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Population Biology |
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
Received for publication December 11, 2003. Accepted for publication July 2, 2004.
| ABSTRACT |
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Key Words: Astragalus conservation endemic Fabaceae genetic diversity Idaho, USA ISSR
| INTRODUCTION |
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Known populations of A. oniciformis are spread throughout Lincoln, northern Minidoka, and southern Blaine Counties, Idaho. However, in the eastern portion of its range, several populations are separated from the central populations by the Minidoka Flow, an inhospitable, 12.8 km wide, basaltic lava flow. This flow has been dated at 3600 yr (Moseley and Popovich, 1995
) and is too young for erosional or depositional processes to form suitable habitat for A. oniciformis. In the western portion of its range, two populations, located 9.39.6 km west of Shoshone, have not been relocated and their current status is unknown (Moseley and Popovich, 1995
).
Astragalus oniciformis is a prostrate, caulescent perennial herb that establishes in sandy areas (often disturbed) or sandy, aeolian pockets on basaltic lava flows (Barneby, 1964
). Throughout its range, it occurs with Artemisia tridentata Nutt. var. wyomingensis (Beetle & Young) Welsh and Hesperostipa comata (Trin. & Rupr.) Barkworth. Astragalus oniciformis is a short-lived perennial with populations that can vary dramatically between droughts and cool, wet, prolonged growing seasons. Spikes of recruitment followed by population decline make managing this species difficult. It prefers open, stabilized, sandy pockets (often previously burned), but it has never been found in unstable sand dune environments (Moseley and Popovich, 1995
; Popovich and Pyke, 1995
). These pockets overlie extensive basaltic lava flows. In the eastern portion of its range, A. oniciformis populations are found in aeolian deposits on and surrounded by basalt flows ranging in age from 3600 to 12 000 yr. These flows originated in the Craters of the Moon Lava Field (Moseley and Popovich, 1995
).
Habitat fragmentation and disturbance due to rangeland improvements can have major impacts on populations of A. oniciformis. The type and frequency of disturbance has had different effects on this taxon (Popovich and Pyke, 1995
). The long-term impacts of grazing have not been investigated; however, moderate grazing levels may not be detrimental. In a study assessing mortality after heavy trampling by livestock, initial direct damage to plants was high, but a majority appeared to recover during the next growing season, perhaps due to the heavy tap roots and low caudices characteristic of A. oniciformis. Recruitment at trampled sites was not different from that of untrampled areas nearby (S. Popovich and D. Pyke, United States Geological Survey Biological Resources Division [USGS-BRD], unpublished data).
In general, A. oniciformis can persist in areas that have been revegetated after fire by drill or aerial seeding to non-native grasses. These forms of range improvements are lighter disturbances than others that heavily disturb or "plow" the soil surface using an offset-disk range-plow. When compared to adjacent untreated areas over a two- or three-year period, A. oniciformis density and reproduction at revegetated sites using drill or aerial seedings were similar. However, the long-term effects of these range improvement techniques on A. oniciformis recruitment and persistence have not been investigated (Popovich and Pyke, 1995
; S. Popovich and D. Pyke, USGS-BRD, unpublished data).
Inter-simple sequence repeat (ISSR) markers were selected to determine the levels and distribution of genetic differentiation among populations of A. oniciformis. The ISSR markers have recently become widely used in population studies because they are highly variable; require less investment in time, money, and labor than other methods (Wolfe and Liston, 1998
; Harris, 1999
); and exhibit Mendelian inheritance (Gupta et al., 1994
; Tsumura et al., 1996
).
The ISSRs can generate higher percentages of polymorphic loci than other methods (Esselman et al., 1999
). Differences in levels of polymorphism can exist between ISSR and allozyme data (Esselman et al., 1999
), cpDNA restriction site analyses (King and Ferris, 2000
), random amplified polymorphic DNA (RAPD) data (Jain et al., 1999
), and amplified fragment-length polymorphism (AFLP) data (Arcade et al., 2000
). These can result in different estimates of diversity. Despite this, ISSRs have been as reliable and genetically informative as RFLP analyses (Nagaoka and Ogihara, 1997
; Huang and Sun, 2000
).
