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(American Journal of Botany. 1999;86:669-676.)
© 1999 Botanical Society of America, Inc.

High population differentiation and genetic variation in the endangered Mexican pine Pinus Rzedowskii (Pinaceae)1

Patricia Delgado, Daniel Piñero2, Alvaro Chaos, Nidia Pérez-Nasser and Elena R. Alvarez-Buylla

Departamento de Ecología Evolutiva Instituto de Ecología, Universidad Autónoma de México, Apartado Postal 70-275, México D. F., 04510 México

Received for publication January 19, 1998. Accepted for publication September 16, 1998.


    ABSTRACT
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Pinus rzedowskii is an endangered pine species from Michoacán (central México), which has been previously reported from only three localities. Classified within the subgenus Strobus, it exhibits intermediate morphological characters between subgenera Strobus and Pinus. We analyzed genetic aspects that could shed light on the evolution and conservation of this species. The genetic structure of nine populations was examined using 14 isozyme loci. Pinus rzedowskii has a relatively high level of genetic variation with 46.8% of the loci assayed being polymorphic, a total of 35 alleles, and a mean heterozygosity per population of 0.219. We calculated Wright's FST statistic to estimate gene flow indirectly and to evaluate whether or not there was genetic structuring among populations. We found a marked differentiation among populations (FST = 0.175) and significant inbreeding (FIS = 0.247). No pattern of isolation by distance was found. We also constructed a dendrogram based on a genetic distance matrix to obtain an overview of the possible historical relationships among populations. Finally, we found a convex relationship between the genetic distance among populations and the number of ancestral lineages, suggesting that demographically this species has not been at risk recently. Although endangered, with small and fragmented populations, P. rzedowskii shows higher levels of genetic variation than other conifer species with larger populations or similar conservation status.

Key Words: conservation • gene flow • genetic structure • Pinaceae • Pinus rzedowskii.


    INTRODUCTION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Most conifers have high levels of genetic variation, as inferred from isoenzymatic markers (O'Malley, Allendorf, and Blake, 1979 ; Yeh and Layton, 1979 ; Yeh and El-Kassaby, 1980 ; Yeh and O'Malley, 1980 ; Weber and Stettler, 1981 ; Guries and Ledig, 1982 ; Hiebert and Hamrick, 1983 ; Ledig and Conkle, 1983 ; Furnier and Adams, 1986 ; Li and Adams, 1989 ; Merkle and Adams, 1987 ; Ledig, 1998 ), and relatively little genetic differentiation among populations ( <15%; Ledig, 1998 ). However, most studies have focused upon wide-ranging species and less attention has been paid to species with fragmented and restricted distributions and small population sizes (Szmidt, 1982 ; Ledig and Conkle, 1983 ; Mejnartowicz and Bergmann, 1985 ; Niebling and Conkle, 1990 ). The common explanation for the low genetic differentiation found in conifer species is based on the reproductive systems particular to this group: in most conifers, seed and pollen are wind dispersed and this allows a more efficient gene flow among distant populations. However, this pattern can be modified by other factors, such as environmental fluctuations, historical events, and microspatial habitat selection (Hamrick and Godt, 1990 ).

Here, we present a study on the levels of genetic variation in and patterns of genetic differentiation among populations of Pinus rzedowskii (Madrigal et Caballero), an endangered species from Michoacán, México. Our goal was to provide baseline information for this conservationally important and morphologically intriguing species (Madrigal and Deloya, 1969 ; Delgado, 1997 ). Pinus rzedowskii is represented by small populations, its distribution is extremely restricted and fragmented, and it is listed as an endangered species (Mexican government order, NOM-PA-CRN-001/93). Pinus rzedowskii exhibits traits representative of both subgenera Strobus and Pinus: dorsal umbo, winged seeds, and wood anatomy typical of hard pines; number and position of resin canals, resin secondary compound composition and wood composition typical of soft pines (Madrigal and Deloya, 1969 ; Perry, 1991 ). Finally, the small population sizes of this species and extremely restricted and fragmented geographic distributions offer an excellent opportunity to determine whether the quantity and distribution of genetic variation are related to population size and degree of isolation. We expected P. rzedowskii populations to show low levels of genetic variation and low population structuring. The results are surprising, however, in that P. rzedowskii is not genetically impoverished and shows a marked genetic structure. Furthermore, historical demography results strongly suggest that population densities of this endangered pine have been increasing steadily.


