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Genetic Composition and Diploid Hybrid Speciation of a High Mountain Pine, Pinus densata, Native to the Tibetan Plateau
Xiao-Ru Wanga,d, Alfred E. Szmidtb, and Outi Savolainenca Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China,
b Department of Biology, Graduate School of Science, Kyushu University, Fukuoka 812-8581, Japan,
c Department of Biology, Oulu University, 90570 Oulu, Finland
d National Institute for Working Life, 907 13, Umeå, Sweden
Corresponding author: Xiao-Ru Wang, National Institute for Working Life, P.O. Box 7654, S-907 13 Umeå, Sweden., xiao-ru.wang{at}niwl.se (E-mail)
Communicating editor: D. CHARLESWORTH
| ABSTRACT |
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Pinus densata has been suggested to have originated from hybridization events involving P. tabulaeformis and P. yunnanensis. In this study, allozyme differentiation at 12 loci was studied in 14 populations of P. tabulaeformis, P. densata, and P. yunnanensis from China. The observed genetic composition of P. densata supported the hybrid hypothesis and showed varying degrees of contribution from P. yunnanensis and P. tabulaeformis among its populations. These data, together with previous chloroplast DNA results, indicated different evolutionary histories among P. densata populations. To examine the possibility of ongoing hybridization among the three species, we analyzed patterns of linkage disequilibria between allozyme loci in ovule, pollen, and zygote pools. None of these tests suggested that there is significant ongoing gene exchange, implying that populations of P. densata have a stabilized hybrid nature. The normal fertility and high fecundity of P. densata indicate that this hybrid is maintained through sexual reproduction. P. densata represents an example of diploid hybrid speciation in an extreme ecological habitat that is both spatially and ecologically separated from that of its parents.
IN plants, hybridization and introgression are known to be important evolutionary forces (![]()
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The occurrence of several crossable sympatric species from the genus Pinus in Asia has led to suggestions that some species arose as a result of hybridization (![]()
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Hybridization and introgression have been reported for several other conifer species complexes where hybridization goes on in the narrow hybrid zone of sympatry of the parental taxa (e.g., ![]()
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Detailed studies on population genetic structure are important for understanding the effects of introgression on the maintenance of species differences, hybrid population dynamics, and the potential differences in the evolutionary biology of organellar vs. nuclear genes (![]()
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In our previous analysis, only one population of each of the three species, P. tabulaeformis, P. densata, and P. yunnanensis, was analyzed for allozyme variation (![]()
| MATERIALS AND METHODS |
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Seed material:
Bulked seed samples were obtained from eight natural populations of P. tabulaeformis (Pt-1, -2, -3, -5, -6, -8, -9, and -10), three populations of P. densata (Pd-1, -2, and -7) and three populations of P. yunnanensis (Py-1, -2, and -3) from the natural range of each species in China. The geographic distribution of these populations is presented in Fig 1. Two populations of P. tabulaeformis (Pt-9 and Pt-10) and one population of P. yunnanensis (Py-1) originated from the region of close sympatry with P. densata (Fig 1). The remaining populations of P. tabulaeformis and P. yunnanensis were located outside the range of P. densata. Of the three populations of P. densata, one population (Pd-7) was located in the region of sympatry with P. yunnanensis, while the remaining two populations originated from the north-central part of its distribution, which is outside the ranges of both putative parental species (Fig 1). The exact number of trees included in these collections is unknown, but appears to be >50. The megagametophyte and embryo from each seed were separated and analyzed simultaneously for all the enzyme systems used in this study. From 100 to 195 megagametophytes and their corresponding embryos were analyzed from each population.
Allozyme analyses:
For allozyme electrophoresis, seeds were germinated for
14 days until a 3-mm radicle emerged from the seed coat. Enzymes were extracted as previously described (![]()
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Statistical analysis:
Diversity measurements:
Allozyme frequencies, expected (He, ![]()
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PifPim, where Pif and Pim are the allelic frequencies for ovule and pollen, respectively.