Typically ISSRs have been used in studies of cultivated species to produce genetic linkage maps (Kojima et al., 1998
; Cekic et al., 2001
) and to determine the relatedness of lines of agriculturally important species (de Oliveira et al., 1996
; Jain et al., 1999
; Chowdhury et al., 2002; Mondal, 2002
). The ISSRs have also been instrumental in determining variability and correcting misidentifications in large germplasm collections (Fang et al., 1997
; Gilbert et al., 1999
; Lanham and Brennan, 1999
; Charters and Wilkinson, 2000
).
The ISSRs have also been used to determine the genetic diversity of species of conservation concern (Esselman et al., 1999
; Camacho and Liston, 2001; McGlaughlin et al., 2002
; Smith and Bateman, 2002
), the origin of rare endemic taxa such as Sophora toromiro Skottsb. (Fabaceae; Maunder et al., 1999
), and the closest native species related to Ipomoea batatas (L.) Lam. (Convolvulaceae; sweet potato; Huang and Sun, 2000
). In other studies, ISSRs have been successful in distinguishing between subspecies of Plantago major L. (Plantaginaceae), a cosmopolitan species (Wolff and Morgan-Richards, 1998
), and in determining the levels of genetic variation between sympatric species of Alnus (Betulaceae) in Italy (King and Ferris, 2000
).
Several population-level studies have also used ISSR markers. In Calamagrostis porteri A. Gray subsp. insperata (Swallen) C. W. Greene (Poaceae), moderate genetic differentiation was found among populations (Esselman et al., 1999
). Comparatively, ISSR variability showed little genetic differentiation between populations of the rare variety Eriogonum shockleyi S. Watson var. packardae Reveal and the widespread var. shockleyi (Smith and Bateman, 2002
) and among populations of the self-fertilizing species, Botrychium pumicola Coville (Camacho and Liston, 2001
). In another study involving the rare taxon Abronia umbellata Lam. subsp. breviflora (Standl.) Munz (Nyctaginaceae), ISSR markers were useful in determining the genetic diversity of reintroduced Oregon populations (McGlaughlin et al., 2002
).
In this study, populations of A. oniciformis and A. mulfordae were sampled (1) to test the reliability of ISSR markers in populations of A. oniciformis and their utility among closely related species, (2) to examine the levels and distribution of intra- and interpopulational genetic variation of A. oniciformis, (3) to determine if several thousand years of geographic isolation induced significant genetic differentiation in the populations isolated by the rift lava flow (rift populations), and (4) to recommend conservation measures, based on results of the genetic analyses, that preserve the genetic integrity and diversity of this narrow endemic Astragalus.
| MATERIALS AND METHODS |
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Fifteen individuals from each population, for a total of 135 samples, were used for ISSR analyses. Individuals were randomly sampled from throughout the known geographic extent of each population. Additionally, individuals were sampled at least 10 m apart to minimize sampling of progeny. Between 20 and 80 mg of leaf material was collected from each individual. Leaf samples were air dried and then stored at 20°C until the DNA was extracted. Genomic DNA was extracted and purified using the DNeasy plant mini kit (QIAGEN, Chatsworth, California, USA). The ISSR reactions and polymerase chain reaction (PCR) protocols followed Camacho and Liston (2001)
. The PCR products were analyzed in 1.5% agarose gels and stained in an ethidium bromide solution on an orbital shaker.
