift and with existing knowledge of the structure of this population and thus does not imply the action of other evolutionary processes. The overall magnitude (normalized disequilibrium) of associations was greater for maternally inherited mtDNA than for paternally inherited cpDNA, though this difference was neither large nor significant. Such significant disequilibria involving the paternally inherited organelle indicate that not only are there a limited number of seed parents, but the effective number of pollen parents is also limited.
CYTONUCLEAR disequilibrium is the nonrandom association of alleles or genotypes at a nuclear locus with haplotypes at cytoplasmically inherited organellar DNA (![]()
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Migration creates cytonuclear disequilibria primarily when disequilibria exist in the migrant pool (![]()
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Like linkage disequilibrium between nuclear loci, cytonuclear disequilibria are also affected by genetic drift. Thus, some linkage disequilibrium (![]()
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Because many different factors can create cytonuclear associations, it can be difficult, in the absence of external information, to determine which of the several forces are at work in any observed instance of cytonuclear disequilibrium (![]()
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| METHODS |
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Study population:
The study population consists of 217 permanently marked trees in a natural all-aged stand of ponderosa pine (P. ponderosa Laws. var. scopulorum Engelm., Pinaceae). The population is located at 1740 m above sea level on a south-facing slope near Boulder, Colorado, and has been the site of ongoing research for 20 years (e.g., ![]()
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The genetic consequences of this movement may include founding events on a very local scale. The spatial arrangement of genetic markers in this population has been described in ![]()
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6 m diameter on average (P < 0.05; ![]()
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Cytonuclear disequilibria:
Because trees in the stand are permanently marked, the composite three-genome genotype of each tree could be reconstructed for 182 of the original 217 trees on the site using the organellar haplotypes and allozyme genotypes determined in the above studies. This represents a complete census of surviving trees on the site. We analyzed these data for disequilibria (i) between allozymes and maternally inherited mtDNA, (ii) between allozymes and paternally inherited cpDNA, (iii) between allozymes and the joint mtDNA-cpDNA cytotype, (iv) between the two organellar genomes, and (v) among nuclear allozyme loci. Methods for the estimation of true three-way disequilibria (i.e., nuclear-mtDNA-cpDNA; ![]()
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We proceeded in three steps. First, we tested each locus-organelle combination for significant overall departures from random association. Because exact tests are computationally impractical for overall associations (i.e., for all allele-haplotype and genotype-haplotype combinations combined), we employed the Monte Carlo approach of ![]()
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D2/n (![]()
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| RESULTS |
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Linkage disequilibrium was not significant between any pair of nuclear loci (
2 < 3.84 for all pairs). In addition, there was no association between mtDNA haplotype and cpDNA haplotype (
2 = 0.016, not significant).
Table 1 lists the significance (P values from the Monte Carlo approximation) of overall association between alleles or genotypes at each nuclear locus and mtDNA, cpDNA, and joint mtDNA-cpDNA cytotype. This represents the test for overall nonrandom association between genotypes or alleles and haplotypes. For most loci, disequilibria are not statistically different from zero. However, 13 significant associations (P < 0.05) are observed where only 3 are expected by random chance. Three loci show associations with mtDNA (Fe, Got, and Udp), while two are significantly associated with cpDNA (Per and Sdh). Significant associations between nuclear loci and the joint mtDNA-cpDNA cytotype were observed only for loci that showed a significant association with either cpDNA or mtDNA alone (Table 1). Thus the joint disequilibrium measures repeat the information contained in the two-way measures and are not discussed further here.
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For all loci showing a significant overall association between alleles or genotypes and one of the organelles, the association could be attributed to one particular nuclear genotype or allele (Table 2). For example, the association between Fe genotypes and mtDNA (P < 0.02; Table 1) was entirely attributable to the fact that there were significantly more BB homozygotes carrying mtDNA haplotype m (and fewer with haplotype M) than expected under a random association (P < 0.0025; Table 2). None of the other Fe genotypes showed significant association with the mtDNA haplotypes, although there is no a priori reason why they should not. For all loci, the difference between observed and expected numbers of individuals exhibiting a particular cytonuclear genotype (O - E) was small (Table 2). In the case of the Fe-mtDNA association, we observed only 8 more individuals with the BB-m genotype than the 11 that are expected under random association. Similar results were observed for the allelic associations (not shown).