The fit of genotypic frequencies to the Hardy-Weinberg (H-W) expectation was tested using the exact test (![]()
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Population differentiation was analyzed for polymorphic loci in ovules, pollen, and zygotes by F-statistics (![]()
) values and the probability test (exact G-test, ![]()
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Linkage disequilibria:
To examine the possibility of ongoing hybridization among the three species, we analyzed patterns of linkage disequilibria between loci in ovule, pollen, and zygote pools. Measures of linkage disequilibrium were calculated as described by ![]()
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Allozyme admixture:
The relative contributions from P. tabulaeformis and P. yunnanensis to the investigated populations were estimated using a least-squares procedure developed by ![]()
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| RESULTS |
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Allele frequency:
Twelve loci were inferred for ovules, pollen, and zygotes in each of the 14 investigated populations. Of these 12 loci, 9 were polymorphic (frequency limit for most common allele: 0.95) in at least 1 population. Allozyme frequencies in zygotes for each of the 3 populations of P. densata are given in Table 1 and were compared to the mean allozyme frequencies found for P. tabulaeformis and P. yunnanensis. Allozyme frequencies for individual populations of P. tabulaeformis and P. yunnanensis can be obtained upon request from the senior author. The most polymorphic loci included Pgm-1, Fes, Lap-2, Got-3, and Sdh-1. Little polymorphism was found at the Mdh-1, Mdh-2, and Gdh-1 loci. Distinct differences were found at the Lap-2 locus, which was highly variable in P. yunnanensis and P. densata but nearly monomorphic in P. tabulaeformis. The Sdh-1 locus, however, was more variable in P. tabulaeformis and P. densata than in P. yunnanensis. The Got-3 locus was highly polymorphic in all three species, but for different alleles (Table 1). At all the loci that varied markedly between P. tabulaeformis and P. yunnanensis, P. densata nearly always showed an intermediate allozyme composition, with Pd-7 tending to be more similar to P. yunnanensis. Alleles restricted to P. tabulaeformis and P. yunnanensis were detected at several loci, e.g., Pgm-1 and SDh-1, and they were also often found in P. densata. At other loci, most of the unique alleles for P. tabulaeformis and P. yunnanensis had very low frequencies (<0.05) and they were not always detected in P. densata. Among all the 12 loci examined, only two alleles specific to P. densata were detected, at Got-3 and SDh-2, with frequencies ranging from 0.004 to 0.075.
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Allele frequency differences between the two gametic pools were very minor (data not shown). If allelic differences between ovule and pollen pools were present, the expected heterozygosity would be higher than the H-W expectation. The effect of allelic differences on estimates of expected heterozygosity is shown in Table 2. The expected heterozygosity (He') based on the allele frequencies in the ovules and pollen was calculated for each locus, and the mean value for each population is listed in Table 2. The difference in He' compared to He based on allele frequencies in zygotes is negligible. Thus, in the following H-W test and FI estimates, allele frequencies in the zygotic population were used.
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Diversity measures and population differentiation:
A summary of genetic variability measures at 12 loci in the investigated populations is given in Table 2. The average proportion of polymorphic loci ranged from 50% in P. yunnanensis to 67% in P. densata. The average observed heterozygosity in zygotes was 0.193, 0.194, and 0.178 for P. tabulaeformis, P. densata, and P. yunnanensis, respectively, and the corresponding numbers for the expected heterozygosity in zygotes were 0.205, 0.232, and 0.190 (Table 2). Comparison between the ovule and pollen pools revealed very similar gene diversity but slightly higher values in the ovules of each species (Table 2). In both the ovule and pollen, as well as in the zygote pools, P. densata had the highest gene diversity among the three pines.