Two samples from a single population were used for initial primer screening. Band sizes were estimated using a 100-base pair (bp) ladder (New England Biolabs, Beverly, Massachusetts, USA). Loci were named based on the primer used and estimated band size. Duplicate reactions were run for all ISSR analyses to determine the reproducibility of banding patterns. All genetic analyses were run on both primers separately and together to determine the contribution of each to the combined genetic results. Loci of band size lower than 400 bp were eliminated due to having an incomplete data set of these loci. Electrophoretic runs as long as 12 h at 70 V were needed to resolve these bands. Many of the first gels were run for only 33.5 h at 130 V. The longer runs were instituted so bands within 25 bp of each other would separate further to make scoring easier.
Bands were scored as present or absent (Fig. 2). The number of polymorphic loci, measures of the distribution of genetic diversity, Nei's genetic identity (h; 1973), and Shannon index of phenotypic diversity (I; King and Schaal, 1989
) were computed with PopGene32 (Yeh et al., 2000
), assuming all loci were dominant and in Hardy-Weinberg equilibrium. An unbiased genetic identity matrix (Nei, 1978
) was generated by PopGene32 and used to create unweighted pair-group method arithmetic average (UPGMA) and neighbor-joining (NJ) dendrograms using NTSYSpc 2.02 (Rohlf, 1997
). The deviation from Hardy-Weinberg expectations due to population subdivision (FST) and other estimates of population-level genetic differentiation were determined using a hierarchical analysis of molecular variance (AMOVA; Excoffier et al., 1992
) computed with Arlequin 1.1 (Schneider et al., 1997
), which assumes these data are haplotypic. For the estimation of genetic distances between populations, a pairwise population FST matrix was generated by Arlequin 1.1, and an unbiased genetic distance matrix (Nei, 1978
) was generated by PopGene32.
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Correlation between the pairwise FST and unbiased genetic distance matrices, between the pairwise FST and unbiased genetic identity matrices, and between Nei diversity (h) and Shannon diversity (I) were conducted in SYSTAT for Windows version 6.0 (SPSS, Chicago, Illinois, USA). All P values in statistical analyses were significant at the <0.05 level.
Estimation bias can lead to the overestimation of parameters by as much as 5% in the dominant marker data produced by RAPD and ISSR analysis (Lynch and Milligan, 1994
). To reduce this bias, Lynch and Milligan proposed pruning any locus with a band frequency of higher than 1 (3/N), where N is the number of individuals sampled. This pruning procedure was implemented with the A. oniciformis data set prior to the genetic analyses. Loci were tested for significant single population linkage disequilibria (Weir, 1979
) and Ohta's two-locus analysis of population subdivision (1982a, b; both tests for linkage disequilibria) using PopGene32.
| RESULTS |
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Significant linkage disequilibria occurred between locus 841775 and locus 841475 in A. oniciformis. Weir's significant single population linkage disequilibria (1979) and Ohta's two-locus analysis of population subdivision (1982a, b) showed significant linkage between these two loci. Based on these results, locus 841775 was deleted from all genetic analyses. Loci 841775 and 841475 were not linked in A. mulfordae.
For a locus to be pruned according to Lynch and Milligan (1994)
in the A. oniciformis ISSR data (N = 120), the frequency of the band had to be 0.975 or higher. Because no locus was present at a frequency higher than 0.88, the Lynch and Mulligan pruning procedure was not implemented.
The number of polymorphic loci within each population and their diversity indices varied depending upon whether the primers were analyzed separately or together. In a combined analysis (Table 3), population SD had the highest number of polymorphic loci, 28 (h = 0.1856, I = 0.2895). Populations MB and SB were the most depauperate, with 19 and 21 polymorphic loci, respectively (MB: h = 0.1412, I = 0.2182; SB: h = 0.1189, I = 0.1949). The analysis of primer 818 showed that DS had 23 polymorphic loci (h = 0.2339, I = 0.3596) and SD had 21 (h = 0.2043, I = 0.3145). Population LTR had the lowest, 14 polymorphic loci (h = 0.1396, I = 0.2172). The analysis of primer 841 showed that CBS and LTR both had nine polymorphic loci (CBS, h = 0.1545, I = 0.2571; LTR, h = 0.1421, I = 0.239). Populations DS, GR2, and MB had the lowest number of polymorphic loci, four (DS, h = 0.061, I = 0.1058; GR2, h = 0.0982, I = 0.1512; MB, h = 0.061, I = 0.1058).
