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Genetics and Molecular Biology |
2Department of Ecology and Evolutionary Biology, Tulane University, 6823 St. Charles Avenue, New Orleans, Louisiana 70118 USA; 3Department of Biological Sciences, Loyola University, New Orleans, Louisiana 70118 USA
Received for publication January 7, 2003. Accepted for publication April 24, 2003.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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Key Words: Agrostis • bentgrass • geothermal • Gramineae • heat tolerance • Kamchatka, Russia • Lassen Volcanic National Park, California • Poaceae • thermal • Yellowstone Naitonal Park, Wyoming
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). Species in this genus are particularly known for their ability to form morphologically similar ecotypes in response to heavy metals and other unusual edaphic conditions (Jain and Bradshaw, 1966
; McNeilly, 1968
; Wu et al., 1975
; Hogan and Courtin, 1977
; Karataglis, 1980a
, b
; Archambault and Winterhalder, 1995
). Such Agrostis ecotypes are often inter-fertile, and cross-pollinating, but the selection pressure exerted by differing soil characteristics is great enough to maintain genetic differences between populations only meters apart. Based on experimental manipulations and field observations, Karataglis et al. (1980b)
and Archambault and Winterhalder (1995)
estimated that the formation of Agrostis ecotypes is rapid and probably frequent, with the same ecotype evolving independently in different locations.
Two Agrostis taxa in geothermally influenced habitats of Yellowstone National Park, Wyoming, USA, have geographic distributions that suggest ecotype formation in response to soil temperature extremes or unique soil chemistry (M. T. Tercek, personal observations). Agrostis rossiae Vasey is endemic to Yellowstone thermal areas (Swallen, 1948
), while Agrostis scabra Willdenow occurs both in thermal areas and in a variety of nonthermal habitats throughout the northern latitudes (Hitchcock, 1950
; M. T. Tercek, personal observations). The thermal form of A. scabra, despite keying out as A. scabra in the local floras, differs from the nonthermal form in its shorter stature (8–20 cm vs. 15–30 cm), more rapid growth, and annual habit, all characteristics shared with A. rossiae (Table 1). Agrostis rossiae can be distinguished from A. scabra by its compressed, rather than spreading panicle (Hitchcock, 1950
). In 1999, one of the present authors (M. T. Tercek) discovered that every Yellowstone thermal Agrostis population (A. rossiae as well as thermal A. scabra) is surrounded by a nonthermal A. scabra population that appears to be reproductively isolated from the adjacent thermal population by its later flowering time. Seeds of thermal Agrostis populations germinate from December to January, when all nonthermal areas of the park are covered with snow. The thermal plants are killed by rising soil temperatures in mid-June. Nonthermal A. scabra populations do not initiate new growth from their perennial roots until late June, when the snow has completely melted, and they flower in mid-July to mid-August. A number of populations were found to be growing around a relatively localized heat source (e.g., a single steam vent), and in these cases, the nonthermal population was distributed concentrically around the thermal population.
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; J. Whipple, National Park Service, personal communication). Dorn (1989)
reported that A. rossiae is restricted to the Upper Geyser Basin, where Old Faithful geyser is located. However, many more populations have since been found (M. T. Tercek, personal observation; J. Whipple, National Park Service, personal communication). Although there are many thermal areas in Yellowstone, A. rossiae and thermal A. scabra populations occur only in the western part of the park. In most cases, a particular thermal population consists of only one of those taxa, not both. The thermal habitats in which Agrostis taxa occur tend to be located on glacial deposits at a slightly higher elevation than nearby hot springs and consequently contain numerous fumaroles (steam vents) and relatively little geothermal water and are permeated by steam and other trace gasses, including hydrogen sulfide, which acidifies the soil (pH 3.0–4.5). These habitats are usually dominated by the moss Racomitrium canescens, and contain a heat-tolerant grass, Dichanthelium lanuginosum, and a small number of annual forbs.