Exact tests for departure from H-W equilibrium in the zygotes revealed that, among the eight populations of P. tabulaeformis, two populations (Pt-2 and Pt-5) showed significant deviation from H-W expectations (Table 2). All the three populations of P. densata and one population of P. yunnanensis (Py-1) showed deviation from H-W expectations. However, although statistically significant all the FI values were small and close to zero. The average FI for each population ranged between -0.019 and 0.043 in P. tabulaeformis, between 0.038 and 0.097 in P. densata, and between 0.007 and 0.021 in P. yunnanensis, at the seed stage (Table 2). All populations, except one (Pt-10), had positive fixation indices, indicating slight homozygote excess.
Single locus estimates of population differentiation (Fst) are presented in Table 3. In P. tabulaeformis all 12 polymorphic loci gave significant Fst values among the zygote populations. In P. densata 9 of the 10 polymorphic loci, and in P. yunnanensis 7 out of 11 loci, were significantly differentiated among the zygote populations. Mean Fst values in zygotes ranged from 0.023 (P. yunnanensis) to 0.086 (P. densata). Within each species, the average Fst values for ovule, pollen, and zygote populations were very similar, although slightly higher Fst values were found for ovules in P. tabulaeformis and P. yunnanensis. In P. densata, however, the pollen pools gave the highest Fst (0.097). Compared to P. tabulaeformis and P. yunnanensis, P. densata had noticeably higher Fst values for all the ovule, pollen, and zygote populations.
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Linkage disequilibrium test:
Results of the linkage disequilibria tests in ovules, pollen, and zygotes are summarized in Table 4. The numbers of significant loci associations among all the possible pair-wise loci combinations were low and similar in all three species. For example, in P. tabulaeformis, 9 and 1 out of 66 loci combinations were found in close association in zygote populations of Pt-1 and Pt-6, respectively. In the pollen pool of Pt-6, all 55 possible loci combinations were found to be in random association. Similarly, in the pollen pool of Pd-7 and zygote pool of Py-1, all loci were found in random association. Compared to P. tabulaeformis and P. yunnanensis, P. densata did not show a noticeably higher degree of disequilibrium in ovule, pollen, and zygote pools.
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Continuing admixture of different gene pools could generate linkage disequilibrium due to different allelic frequencies between the parental populations. The power for detecting linkage disequilibrium is highest between polymorphic loci (e.g., Fes, Pgm-1, Sdh-1, and Got-3). If continuing hybridization were the cause of linkage disequilibrium, we would expect that P. densata would have more disequilibrium than the parental populations. In addition, we would also expect to find that those loci that were highly differentiated between the parental populations (such as Sdh-1 and Got-3) would be more often involved in significant disequilibria than those that were equally polymorphic in all species, without differentiation between the supposed parental species (such as Pgm-1 and Fes, Table 1). In fact, this is not the case. Among the significant disequilibria of Pd-1 and Pd-2, these two groups of loci are equally frequently involved in the few significant pairs of disequilibria.
Gene admixture analysis and population clustering pattern:
The allozyme composition in each population was analyzed for the respective gene admixtures from reference species of P. yunnanensis and P. tabulaeformis. Of the three populations of P. densata, populations Pd-1 and Pd-2 had similar amounts of apparent allozyme mixture from P. yunnanensis (57.8 and 60.4%, respectively, Fig 2), while population Pd-7 showed a very strong affinity to P. yunnanensis (100%, Fig 2). The sampled populations of the two reference species, P. tabulaeformis and P. yunnanensis, showed nearly no admixture from each other and appeared to be nearly pure representatives of their respective species (data not shown).
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The UPGMA tree based on NEI's (1978) unbiased genetic distance for all populations revealed three distinct groups of populations with strong bootstrap support (Fig 3). The eight populations of P. tabulaeformis showed little differentiation and clustered as one group. Another major cluster was composed of the three P. yunnanensis populations and one population of P. densata (Pd-7). The third group comprised the other two populations of P. densata (Pd-1 and Pd-2) from the north-central part of its distribution.