    MATERIALS AND METHODS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Study area
The study area (in the Sierra Madre del Sur mountain range; Fig. 1) belongs to the Municipio of Coalcomán, Michoacán, México. It is located between 102°55' and 103°00' longitude West and 18°54' and 18°39' latitude North. Three of the study sites correspond to those described previously (Madrigal and Deloya, 1969 ; Farjon and Styles, 1997 ). These are SOL3, CHI6, and PIN8 (Table 1). There are a total of 12 populations in an approximate area of 1.6 million ha. Of these, four have very low densities (SOL3, TEJ10, DUR11, and TAB12; Table 1) and of these only SOL3 was included in this study. Mean annual rainfall is 1500 mm, mainly between July and October. Average annual minimum and maximum temperatures are -5° and 30°C, respectively. Pinus rzedowskii populations have only been found on cambisol soils (~160 ha). These soils are poorly developed, with a subsoil layer that is more like a rock layer and an accumulation of materials such as clay, iron, and manganese. The topography is very rugged, with slopes from 85° to 90°. Vegetation types are wide ranging, with pine-oak, oak, subdeciduous, and deciduous tropical forest. However, most of the area is covered with pine-oak forest.



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Fig. 1 Known localities for P. rzedowskii in México. Population codes used are as in Table 1 .

 

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Table 1. Localities and densities of Pinus rzedowskii populations (Michoacán, México). All populations except TEJ10, DUR11, and TAB12 were used for genetic analysis. Approximate total number of P. rzedowskii = 6000–6500 individuals.

 
P. rzedowskii usually grows in patches alongside populations of P. herrerai, P. michoacana, P. pseudostrobus, P. oocarpa, and P. leiophylla. All these species belong to the subgenus Pinus (hard pines; Critchfield and Little, 1966) and P. rzedowskii is the only species found in the region that belongs to the subgenus Strobus (soft pines; Madrigal and Deloya, 1969 ). It is also one of only two soft pine species that have been described for the state of Michoacán, the other being P. ayacahuite var. veitchii. Pinus rzedowskii trees range in height from 15 to 50 m, with irregular treetops, diameters of up to 120 cm and a dark bark, 3-6 cm thick (Delgado, 1997 ).

Sample collection
Primary growth branches with developing buds were collected and kept in polyethylene sealed bags in ice. In the laboratory, a replicate from each individual was stored in a cold room at 4°C and another one was kept in an ultrafreezer at -70°C. Three hundred and ten individuals (6-200 yr old) were sampled (Table 2). Samples were obtained from nine populations (excluding DUR11, TEJ10, and TAB12; Table 1) clearly restricted to patches of limey soil. Due to the terrain's rugged topography, a single sampling strategy was unwarranted. Three kinds of sampling schemes were followed, according to local conditions: in most populations an altitudinal transect was made from the upper part of a slope towards the lower part of the distribution area. Population ALB5 (Table 1) was sampled at five points in the population's margins and one in the middle, as this population was more readily accesible. In sparser populations, such as CHI6 and SOL3, all individuals were sampled.


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Table 2. Levels of allozyme variation within nine populations of P. rzedowskii from Michoacán, México (standard errors are shown in parentheses). Population codes are as in Table 1.

 
Electrophoresis
Buds 1-2 cm long were ground in a mortar using an extraction buffer with three parts Veg II buffer (Cheliak and Pitel, 1984 ) and one part Yeh and O'Malley's buffer (1980 ). The extract was absorbed into chromatography paper wicks, which were put in Eppendorf tubes and stored in an ultrafreezer at -70°C for later use. Gels were prepared with 12% w/v hydrolyzed starch. Three buffer systems (Miles et al., 1977 ; Mitton et al., 1977 ; Conkle et al., 1982 ) and 12 enzymes with good resolution were used. A total of 14 loci were analyzed. Staining recipes were from Hakim-Elahi (1981) for APX-1, APX-2, and CPX-2, Conkle et al. (1982) for MNR-1 and GDH-2, Soltis et al. (1983) for EST-2 and F-EST-2, Werth, Karlin, and Guttman (1982) for LAP-1, and Selander et al. (1986) for IDH-2. Loci and alleles were designated based upon relative protein mobility. Loci marked with number 1 are those farthest from the cathode.

