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Population Biology |
2Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 USA; 3Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309 USA
Received for publication May 21, 2004. Accepted for publication November 24, 2004.
ABSTRACT
Climate change during the Quaternary played an important role in the differentiation and evolution of plants. A prevailing hypothesis is that alpine and arctic species survived glacial periods in refugia at the periphery of glaciers. Though the Rocky Mountains, south of the southernmost extent of continental ice, served as an important glacial refuge, little is known about how climate cycles influenced populations within this region. We inferred the phylogeography of Sedum lanceolatum (Crassulaceae) within the Rocky Mountain refugium to assess how this high-elevation plant responded to glacial cycles. We sequenced 884 base pairs (bp) of cpDNA intergenic spacers (tRNA-L to tRNA-F and tRNA-S to tRNA-G) for 333 individuals from 18 alpine populations. Our highly variable markers allowed us to infer that populations persisted across the latitudinal range throughout the climate cycles, exhibited significant genetic structure, and experienced cycles of range expansion and fragmentation. Genetic differentiation in S. lanceolatum was most likely a product of short-distance elevational migration in response to climate change, low seed dispersal, and vegetative reproduction. To the extent that Sedum is a good model system, paleoclimatic cycles were probably a major factor preserving genetic variation and promoting divergence in high-elevation flora of the Rocky Mountains.
Key Words: alpine • climate cycles • cpDNA • Crassulaceae • genetic diversity • historical biogeography • Quaternary • Rocky Mountain refuge • Sedum lanceolatum
During the long glacial episodes of the Quaternary (from two million years ago to the present) many taxa were restricted to one or a few regional refugia (Webb and Bartlein, 1992
; Hewitt, 1996
). Evidence from studies on European flora (reviewed in Taberlet et al., 1998
; Stehlik, 2000
) suggests that glacial refugia were located at the periphery of ice sheets (Tollefsrud et al., 1998
; Despres et al., 2002
; Holderegger et al., 2002
; Schönswetter et al., 2002
) and that some populations persisted on ice-free nunataks protruding above the glaciers (Stehlik, 2002
; Stehlik et al., 2002b
; Tribsch et al., 2002
; Schönswetter et al., 2003
). Though less information is available for North American taxa, several important Ice Age refugia have been proposed and supported empirically, including Beringia, the Rocky Mountains south of the southernmost extent of sheet ice, and coastal regions to the southeast and west of the ice sheets (Hultén, 1937
; Mooney and Billings, 1961
; Steinhoff et al., 1983
; Cwynar and MacDonald, 1987
; Sewel et al., 1996
; Soltis et al., 1997
; Comes and Kadereit, 1998
; Tremblay and Schoen, 1999
; Abbott et al., 2000
; Abbott and Brochmann, 2003
; Abbott and Comes, 2003
; Dobes et al., 2004
). Populations inhabiting the area of the Rocky Mountain glacial refugium harbor high levels of genetic variation, presumably because Pleistocene conditions promoted the persistence and differentiation of populations in this region (Golden and Bain, 2000
; Dobes et al., 2004
). These molecular studies corroborated previous findings from the pollen and plant macrofossil records, which revealed that as the climate warmed and ice receded, low-elevation plants expanded their ranges northward, while high-elevation taxa retreated upslope and that the response to climate change varied predictably between the Northern and Southern Rockies (Fall, 1997
; Vierling, 1998
).
The Rocky Mountains, south of the Laurentide and Cordilleran ice sheets, served as one of the most important glacial refuges for high-latitude and high-elevation flora in North America. Within this ice-free area, the Rocky Mountains are divided into three physiographic regions (Brouillet and Whetstone, 1993
): the Northern Rockies of Montana, the Central Rockies from Montana to the Wyoming Basin, and the Southern Rockies that extend from the Wyoming Basin south into New Mexico (Fig. 1). The Rocky Mountains comprise a topographically and climatologically heterogeneous cordillera along the Continental Divide with elevations ranging roughly from 1000 to 4000 m. Climate is highly variable due to topography, but in general the Northern Rockies receive moisture during winter from the northern Pacific while the Southern Rockies are more affected by subtropical summer monsoons (Thompson and Anderson, 2000
; Kittel et al., 2002
). At the time of the Last Glacial Maximum (about 18 000 yr ago), the Cordilleran and Laurentide Ice Sheets extended south into northern Montana, but the highest peaks rose above the ice as nunataks (Carrara, 1989
). Most of the central Rockies was covered by a 1000 m thick layer of ice (Pierce, 1979
) whereas in the south, mountain glaciers were more localized and not as continuous (Elias, 1996
).
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). During glacial periods, the alpine habitat was broadly distributed and interconnected, except for a discontinuity associated with the Wyoming Basin (Fig. 2A; Pewe, 1983
; Elias, 1996
). Interconnection during the glacial periods might have facilitated genetic and demographic cohesion across a broad geographic range. By contrast, contemporary surveys of the distribution of alpine habitat in the Rocky Mountains shows a highly dissected archipelago of habitat islands confined to high elevations (Fig. 2B; Küchler, 1985
). In the current interglacial, many populations of alpine species are isolated and probably exhibit different demographic characteristics.
