ª 2004 The American Genetic Association Journal of Heredity 2004:95(2):136–143 DOI: 10.1093/jhered/esh019 Genetic Roots of the Red Deer (Cervus elaphus) Population in Eastern Switzerland R. KUEHN, H. HALLER, W. SCHROEDER, AND O. ROTTMANN From the Wildlife Biology and Wildlife Management Unit, Department for Ecosystem and Landscape, Technical University Munich-Weihenstephan, D-85354 Freising, Germany (Kuehn and Schroeder), Swiss National Park, CH-7530 Zernez, Switzerland (Haller), and Department for Animal Science, Technical University Munich-Weihenstephan, D-85354 Freising, Germany (Rottmann). We thank all wildlife, national park, and forest officers involved for their helpful support and all the hunters for making the samples available. We would like to give special thanks to Dr. R. Gross for useful discussions in population genetic computations and Dr. Foerster for laboratory assistance. We also thank U. Puszkarz for criticism and comments on the manuscript. This work was supported by the Swiss National Park. Address correspondence to R. Kuehn at the address above, or e-mail: [email protected]. Abstract Overhunting of red deer (Cervus elaphus) in eastern Switzerland led to its extinction in the second half of the 17th century. Natural recolonization must have taken place later, because red deer were seen again in the canton of the Grisons (eastern Switzerland) in the 1870s. According to historical data, three different populations could have served as the source population. To determine the genetic origin of the eastern Swiss red deer population, we collected samples from five different subpopulations in the canton of the Grisons as well as from four adjacent populations in Germany, Liechtenstein, Austria, and Italy. We analyzed the samples by genotyping 18 microsatellite loci. FST values, assignment tests, correspondence analysis, and fuzzy clustering clearly pointed to Liechtenstein as the most probable source population for the red deer in eastern Switzerland. In addition, our analyses revealed high gene diversity in all examined populations. Gene flow and the high genetic admixture are discussed. Colonization of a new habitat or recolonization after extinction are fundamental processes in metapopulation biology (Hanski 1998). The genetic structure of a metapopulation is shaped by the geographical scale and pattern of dispersal leading to colonization (Harrison and Hastings 1996; Wade and McCauley 1988). The emigration of colonists from an established population can be induced by resource competition and niche availability (Baker 1978; Johnson 1969). Dispersal distance, the number of colonists, and the frequency of emigration also determine the frequency of recolonization and therefore the spatial genetic structure of the metapopulation. F statistics can be used to identify newly colonized sites and to indicate the mode of colonization (Slatkin 1977; Wade and McCauley 1988). In many cases, genetic differentiation is minimal, preventing Fstatistic approaches from identifying the source of colonists unambiguously (Gaggiotti et al. 2002). In addition, Whitlock and McCauley (1999) mentioned that estimates of dispersal from FST should be undertaken with great caution, and only if the biological question behind the attempt at estimating 136 dispersal depends on knowing migration rates within very large bounds. In this study, we want to analyze the mode of colonization of red deer (Cervus elaphus) in eastern Switzerland. In view of the difficulties of the F-statistic approach, we additionally used assignment tests, correspondence analysis, and fuzzy clustering to identify the possible source population. Originally red deer were present in all parts of Switzerland. According to historical documents, which were collated for a comprehensive study of the history, population development, and habitats of red deer in and around the Swiss National Park (Haller 2002), overhunting led to their virtual extinction in the canton of the Grisons (eastern Switzerland) by the second half of the 17th century. Only after an increase in red deer in the neighboring countries of Liechtenstein, Austria, and Italy (South Tyrol), coupled with enforcement of hunting regulations, did a red deer population reestablish itself in the canton of the Grisons in the second half of the 19th century. Toward the end of the 19th century, red deer were seen in Praettigau, an area in the Kuehn et al. Red Deer in Switzerland a particularly distinct spreading dynamism. (2) Individuals from the population in South Tyrol (Vinschgau) dispersed to Muestair. This colonization was not very successful because of poaching along the dispersal route between these two regions. (3) The red deer population of the Ammergebirge spread from southern Germany and repopulated adjacent Austrian valleys (e.g., Paznaun) and also the Engadin Valley in Switzerland (Unterengadin, Mittelengadin, and Oberengadin). In this study, genetic methods were used to reveal the relationships between the populations and to reconstruct the