Because of the consistent geographic association of the thermal and nonthermal populations, we initially hypothesized that the thermal populations may have arisen independently in each thermal area as an ecotype of nonthermal Agrostis scabra (Jain and Bradshaw, 1966
; McNeilly, 1968
; Wu et al., 1975
; Hogan and Courtin, 1977
; Karataglis, 1980a
, b
; Archambault and Winterhalder, 1995
). Preliminary greenhouse experiments showed that Agrostis rossiae, thermal A. scabra, and nonthermal A. scabra maintain their morphological differences (Table 1) when grown from seed in a variety of soils and under both hot and cold temperature extremes, suggesting that they are genetically distinct (M. T. Tercek, unpublished data). Furthermore, these taxa experience no reduction in seed set when their inflorescences are isolated from external pollen sources, suggesting that they are capable of self-pollination or are apomictic. The present study was part of a larger effort to determine the ecological and genetic factors contributing to the endemism of A. rossiae, the historical relationships between the thermal and nonthermal Agrostis populations, and whether or not ecotype formation is taking place in response to selection pressures imposed by the geothermal habitats. These questions have practical as well as theoretical interest: if A. rossiae is merely an ecotype of nonthermal A. scabra, it may not be worthy of conservation effort.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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), and A. scabra var. geminata was collected from a thermal plant community in the Boiling Springs Lake thermal area of Lassen Volcanic National Park, California, USA (Gillett et al., 1995
). Samples were collected over the entire geographic range of each population, with an effort to collect plants at least 1 m from each other. Because some populations were quite small, this was not always possible. Approximately 5–8 cm of leaf was collected from each plant and stored in silica gel until DNA was extracted. In addition to the field-collected plants, a single specimen was obtained from a thermal community located in the Valley of the Geysers, Kamchatka Peninsula, Russian Federation. Eight seeds from the latter specimen were propagated, and the progeny were identified as Agrostis pauzhetica Probatova, which is apparently endemic to that region (Probatova, 1984
). Agrostis scabra var. geminata and A. pauzhetica resemble thermal A. scabra, but they sometimes have awned lemmas. Voucher specimens for all taxa are deposited at the Tulane University herbarium (NO).
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. DNA samples were quantified with a spectrophotometer and diluted with TE (Tris-EDTA) buffer. Each 25-µL polymerase chain reaction (PCR) contained 10 mmol/L Tris-HCl, 50 mmol/L KCl, 0.8 mmol/L dNTPs; 1 unit Taq polymerase, 0.2 µmol/L primer, 3 mmol/L MgCl2, and approximately 2 ng of template. The PCR reactions were treated for 3 min at 94°C, followed by 40 cycles of 1 min at 94°C, 1 min at 40°C, and 1 min at 72°C, followed by a final extension step of 15 min at 72°C (Golembiewski et al., 1997
). Amplifications were resolved on a 1.5% agarose gel (150 V for 5 min, followed by 100 V for 2 h) and stained with ethidium bromide. Forty random decamer primers (RAPDs primers 701–740, University of British Columbia, Vancouver, British Columbia, Canada) were screened and four were chosen for their repeatability and quality of staining (primers 702, 713, 719, 721).
The scoring of each individual was based on at least two separate PCR reactions. The NTSYSpc 2.1 genetics package (Rohlf, 2000
) was used to produce UPGMA phenograms of all individuals, using the Jaccard, Simple Matching, and Dice similarity coefficients. Population gene frequencies were calculated using the methods of Lynch and Milligan (1994)
, and NTSYSpc was used to produce population-level UPGMA phenograms based on Nei's (1978)
unbiased genetic distance, which is suitable for small population sizes. The UPGMA phenograms based on other similarity measures had the same topology (not shown). The population-level data were also visualized with the principal components analysis module of NTSYSpc. The FREETREE program (Pavlicek et al., 1999
) was used to produce 500 bootstrap pseudoreplicates of the population-level data and to calculate the level of confidence that could be assigned to each cluster in the original UPGMA phenogram.