Data analyses
All estimates were made based on nine polymorphic loci and five monomorphic ones. We obtained allele and genotypic frequencies, genetic identities, and distances following Nei (1975) and fixation indices for each locus and population following Wright (1965) .

Wright's F statistics as well as 99% confidence intervals of their mean values were obtained by bootstrapping over loci for the multilocus estimates and jackknifing over populations for the single-locus estimates (Weir and Cockerham, 1984 ; Alvarez-Buylla et al., 1996a ). To find out whether FIS and FIT values for each locus were significantly different from 0, the statistic {chi}2 = F (2N) (K-1) was obtained with K(K-1)/2 degrees of freedom and where N is the sample size (number of individuals) and K the number of alleles (Li and Horvitz, 1953 ). To determine the significance of FST values per locus, the statistic {chi}2 = (2N) FST(K-1), with (K-1)(s-1) degrees of freedom was used, where s is the number of subpopulations (Workman and Niswander, 1970 ). Gene flow (Nm) estimation was made indirectly using the formula proposed by Crow and Aoki (1984) . Mean Nm value was used to obtain indirect estimates of effective population size per neighborhood (Nb; Slatkin and Barton, 1989 ). Isolation by distance was analyzed with the method proposed by Slatkin (1993) based on an island population structure model. The statistic M = (1 / FST - 1/4) was used in which population pairs with restricted dispersal and in genetic equilibrium would show lower M ratios and where FST are estimates for each pair of populations (Slatkin, 1993 ; Alvarez-Buylla and Garay, 1994 ). The Mantel statistic with 1000 permutations was used to test for significance of the isolation by distance pattern (Rohlf, 1993 ). To describe the genetic relationships among populations, dendograms (UPGMA [unweighted pair group method with arithmetic mean]; Sneath and Sokal, 1973 ; neighbor-joining; Swofford and Olsen, 1990 ) were obtained using the matrix of genetic distances. The reconstructed tree was used to describe the demographic status of the species as proposed by Moritz (1996) for conservation studies. This method is easily applied if phylogenetic relations among populations can be established. It is based on the idea that expanding populations are expected to show a star-like phylogeny that would result in a parabolic relation between the genetic distance, as an estimate of time of divergence, and the logarithm of the number of lineages following the UPGMA analysis. On the contrary, stable populations would show a strongly structured phylogeny and would result in an exponential relationship.


    RESULTS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Variation and genetic structure
Seventeen enzymes were originally assayed, five of which did not show activity. For the 12 remaining enzymes, 14 presumptive loci were resolved. Enzymes APX and EST showed two loci each. From the total of 14 loci analyzed, nine were polymorphic according to the criteria of the most common allele having a maximum frequency of 0.95 (Table 2). There was an average of 1.8 alleles per locus (range, 1.6-2.4 alleles). Percentage of polymorphic loci per population varied from 37.5% (SOL3) to 64.3% (CHI6), with a mean value of 46.8%. Observed heterozygosity varied from 0.129 (VAR7) to 0.239 (VP11), with an average of 0.162, and expected heterozygosity from 0.183 (PVA2) to 0.304 (CHI6), with an average of 0.219.

Two alleles were found for loci Apx-1, Cpx-1, Lap-1, Idh-2, and Gdh-2, four alleles for loci Apx-2, Est-2, and Sdh-2, and five alleles for locus Got-1. Allele frequencies were significantly different among populations using a multiple comparisons G test (Sokal and Rohlf, 1981 ; data not shown). Twenty-eight out of 59 fixation indices were significantly different (P < 0.05; data not shown) from those expected under Hardy-Weinberg equilibrium. Twenty-four of these indices were positive. This indicates an excess of homozygotes for several loci in several populations.