dispersal routes in order to define the origin of the red deer population of eastern Switzerland. Historical data were used to formulate the following question: Did the source of the eastern Swiss red deer originate from Liechtenstein (i.e., gene flow from the northwest), from South Tyrol in Italy (i.e., gene flow from the southeast), or was the possible source population located in the Ammergebirge along the GermanAustrian border? Despite the fact that the Ammergebirge population inhabits an area distant from the Grisons, we were interested in exploring the possibility that long distance gene flow via the Alps could have happened. To determine the genetic roots of eastern Swiss red deer, we analyzed five populations from eastern Switzerland and four from adjacent countries (Austria, Germany, Italy, and Liechtenstein). Eighteen microsatellites were genotyped in order to investigate which population of the adjacent countries was the possible source. Furthermore, we examined the influence of founding on gene diversity. Material and Methods Animals A total of 207 red deer of different sex and age, originating from eight populations, were shot during the 1997 and 1998 hunting seasons, and heart tissue (20 g) was collected from each animal and stored at 208C. In addition, one popFigure 1. Locations (circle) of five Swiss [Praetigau (PR), ulation from a previous investigation (Kuehn et al. 2003) was Oberengadin (OE), Mittelengadin (ME), Unterengadin (UE), used in this study. Samples were taken from five different Muestair (MU)] and four adjacent [Paznaun (PZ, Austria), Swiss areas within the canton of Grisons (Figure 1): Ammergebirge (AG, Germany), Vinschgau (VI, Italy), Mittelengadin (ME), Muestair (MU), Oberengadin (OE), Liechtenstein (FL)] red deer populations. The arrows indicate Praettigau (PR), and Unterengadin (UE). Four populations the possible dispersal routes of red deer after 1860 based on Haller’s (2002) analysis of historical data. The years stand for the from adjacent areas were also examined: Ammergebirge (Germany; previous study, AG; Kuehn et al. 2003), first evidence of red deer in the particular regions. Liechtenstein (FL), Paznaun (Austria, PZ), and Vinschgau (Italy, VI). Historical and demographic data used in this north of the canton bordering Austria. By 1916 animals were study were summarized by Haller (2002) and originated prialso sighted in the Val Muestair, in the southeastern part of marily from the Swiss National Park and the hunting agency the canton. In the first half of the 20th century, red deer of the Grisons. could be found throughout the canton, and by the second half, populations had reached the carrying capacity of their habitats. At the same time, large areas in the central Alps DNA Isolation and Microsatellite Analysis were repopulated. The DNA was isolated according to Hogan et al. (1986). According to historical data, three different dispersal Eighteen microsatellite loci, mostly derived from cattle or processes took place toward the end of the 19th century sheep, were used for genotyping all populations: BM1818, (Figure 1): (1) Red deer from the population in Liechtenstein Cer14, CSPS115, CSRM60, CSSM14, CSSM16, CSSM19, dispersed to the canton of the Grisons. These exhibited CSSM22, CSSM66, ETH3, ETH225, Haut14, Haut24, 137 Journal of Heredity 2004:95(2) ILSTS06, INRA35, IOBT918, IOBT965, and MM12 (Kuehn et al. 2003). Generally the loci are physically mapped on different chromosomes of Cervus (Slate et al. 2002). To reduce the time and cost of the genotyping analyses, multiplex polymerase chain reactions (PCRs) and multiplex loading were used according to Kuehn et al. (2003). The genotypes were scored on an ABI PRISM 377 DNA Sequencer (Applied Biosystems/Perkin Elmer). The proportion of missing genotypes was less than 5% per locus. Descriptive Statistics and Population Differentiation We documented the extent of intra- and interpopulation genetic diversity based on the allelic composition of the nine sample areas. We used the program GENETIX v. 4.02 (Belkhir et al. 1996–2001) to generate allele frequency tables, to calculate the average number of alleles per locus, and to calculate expected and observed heterozygosity (He, Ho). GENEPOP v. 3.3 (Raymond and Rousset 1995b) was used to test the genotypic distribution for conformity to HardyWeinberg expectations, to test the loci for genotypic disequilibrium, and to assess the significance of allelic differentiation between pairs of populations. This program was also used to calculate the pairwise population differentiation, FST. All probability tests were performed applying the Markov chain algorithm (Guo and Thomson 1992; Raymond and Rousset 1995a). Sequential Bonferroni adjustments (Rice 1989) were used to correct for the effect of multiple tests. In order to assess the possible impact of demographic changes on genetic diversity due to colonization, we used the heterozygosity excess test, estimated and tested by the Wilcoxon signed rank test in the BOTTLENECK (Cornuet and Luikart 