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), little is known about how plant populations responded to the dynamic climatic history of the Pleistocene. Given the expanding/contracting response of the alpine tundra to climate change, as outlined above, we expected populations to have mixed during glacial periods and become isolated during interglacials. Overall, we predicted that these cycles would yield a high degree of genetic diversity within the region as found in other glacial refugia (Comes and Kadereit, 1998
), no loss of genetic diversity associated with increasing latitude because populations could have persisted across the range throughout the climate cycles, and high levels of genetic differentiation among populations due to isolation on sky islands during interglacials. Herein we adopted population genetic and phylogenetic approaches to evaluate the history of 18 alpine populations, ranging from northern Montana that was blanketed in sheet ice to southern Colorado where ice-free habitat existed throughout the climate cycles. MATERIALS AND METHODS
Study organism
After its initial discovery by the Lewis and Clark expedition, Sedum lanceolatum Torr. (Crassulaceae), the yellow stonecrop, was found to be widespread throughout the western cordillera of North America, ranging from New Mexico to Alaska (Clausen, 1975
). Plants are patchily distributed over a broad range of elevations, from 1700 m in the Great Plains to 4048 m in the alpine tundra of the Rocky Mountains. Sedum lanceolatum is a tufted, slow-growing, perennial herb that inhabits sandy soils and rocky outcrops of limestone, sandstone, marble, andesite, basalt, granodiorite, and granite (Clausen, 1975
). Yellow, pentamerous flowers, occurring in terminal cymes, are pollinated by a variety of insects, including Diptera, Hymenoptera, and Lepidoptera (Scott, 1973
; Clausen, 1975
), but self-pollination is possible (Clausen, 1975
). Although the small seeds (1.0 mm x 0.4 mm) generally drop to the ground and germinate, they are lightweight, and long-distance dispersal may occur (Clausen, 1975
). Vegetative reproduction occurs readily in S. lanceolatum when leafy rosettes separate from primary stems and take root (Clausen, 1975
). Within Sedum, hybridization is common. Diploid, tetraploid, and hexaploid populations of S. lanceolatum exist, but can be differentiated morphologically (Clausen, 1975
). Finally, though populations are generally large (Jolls, 1980
), population density, ratio of seedlings to adults, average number of leaves per rosette, height of inflorescence, and number of flowers per plant decrease with increasing elevation (Jolls, 1980
).
Sampling
Sedum lanceolatum was collected from 18 alpine sites throughout the Rocky Mountains, from southern Colorado, which was greatly impacted by mountain glaciers, to northern Montana where continental ice sheets buried the landscape but populations could have persisted on nunataks (Fig. 1, Table 1). All specimens were morphologically similar and we used this criterion to limit comparison to individuals with the same ploidy. At each location, leaves from approximately 20 spatially separated individuals were taken, for a total of 333 samples (Table 1). Seven of the collection sites were within national parks: Glacier National Park (permit # GLAC-2001-SCI-0020), Yellowstone National Park (permit # YELL-2001-SCI-0212), Grand Teton National Park (permit # GRTE-2001-SCI-0009), and Rocky Mountain National Park (permit # ROMO-2001-SCI-0037). Specimens were transported on dry ice and stored at –80°C at the University of Colorado, Boulder, Colorado, USA.
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) because in angiosperms, cpDNA is nonrecombinant, maternally inherited, dispersed via seed, permitting history to be separated from more recent gene flow due to pollen (McCauley, 1995
), and evolves at a rate that retains intraspecific patterns and processes (Palmer, 1987
; Comes and Kadereit, 1998
). We sequenced two intergenic spacers from the chloroplast genome: the noncoding regions between tRNA-L and tRNA-F (304 base pairs [bp]) and between tRNA-S and tRNA-G (580 bp), for a total of 884 bp. Amplification of the desired markers was accomplished by using specific primers for those regions: tRNA-L: (5'-ATTTGAACTGGTGACACGAG-3') and tRNA-F: (5'-GGTTCAAGTCCCTCTATCCC-3') (Fujii et al., 1999
) and tRNA-S: (5'-GCCGCTTTAGTCCACTCAGC-3') and tRNA-G: (5'-GAACGAATCACACTTTTACCAC-3') (Hamilton, 1999
). Each 50 µL reaction volume contained 2.25 mmol/L MgCl2, 0.02 mmol/L dNTPs, 0.05 mmol/L of each primer, 2.5 units of Promega (Madison, Wisconsin, USA) B Taq polymerase, Promega 10x reaction buffer, and approximately 100 ng of genomic DNA. The thermal cycler profile was one cycle at 96°C for 5 min, 40 cycles at 96°C for 45 s, 52°C for 1 min, 72°C for 1 min 30 s, and one extension cycle at 72°C for 7 min. Polymerase chain reaction (PCR) products were cleaned with ExoI-SAP (0.5 µL exonuclease I, 0.5 µL shrimp alkaline phosphatase; 37 for 15°C min and 85°C for 15 min). Forward and reverse strands were cycle sequenced with the same PCR primers, using BigDye Terminator version 3.1 Cycle Sequencing kit (Applied Biosystems, Hayward, California, USA). For the cycle sequencing reaction, the thermal cycler profile was 25 cycles at 96°C for 10 s, 50°C for 5 s, and 60°C for 4 min. Cycle sequence products were cleaned with Performa DTR 96-well Standard Plate Kit (Edge BioSystems, Gaithersburg, Maryland, USA). Sequencing was performed by the DNA Sequencing and Synthesis Facility at Iowa State University, Ames, Iowa, USA. Sequences were edited on Sequencher version 4.1.2 software (Gene Codes, Ann Arbor, Michigan, USA) and aligned with Clustal X (Thompson et al., 1997
). Because recombination is limited in the chloroplast genome (McCauley, 1995
), sequences from the two intergenic spacers were combined in all analyses. For all analyses, indels were considered to be a single polymorphic position (Widmer and Baltisberger, 1999
; Stehlik et al., 2002a
), unless sites within indels varied between haplotypes. In these cases, indels were reduced in length to the minimum number of polymorphic sites needed to represent the variation within the indel.