All three of Wright's F statistics for polymorphic loci were positive and significantly (P < 0.01; Table 3) different from zero for all loci except FIS and FIT for locus Est-1.


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Table 3. FIS, FST, FIT, Nm, and Nb estimates for nine polymorphic loci in nine populations of P. rzedowskii (Michoacán, México).

 
The mean FIS value is quite high (0.247, with a 99% confidence interval from 0.151 to 0.482), which suggests that on average there is an excess of homozygotes. FST values are very heterogeneous (0.083-0.388; Table 3) with an average value of 0.175. That is, ~17% of the genetic variation is explained by differences among populations. All FST values were significantly different from zero. Therefore, many of the values obtained for FIT are due to differences among populations. FIT values ranged from 0.083 to 0.902, with a mean of 0.405 and a confidence interval between 0.256 and 0.816 (P < 0.05). Gene flow (Nm) estimates ranged from 0.14 to 3.48 (average = 1.5), which suggests that there is relatively little genetic exchange among P. rzedowskii populations. Effective neighborhood size (Nb; Slatkin and Barton, 1989 ) was also low (0.88 to 21.88, with a mean of 9.0), suggesting that few individuals are contributing allelic variants and that gene flow may be insufficient to prevent differentiation among populations (Table 3).

Genetic relatedness among populations and isolation by distance
Estimators of genetic identity were heterogeneous (Table 4). The largest genetic identity was 0.986, between populations AGU9 and PIN8, and the smallest was 0.870, between populations ALB5 and SOL3. No specific pattern was found to match the distances separating the populations. This was confirmed using both Slatkin's (1993) method in which no significant relationship was found between a logarithmic estimate of gene flow and geographic distance among populations (data not shown) and the Mantel test on data from Table 4 ({rho} = 0.11, P = 0.460). This suggests that the populations' structure appears not to be due to differences in gene flow produced by an isolation by distance model.


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Table 4. Genetic identities (above the diagonal) and geographic distances (below the diagonal) between population pairs of P. rzedowskii (Michoacán, México). Mean genetic identity = 0.929; mean geographic distance = 7.6 K). Population codes are as in Table 1.

 
The dendrogram (Fig. 2) shows two well-defined groups. The first one contains six populations and includes the populations with the most genetic variation and a higher number of individuals (between 60 and 3500 individuals per population; average = 1242 individuals). The second group includes the three populations with the lowest number of individuals (9, 50–60, and 200 individuals; average = 115 individuals). Almost the same topology was obtained with the neighbor-joining algorithm, the only difference being the fact that population CHI6 was sister to the group formed by PIN8, AGU9, and ALB5 instead of being closer to FRE4 (as shown in Fig. 2).



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Fig. 2. Phenogram among populations of P. rzedowskii (UPGMA; Sneath and Sokal, 1973). Population codes are as in Table 1 .

 

    DISCUSSION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Genetic variation and structure
Genetic variation in pines has been extensively studied (Ledig, 1998 ). We expected that P. rzedowskii with small and fragmented populations would have low levels of genetic variation. However, it shows genetic variation levels similar to those found for other pine species with large and continuous populations (Hamrick, Mitton, and Linhart, 1981 ; Niebling and Conkle, 1990 ). For instance, mean allele number per locus (1.8) is comparable to values found in P. maximinoi (1.7; Mathenson, Bell, and Barnes, 1989 ), P. attenuata and P. muricata (1.7 for both; Millar et al., 1988 ). Unlike P. rzedowskii, these species are wide-ranging and have large population sizes. Expected heterozygosity in P. rzedowskii (0.219) was higher than the estimate reported for P. muricata (0.120; Millar et al., 1988 ), a wide-ranging species with fragmented populations. The percentage of polymorphic loci is higher in P. rzedowskii (46.8) than in P. torreyana (3.4; Ledig and Conkle, 1983 ), a species with restricted distribution and only two small populations (2000 and 7000 individuals). Another interesting species is P. washoensis, an endangered pine from California (expected heterozygosity = 0.148; Niebling and Conkle, 1990 ), which like P. rzedowskii has higher variability than that found in species of wider distribution. Observed heterozygosity in P. rzedowskii (0.162; Table 2) was significantly lower than expected heterozygosity (0.210). In contrast, in most studied pine species inbreeding is rare (Ledig, 1998 ). Pinus rzedowskii shows both fixation indices and FIS statistics that deviate from Hardy-Weinberg equilibrium, revealing a moderate inbreeding level.