The Arlequin genetics package (Schneider et al., 2000
) was used to perform an analysis of molecular variance (AMOVA), which uses bootstrapped permutations of the data to test an hypothesized population genetic structure. Arlequin's AMOVA module was configured to test five different hypothesized population structures. The first hypothesis treated A. rossiae, thermal A. scabra, Kamchatka thermal Agrostis (A. pauzhetica), and Lassen thermal Agrostis (A. scabra var. geminata) as separate operational taxonomic units (OTUs). The other three hypotheses combined the thermal populations into successively larger OTUs, and the final hypothesis grouped the thermal populations with nonthermal A. scabra, which was determined by the UPGMA to be most closely related to the thermal populations. Because the AMOVA tests for levels of differentiation among groups of taxa, A. idahoensis, A. exarata, and A. variabilis were also included in the analysis as outgroups because the principal components analysis indicated that they were more closely related to the thermal cluster than other sampled taxa (Table 4). The AMOVA procedure also provides estimates of the population differentiation statistic, FST, which is calculated as the percentage of the bootstrapped variation that is not partitioned within the populations (Excoffier et al., 1992
). These AMOVA FST estimates were compared to GST values calculated following the methods of Nei (1973)
, which is equivalent to FST when there are only two alleles possible (Nei, 1973
). Culley et al. (2002)
have shown that the GST of Nei (1973)
is not always comparable to the GST used in the widely cited review by Hamrick and Godt (1989)
. We chose Nei's formula because it is used more frequently in the literature (Culley et al., 2002
) and can be directly compared to the recent review of RAPDs studies by Nybom and Bartish (2000)
. In the Nei (1973)
method, the values of total expected heterozygosity (Ht) for a taxon and within-population heterozygosity (Hs) are averaged over all polymorphic loci and then entered into the formula GST = (Ht – Hs)/Ht, where Hs = 1/L 
1 – pi2 – qi2, pi is the frequency of the amplified allele at the ith locus in a population, qi is the frequency of the null allele for the ith locus, and L is the number of loci.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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unbiased similarity), and the UPGMA of all 374 individuals had the same topology as the UPGMA of the population-level data, with individuals from each population grouping together (not shown). Furthermore, a population-level UPGMA using raw RAPDs band frequencies (percentage of occurrence of each band in each population) was identical to one in which gene frequencies were calculated using the methods of Lynch and Milligan (1994)
, which correct for the dominance of RAPDs bands.
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formula (Table 3). With one exception (populations MAR and PSAR.2, where FST = 0), fixation indices calculated by Arlequin between all possible pairs of populations ranged between 0.69 and 0.99, and they were all significantly nonzero (data not shown). |
DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). In Lassen Volcanic National Park, California, this thermal taxon is called A. scabra var. geminata (Gillett et al., 1995
), and in Kamchatka, it is called A. pauzhetica (Probatova, 1984
). The same grouping of all thermal plants was obtained when the data were analyzed at the population and individual levels; the individuals from each population all clustered together as discrete groups. Contrary to our original hypothesis, the thermal populations do not appear to be independently evolved ecotypes of parapatric, nonthermal A. scabra. There is no relationship between geographic proximity and the genetic distance between thermal and nonthermal populations. Instead, the UPGMA shows that all nonthermal A. scabra populations, as a group, are distantly related to the thermal taxa. Indeed, the fact that nonthermal A. scabra did not plot any nearer to the thermal taxon than did A. exarata, A. idahoensis, or A. variabilis on the principal components analysis (Fig. 2), combined with the low bootstrap support for its UPGMA clustering with the thermal populations, suggests that nonthermal A. scabra may not be the sister taxon of the thermal populations. It is possible that the nonthermal sister taxon of the thermal populations was not included in the present study but may be found near other sites of thermal activity in the Pacific ring, where Agrostis species have been reported to occur, e.g., the Aleutian Islands or Big Windy Preserve, Alaska, USA (Juday, 1998
).
Agrostis rossiae and thermal A. scabra are intermingled on the UPGMA, despite the fact that they maintain separate morphologies (Table 1) when grown under uniform conditions (M. T. Tercek, unpublished data). The low bootstrap values assigned to the terminal branches of the thermal portion of the UPGMA indicate that our data set do not support any definite conclusions regarding the separation of these two taxa. This result could be explained by a possibly recent divergence of A. rossiae and thermal A. scabra or by continued hybridization between the two. With regard to the first possibility, it is well known that gene trees do not always agree with species trees (Avise, 1989
; Maddison, 1997
). The markers used in the present study may be too conservative to resolve such recently diverged populations. With regard to the second possibility, no morphological hybrids of A. rossiae and thermal A. scabra have been observed. However, even if infrequent hybridization was occurring, it is possible that morphological differences may be maintained by natural selection despite the detection of gene flow by neutral markers (Nesbitt et al., 1995
; Harrison et al., 1997
; Olfelt et al., 2001
). Agrostis rossiae and thermal A. scabra do have mostly separate geographical distributions, which could reflect a difference in habitat requirements. Agrostis rossiae is restricted to the vicinity of the Firehole River drainage, while thermal A. scabra occurs primarily north and south of this area. Laboratory experiments have shown that they differ in tolerance to soil acidity (M. T. Tercek, unpublished data). However, transplantation experiments have shown that A. rossiae and thermal A. scabra both survive to maturity in each other's habitat, and the population differentiation indices (FST, GST) suggest that there is low gene flow between Agrostis populations. Our Nei (1973)
GST values of 0.8011–0.9400 (Table 3) were higher than those reported for self-pollinating taxa (0.7) by Nybom and Bartish (2000)
, and the AMOVA-derived FST values calculated between all possible pairs of populations (Fst = 0.69–0.99, data not shown) indicate that gene flow seldom occurs between thermal Agrostis populations that are in some cases only meters apart. These findings contradict Despain's (1990)
speculation that seed dispersal among A. rossiae populations is frequently achieved by ungulates that migrate between Yellowstone's thermal areas during the winter, but these findings do agree with experiments that suggest A. rossiae and thermal A. scabra are self-pollinating or apomictic, having no reduction in seed set when isolated from external pollen sources (M. T. Tercek, unpublished data). Preliminary attempts to cross-pollinate A. rossiae and thermal A. scabra were unsuccessful, but more rigorous experimentation is needed before a definite conclusion can be reached.