Analyses of genetic variation and population differentiation
Measures of within-population genetic variation and among-population genetic differentiation were estimated to test the predictions of the expansion hypotheses. Within population genetic diversity was estimated as the average pairwise nucleotide diversity (
) and based on the relationship between the number of segregating sites and the number of alleles sampled (
W). Linear regressions were performed using both estimators of to evaluate the relationship between latitude and genetic diversity (). In addition, regions with high levels of genetic variation were used to implicate the location of refugia (Comes and Kadereit, 1998
; Hewitt, 1999
). To test whether or not populations had been isolated on sky islands and to examine hierarchical population structure, we estimated the degree of differentiation among populations (FST) and performed an analysis of molecular variation (AMOVA). For the AMOVA, variation was partitioned at three levels: among northern, central, and southern biogeographic regions (Brouillet and Whetstone, 1993
); among populations within regions; and within populations. We also tested for isolation-by-distance following Rousset (1997)
using linear regression of standardized pairwise population FST [–FST/(1–FST)] on the logarithm of geographic distance. All calculations were performed on Arlequin version 2.0 (Schneider et al., 1997
).
Phylogenetic and nested clade analyses
Two approaches were taken to infer phylogenetic relationships among haplotypes. First, the intraspecific phylogenetic relationships among haplotypes was inferred using Bayesian posterior probabilities implemented with MRBAYES version 2.0 (Huelsenbeck and Ronquist, 2001
) using four-chain Metropolis-coupled Markov chain Monte Carlo (MCMCMC) analysis. Base frequencies were determined empirically and substitution rates and the gamma distribution were estimated. The first 400 000 generations were discarded as the "burn-in." Chains were sampled every 100 generations and inferences were based on a total of 5000 sampled trees. A consensus tree with posterior probabilites was generated in PAUP version 4.10b (Swofford, 2001
) from the base frequency, substitution rate, gamma distribution, and 5000 Bayesian trees.
We also used statistical parsimony (Templeton et al., 1992
), implemented on TCS 1.13 (Clement et al., 2000
), for estimating the relationships among haplotypes. The resulting genealogy was tested for geographic structure using nested clade analysis (NCA; Templeton et al., 1995
) implemented on GeoDis (Posada et al., 2000
). While NCA permits the examination of potential population processes underlying the geographic distribution of genetic variation (Templeton, 1998
), it is unable to statistically examine alternative inferences (Knowles and Maddison, 2002
), and thus caution is warranted when interpreting these analyses. The few studies of plant phylogeography that incorporated NCA support its utility in elucidating processes that have shaped genetic patterns when compared with more traditional approaches such as AMOVA (see Stehlik, 2002
; Dobes et al., 2004
).
RESULTS
Chloroplast sequence data
Approximately 304 bp of intergenic spacer between tRNA-L and tRNA-F and 580 bp between tRNA-S and tRNA-G were sequenced from 333 individual plants for a total of 884 bp of chloroplast intergenic spacer per sample (Genbank accession numbers: AY704273– AY704317 for tRNA-L to tRNA-F and AY704318–AY704362 for tRNA-S to tRNA-G). In surprising contrast to other studies that showed very low levels of sequence variation for cpDNA (e.g., Stehlik et al., 2002a
; Holderegger and Abbot, 2003
), 45 haplotypes were identified in S. lanceolatum. The sequence data revealed three indels, which varied in length from 1 to 7 bp, four regions of single nucleotide repeat length polymorphisms (strings of 6–7 A's, 13–18 A's, 8–10 T's, 7–10 T's, and 7–8 T's), and an additional seven variable sites. After converting the indels to one base substitution each, we described 20 variable sites for the 45 haplotypes, of which 16 sites were parsimony informative.
Population genetic analysis
The average pairwise nucleotide diversity within populations, , ranged from 0.0 to 4.6 (Table 1). We found no relation between genetic diversity, as measured by or W, and latitude (Table 1; for , r = 0.01, P = 0.96; for W, r = 0.01, P = 0.67). Moreover, estimates of genetic diversity were highly variable among sites at similar latitudes, but generally lower in the mid-latitudes around the Greater Yellowstone Ecosystem. The high levels of genetic variation associated with northern and southern regions suggest the presence of two refugia (Comes and Kadereit, 1998
). These findings on the distribution of genetic variation suggest that, generally, populations persisted across the latitudinal range sampled for this species throughout the climate cycles.