Pinus rzedowskii has significant levels of genetic differentiation among populations, with 17.5% of the total variation due to differences among populations. The mean FST value for P. rzedowskii is higher than that found in most studied conifers, most of which are wide-ranging species (Table 5). However, the FST values found for P. rzedowskii are within the range of values reported for species with discontinuous distributions and large populations. For instance, P. cembra has an FST value of 0.32 (Szmidt, 1982 ), P. nigra has a value of 0.135 (Nicolié and Tucié, 1983 ), and P. torreyana has a value of 1.0 with different alleles fixed in each one of its two populations (Ledig and Conkle, 1983 ). Bermejo (1993) and Mathenson, Bell, and Barnes (1989) also found relatively high FST values in P. engelmanii, P. oocarpa, and P. caribea (0.13, 0.1, and 0.13, respectively). This could be related to the species' distributions on rugged mountain ranges (Perry, 1991 ) where topography could act as a natural barrier to gene flow.


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Table 5. Genetic variation and population structure of several species of Pinus. The type of distribution (wide vs. narrow), the number of loci analyzed, the mean number of alleles per locus (A), the expected heterozygosity (He), and estimates for population differentiation (GST or FST) are reported.

 
Small population size and isolation promote heterozygosity loss through inbreeding and allele loss through genetic drift. For instance, allele 5 (Got-1) was found only in population CHI6, while allele 4 (Sdh-2) was found only in population FRE4. These alleles, fixed in one population but not in others, contribute to the high FST values. Therefore, the genetic structuring observed in P. rzedowskii may be due in part to inbreeding but mainly to genetic drift.

Higher FST values can result from reduced population sizes and gene flow (Wright, 1965 ; Slatkin, 1993 ). The mean gene flow per generation (1.5) estimated for P. rzedowskii is lower than that reported for other species of conifers (Table 5). This indicates that there is little genetic exchange among populations, although there may be enough to prevent complete isolation among them. Gene flow as estimated by Nm and neighborhood size (Nb) are directly related. For P. rzedowskii, Nb estimates are 9.0 individuals per population but these estimations were made indirectly and are therefore preliminary. Data on cone production (less than a cone per reproductive tree per year) and seedling recruitment (less than one per tree per year; Delgado, 1997 ) support the idea that only a few individuals reproduce, yielding low effective population size.

Genetic relations and isolation by distance
The isolation by distance analysis does not show any significant pattern, suggesting that the distribution of genetic variation may not be explained by the geographic distances separating the populations (data not shown). The analysis of genetic relationships among populations shows this clearly. The six populations with the highest population sizes (VPI1, FRE4, ALB5, CHI6, PIN8, and AGU9; average, 1069 individuals; Table 1) and the highest levels of genetic variation (average polymorphism = 51% and average expected heterozygosity = 0.24; Table 2) formed one group. The rest of the populations form a second group and include the ones with the smallest population sizes (average = 90 individuals) and the least genetic variation (average polymorphism = 38% and average expected heterozygosity = 0.18). The two populations found at the north end of the distribution (CHI6 and SOL3) belong to different groups. The grouping by population size suggests that genetic drift may be the main evolutionary force acting on the distribution of genetic variation in this species.

In addition to soil characteristics of the sites where P. rzedowskii populations are established (limey soils) and the species' life history (slow growing, long lived), its reproductive behavior seems to play a role in explaining its patterns of genetic variation. Probably, gene flow rates are more likely to be affected by microgeographic features (such as the limey soil and the rugged topography) that isolate populations to different extents. Also, P. rzedowskii shows reproductive asynchrony. During four consecutive years (1992-1995) only modest cone production has been observed (a maximum of 15 cones per tree) and only a few individuals have reproduced at all (21 out of 300). There is no evidence of a large annual seed production during the last 6 yr (Delgado, 1997 ). Reproductive asynchrony has probably increased genetic differentiation because genetic exchange is occurring only among a few reproductive individuals within populations. This enhances local inbreeding. The observed heterozygote deficit suggests significant inbreeding levels, which, together with reduced population sizes and microgeographic isolation, might underlie the observed genetic structure.

