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(American Journal of Botany. 2000;87:591-596.)
© 2000 Botanical Society of America, Inc.

RAPD marker diversity within and divergence among species of Dendroseris (Asteraceae: Lactuceae)1

Elizabeth J. Esselman2, Daniel J. Crawford8,3, Soren Brauner4, Tod F. Stuessy5, Gregory J. Anderson6 and Mario Silva O7

2 Department of Biological Sciences, Southern Illinois University at Edwardsville, Edwardsville, Illinois 62026 USA; 3 Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio 43210 USA; 4 Department of Biology, Ashland Uiversity, Ashland, Ohio 44805 USA; 5 Department of Higher Plant Systematics and Evolution, Institute of Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria; 6 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 USA; and 7 Departamento de Botánica, Universidad de Concepción, Concepción, Chile

Received for publication February 25, 1998. Accepted for publication July 27, 1999.

ABSTRACT

Random Amplified Polymorphic DNA (RAPD) markers were used to measure genetic diversity within and divergence among species of Dendroseris (Asteraceae: Lactuceae), a genus endemic to the Juan Fernandez Islands, Chile. Results were compared to previous studies employing allozymes. For five of the species, RAPD banding patterns distinguished all individuals examined, and different mutilocus genotypes were found even in species exhibiting no allozyme diversity. RAPD band diversities ranged from 0.003 to 0.022 within species; >90% of total diversity was among species and <10% within them. Relative levels of allozyme and RAPD diversity were similar for some species, particularly those with highest and lowest diversities, but overall there was no significant correlation. Relationships inferred from a neighbor-joining tree generated from RAPD bands were similar to results obtained from morphology, chloroplast DNA (cpDNA) restriction site mutations, and sequences from the internal transcribed spacer regions of nuclear ribosomal DNA (ITS), but somewhat better resolution was achieved. Relationships shown by allozymes differed from trees based on other data; this ostensibly is a result of the sharing of ancestral alleles and the absence of alleles generated subsequent to speciation. Dendroseris represents an example where RAPD markers, because of their greater variability, provide a useful alternative to allozymes for assessing diversity in rare species endemic to oceanic islands and for resolving relationships among the species.

Key Words: allozymes • Asteraceae • Dendroseris • genetic diversity • Juan Fernandez Islands • RAPD markers

Endemic species have, on average, low genetic diversity at allozyme loci relative to vascular plants in general (Hamrick and Godt, 1989, 1996 ), and species endemic to oceanic islands have even lower mean diversity (De Joode and Wendel, 1992 ; Frankham, 1997 ). For some endemic congeners on oceanic islands there is minimal interspecific divergence at allozyme loci, and thus little resolution of relationships among species is achieved with enzyme electrophoresis (Helenurm and Ganders, 1985 ; Lowrey and Crawford, 1985 ; Francisco-Ortega et al., 1996 ). Because allozymes have sometimes proven insufficiently variable for assessing genetic diversity within and among populations of rare endemic plants (e.g., Waller, O'Malley, and Gawler, 1987 ; Lesica et al., 1988 ; Soltis et al., 1992 ; Crawford et al., 1994 ), attention has turned to more variable regions of the genome. A more recently employed approach in plant systematics and population biology is random amplified polymorphic DNA (RAPD) markers, a PCR (polymerase chain reaction)-based technique (Hadrys, Balick, and Schierwater, 1992 ; Whitkus, Doebley, and Wendel, 1994 ; Brunell and Whitkus, 1997 ; Spooner, Ugarte, and Skroch, 1997 ; Whitkus et al., 1998 ; Wolfe and Liston, 1998 ).

The genus Dendroseris (Asteraceae: Lactuceae) is endemic to the Juan Fernandez Islands, which are of volcanic origin, located some 600 km west of mainland Chile at 33°S latitude, and consist of two main islands. Masatierra is four million years old and nearer continental Chile, while Masafuera is one to two million years in age and more distant from the continent (Stuessy et al., 1984 ). Dendroseris consists of rosette trees and shrubs and is extremely variable morphologically. Sanders et al. (1987) placed the 11 species (making Dendroseris the largest genus in the archipelago) into three subgenera: (1) subg. Dendroseris consisting of D. litoralis Skottsb., D. macrantha (Bertero & Dcne.) Skottsb., D. macrophylla D. Don, and D. marginata (Bertero & Dcne.) Hook. & Arn.; (2) subg. Phoenicoseris with D. berteroana (Dcne.) Hook. & Arn., D. pinnata (Bertero ex Dcne) Hook & Arn., and D. regia Skottsb.; and (3) subg. Rea composed of D. gigantea Johow, D. micrantha (Bertero & Dcne.) Hook. & Arn., D. neriifolia (Dcne.) Hook. & Arn., and D. pruinata (Johow) Skottsb. Various aspects of the genus have been discussed in earlier papers (Crawford, Stuessy, and Silva O., 1987 ; Crawford et al., 1992, 1998 ; Sanders et al., 1987 ; Sang et al., 1994 ), but it should be emphasized that natural populations of Dendroseris are very small (almost always fewer than ten plants), few in number, and widely scattered.