Several lines of evidence indicated that S. lanceolatum exhibited strong geographic structure. First, 39 out of 45 haplotypes (87%) were restricted to only a single locality (we refer to these haplotypes as private alleles) (Table 1). Second, nearly all pairwise population comparisons of FST were significant (not shown). Third, regression of FST/(1 – FST) against the logarithm of geographic distance showed a strong signal of isolation-by-distance (r = 0.21, P < 0.01). Finally, the results of the AMOVA (Table 2) were consistent with our other findings and showed significant genetic structure at all hierarchical levels. The majority of variation (52%) was explained by differences among populations within regions. Differences among northern, central, and southern regions explained 38% of the variation. Only 18% of the variation occurred within populations. Overall, the genetic structure and high degree of differentiation between populations suggests extremely low rates of gene flow among biogeographic provinces or among populations within regions and long-term isolation of high-elevation S. lanceolatum populations on multiple sky islands.
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The genealogy of S. lanceolatum haplotypes inferred using statistical parsimony (Fig. 3) included 28 unsampled, hypothetical ancestors in addition to the 45 sampled haplotypes. Only one haplotype (Y5) was broadly distributed. The deepest divergence between clades (clades 4-1 and 4-2) corresponded to populations north and south of the Wyoming Basin. The internal position of the geographically widespread haplotype implies that it is probably of ancestral origin, but we did not determine an ancestral root for the cladogram. Again, this disjunct distribution of haplotypes corroborates our AMOVA findings and implies long-term separation of northern and southern populations in two region-scale refugia and little gene flow among any sites.
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= 0.05 (boxes in Fig. 3 and all those shown in Fig. 4). Using Templeton et al. (1995)
inference key, we inferred that the history of S. lanceolatum included several cycles of fragmentation and range expansion (Table 3). In the north, range expansion (clade 4-1) was followed by restricted gene flow (clades 3-2) then range expansion again (clade 3-1, 2-4, 2-1) and finally more restricted gene flow (clade 2-2) and fragmentation (clades 1-1, 1-3). The southern clade was more influenced by restricted gene flow and fragmentation events (clades 4-2, 3-3, 2-9, 2-7), but did exhibit range expansion (clade 2-6) followed by a recent fragmentation event (clade 1-8). Overall, the north experienced oscillation between expansion and fragmentation or isolation of populations whereas the predominant inference in the south was one of fragmentation and isolation.
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Because of the large amount of variation observed in the cpDNA intergenic spacers of S. lanceolatum, we were able to discern a high level of geographic structure in this species. The chloroplast genome has historically been considered to exhibit low variation (Schaal et al., 1998
; reviewed in Widmer and Baltisberger, 1999
). Recently, however, several studies have found high levels of variation within chloroplast regions and that the degree of variation differs among taxa (Soltis et al., 1991
; Dobes et al., 2004
) and between markers within the genome (Gaut et al., 1993
; Gielly and Taberlet, 1994
; Widmer and Baltisberger, 1999
). Most of the variation occurs in large single-copy regions (Schaal et al., 1998
), as in our study. The few studies that used cpDNA sequence data from intergenic spacers (e.g., Fujii et al., 1999
; Dobes et al., 2004
) were highly successful at inferring the historic biogeography of a species in response to Quaternary climate change. Our cpDNA intergenic markers exhibited an unusually high level of sequence variation (2.26%) in comparison to other studies and permitted well-resolved inferences of the S. lanceolatum genealogy and genetic structure. Undoubtedly, S. lanceolatum is not alone in its rate of sequence evolution for cpDNA intergenic spacer regions, and increased sampling will most likely reveal that other species harbor extensive variation in cpDNA.
The Rocky Mountains south of the contiguous ice sheets is topographically and climatologically heterogeneous, with abrupt changes in elevation, resources, climate, and abundance of alpine habitat. The disjunct geography and topography of the Rocky Mountains suggest isolation between the northern and southern Rockies across the Wyoming Basin. Both climatic (low precipitation) and geographic (low elevation) barriers meet at approximately 42° N latitude on the Continental Divide. The Wyoming Basin has acted as a formidable barrier to gene flow between the north and south for high-elevation organisms (Noonan, 2001
; DeChaine and Martin, 2004
).
The genetic structure in S. lanceolatum implies that both climate and geography within the Rocky Mountains played major roles in shaping the distribution of genetic variation and historic biogeography of this species. A genetic split across the Wyoming Basin is immediately apparent from the data. The distribution of genetic diversity (Table 1), as measured by and W showed no relationship with latitude in S. lanceolatum, but rather revealed two centers of diversity within the region, demonstrating that populations persisted across the latitudinal range of the Rocky Mountain refugium throughout the paleoclimatic cycles. We also found that populations were highly differentiated, implying a low frequency of gene flow and long distance colonization, as expected (Van der Velde and Bijlsma, 2003
). Moreover, genetic diversity was structured at all hierarchical levels. While genetic divergence was strong among the northern, central, and southern regions, the greatest degree of differentiation occurred among populations within regions (Table 2). The signal of isolation-by-distance also implied limited gene flow among populations up and down the cordillera. The significant geographic structure associated with the intraspecific phylogeny for S. lanceolatum further illustrated northern and southern centers of diversity and long-term isolation of populations. Moreover, some of the highest levels of within-population genetic variation and an assortment of private alleles were observed for the most northern populations in Glacier National Park (Table 1), indicating that populations either persisted on the highest peaks, or nunataks, that protruded above glacial ice or that other local, peripheral refugia existed during the last glacial period.