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An NJ dendrogram of Nei's (1978)
unbiased genetic identity (not shown) grouped no populations separated by less than 25 km as most similar (unbiased genetic identity = 0.9691 0.9856). The result of nearby populations not being most similar was also found in a UPGMA (not shown) dendrogram. However, the NJ and UPGMA topologies were incongruent.
AMOVA analyses of the combined 818 and 841 data (Table 4) found that 88.69% of the variation was significantly attributed to the variation within populations (P < 0.001) and that differentiation between the rift populations and the western populations was not significant (P = 0.97). The results for the separate AMOVA analyses of primer 818 (88.64% of variation) and primer 841 (88.2% of variation) had nearly identical results.
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The GST values for the combined and separate analyses, are nearly identical to the FST values in the AMOVA analyses, between 0.112 and 0.118. An additional AMOVA analysis was performed on the combined A. oniciformis data and A. mulfordae data, testing whether a significant amount of variation was explained by groups of all A. oniciformis populations and a group of the single A. mulfordae population. A weakly significant (P = 0.1) 17.34% of the variation was explained by this grouping.
A Mantel test using geographic distance and Nei's (1978)
unbiased genetic distance matrix found a weakly negative correlation (t = 0.34809, P = 0.0780). Another Mantel test using the geographic distance matrix and pairwise FST genetic distance matrix found that they are not significantly correlated (t = 0.27905, P = 0.1135).
| DISCUSSION |
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Especially in studies with small sample sizes, dominant markers can lead to parameter estimation bias (Lynch and Milligan, 1994
; Isabel et al., 1999
). This bias cannot be corrected by increasing either the number of populations or the number of markers sampled (Isabel et al., 1999
). Pruning of dominant marker loci with high frequency proved to be the most effective means of reducing parameter estimation bias (Lynch and Milligan, 1994
; Isabel et al., 1999
). Parameter estimation bias can be reduced by the Lynch and Milligan (1994)
test, and because no bands in the A. oniciformis data were present at a high enough frequency to be pruned, this bias in these data is low. Also, the AMOVA procedure in Arlequin assumes the data are codominant and haplotypic. The ISSR data could cause bias in parameter estimation because ISSR markers are dominant and not haplotypic. In addition to the identical FST values and GST values, the topology of the UPGMA dendrograms of the pairwise FST and Nei's unbiased genetic distance were nearly identical, differing only in branch lengths and the grouping of the SB and SC populations. The significant correlation between the pairwise FST values (calculated by NTSYSpc) and the Nei's unbiased genetic distance values (calculated by PopGene32) is further evidence that bias was low in these data.
Violation of assumptions of software algorithms can also lead to inaccurate results. The analyses used in PopGene32 assume that all data are in Hardy-Weinberg equilibrium. Because no codominant ISSR locus was found and codominant data do not exist for A. oniciformis, the assumption that the data meet Hardy-Weinberg expectations could not be tested. The nearly identical FST values from the AMOVA analysis and the GST values from the PopGene32 analysis are evidence that potential problems arising from the violation of certain assumptions of the software did not occur. Inter-simple Sequence repeat studies generally use the same software algorithms and methodologies used in this study, but the ISSR data in very few of these studies are tested to determine the extent to which the potential violations bias the results. Multiple tests have been performed on our data, and bias has been found to be low.
Because RAPD and ISSR markers are sampled randomly from throughout the genome including nuclear and organellar DNA, these can produce problematic data sets due to the different population genetic histories of these regions (Harris, 1999
). In this study, two different primers were analyzed. The two ISSR primers (UBC-818, which had a highly polymorphic banding pattern, and UBC-841, which had a more monomorphic banding pattern) produced, in separate and combined analyses, nearly identical results. These results were verified in the AMOVA analyses, indicating this also was not a problem in these data. Overall, the data from populations of A. oniciformis demonstrate the robustness of ISSR markers.