In earlier studies (Crawford, Stuessy, and Silva O., 1987 ; Crawford et al., 1998 ), we reported on allozyme diversity within and divergence among species of Dendroseris; both low diversity and divergence were found. Thus, Dendroseris fits the general (but not universal) pattern of many insular endemics (Helenurm and Ganders, 1985 ; Lowrey and Crawford, 1985 ; Witter and Carr, 1988 ). The purposes of the present study were to use RAPD markers to assess genetic diversity within and divergence among species of Dendroseris and to compare the results with those obtained from allozymes.

MATERIALS AND METHODS

Total DNA was extracted from plants collected in the field; leaves were either dried (placed in sealable plastic bags with silica gel) or placed on ice and retained at 4°C until extracted in the laboratory at The Ohio State University, Columbus, Ohio, USA. A total of 35 individuals from 25 populations and seven species was included in the study (Table 1). The CTAB (hexadecyltri-methylammonium bromide) method of Doyle and Doyle (1987) was used to extract total DNA. DNAs were purified by banding on cesium chloride-ethidium bromide gradients (Palmer, 1986 ). Amplifications, electrophoretic separation of the amplified products, and staining were performed as described by Brauner, Crawford, and Stuessy (1992) . The 11 primers used were from the "A" kit purchased from Operon Technologies, Alameda, California, USA; these included primers 1, 3, 4, 8, 9, 11, 13, 14, 15, 18, and 20. In most instances, DNA from each plant was amplified with the same primer more than once, and the banding patterns were compared.


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Table 1. Populations of Dendroseris used as sources of DNA

 
Fragment sizes were designated as loci, and bands were shared as diallelic characters (present = 1, absent = 0). Only those loci amplifying strongly in each instance were scored and included in the analyses. The number of multilocus genotypes (unique arrays of loci) was calculated for each species. RAPD locus diversity was calculated with the Shannon-Weaver information statistic employing the Brilliouin formula for eliminating the bias of finite sample size (Peet, 1974 ; Whitkus et al., 1998 ). Diversity was estimated for each species and across all species. Apportionment of diversity within and between species was determined according to Lewontin (1972) . The rationale for employing these methods for estimating RAPD locus diversity was given in Whitkus et al. (1998) . A neighbor-joining tree was constructed from RAPD locus similarities (the coefficient of Dice [1945] ) among species of Dendroseris. Genetic distances among species at allozyme loci (Crawford, Stuessy, and Silva O., 1998 ) were used to produce a neighbor-joining tree.

RESULTS

A total of 215 loci was scored for the 11 RAPD primers for a mean of 19.5 loci per primer. Diversity within species ranged from 0.003 in D. neriifolia to 0.022 in D. micrantha (Table 2) with a mean of 0.012 for all species. About 90% of the total diversity resided between and 10% within species. For the species D. litoralis, D. marginata, D. micrantha, D. neriifolia, and D. pruinata, each plant had a different array of RAPD loci (multilocus genotype). The five plants of D. berteroana have three different patterns, while the 13 plants of D. pinnata express four different genotypes. Total diversity (Ht; Nei, 1973 ) at allozyme loci is also shown in Table 2 (from Crawford et al., 1998 ); these values ranged from no diversity in D. berteroana and D. pruinata to 0.071 for D. litoralis. Only one plant of D. marginata was examined for allozymes so Ht was not calculated for it.


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Table 2. Total gene diversity (Ht) at allozyme loci and RAPD bands and RAPD band diversity for six species of Dendroseris.

 
Mean RAPD locus similarities for individuals of different species ranged from 0.243 to 0.575, with an average of 0.405 for all pairwise comparisons. The neighbor-joining tree based on these similarities has three major groups corresponding to the subgenera of Dendroseris (Fig. 1). Genetic identities (Nei, 1972 ) between species of Dendroseris at allozyme loci ranged from 0.73 for D. marginata and D. pruinata to 0.99 for D. berteroana and D. pinnata (Crawford et al., 1998 ). Mean identity values for species within subg. Dendroseris, subg. Phoenicoseris, and subg. Rea were 0.91, 0.99, and 0.85, respectively. Mean identities between subgenera ranged from 0.79 for subg. Dendroseris and subg. Rea to 0.90 for subg. Dendroseris and subg. Phoenicoseris. The neighbor-joining tree based on genetic identities at allozyme loci had Dendroseris micrantha and D. pruinata of subg. Rea, and D. berteroana and D. pinnata of subg. Phoenicoseris each forming groups. However, other groups did not correspond to subgeneric assignments; D. litoralis and D. marginata (subg. Dendroseris) do not occur together and D. neriifolia is not included with the other two species of subg. Rea (Fig. 2).