Though high elevation species are expected to exhibit low levels of differentiation among populations due to population mixing during relatively long glacial periods (Winograd et al., 1997
), S. lanceolatum exhibited high levels of genetic differentiation. High-elevation populations could have remained isolated throughout the paleoclimatic cycles by migrating up- and downslope with little opportunity for interpopulation gene flow. Isolation of populations, whether on a chain of interglacial sky-islands or glacial nunataks within the confines of Cordilleran ice, could have led to genetic differentiation among populations. While downslope migration, expansion, and connection of previously fragmented habitat during glacial periods (or during interglacials for northern populations) might have promoted population admixture, which could lead to increased genetic diversity (Walter and Epperson, 2001
), population mixing could have been inhibited by the persistent presence of individuals at a site or within a region throughout the glacial cycles (Soltis et al., 1997
). This could account for the observed high frequency of private alleles and geographic structure in the haplotypes of S. lanceolatum. When populations receded upslope, and experienced another period of isolation, they likely became further differentiated, while preserving genetic variation across the species' distribution.
Historic events inferred through NCA revealed that northern clades were more affected by expansion events, while those in the south responded to fragmentation of habitat (Table 3, Fig. 3), which was probably due to differences in topography and the extent of ice. The south is more topographically heterogeneous and was not impacted by sheet ice, while the north experienced a higher degree of connectivity during glacial periods with more of an opportunity for gene flow and colonization of novel habitat. For the alpine tundra, population processes were probably uncoupled across the latitudinal range due to the varying effects of ice. During glacial periods, northern populations were probably isolated on nunataks or in peripheral refugia, while in the south populations broadened their ranges and became connected with downslope migration of alpine habitat. In contrast, glacial retreat probably served to connect the disparate northern populations, while interglacial warming marooned more southerly populations on fragmented sky islands.
Unfortunately, fossil pollen of alpine plant species is scarce and Sedum pollen has not been identified from glacial deposits or regions south of the ice sheets, so direct comparison with the palynological record is not possible. Nonetheless, our findings match palynological records for other high-elevation taxa in the Rocky Mountains, including elevational migration of the alpine tundra and treeline and a differential response of flora north and south of the Wyoming Basin (Whitlock, 1993
; Fall, 1997
; Vierling, 1998
).
The phenomenon of "chloroplast capture" cannot be ruled out as a factor affecting the geographic structure of haplotypes in our study. In the absence of reproductive barriers, interspecific gene flow can cause the introgression of one species' chloroplast into a population of another species with reticulation of chloroplast lineages but permanence of morphological traits (reviewed in Schaal et al., 1998
). Several examples have been documented, including sunflowers (Rieseberg et al., 1990
), poplars (Smith and Sytsma, 1990
), oaks (Whittemore and Schaal, 1991
), and the sister family to Crassulaceae, the Saxifragaceae (Soltis et al., 1991
). Members of the genus Sedum frequently hybridize (Clausen, 1975
) and thus chloroplast introgression is likely. For nearly all of our collecting sites S. lanceolatum was the only species of Sedum present. Nonetheless, comparisons with other co-distributed species in the genus are warranted.
Biogeographic responses of flora to recurrent cycles of climate change greatly impact the evolution of a species (Stebbins, 1984
) and that response is species dependent (Jackson and Overpeck, 2000
), based on seed-dispersal abilities, pollination strategies, life span, and whether the species is asexual, a self-pollinator, or outcrossing. Several life history traits in S. lanceolatum (Clausen, 1975
), including a long-lived perennial habit, slow growth, local outcrossing through insect pollination, vegetative reproduction, and limited or short-distance seed dispersal, undoubtedly influenced the high degree of isolation and spatial stability of this species. High levels of differentiation among regions without the loss of genetic variation is presumably due in part to long life span, vegetative propagation, and local selection (Hamrick and Godt, 1990
; Reisch et al., 2003
), in contrast to outcrossing plants (Hamrick et al., 1991
). The wide range of altitudes and soil types inhabited by S. lanceolatum suggests that localized adaptation may be contributing to the high genetic differentiation among sky island populations in this species.
Summary of conclusions
The expanse of the Rocky Mountain cordillera running south of the Pleistocene continental ice sheets has been a major influence on the evolution of plants in North America. Our inferences from the high-resolution cpDNA markers of S. lanceolatum suggest that high-elevation populations underwent extensive genetic divergence in response to habitat fragmentation associated with the paleoclimatic cycles. Not only was this region an important glacial refugium that preserved genetic diversity of arctic and alpine taxa throughout glacial periods, but its varied topography also promoted genetic differentiation of populations during warm interglacials.