1996) computer program, assuming one step and multistep mutation models. The R-PACKAGE software (Casgrain 2001) was used to calculate the geographical distances (in kilometers) separating sampling locations based on the approximate latitudes and longitudes for each region. To estimate the likelihood of an individual’s multilocus genotype occurring in a given population, the exclusionsimulation test accompanied by the Bayesian approach of assignment test (GENECLASS v. 1.0.02; Cornuet et al. 1999) was used. This method considers each population separately and does not assume a priori that the ‘‘true’’ population of origin has been analyzed. The mean probability of belonging was calculated based on the probability of the individual assignment, which makes the percentage of admixture detectable and visualizes it in circular charts. The extent of population differentiation, or more precisely the admixture of the red deer population in eastern Switzerland, based on microsatellite allelic frequencies, was further assessed by performing a correspondence analysis (CA) (Benzérci 1973) using STATISTICA 6.0. The application of this analysis to genetic data was developed by Greenacre and Degos (1977) and She et al. (1987). The genetic data were transformed into a contingency table (samples 3 alleles), in which each sample was described by 138 the allelic frequencies. The Euclidian distance, centered on the marginal distribution of the contingency table, was used to measure the pairwise population relatedness in the kdimensional space (k ¼ number of alleles). The factors were tabulated according to their eigenvalues and scattered in three dimensions. Population similarity is based on the lowest variation between these three dimensions. In order to further investigate whether the revealed levels of similarity are indeed the result of natural recolonization, fuzzy grouping into different classes of populations was calculated with the algorithm based on Ohmayer (1982), Ohmayer and Seiler (1985), and Medjugorac (1995). Using the Cavalli-Sforza chord distance, this fuzzy-grouping algorithm, in conjunction with the great deluge algorithm (Dueck 1989), estimates the probability of populations belonging to different classes. Fuzzy cluster analysis methods partition a dataset into classes in which similar data are assigned to the same class and dissimilar data to different classes by minimizing the within-class sum of square errors. Membership degrees ranging from zero to one are used instead of assignments. A total of 150,000 iterations were performed with a fuzzy exponent of two for estimating three to five classes. The optimum number of classes was established on the basis of minimizing the fuzziness performance index (FPI) and the modified partition entropy (MPE). The FPI estimates the degree of fuzziness and the MPE estimates the degree of disorganization generated by a specified number of classes (Roubens 1982). In addition, we tested for the presence of population structure by assigning individuals to populations using the STRUCTURE program (Pritchard et al. 2000). This program uses a model Bayesian approach with a Markov chain Monte Carlo algorithm and provides a probability value that can be interpreted directly as a probability of origin of each individual in populations or classes. The method is described by Pritchard et al. (2000). A total of 50,000 iterations with 5000 burn-ins were performed, under the assumption that the regional provenance of the individuals is not known and that there is gene flow between populations. The individuals were assigned to four groups and the probability of belonging was compared with the fuzzy grouping. Results Linkage and Hardy-Weinberg Equilibrium The test for genotypic disequilibrium for each pair of the 18 microsatellite loci across all populations gave two significant values (P , .05) for 153 comparisons; seven significant values are expected by chance at the 5% level. After Bonferroni correction for multiple tests, one combination was significant (P , .00033) at the experimental level. When each population was tested separately, a linkage equilibrium between all pairs of loci was observed. The probability test by the Markov chain method for the Hardy-Weinberg equilibrium (Haldane 1954) showed two to Kuehn et al. Red Deer in Switzerland Table 1. Number of sampled animals (n), historical background, and geographic coordinates as demographic parameters, and mean alleles per locus (na), mean expected heterozygosity (He), and mean observed heterozygosity (Ho) in studied red deer populations over all loci Population n Historical background Longitude Latitude na He Ho Ammergebirge (AG) Fuerst. Liechtenstein (FL) Mittelengadin (ME) Muestair (MU) Oberengadin (OE) Praettigau (PR) Paznaun (PZ) Unterengadin (UE) Vinschgau (VI) 43 28 29 27 26 28 13 29 27 Possible founder Possible founder Founded Founded Founded Founded Founded Founded Possible founder 11.07 9.52 10.10 10.42 9.83 9.70 10.23 10.30 10.77 47.60 47.13 46.70 46.60 46.50 46.93 47.00 46.80 