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Systematics |
Division of Environmental and Evolutionary Biology, Sir Harold Mitchell Building, University of St. Andrews, St. Andrews KY16 9TH, UK
Received for publication September 5, 2002. Accepted for publication January 10, 2003.
| ABSTRACT |
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Key Words: contact zones intraspecific evolution ITS lineage sorting long-distance dispersal phylogeography, psbAtrnH cpDNA Saxifraga oppositifolia Saxifragaceae
| INTRODUCTION |
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The circumpolar cushion plant S. oppositifolia has been an important model species for the analysis of the Quaternary phylogeography and evolution of Arctic-Alpine species and also for examining the relevance of intraspecific polymorphisms in adaptation to environmental heterogeneity at small spatial scales and to climate change (e.g., Crawford et al., 1993). In particular, the species has been the subject of several molecular genetic studies examining restriction fragment length polymorphisms (RFLPs) of cpDNA and random amplified polymorphic DNA (RAPDs; Abbott et al., 1995
, 2000
; Gabrielsen et al., 1997
; Gugerli et al., 1999
; Holderegger et al., 2002
). Based on fossil evidence and a study of cpDNA phylogeography, Abbott et al. (2000)
suggested that S. oppositifolia was relict to the Arctic in western Beringia (northeastern and north-central Siberia) during the late Tertiary, before it migrated eastwards and westwards to obtain a circumpolar distribution. There is also reliable macrofossil and molecular evidence showing that the species survived the Pleistocene glaciations in several major refugial regions of the Alaskan and Canadian high Arctic, of northern Siberia, and of Eurasia to the south and east of the main ice sheets (Abbott and Brochmann, 2003
). The present study evaluates whether these phylogeographical patterns are supported by cpDNA and nrDNA sequences. Specifically, we asked whether glacial survival in different major glacial refugia resulted in the evolution of distinct intraspecific lineages in S. oppositifolia, as could be expected because of genetic drift or differential adaptive selection during long-term isolation. We analyzed the psbAtrnH spacer of the chloroplast genome (Sang et al., 1997
) and the ITS region of nrDNA of samples of S. oppositifolia from almost the species' entire distribution. For comparison, some closely related taxa (species or subspecies) occurring within the distribution area of S. oppositifolia were included.
| MATERIALS AND METHODS |
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DNA extraction
Genomic DNA was extracted from 80 mg of dried leaf material using the hexadectyltrimethylammoniumbromide (CTAB) protocol of Whittemore and Schaal (1991)
with the modifications and cleaning steps given in Milne et al. (1999)
. Total DNA was additionally cleaned with 7.5 mol/L ammonium acetate and a Wizard DNA cleanup kit (Promega, Madison, Wisconsin, USA).
The psbAtrnH sequencing
Amplifications of the psbAtrnH intergenic spacer of cpDNA using the primers psbAF and trnHR (Operon, Alameda, California, USA) from Sang et al. (1997)
were performed in 50 µL volumes containing 24.1 µL of ddH2O, 10 µL of Q-solution (enhancing the quality of the PCR product; Qiagen, Valencia, California, USA), 4 µL of 25 mmol/L MgCl2, 2.5 µL of a 2 mmol/L dNTP solution in equimolar ratio, 1 µL of each primer at 10 pmol/µL, 0.4 µL of Taq DNA-polymerase A (5 units/µL; Promega, Madison, Wisconsin, USA), 5 µL of the provided 10x enzyme buffer, and 2 µL of genomic DNA at 20 ng/µL. Polymerase chain reaction (PCR) was performed with a PTC-100 thermocycler (MJ Research, Waltham, Massachusetts, USA) set at an initial 1 min at 94°C, followed by 30 cycles of 1 min at 94°C, 1 min at 55°C, and 2 min at 72°C with a final extension of 10 min at 72°C.