FOOTNOTES
1 The authors thank Glacier National Park, Yellowstone National Park, Grand Teton National Park, and Rocky Mountain National Park for permission to collect plants. The work was funded by an NSF Doctoral Dissertation Improvement Grant, the University of Colorado, EPOB Graduate Student Research Grants and Fellowships, the Beverly Sears Graduate Student Grants, the John W. Marr Ecology Fund, the Indian Peaks Wilderness Association, Canon-National Parks Scholarships, the Edna Bailey Sussman Fellowship, and the Colorado Mountain Club Academic Fellowship, with additional support from the Southern Rockies Ecosystem Project. For help collecting specimens, we thank Gerald DeChaine, Mathew Burt, and Thomas Walla. We also thank Deane Bowers, William Bowman, Yan Linhart, Tom Veblen, and two anonymous reviewers for valuable discussions and feedback. 
4 Author for correspondence (dechaine{at}fas.harvard.edu
)
LITERATURE CITED
Abbott R. J C Brochmann 2003 History and evolution of the arctic flora: in the footsteps of Eric Hultén. Molecular Ecology 12: 299-313[CrossRef][Medline]
Abbott R. J H. P Comes 2003 Evolution in the Arctic: a phylogeographic analysis of the circumarctic plant, Saxifraga oppositifolia (Purple saxifrage). New Phytologist 161: 211-224[CrossRef][ISI]
Abbott R. J L. C Smith R. I Milne R. M. M Crawford K Wolff J Balfour 2000 Molecular analysis of plant migration and refugia in the Arctic. Science 289: 1343-1346
Brouillet L R. D Whetstone 1993 Climate and physiography. In Flora of North America North of Mexico Editorial Committee [eds.], Flora of North America, 15–46. Oxford University Press, New York, New York, USA
Carrara P. E 1989 Late Quaternary glacial and vegetative history of the Glacier National Park Region, Montana. U.S. Ecological Survey Bulletin No. 1902
Clausen R. T 1975 Sedum of North America north of the Mexican Plateau. Cornell University Press, Ithaca, New York, USA
Clement M D Posada K. A Crandall 2000 TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659[CrossRef][Medline]
Comes H. P J. W Kadereit 1998 The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science 3: 432-438[CrossRef][ISI]
Cwynar L. C G. M MacDonald 1987 Geographical variation of lodgepole pine in relation to population history. American Naturalist 129: 463-469[CrossRef][ISI]
DeChaine E. G A. P Martin 2004 Historic cycles of fragmentation and expansion in Parnassius smintheus (Papilionidae) inferred using mitochondrial DNA. Evolution 58: 113-127[ISI][Medline]
DeLorme. 1998a Colorado atlas and gazetteer. DeLorme, Yarmouth, Massachusetts, USA
DeLorme. 1998b Idaho atlas and gazetteer. DeLorme, Yarmouth, Massachusetts, USA
DeLorme. 1998c Montana atlas and gazetteer. DeLorme, Yarmouth, Massachusetts, USA
DeLorme. 1998d Wyoming atlas and gazetteer. DeLorme, Yarmouth, Massachusetts, USA
Despres L S Loriot M Gaudeul 2002 Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers. Molecular Ecology 11: 2337-2347[CrossRef][Medline]
Dobes C. H T Mitchell-Olds M. A Koch 2004 Extensive chloroplast haplotype variation indicates Pleistocene hybridization and radiation of North American Arabis drummondii, A. x divaricarpa, and A. holboellii (Brassicaceae). Molecular Ecology 13: 349-370[CrossRef][Medline]
Elias S. A 1996 The Ice Age history of national parks in the Rocky Mountains. Smithsonian Institution Press, Washington, D.C., USA
Fall P. L 1997 Timberline fluctuations and late Quaternary paleoclimates in the southern Rocky Mountains, Colorado. Geological Society of America Bulletin 109: 1306-1320
Fujii N K Ueda Y Watano T Shimizu 1999 Further analysis of intraspecific sequence variation of chloroplast DNA in Primula cuneifolia Ledeb. (Primulaceae): implications for biogeography of the Japanese alpine flora. Journal of Plant Research 112: 87-95[CrossRef][ISI]
Gaut B. S S. V Muse M. T Clegg 1993 Relative rates of nucleotide substitution in the chloroplast genome. Molecular Phylogeny and Evolution 2: 89-96
Gielly L P Taberlet 1994 The use of chloroplast DNA to resolve plant phylogenies: non-coding vs. rbcL sequences. Molecular Biology and Evolution 11: 769-777[Abstract]
Golden J. L J. F Bain 2000 Phylogeographic patterns and high levels of chloroplast DNA diversity in four Packera (Asteraceae) species in southwestern Alberta. Evolution 54: 1566-1579[ISI][Medline]
Hamilton M. B 1999 Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8: 513-525[CrossRef][Medline]
Hamrick J. L M. J. W Godt 1990 Allozyme diversity in plant species. In A. H. D. Brown, M. T. Clegg, A. L. Kahler, and B. S. Weir [eds.], Plant population genetics, breeding, and genetic resources. Sinauer, Sunderland, Massachusetts, USA