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The spatial arrangement of the organellar haplotypes is presented in Fig 1, a and d. Mitochondrial haplotypes show significant clustering in space (P < 0.05), while cpDNA haplotypes do not (![]()
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Under random genetic drift, some loci will drift to a positive and some to a negative association between allele A and the organellar haplotype M (where allelic labels are arbitrarily assigned). Thus, the variance of D across loci will be inversely related to the effective population size (![]()
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0.005, and Var(D) for cytoplasmic disequilibria is typically about twice that for nuclear loci (![]()
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50%.
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| DISCUSSION |
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Disequilibrium and drift:
The nonrandom association of nuclear alleles or genotypes with organellar haplotypes can arise from a number of evolutionary forces that fall into three categories (![]()
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Significant associations between nuclear and organellar polymorphisms are observed in this population for both the mitochondrial and chloroplast genomes (Table 1). Five nuclear loci show associations that are significant and for which the normalized disequilibrium D* is quite large (Table 2). However, despite large normalized disequilibria, the absolute magnitude of the difference between the observed and expected number of individuals carrying each combination is quite small, typically 510 individuals. Such small deviations (though statistically significant) are consistent with the action of genetic drift, which in this case we ascribe to very localized founder events (see below). Since many populations fluctuate over time, such drift-induced cytonuclear disequilibria are likely to occur in a wide variety of species.
A common feature of cytonuclear disequilibria caused by migration patterns in hybrid zones is consistency in both the magnitude and direction of disequilibrium across all nuclear loci. For the Hyla example (![]()
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The spatial patterns have been superimposed on the disequilibria by the differential dispersal abilities of seed and pollen. The clusters of mtDNA haplotypes presumably reflect recent founding of that patch by a maternal tree that had that haplotype. If the founding tree also carried a relatively uncommon allozyme allele, then the nuclear allele and mtDNA haplotype would become associated because both are present in the matrilineal family that descended from that individual. Moreover, these individuals would be clustered in space due to limited seed movement. Thus the reduction of Ne that produced the drift seems likely to have been due to very localized founder events surrounding the trees that were reproductive at the time the population began to expand and increase in density (
100 years ago; ![]()
Very few data exist for cytonuclear disequilibria involving a paternally inherited organelle. The data of ![]()
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0.065 for Ne = 10 and 0.013 for Ne = 50. The observed value for cpDNA (0.038; Table 3) falls within this range. Since the census size of the population is 217, the effective number of pollen parents appears to be between one-twentieth and one-quarter of the census size.
Thus, the number of pollen founders in this population appears to have been almost as limited as the number of seed founders. We might predict that fewer seed parents contribute to the founding of a new population than pollen parents because of the greater potential for pollen immigration and thus a lower effective population size of females than males. Although chloroplasts do show slightly lower values of normalized disequilibrium and its variance (0.038) than do mitochondria (0.078), this difference is not significant, such that the effective population size of males appears to be at most only slightly greater than that of females. Data on the reproductive output of each tree have been collected over the last 20 years (cf. ![]()
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Alternatives to drift:
Cytonuclear disequilibria can result from migration primarily where immigrants themselves exhibit cytonuclear associations, or where seed and pollen immigrants are genetically differentiated at nuclear or paternally inherited organellar markers (![]()
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Alternatively, selective scenarios can be imagined that would produce the observed level of differentiation, but these, too, require a number of assumptions. In several hybrid zones, fitness interaction has been demonstrated between the nuclear and organellar genomes (e.g., ![]()
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We therefore interpret the disequilibria as consistent with existing knowledge of the population (![]()
| ACKNOWLEDGMENTS |
|---|
We thank C. J. Basten for his generous help in providing the computer program that calculated the estimates of disequilibrium. Numerous field assistants helped with the collection of data. The final manuscript was greatly improved by the comments of M. A. Asmussen and two anonymous reviewers. Collection of the allozyme and reproductive data was funded by National Science Foundation grants BSR 8918478 and DEB 9120065 to Y.B.L. and J.B.M., and U.S. Department of Agriculture grant 95-37101 to Y.B.L. Organellar data collection was funded by a National Science Foundation Doctoral Dissertation Improvement Grant to R.G.L.
Manuscript received November 23, 2000; Accepted for publication March 9, 2001.
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