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Fig. 1. Neighbor-joining tree for species of Dendroseris based on similarities of RAPD banding patterns. The tree is midpoint rooted but branch lengths from the graph matrix are shown. Species designations are the first three letters of the names given in Table 1

 


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Fig. 2. Neighbor-joining tree species of Dendroseris based on Nei's (1972) genetic distance at allozyme loci (from Crawford et al., 1998 ). The tree is midpoint rooted, but lengths from the graph matrix are shown on the branches. Species designations are the same as in Fig 1

 
DISCUSSION

Although allozymes have been widely and effectively used to assess genetic diversity within and between plant populations (Hamrick and Godt, 1989, 1996 ), they are sometimes of limited value for rare plants because of the low level or total lack of variation (Lowrey and Crawford, 1985 ; Waller, O'Malley, Gawler, 1987 ; Crawford, Stuessy, and Silva O., 1987; Crawford et al., 1994 ; Lesica et al., 1988 ; Soltis et al., 1992 ). Given the paucity of allozyme variation, PCR-based markers have been employed as an alternative with RAPD markers being commonly used (Hadrys, Balick, and Schierwater, 1992 ; Whitkus, Doebley, and Wendel, 1994 ; Brunell and Whitkus, 1997 ; Wolfe and Liston, 1998 ). Available data indicate that RAPD marker diversity is usually equal to or greater than allozyme variation in plant species (e.g., Peakall, Smouse, and Huff, 1993 ; Szmidt, Wang, and Lu, 1996 ; Ayres and Ryan, 1997 : Esselman et al., 1999 ). Few studies are available comparing allozyme and RAPD diversity in rare island endemics, but indications are that the latter are more variable than the former; for example, no allozyme variation was found in Lactoris fernandeziana (Lactoridaceae) (Crawford et al., 1994 ), whereas RAPD diversity was detected (Brauner, Crawford and Stuessy, 1992 ).

Species of Dendroseris are among the very rarest taxa in the Juan Fernandez archipelago (Stuessy et al., 1998 ), with D. neriifolia known from only three plants, D. marginata and D. litoralis from several plants and one or two populations, D. pruinata from only one population with more than five plants and three or four smaller populations, and D. berteroana and D. pinnata occurring in very small (usually five or fewer individuals) scattered populations. The relatively small numbers of plants examined in this study are direct reflections of the rarity of the genus. Our results demonstrate the utility of RAPD markers for detecting variation in very rare species. For example, the total lack of allozyme diversity in D. berteroana and D. pruinata (Table 2; Crawford et al., 1998 ) might be taken as evidence that the species are genetically homogenous and thus any individual and/or population represents the diversity found in the species as a whole. By contrast, RAPD markers show that each individual of D. pruinata is distinct and 60% of the D. berteroana individuals examined can be distinguished. Every individual of the four species D. litoralis, D. marginata, D. micrantha and D. neriifolia has a unique array of RAPD loci, and four multilocus genotypes were detected among the 13 plants of D. pinnata examined.

Another question is whether allozymes and RAPD markers provide similar estimates of the relative levels of diversity for species of Dendroseris. Because RAPD markers are inherited primarily as dominants, the banding patterns cannot be analyzed routinely by the gene diversity statistics commonly employed for allozyme data unless one can assume populations are in Hardy-Weinberg equilibrium (Swenson et al., 1995 ) or segregation can be observed in haploid tissue such as female gametophytes of conifers (Bucci and Menozzi, 1993 ; Isabel, Beaulieu, and Bosquet, 1995 ; Szmidt, Wang, and Lu, 1996 ) so that band frequencies can be directly interpreted as allelic frequencies. Because this was not possible in the present study, the Shannon-Weaver statistic was employed for comparisons to species diversity at allozyme loci. Relative rankings for allozyme and RAPD locus diversity are not correlated (Spearman rank correlation). However, the two species with highest allozyme diversity, D. litoralis and D. micrantha, also exhibit highest RAPD diversity, and D. berteroana has low diversity with both markers (Table 2). There is no correlation between the number of plants examined and the level of RAPD diversity detected (Spearman rank correlation), so the results do not appear to be an artifact of sampling.