Hamrick J M. J. W Godt D. A Murawski M. D Loveless 1991 Correlations between species traits and allozyme diversity: implications for conservation biology. In D. Falk and K. E. Holsinger [eds.], Genetics and conservation of rare plants, 75–86. Oxford University Press, New York, New York, USA
Hewitt G 1996 Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58: 247-276[CrossRef]
Hewitt G 2000 The genetic legacy of the Quaternary ice ages. Nature 405: 907-913
Hewitt G. M 1999 Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society 68: 87-112[CrossRef][ISI]
Holderegger R R. J Abbott 2003 Phylogeography of the arctic-alpine Saxifraga oppositifolia (Saxifragaceae) and some related taxa based on cpDNA and ITS sequence variation. American Journal of Botany 90: 931-936
Holderegger R I Stehlik R. J Abbott 2002 Molecular analysis of Pleistocene history of Saxifraga oppositifolia in the Alps. Molecular Ecology 11: 1409-1418[CrossRef][Medline]
Huelsenbeck J. P F Ronquist 2001 MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755
Hultén E 1937 Outline of the history of arctic and boreal biota during the Quaternary Period. Lehre J. Cramer, New York, New York, USA
Jackson S. T J. T Overpeck 2000 Responses of plant populations and communities to environmental changes of the late Quaternary. Paleobiology 26: 194-220[CrossRef][ISI]
Jolls C. L 1980 Variation in the reproductive biology of Sedum lanceolatum Torr. (Crassulaceae) along an elevational gradient in the front range, Colorado. Ph.D. dissertation, University of Colorado, Boulder, Colorado, USA
Kittel T. G. F P. E Thornton J. A Royle T. N Chase 2002 Climates of the Rocky Mountains: historical and future patterns. In J. S. Baron [ed.], Rocky Mountain Futures, 59–82. Island Press, Washington, D.C., USA
Knowles L. L W. P Maddison 2002 Statistical phylogeography. Molecular Ecology 11: 2623-2635[CrossRef][Medline]
Küchler A. W 1985 National atlas potential natural vegetation. In National atlas of the United States of America. Department of the Interior, U.S. Geological Survey, Reston, Virginia, USA
McCauley D. E 1995 The use of chloroplast DNA polymorphism in studies of gene flow in plants. Trends in Ecology and Evolution 10: 198-202
Mooney H. A W. D Billings 1961 Comparative physiological ecology of arctic and alpine populations of Oxyria digyna. Ecological Monographs 31: 1-29[CrossRef]
Noonan G. R 2001 Systematics and cladistics of the North American subgenus Anadaptus Casey (Genus Anisodactylus Dejean) and a geographic information system analysis of the biogeography of included species. Annals of the Entomological Society of America 94: 301-332[CrossRef]
Palmer J. D 1987 Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. American Naturalist 130: S6-S29[CrossRef]
Pewe T. L 1983 The periglacial environment in North America during Wisconsin time. In S. C. Porter [ed.], Late Quaternary environments of the United States, 157–189. University of Minnesota Press, Minneapolis, Minnesota, USA
Pierce K. L 1979 History and dynamics of glaciation in the northern Yellowstone National Park area. U.S. Geological Survey Professional Paper 729-F
Posada D K. A Crandall A. R Templeton 2000 GeoDis: a program for the cladistic nested clade analysis of the geographic distribution of genetic haplotypes. Molecular Ecology 9: 487-488[CrossRef][Medline]
Reisch C P Poschlod R Wingender 2003 Genetic variation of Saxifraga paniculata Mill. (Saxifragaceae): molecular evidence for glacial relict endemism in central Europe. Biological Journal of the Linnean Society 80: 11-21
Reiseberg L. H S Beckstrom-Sternberb K Doan 1990 Helianthus annuus ssp. texanus has chloroplast DNA and nuclear ribosomal RNA genes of Helianthus debilis ssp. cucumerifolius. Proceedings of the National Academy of Sciences, USA 87: 593-597
Rousset F 1997 Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228[Abstract]
Schaal B. A D. A Hayworth K. M Olsen J. T Rauscher W. A Smith 1998 Phylogeographic studies in plants: problems and prospects. Molecular Ecology 7: 465-474[CrossRef]
Schneider S J Kueffer D Roessli L Excoffier 1997 Arlequin version 1.l: a software for population genetic data analysis. Genetics and Biometry Laboratory. University of Geneva, Geneva, Switzerland
Schönswetter P A Tribsch G. M Schneeweiss H Niklfeld 2003 Disjunctions in relict alpine plants: phylogeography of Androsace brevis and A. wulfeniana (Primulaceae). Biological Journal of the Linnean Society 141: 437-446
Schönswetter P A Tribsch G. M Barfuss H Niklfeld 2002 Several Pleistocene refugia detected in the high alpine plant Phyteuma globulariifolium Sternb. & Hoppe (Campanulaceae) in the European Alps. Molecular Ecology 11: 2637-2647[CrossRef][Medline]
Scott J. A 1973 Population biology and adult behavior of the circumpolar butterfly Parnassius phoebus (Papilionidae). Entomologia Scandinavia 4: 161-168