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| DISCUSSION |
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Genetic structure of P. densata populations:
In general, we observed similar patterns of gene diversity and population differentiation in ovule, pollen, and zygote pools of all three species. All the populations had fixation index very close to zero, suggesting they can be regarded as random mating populations. The partitioning of the gene diversity revealed that most of this diversity occurred within populations of each species and only 2.38.6% (Fst) of it resided among populations of each species. This range of Fst values is within the commonly observed degree of population differentiation for wind-pollinated conifers with continuous distributions (see ![]()
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Gene admixture analysis based on allozyme frequencies revealed that P. tabulaeformis and P. yunnanensis provided nearly equal contributions to the allozyme composition of populations Pd-1 and Pd-2. Population Pd-7, however, appeared to be much more strongly related to P. yunnanensis. On the UPGMA tree, Pd-7 grouped with the P. yunnanensis populations, although farther from them than the distance they spanned. These findings agree well with the results from a previous cpDNA analysis (![]()
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The heterogeneity in allozyme and cpDNA composition among P. densata populations suggests that different populations of P. densata have had different evolutionary histories. It seems that P. yunnanensis and another species were involved in the origin of P. densata, and P. tabulaeformis was involved locally. Thus, P. densata might be multiply derived or certain populations might have been in contact with one or the other parental species in the past, leading to the observed differences in allele and haplotype frequencies among its populations. Population Pd-7 showed very similar allozyme composition to P. yunnanensis. This might be suggestive of introgression with its parents in the marginal populations. Given the huge and complex geographic region occupied by P. densata it is not surprising to discover different factors involved in the evolution of different populations.
Speciation and maintenance of P. densata:
Homoploid speciation in plants involves different processes and mechanisms from polyploid speciation (![]()
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P. densata represents another example of diploid hybrid speciation that involves isolation and adaptation in an extreme habitat. P. densata differs from many other plant hybrids in its stability as a well-recognized species. It occupies a huge territory at high elevations that is not accessible to the putative parents and other pines in the region. In this environment, the putative parental species cannot grow. However, P. densata forms extensive, pure forests and regenerates well. In contrast to hybrid zones that are maintained by intensive current gene flow, the origin of P. densata is hypothesized to be ancient and to be related to the uplift of the Tibetan plateau, which would date back to at least 20 mya (![]()
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108 mya (![]()
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Estimates of the degree of nonrandom associations among gene loci lend further support to the hypothesis that populations of P. densata have a stabilized hybrid nature. If significant gametic disequilibrium is detected among unlinked neutral markers, like allozymes, current gene flow would be expected to be one of the factors maintaining the hybrid genetic structure (![]()
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The high proportion of mixed allozyme and cpDNA composition in P. densata populations does not indicate strong selection acting for or against a particular mating direction. Artificial hybridization experiments have shown that genetic barriers among the Asian pines in the subgenus Pinus are weak. Most of the species can cross with each other and produce viable seeds (![]()
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It should be pointed out that our sampling in the close-sympatric regions is not extensive, due to the complex and inaccessible terrain. Detailed sampling of P. densata from areas to both the north and south linking to the P. tabulaeformis and P. yunnanensis populations would be needed to accurately assess the gene flow in the species complex. In addition, artificial hybridization involving P. densata with either of the putative parents would be of great value in clarifying several aspects related to this speciation event, such as the feasibility of backcrossing, the viability and fertility of the backcross progeny, the genetic structure of these progeny populations, and the potential differences in the evolutionary biology of organellar vs. nuclear genes. Furthermore, information on maternally inherited mtDNA markers, in combination with the paternal cpDNA and biparental nuclear genome data, would shed new light on the evolution of P. densata.
| ACKNOWLEDGMENTS |
|---|
This study was supported by grants from the Chinese Academy of Sciences, the National Natural Science Foundation of China (NSFC-30070058), the Swedish Council for Forestry and Agricultural Research, and the Swedish International Development Agency.
Manuscript received February 12, 2001; Accepted for publication June 22, 2001.
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