The PCR products were cleaned with a Wizard PCR prep kit (Promega, Madison, Wisconsin, USA). Sequence analysis in forward and reverse directions was performed on an ABI PRISM 377 automated sequencer (Applied Biosystems, Foster City, California, USA) according to the manufacturer's instructions (4.75% Long Ranger gels) using the Dye Deoxy Terminator sequencing kit. For cycle sequencing (35 cycles of 10 s at 96°C, 5 s at 50°C, and 90 s at 60°C), 0.5 µg of template DNA, and 5 pmol of the same primers as given above were used. Sequences were edited on SEQUENCE NAVIGATOR 1.0 (Applied Biosystems, Foster City, California, USA) and manually aligned with the psbAtrnH sequence of Saxifraga spathularis (GenBank accession number AF374742) using SEQUENCHER 3.0 (Applied Biosystems, Foster City, California, USA). For each sample, the PCR reaction and the sequence determination were repeated at least twice. No statistical treatment was applied, because we found only two phylogenetically informative haplotypes.
GenBank accession numbers for psbAtrnH are: S. oppositifolia 217-base pair (bp) sequence "with indel 1" (sample 9), AF502090; S. oppositifolia 201-bp sequence "without indel 1" (sample 22), AF502091; S. biflora (sample 2), AF504550; S. blepharophylla (sample 3), AF504548; S. smalliana (sample 4), AF504549; S. aizoides (sample 1), AF504551 (Table 1, Fig. 2).
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For parsimony analysis of ITS sequences, we used PAUP 4.0 (Sinauer, Sutherland, Massachusetts, USA) taking into account both nucleotide substitution and indel information (coded as present or absent irrespective of indel length) with heuristic search, Fitch algorithm, steepest descent, ACCTRAN, tree bisection reconnection (TBR) swamping, and MULPARS in effect. Saxifraga aizoides served as outgroup, and bootstrap estimates were based on 1000 replicates. As an alternative analysis, we additionally generated a neighbor-joining clustering based on uncorrected DNA-DNA distances with PAUP 4.0, again using 1000 bootstrap replicates for significance testing.
GenBank accession numbers for ITS15.8SITS2 are as follows: S. oppositifolia (sample 22), AF502089; S. biflora (sample 2), AF504546; S. blepharophylla (sample 3), AF504545; S. smalliana (sample 4), AF504544; S. aizoides (sample 1), AF504547 (Table 1).
The complete data set on the psbAtrnH and ITS sequences is available from the first author upon request.
| RESULTS |
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Saxifraga blepharophylla (217 bp), S. biflora (217 bp), and S. aizoides (207 bp) all showed psbAtrnH sequences with indel 1 (Fig. 2) in accordance with their geographical origin (Fig. 1). The latter also held for S. smalliana from Alaska with a 201-bp sequence without indel 1 (Figs. 1 and 2). Otherwise, S. blepharophylla showed none, while S. biflora and S. smalliana each had one additional nucleotide substitution not found within the S. oppositifolia samples. These substitutions were noninformative with respect to parsimony. Saxifraga aizoides exhibited two additional indels (indel 2, 1 bp; indel 3, 9 bp) and a single additional nucleotide substitution (Fig. 2).
The ITS sequences
The consensus ITS15.8SITS2 sequence of the 19 S. oppositifolia samples had a length of 676 bp. Within S. oppositifolia, ITS1 exhibited four parsimony informative and 12 noninformative nucleotide substitutions as well as two informative and four noninformative indels. ITS2 showed less variation: one informative and one noninformative nucleotide substitution and a single informative indel. Even the 5.8S region exhibited one informative and one noninformative nucleotide substitution. Hence, nine phylogenetically informative sites were found within the entire ITS data set of S. oppositifolia. Pairwise sequence differences among samples ranged between zero and 10 (26 in total).
In S. biflora (sequence length: 675 bp), S. smalliana (676 bp), and S. blepharophylla (675 bp), only the latter showed a single nucleotide substitution otherwise not found within the ITS variation of the 19 S. oppositifolia samples. In contrast, S. aizoides (675 bp) exhibited 31 additional nucleotide substitutions compared with the other four taxa in the analysis.