Self-pollination is also consistent with the low within-population heterozygosities found for the thermal Agrostis taxa (A. rossiae = 0.0114, thermal A. scabra = 0.0097). These values are even lower than the mean cited for self-pollinating taxa (0.091) by Nybom and Bartish (2000)
. However, the nonthermal taxa in our study had similarly low heterozygosities (Table 3), consistent with results reviewed by Gitzendanner and Soltis (2000)
, who found a correlation between diversity estimates in rare species and their widespread congeners. The low genetic diversity found in this study is therefore not likely due to the small population sizes of the thermal taxa, but instead to something that is shared by other members of the genus, e.g., self-pollination. James and Brown (2000)
reported similar within-population heterozygosity (0.0053–0.0224) for the Australian endemic A. adamsonii.
The AMOVA showed that grouping all the thermal populations together in a single OTU produces a situation in which there is more variation partitioned among the OTUs than within them (Table 4). Splitting this hypothesized thermal OTU into its component parts does not greatly change the partitioning of variation, but grouping it with its closest relative, nonthermal A. scabra, increases the variation within OTUs from 35% to 46% (Table 4). It therefore seems reasonable to consider all the thermal populations as a single taxonomic unit that is separate from nonthermal A. scabra. Olfelt et al. (2001)
used an AMOVA to reach a similar conclusion in their delineation of Sedum taxa.
The phenogram presented here (Fig. 1) may serve as a working hypothesis of the historical relationships among the study taxa until data from more explicitly phylogenetic methods become available. Cladistic methods are often considered preferable to phenetic methods for hypothesizing historical relationships (Li, 1999
), and some authors have pointed out that RAPDs bands may not always be homologous among taxa (e.g., Rieseberg, 1996
). However, the results of the present study corroborate the morphological taxonomic work of Bjorkmann (1960)
and Carlbom (1968)
in their separation of taxa that possess a palea (A. capillaries, A. humilis, and A. thurberiana) from those that do not, and they confirm the grouping of A. mertensii with nonthermal A. scabra, which could be predicted from their morphological similarity (M. T. Tercek, personal observation). More generally, several authors have found RAPD-based phenograms to be similar to trees produced by other methods, including morphological cladistics (e.g., James and Brown, 2000
; Fjellheim et al., 2001
; Olfelt et al., 2001
), inter-simple sequence repeats (ISSR) (Ayres and Strong, 2001
), restriction fragment length polymorphisms (RFLP) (Nocelli et al., 1999
), and isozymes (e.g., Sun and Wong, 2001
).
In conclusion, RAPD data suggest that thermal Agrostis populations of North American and Kamchatka, regardless of their geographic location, are historically related and may comprise a monophyletic taxon, although explicitly cladistic methods, based on other characters, should be used to confirm this conclusion. Field botanists and systematists should be aware that nonthermal A. scabra can be easily confused with thermal A. scabra (Hitchcock and Cronquist, 1973
; Dorn, 2001
), but they can be distinguished morphologically (Table 1). Additional research is needed before the thermal populations can be given taxonomic rank. In particular, it is important to verify the apparent consanguinity of A. rossiae and thermal A. scabra. Because they are morphologically distinct, appear to be autogamous, and probably do not hybridize in the field, they are best treated as separate species until more information is available.
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FOOTNOTES |
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LITERATURE CITED |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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