Scott R. W 1995 The alpine flora of the Rocky Mountains, vol. 1, The Middle Rockies. University of Utah Press, Salt Lake City, Utah, USA
Sewell M. M C. R Parks M. W Chase 1996 Intraspecific chloroplast DNA variation and biogeography of North American Liriodendron L. (Magnoliaceae). Evolution 50: 1147-1154[CrossRef][ISI]
Smith S. L K. J Sytsma 1990 Evolution of Populus nigra (sect. Aigeiros): introgressive hybridization and the chloroplast contribution of Populus alba (sect. Populus). American Journal of Botany 77: 1176-1187[CrossRef][ISI]
Soltis D. E M. A Gitzendanner D. D Strenge P. S Soltis 1997 Chloroplast phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution 206: 353-373[CrossRef][ISI]
Soltis D. E P. S Soltis T. G Collier M. L Edgerton 1991 Chloroplast DNA variation within and among genera of the Heuchera group (Saxifragaceae): evidence for chloroplast transfer and paraphyly. American Journal of Botany 78: 1091-1112[CrossRef][ISI]
Stebbins G. L 1984 Polyploidy and the distribution of the arctic-alpine flora: new evidence and a new approach. Botanica Helvetica 94: 1-13[ISI]
Stehlik I 2002 Glacial history of the alpine herb Rumex nivalis (Polygonaceae): a comparison of common phylogeographic methods with nested clade analysis. American Journal of Botany 89: 2007-2016
Stehlik I 2000 Nunataks and peripheral refugia for alpine plants during quaternary glaciation in the middle parts of the Alps. Botanica Helvetica 110: 25-30
Stehlik I F. R Blattner R Holderegger K Bachmann 2002a Nunatak survival of the high alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages. Molecular Ecology 11: 2027-2036[CrossRef][Medline]
Stehlik I J. J Schneller K Bachmann 2002b Immigration and in situ glacial survival of the low-alpine Erinus alpinus (Scrophulariaceae). Biological Journal of the Linnean Society 77: 87-103[CrossRef][ISI]
Steinhoff R. J D. G Joyce L Fins 1983 Isozyme variation in Pinus monticola. Canadian Journal of Forestry Research 13: 1122-1132
Swofford D. L 2001 PAUP*: phylogenetic analysis using parsimony (* and other methods), version 4.0b8a. Sinauer, Sunderland, Massachusetts, USA
Taberlet P L Fumagalli A.-G Wust-Saucy J.-F Cosson 1998 Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology 7: 453-464[CrossRef][Medline]
Templeton A. R 1998 Nested clade analysis of phylogeographic data: testing hypothesis about gene flow and population history. Molecular Ecology 7: 381-397[CrossRef][Medline]
Templeton A. R K. A Crandall C. F Sing 1992 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633[Abstract]
Templeton A. R E Routman C. A Phillips 1995 Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140: 767-782[Abstract]
Thompson J. D T. J Gibson F Plewniak F Jeanmougin D. G Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24: 4876-4882
Thompson R. S K. H Anderson 2000 Biomes of western North America at 18,000, 6000 and 0 14C yr BP reconstructed from pollen and packrat midden data. Journal of Biogeography 27: 555-584[CrossRef][ISI]
Tollefsrud M. M K Bachmann K. S Jakobsen C Brochmann 1998 Glacial survival does not matter. II. RAPD phylogeography of Nordic Saxifraga cespitosa. Molecular Ecology 7: 1217-1232[CrossRef]
Tremblay N. O D. J Schoen 1999 Molecular phylogeography of Dryas integrifolia: glacial refugia and postglacial recolonization. Molecular Ecology 8: 1187-1198[CrossRef][Medline]
Tribsch A P Schönswetter T. F Stuessy 2002 Saponaria pumila (Caryophyllaceae) and the Ice Age in the European Alps. American Journal of Botany 89: 2024-2033
Van der Velde M R Bijlsma 2003 Phylogeography of five Polytrichum species within Europe. Biological Journal of the Linnean Society 78: 203-213[CrossRef]
Vierling L. A 1998 Palynological evidence for late- and postglacial environmental change in central Colorado. Quaternary Research 49: 222-232
Walter R B. K Epperson 2001 Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations. Molecular Ecology 10: 103-111[CrossRef][Medline]
Webb III T P. J Bartlein 1992 Global changes during the last 3 million years: climatic controls and biotic responses. Annual Review of Ecology and Systematics 23: 141-173
Whitlock C 1993 Postglacial vegetation and climate of Grand Teton and southern Yellowstone National Parks. Ecological Monographs 63: 173-198[CrossRef][ISI]
Whittemore A. T B. A Schaal 1991 Interspecific gene flow in oaks. Proceedings of the National Academy of Sciences, USA 88: 2540-2544
Widmer A M Baltisberger 1999 Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure. Molecular Ecology 8: 1405-1415[CrossRef][Medline]
Winograd I. J J. M Landwehr K. R Ludwig T. B Coplen A. C Riggs 1997 Duration and structure of the past four interglaciations. Quaternary Research 48: 141-154[CrossRef][ISI]
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