Elucidating phylogenetic relationships among congeneric species (or closely related genera) on oceanic islands is necessary for understanding adaptive radiation and the evolution of characters in the closely related yet often morphologically and ecologically divergent species (Baldwin et al., 1998 ). Exclusive use of morphological characters could be less than optimal for reconstructing phylogenies because of selection for similar character states as different lineages radiate into similar habitats on the islands. Molecular data have been employed in addition to morphology for generating phylogenetic hypotheses for insular groups, but a recurring problem has been poor resolution, usually due to lack of variation (Baldwin et al., 1998 ). That is, the commonly employed molecular approaches for resolving relationships among congeneric continental species are often inadequate for insular endemics, ostensibly because radiation and speciation have been too rapid relative to the molecular sequences employed. Dendroseris is typical of various other insular endemics where both chloroplast DNA restriction site mutations (Crawford et al., 1992 ) and sequences from the internal transcribed spacer region of nuclear ribosomal DNA (ITS) (Sang et al., 1994 ) failed to provide complete resolution of species relationships. Both phylogenies are similar in having an unresolved polytomy at the base with D. neriifolia (subg. Rea), D. micrantha and D. pruinata (subg. Rea), subg. Dendroseris, and subg. Phoenicoseris constituting each of the four lineages.

The neighbor-joining tree from allozymes (Fig. 2) is similar in certain respects to trees based on morphology, cpDNA restriction sites, and ITS sequences. For example, D. micrantha–D. pruinata (subg. Rea), and D. berteroana–D. pinnata (subg. Phoenicoseris) group together. However, the allozyme tree differs in several significant respects from those portrayed by morphology and other molecular data; the two species of subg. Dendroseris do not cluster together because D. marginata joins with subg. Phoenicoseris before D. litoralis (Fig. 2). The high similarities between species of subgenera Dendroseris and Phoenicoseris are probably the result of sharing alleles present in their common ancestors; there are no high-frequency alleles differentiating species of the two subgenera. The position of D. neriifolia in the tree shows it to be quite distinct from all other species, with no support for its inclusion in subg. Rea where it is now placed (Sanders et al., 1987 ) (Fig. 2). Dendroseris neriifolia has three unique alleles, whereas only one unique allele was detected in one other species (Crawford et al., 1998 ). Allozymes apparently have evolved too slowly during the radiation of Dendroseris to provide useful data for resolving relationships.

RAPD banding patterns have been used for elucidating relationships between subspecies (Wolff and Morgan-Richards, 1998 ) and congeneric species (Adams and Demeke, 1993 ; Campos, Raelson, and Grant, 1994 ; Brummer, Bouton, and Kochert, 1995 ; Catalan et al., 1995 ; Stammers et al., 1995 ; Lannér, Bryngelsson, and Gustafsson, 1996 ; Spooner et al., 1996 ; Spooner, Ugarte, and Scroch, 1997 ). The tree for Dendroseris species produced from RAPD loci is highly concordant with trees from cpDNA restriction sites and ITS sequences (Crawford et al., 1992 ; Sang et al., 1994 ), with the species of subgenera Dendroseris and Phoenicoseris grouping together, and D. micrantha and D. pruinata of subg. Rea forming a group (Fig. 1). In addition, D. neriifolia of subg. Rea occurs with the two other species of subg. Rea, whereas the cpDNA, allozyme, and ITS data failed to resolve the position of D. neriifolia (Crawford et al., 1992a ; Sang et al., 1994 ) (Figs. 1, 2). This suggests that because RAPD loci evolve more rapidly than allozyme loci the common ancestor of the three species of subg. Rea had sufficient time to accumulate mutations prior to the origin of the three species. The fact that the neighbor-joining tree based on RAPD bands is highly concordant with trees generated from morphological and other molecular data indicates that RAPD markers provide an accurate portrayal of relationships in Dendroseris. Judging from the results for Dendroseris, RAPD markers may offer an additional source of data for assessing genetic diversity within and relationships among closely related and rapidly radiating groups of rare plants endemic to oceanic islands. These rare endemics are of concern for conservation, and RAPD loci may prove useful for identifying particular populations or lineages for preservation when other methods fail to detect variation or resolve relationships.

FOOTNOTES

1 The authors thank CONAF of Chile for permission to do field work in Robinson Crusoe Islands National Park, including field guides Alfonso Andauer, Oscar Chamorro, Miguel Garcia, Ivan Laceva, Bernardo Lopez, and Ramon Schiller; Richard Whitkus and Andrea Wolfe for valuable comments on the manuscript, and Bette Hellinger who word processed the manuscript with her usual accuracy. Financial support was provided by the National Science Foundation from grants INT-7721637, BSR-08306436, BSR-8906988, and DEB-9500499 to D. J. Crawford, T. F. Stuessy, and G. J. Anderson, and by FONDECYT of Chile through projects FNC 1996008-22 and 796-00-15 to M. Silva O. Back

2 Author for correspondence. Back

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X.-J. GE, Y. YU, Y.-M. YUAN, H.-W. HUANG, and C. YAN
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