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Contrasting the Distribution of Chloroplast DNA And Proc. Nati. Acad. Sci. USA Vol. 91, pp. 8127-8131, August 1994 Population Biology Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: Implications for studies of gene flow in plants DAVID E. MCCAULEY Department of Biology, Vanderbilt University, Nashville, TN 37235 Communicated by Michael T. Clegg, May 2, 1994 ABSTRACT The distribution of chloroplast DNA (cp- literature showing that intraspecific cpDNA variation can be DNA) length variants was analyzed within and among 10 local detected in a variety of species and that such variation populations of Sikne alba, a dioecious angiosperm. The pop- generally shows considerable spatial structure (1, 2, 4, 9-12). ulations displayed considerable allele frequency variation, re- However, comparisons to nuclear variation are limited. Since sulting in an estimate of Wright's Ft of 0.67 over a 25 x 25 km most of the published studies have been conducted on a portion ofthe species' range. By contrast, a concurrent analysis spatial scale that encompasses a major portion ofthe species' of the genetic structure of these same populations based on range, the questions ofwhether cpDNA variation can be used seven polymorphic allozyme loci yielded an estimate of Fat of to document genetic structure at relatively fine geographic 0.13. The two Ft estimates are significantly different from one scales and how the relative magnitudes of the within- and another when their respective confidence limits are estimated among-population components of that variation compare to by jackknifing. The results of a breeding study were consistent the local distribution of nuclear variants remain open. This with maternal inheritance of the cpDNA variants. With ma- paper represents one of the first attempts to address these ternal inheritance the genetic structure of the cpDNA should issues in natural populations of a plant species. reflect seed movement, whereas the genetic structure of the Here I report on the use of PCR-based cpDNA variants in nuclear-encoded allozyme loci should reflect the movement of the analysis of the genetic structure of local populations of a both seeds and pollen. Comparison of the two markedly dioecious angiosperm, Silene alba (= Silene latifolia, Caryo- different Fst estimates in the context of recent models of the phyllaceae). I show that the distribution of chloroplast DNA population genetics oforganelles suggests that the movement of polymorphisms among populations separated by only a few both seeds and pollen contributes significantly to gene flow. kilometers displays markedly more spatial structure than does the distribution of nuclear-encoded allozyme markers Recently it has been suggested that the study of the genetic when compared using Fq, Wright's (13) measure of genetic structure of plant populations could be greatly facilitated by structure. I further discuss the inferences about the contri- employing markers encoded by chloroplast DNA (cpDNA) bution of seed and pollen movement to gene flow that can be (1-4). One reason is that in species in which cpDNA displays drawn by the joint consideration of these Fst estimates. maternal or maternal-biased inheritance, as is often the case in angiosperms (5, 6), gene flow in cpDNA is restricted, or MATERIALS AND METHODS largely restricted, to incidents of seed movement. Since gene flow in nuclear DNA can occur via the dispersal of either S. alba (white campion) is a patchily distributed roadside seeds or pollen, information about the relative influence of weed in the area of southwestern Virginia in which this study the two sources of gene flow on genetic structure might be was conducted. Long-term studies (14) have identified nu- contained in the comparative behavior of genetic markers merous populations of S. alba, ranging in size from a few to derived from the two genomes. Furthermore, in plant meta- >200 individuals along roadsides within a 15-km radius ofthe populations in which the local demes are subject to frequent Mountain Lake Biological Station in Giles County, VA. Ten extinction and recolonization, the imprint of recent founding representative populations, each consisting of >30 individ- events on genetic structure should be particularly evident in uals, were selected from this area for genetic sampling. the distribution of cpDNA variants, since local demes are Between 20 and 50 individuals were sampled from each site founded by the movement of seeds into empty patches of by removing single leaves. Collection sites were spaced such favorable habitat (7). Thus, chloroplast and nuclear genes that nearest neighbors were separated from one another by could display markedly different patterns of spatial genetic 5-10 km; the greatest distance separating any ofthe sampled structure, particularly in those species in which pollen and sites was -25 km. Note that a number of unsampled popu- seed dispersal patterns differ. Taken together, the two classes lations were distributed along the intervals of roadside that of genetic markers have the potential to