All ITS trees generated exhibited largely unresolved topologies with low bootstrap support irrespective of the methods (parsimony or neighbor-joining) and the settings used. As an example, we present the 50% majority-rule consensus tree of the 25 most parsimonious trees found (Fig. 3). It also had low phylogenetic resolution with a consistency index (CI) of only 0.192. Only two aspects were recurring in the different analyses of the ITS sequences: (1) samples of S. oppositifolia with a cpDNA haplotype without indel 1 (see above; Fig. 2) were mainly grouped in a clade including S. smalliana (top clade in Fig. 3), and (2) S. biflora, S. blepharophylla, and S. smalliana were positioned amongst the S. oppositifolia samples.
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| DISCUSSION |
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The phylogenetic analysis of ITS sequences (Fig. 3) resulted in a poorly resolved topology with low bootstrap support. Hence, the two main cpDNA lineages detected in S. oppositifolia were not precisely reflected in the species' nrDNA sequence variation, although samples of S. oppositifolia with a cpDNA haplotype without indel 1 were mainly grouped together in an ITS clade that included S. smalliana. In view of this poor resolution, a determination of divergence time between the two cpDNA lineages of S. oppositifolia must be left to future studies.
The two cpDNA lineages remained separate throughout their distributions in the study of Abbott et al. (2000)
, except in northern Greenland and north-central Siberia where secondary contact zones appeared to exist. In the present study, we detected one exception to this pattern in that sample 12 of S. oppositifolia from the North Cape in Scandinavia possessed the cpDNA sequence without indel 1, which was not concordant with its geographical location (Fig. 1). A possible explanation for this particular pattern could be rare long-distance dispersal through seed from a population of S. oppositifolia either from northern Greenland or from the Siberian Taymyr Peninsula (Fig. 1). Such long-distance migration is now considered to be rather common in many Arctic plant species (Hagen et al., 2001
; Abbott and Brochmann, 2003
). However, without having a comparative and reliable nuclear gene phylogeny at hand, the alternative explanation of an ancient polymorphism cannot be rejected.
In regions where migrants from different glacial refugia have come into contact, higher levels of genetic diversity can be expected (Comes and Kadereit, 1998
; Stehlik, 2002
). Such postglacial sink regions between the East Asian-North American and the Eurasian lineages of S. oppositifolia are likely to occur in north-central Siberia and northern Greenland/northeastern Arctic Canada, where the two cpDNA lineages co-occur (Abbott et al., 2000
; Fig. 1). In contrast to maternally inherited cpDNA, biparentally inherited nrDNA would be expected to mix easily in such contact zones through sexual reproduction in the mainly outbred S. oppositifolia (Gugerli et al., 1999
). Unfortunately, the unresolved ITS-phylogeny prevented a corresponding phylogeographical analysis. As there are no comparative data available on intraspecific sequence variation in other Arctic plant species, it is not yet possible to infer whether contact zones are general biogeographical features of circumpolar taxa.
The usefulness of ITS for intraspecific phylogenetic analyses
The limited variation in the ITS sequences of S. oppositifolia (i.e., nine phylogenetically informative sites) resulted in a poor resolution of this species' intraspecific evolution and phylogeography. The samples investigated exhibited between zero and 10 pairwise site differences. This ITS variation of individuals covering almost the species' entire distribution area was low compared with the ITS variation found in other Saxifraga species sampled at far smaller spatial scales. Brochmann et al. (1998)
detected 221 divergent sites in pairwise sequence comparisons of four populations of S. cernua collected within only 140 km on the Arctic Svalbard, while values for seven populations of S. globulifera from both sides of the Strait of Gibraltar ranged between zero and 24 differences (Vargas et al., 1999
). Therefore, the applicability of ITS sequences to intraspecific phylogenies (Soltis and Soltis, 1998
) varies within comparatively closely related species and for different geographical scales. This sheds doubt on the accuracy of estimates of divergence times at lower taxonomic levels (Ayala, 1999
) in cases where sequence variation within a studied taxon or a group of taxa is not adequately covered.