Two historical scenarios may account for our results. The first one involves the populations' distribution as being the result of dispersal from a central population. Differentiation levels would therefore be a function of gene flow levels, number of founders, and the time since the founder event. The second scenario involves a single ancestral panmictic population that became fragmented into several patches because of geological events during the Pleistocene (Millar, 1998 ). Here, genetic differentiation would depend on gene flow levels, population sizes, and the degree of geographical isolation. It is difficult to discern which scenario actually took place.

Conservation implications
The information available warrants two management and conservation strategies. The first one would consist of an in situ conservation plan that would define core areas completely free from perturbation, at least for the genetically most diverse populations (namely VPI1, FRE4, ALB5, CHI6, PIN8, and AGU9). This would guarantee the maintenance of most of the species' genetic variation, including uncommon and unique alleles. The latter is the case of alleles found in CHI6 (the only one having Got-1, allele 5), PVA2, and AGU9. Nevertheless, high FST values suggest that all populations are important for conservation because they are differentiated. Conservation plans for tree species should also consider demographic traits of populations such as population size and recruitment rate (Alvarez-Buylla et al., 1996b ). In that respect, we present a simple analysis (Fig. 3) to get an insight about P. rzedowskii historical demography (Moritz, 1996 ). It is based on the idea that expanding populations are expected to show a star-like phylogeny that would result in a parabolic relation between the genetic distance, as an estimate of time of divergence, and the logarithm of the number of populations following the UPGMA analysis. On the contrary, stable populations would show a strongly structured phylogeny and would result in an exponential relationship. Our results show that since the curve is parabolic, P. rzedowskii populations have increased historically. These results also agree with our genetic data and highlight the importance of maintaining demographically viable populations since recent man produced habitat fragmentation has not yet affected this endangered species. This has probably been due to its longevity (~200 yr) that would produce a time lag before the effects of habitat transformation change both the demography and the genetic structure. Low recruitment has been observed by us in all populations and thus it appears as the most critical aspect for an in situ conservation strategy. Enforcement of methods to guarantee the survival of seedlings seems the most appropriate way to assure the viability of these populations.



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Fig. 3. Number of ancestral lineages of extant taxa at different genetic distance estimates for P. rzedowskii (Michoacán, México) following Moritz (1996) .

 
The second management strategy aims towards ex situ conservation based on seed harvesting and collection of pollen and vegetative tissue. Cone gathering is difficult as cone production is minimal compared to other pine species (Delgado, 1997 ). However, it is critical to recover in the short term as many seeds as possible to obtain a good representation of the species' genetic diversity. Tree nurseries should also be established together with field plots. Reintroduction tests should be carried out with seedlings produced ex situ. The genetic and demographic analyses of this study strongly suggest that despite the small size and population fragmentation of the populations, P. rzedowskii is not at risk of extinction under undisturbed conditions. An encouraging fact is that proposals for the establishment of areas free of anthropogenic perturbation have been made by the local people to government forestry officials. The information gathered in this study may guide, in part, various plans for the in situ and ex situ conservation of this conservationally important and morphologically intriguing pine species.


    FOOTNOTES
 
1 The authors thank Yan B. Linhart, Glenn Furnier, and an anonymous reviewer for reviewing a previous version of the manuscript; León Martínez and Rocío Esteban for helping with the translation and editing; Adrian Quijada, Francisco Ruíz, and the people from Dos Aguas, Michoacán, in particular Ceferino Moreno and Manuel Sapién, for helping with the field work; and Glenn Furnier and Oscar Avila for helping with the laboratory work. The work was supported by grant number 4715-N from Consejo Nacional de Ciencia y Tecnología, México to DP. Back

2 Author for correspondence. Back


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 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
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