Studies of other species of Astragalus using genetic methods such as isozymes, AFLPs, or RAPDs have yielded similar results as ISSR markers have in A. oniciformis and A. mulfordae. In an isozyme study among populations of various species of annual Astragalus, Liston (1992)
found that Nei's genetic identity did not fall below 0.961. The tight range of genetic identities (0.970.99) found in A. oniciformis with ISSR markers is on the high end of the range of values reported by Liston (1992)
.
The genetic identity of 0.95 between A. mulfordae and A. oniciformis is not unusual. Liston (1992)
found a genetic identity of 0.937 between A. breweri A. Gray, a species native to serpentine outcrops in the Coast Range of California, and A. tener A. Gray var. titi (Eastw.) Barneby, which is found in a single population on the Monterey Peninsula of California (Liston, 1992
). Like A. mulfordae and A. oniciformis, these two annual species are not sympatric. The genetic identity obtained in this study between A. mulfordae and A. oniciformis is likely to be inaccurate, because only one population was sampled. A more thorough sampling of populations of A. mulfordae will potentially provide additional loci in A. mulfordae that are currently only present in A. oniciformis, as well as additional loci unique to A. mulfordae.
Geologic features and habitat restrictions have been documented as instrumental in increasing population differentiation in species with limited distributions (Travis et al., 1996
). In Astragalus cremnophylax Barneby, a species native to Kaibab Limestone outcrops on the North Rim and South Rim of the Grand Canyon, genetic differentiation overall among the populations is high,
(an equivalent of FST) = 0.44 (Travis et al., 1996
), compared to A. oniciformis GST = 0.113. Gene flow (Nm) is limited for A. cremnophylax, between 0.2 and 0.4 migrants per generation. Gene flow has been proposed only to occur through pollinators because geographic barriers (the Grand Canyon) and habitat barriers (16 km of dense vegetation) prevent seed dispersal. The population sizes of A. cremnophylax ranged from two to 970 individuals, which makes this species extremely vulnerable to fluctuations in climate and habitat disturbance (Travis et al., 1996
). Astragalus oniciformis has a much wider, continuous distribution (over 80 km), larger population sizes (10 to >10 000) individuals, and higher estimates of gene flow (Nm = 3.913.93). The lack of genetic differentiation among populations, especially when compared to A. cremnophylax, is also evidence of potential gene flow throughout the range of this species.
A wide range of GST and FST values have been obtained in studies of species of Astragalus (Table 5). Liston (1992)
found that within annual species, GST values ranged from 0 to 0.725. The highest values were found in A. pauperculus Greene (0.775) and A. clarianus Jeps. (0.331), two species with narrow distributions in cismontane California. The widespread species had GST values between 0 and 0.254. The highest FST values in Karron et al. (1988)
were found in A. osterhouti (FST = 0.14), which in 1988 had a total of 1500 individuals restricted to three populations. Comparatively, A. pectinatus Douglas ex G. Don (FST = 0.02 and 0.05) and A. pattersoni A. Gray ex Brandegee (FST = 0.01) are widespread species with lower levels of genetic differentiation than observed in this study (Karron et al., 1988
). A
estimate of 0.44, found in A. cremnophylax (Travis et al., 1996
), is additional support that in Astragalus, genetic differentiation and possibly speciation can occur when population size decreases, gene flow decreases, and genetic differentiation among populations increases in endemic species with narrow distributions. Although A. oniciformis has a relatively narrow distribution, its large population sizes, numerous occurrences, and evidently high gene flow among populations has historically resulted in a low potential for genetic differentiation.