Sequence differences between Saxifraga oppositifolia and closely related taxa
The S. smalliana sample from Alaska had a cpDNA haplotype without indel 1 and differed in only one nucleotide substitution from samples of S. oppositifolia from the same region (Figs. 1 and 2). Moreover, its ITS sequence was congruent with the consensus sequence of all S. oppositifolia samples. Saxifraga blepharophylla from the European Alps, often treated as a subspecies of S. oppositifolia (Webb and Gornall, 1989
), exhibited a psbAtrnH haplotype identical to the one found in the Alpine samples of S. oppositifolia (i.e., with indel 1; Figs. 1 and 2), and its ITS sequence had only one nucleotide substitution not found in S. oppositifolia. It may be concluded from this that S. smalliana and S. blepharophylla are very closely related to S. oppositifolia.
Based on the present molecular data, taxonomic conclusions on S. smalliana and S. blepharophylla cannot be drawn. For such an aim, many more samples of these two taxa had to be included in morphological, biosystematic (e.g., common garden transplants or cross pollinations), and molecular genetic analyses. It was nevertheless striking that even the morphologically distinct, but closely related Alpine species S. biflora (Kaplan, 1995
) showed an ITS sequence encompassed by the variation found in S. oppositifolia. In addition, this species' cpDNA sequence (with indel 1) had only one nucleotide substitution differing from the sequences of the other samples investigated (Figs. 1 and 3). Alpine samples of S. biflora and S. oppositifolia were also not distinguishable based on a preliminary survey of cpDNA RFLPs using the Southern blotting technique (R. Holderegger and R. J. Abbott, unpublished data). In natural populations, these two species hybridize, and introgression is observed (Gugerli, 1997
). This may account for the observed lack of differentiation between these two taxa.
All investigated samples, including S. aizoides, either contained or lacked the psbAtrnH indel 1 according to their geographical origin. A corresponding pattern, where individuals do not possess taxon-specific but region-specific cpDNA haplotypes, was found in the European white oaks (Petit et al., 2002
), which was attributed to lineage sorting. Lineage sorting due to the presence of ancestral polymorphisms coupled with differential survival of the variants results in gene phylogenies not matching organismal phylogenies (Page and Holmes, 2000
). It has also been invoked in the evolution of Mediterranean Senecio (Comes and Abbott, 2001
) and Alpine Draba species (Widmer and Baltisberger, 1999
). Whether the geographical pattern of the cpDNA sequences found in several Saxifraga taxa in the present study is due to lineage sorting cannot be answered based on the present data set; there are several alternative explanations. (1) It is possible that indel 1 represents an ancestral state in S. oppositifolia and other Saxifraga species, which the East Asian-North American lineage of S. oppositifolia has lost. (2) Saxifraga smalliana and S. blepharophylla may simply represent subspecies or even varieties of S. oppositifolia of regional origin. Thus, it would not be surprising that they exhibit the main cpDNA haplotype typical for the corresponding regions. (3) Only one sample each of S. biflora and S. aizoides, both from the European Alps, were included in the analysis. While the former species is an Alpine endemic, the latter has a wide circumpolar distribution. It would thus be interesting to investigate whether samples of S. aizoides from other regions, e.g., from North America, also show region-specific cpDNA haplotypes. (4) Ancient hybridization events as found in the Boykinia and Heuchera groups of Saxifragaceae (Soltis and Kuzoff, 1995
; Soltis et al., 1996
) could be involved and might cause similar phylogeographic patterns.
Conclusions
The two main cpDNA haplotypes based on psbAtrnH sequences found in S. oppositifolia were consistent with the existence of two intraspecific evolutionary lineages (East Asian-North American and Eurasian) in this species. In contrast, an analysis of intraspecific ITS variation resulted in low phylogenetic resolution. A possible long-distance dispersal event in S. oppositifolia and the occurrence of putative lineage sorting within a group of taxa of the genus Saxifraga were also indicated by the molecular analyses conducted.
| FOOTNOTES |
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2 Author for reprint requests, present address: Division of Ecological Genetics, WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland (phone: +41 1 739 25 27; FAX: +41 1 739 22 15; rolf.holderegger{at}wsl.ch
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