be quite useful for separated the sampled sites. inferring the demographic processes that underlie genetic Because the goal of this study was to use cpDNA poly- structure, especially when evaluated in the added context of morphisms to estimate the among-population component of recent population genetic models of organelles (3, 4, 8). gene frequency variation, rather than to estimate total nu- Despite the potential value of such studies ofcpDNA, they cleotide diversity, the initial survey for markers focused on are still relatively few. The chloroplast genome is generally a region of the chloroplast genome most likely to vary. To highly conserved and it is not yet clear whether intraspecific that end, a PCR-based approach employed a nested set of variation of the sort needed for studies of population struc- primers expected to anneal within tRNA coding regions, but ture is sufficiently common for cpDNA to be a widely used flanking noncoding regions, either intergenic spacers or an tool in plant population biology. There is a small but growing intron. These primers were designed to amplify regions of DNA that would be expected to be less well conserved than The publication costs of this article were defrayed in part by page charge coding regions (15) (see Fig. 1). Genomic DNA was collected payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. Abbreviation: cpDNA, chloroplast DNA. 8127 Downloaded by guest on September 29, 2021 8128 Population Biology: McCauley Proc. Natl. Acad. Sci. USA 91 (1994) 700 bp 650 bp 450 bp region, respectively. The frequency of these haplotypes was then estimated for samples of 10-15 individuals from each of I1I the 10 study populations. In addition, cpDNA haplotypes trnT trnL trnL trnF were determined for the parents and offspring drawn from three laboratory crosses in which the parents differed at the variable trnL intron site. For comparative purposes, genetic structure was also FIG. 1. Location and alignment of primers designed to anneal to estimated for nuclear loci by the analysis of electrophoretic tRNA gene T, L, or F within the chloroplast genome, as redrawn protein polymorphisms. Population-speciflic allele frequen- from ref. 15. See that paper for primer sequences and positions relative to the published tobacco cpDNA sequence. Cross hatches cies at each of seven polymorphic allozyme loci were esti- represent the approximate location of insertion/deletion polymor- mated from samples of 20-50 individuals taken from the 10 phisms. study populations. The enzymes studied and their EC num- bers are phosphoglucomutase (PGM; 5.4.2.2), glucose-6- from leaf material by a CTAB/chloroform extraction method phosphate isomerase (GPI; 5.3.1.9), shikimate 5-dehydroge- (16) and then used as a template in the PCR. The PCR cycle nase (SKDH; 1.1.1.25), isocitrate dehydrogenase (IDH; was as follows: 1 min at 940C followed by 1 min at 450C and 1.1.1.42), phosphogluconate dehydrogenase (6-PGD; 2 min at 720C. This was repeated 35 times. In the original 1.1.1.44), malate dehydrogenase (MDH; 1.1.1.37), and leucyl survey for variation the outside pair of primers (Fig. 1) was aminopeptidase (LAP; 3.4.11.1), for which a total of 26 used to amplify the entire z1800-bp sequence from several putative alleles could be scored. Allozyme variation was individuals. Separate aliquots (10 1.l) of the 50-Al PCR assayed by starch gel electrophoresis. Tissue preparation and products were then digested with one of several restriction enzyme staining followed standard methods (17). using enzymes. The digestion products were electrophoresed on Genetic structure was quantified by calculating F~t algorithms developed for both haploid and diploid data (18). 4% NuSieve (FMC) agarose minigels and visualized by Fq was selected as a measure of genetic structure because it ethidium bromide staining. While no interindividual variation describes the relative contribution ofamong-population allele in restriction site number was detected, the size of the frequency variation to total genetic variance. This approach restriction fragments varied among individuals in several of facilitates comparing or averaging loci with varying degrees the digests, suggesting length variation owing to insertion/ of absolute polymorphism. Furthermore, the algorithm in- deletion polymorphism. By employing nested combinations cludes sample size corrections that allow comparisons based of primer pairs illustrated in Fig. 1, two variable regions were on samples of different numbers of individuals. Finally, Fq identified, one within the trnL (UAA) intron and one in the (or the related statistic, Gs,) is a variable often used in region that separates the trnL (UAA) and trnF (GAA) coding population genetic studies that relate genetic structure to regions (15). A slight size variation was apparent by inspec- various demographic processes (13, 19, 20). tion after electrophoresis of the uncut PCR products. Visu- For the allozyme data, Fst was first calculated for each alization of the length variants was facilitated by digestion of allele.
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