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The rift populations, GR2 and MB, are separated from all other populations by the 12.8 km wide, inhospitable Minidoka Flow (Moseley and Popovich, 1995
). The lack of genetic differentiation between these two populations and the western populations provides evidence that in A. oniciformis, either the rift populations are the result of two or more recent dispersal events or 3600 yr of separation has not caused significant genetic differentiation between the rift and western populations. Su et al. (2003)
found significant genetic differentiation between subpopulations of several insect-pollinated perennial taxa after only 600 yr of isolation caused by the Great Wall of China. The rift populations of A. oniciformis may not have been completely genetically isolated. Two or more dispersal events have likely occurred, because MB and GR have different levels of polymorphic loci, are not grouped as being similar in the UPGMA or NJ dendrograms, and have a genetic identity of 0.9824, a value in the middle of the range for this species.
Gene flow across this inhospitable boundary has not been completely ruled out because the life histories of the pollinators of A. oniciformis have not been studied (S. Popovich and D. Pyke, USGS-BRD, unpublished data). Popovich and Pyke (1995)
found two rare pollinators on A. oniciformis: Andrena nigerrima, a species not previously reported from west of the Rocky Mountains, and Calliopsis barri, a narrow endemic known only known from a few sites in the northern Great Basin and Columbia Plateau. These pollinators nest exclusively in lava flows and are sensitive to habitat modifications that lead to the loss of nesting microsites. Many of the largest and most genetically diverse populations of A. oniciformis are found in the vicinity of the Minidoka basalt flow. The smallest populations of A. onicifomis are far from even the smallest lava flows, suggesting a correlation between the pollinators and A. oniciformis that warrants further investigation (Popovich and Pyke, 1995
; S. Popovich and D. Pyke, USGS-BRD, unpublished data).
The lack of genetic differentiation among populations and the high level of gene flow within the range of A. oniciformis indicate that current threats to this species, plant community changes in the last 60 yr due to changing fire patterns, habitat alteration due to livestock grazing, and habitat loss due to past rangeland improvements (Moseley and Popovich, 1995
), have not affected the genetic diversity of this species in the short term. Genetic differentiation has not occurred despite these disturbances because of the high gene flow and the numerous, large populations characteristic of A. oniciformis. In addition, the seed bank for A. oniciformis can be potentially large (D. Pyke, USGS-BRD, personal communication), so if genetic differentiation were to occur, it could be several generations before genetic drift is detectable. The techniques in this study were not sensitive enough to detect any recent genetic drift in populations of A. oniciformis. Conserving the numerous, large populations throughout the range of this species and the smaller intervening patches would be one strategy that would help preserve the high gene flow among populations.
The populations located at Picabo (see Fig. 1) near the type locality and the populations along Silver Creek should not be selected as a seed source for habitat restoration or enhancement projects for other populations throughout the range of A. oniciformis. The low levels of polymorphism, low population sizes, and the higher potential for future genetic differentiation make these populations poor candidates. Populations within the continuous central and western range of this species are the best candidates for restoration and enhancement efforts. Any reintroduction efforts will require monitoring techniques similar to those employed by McGlaughlin et al. (2002)
to ensure that the new populations retain the genetic diversity of the founder populations.
Complete conversion of rangeland to non-native grass mixtures without native islands may have detrimental effects on this species by altering potential habitat and creating limits to gene flow. In one study comparing recruitment and persistence of A. oniciformis between disk-plowed and adjacent native sites, preliminary monitoring data show that overall retention of A. oniciformis was substantially greater in the native untreated sites compared to the plowed sites. This was due in part to high rates of initial adult mortality and lower rates of seedling survivorship in the disk-plowed sites. Astragalus oniciformis responds negatively to range conversion practices such as offset-disk range-plowing techniques that disturb the soil horizons with the objective to destroy and replace native vegetation (Popovich and Pyke, 1995
). Such techniques should be discouraged in general within the range of A. oniciformis and especially in the studied populations with high genetic diversity.
| FOOTNOTES |
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2 Present address: Arapaho-Roosevelt National Forests/Pawnee National Grassland, 240 West Prospect, Fort Collins, Colorado 80526 USA ![]()
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