46.36 6.39 7.00 6.61 7.28 6.61 6.72 5.78 6.50 6.89 0.638 0.689 0.675 0.678 0.679 0.676 0.682 0.651 0.668 0.563 0.581 0.567 0.551 0.558 0.599 0.589 0.548 0.506 five significant deviations from the Hardy-Weinberg equilibrium in each population after Bonferroni correction. The populations of FL, ME, and VI showed significant deviations at five loci. Allele Frequency Distribution and Heterozygosity The highest number of alleles (19) was detected at the CSSM19 locus and the lowest (2) at the ETH3 locus. The expected heterozygosity (He) per locus over all populations was between 0.887 (ILSTS06) and 0.321 (CSSM14). On average 9.8 6 5.2 polymorphic alleles per locus were found. Intrapopulation indices are given in Table 1. The mean number of polymorphic alleles per locus and population (na) ranged from 6.4 (AG) to 7.3 (MU). The He of the 18 microsatellites per population ranged from 0.638 to 0.689 and the observed heterozygosity (Ho) ranged from 0.506 to 0.599. No significant differences with respect to the heterozygosity values between the different populations were detectable based on t tests. To assess whether the allelic distributions within populations had been shifted by changes in population sizes due to colonization, we tested for heterozygosity excess using the BOTTLENECK program (Cornuet and Luikart 1996). Based on the infinite allele model (IAM) and the stepwise mutation model (SMM), no population exhibited significant heterozygosity excess (Wilcoxon test, P , .05). Genetic Differentiation and Demography Based on the 18 examined microsatellite loci, pairwise estimates of FST values showed little to moderate (Wright 1978) differentiation, with values ranging from 0.0015 to 0.0999. Within the Engadin valley (ME, OE, and UE), the FST values were very low and no significant P values for population allelic differentiation were detectable after Bonferroni correction (P , .0014; Table 2). Between the populations FL and ME, MU and UE, and OE and PR, the FST values were also very low and the differentiation was not significant after Bonferroni correction. The other populations showed moderate and significant pairwise FST values, indicating that the possible source populations VI and AG are genetically distinct from the remaining populations. At the microsatellite level, the assignment of the individuals’ multilocus genotype based on the exclusionsimulation tests (GENECLASS 1.0.02; Cornuet et al. 1999) revealed that the possible source populations (FL, VI, and AG) had high probability values for the correct assignments of individuals to their origin (53%, 46%, and 71%, respectively). The individuals of the population PZ were also assigned correctly at 71% (Figure 2). In the case of the populations ME, OE, and UE within the Engadin valley, the individuals’ assignments to their populations of origin were much lower (26–32%). In these as well as in the populations MU and PR, a high admixture of the multilocus genotypes, and therefore a high gene flow between the populations, was Table 2. Matrix of FST values according to Weir and Cockerham (1984) (below diagonal) and the approximate geographical distances (in kilometers) (above diagonal) between populations AG Ammergebirge (AG) Fuerst. Liechtenstein (FL) Mittelengadin (ME) Muestair (MU) Oberengadin (OE) Praettigau (PR) Paznaun (PZ) Unterengadin (UE) Vinschgau (VI) 0.0644*** 0.0605*** 0.0896*** 0.0361*** 0.0369*** 0.0892*** 0.0822*** 0.0999*** FL ME MU OE PR PZ UE VI 128 124 65 122 91 27 154 74 30 46 127 26 40 66 49 92 56 35 47 63 41 106 70 19 24 49 48 23 110 110 51 27 73 88 58 40 0.0091** 0.0140*** 0.0197*** 0.0269*** 0.0221*** 0.0127*** 0.0416*** 0.0097*** 0.0035 0.0132*** 0.0253*** 0.0058** 0.0280*** 0.0305*** 0.0498*** 0.0317*** 0.0014* 0.0194*** 0.0015** 0.0434*** 0.0299*** 0.0458*** 0.0647*** 0.0455*** 0.0645*** 0.0240*** 0.0439*** 0.0361*** Significant P value for population allelic differentiation: * P , .05, ** P , .001, *** P , .0001. 139 Journal of Heredity 2004:95(2) Figure 2. Circular charts of adjusted mean probability of belonging of the assigned individuals per population based on the exclusion-simulation test (GENECLASS; Cornuet et al. 1999). The segments show the probability of belonging of the assigned individuals to the population noted below the charts (only percentages greater than 10% are displayed). detectable. Remarkably, however, only 4% of the ME population, 5% of the OE population, and 7% of the UE population exhibited the possible founder genotypes of VI. One percent of ME, 2% of OE, and 2% of UE had genotypes of the population AG. Eight percent of the MU population exhibited genotypes of VI and 0% of the PZ population had genotypes of AG. However, 13–15% of the populations in the Engadin Valley (ME, OE, and UE) exhibited genotypes of the possible source population, FL. Even 13% of the MU population—the population with the highest geographical distance to FL (Table 2)—had genotypes of the FL population. Eleven percent of the VI population exhibited genotypes of the ME population and 13% of the VI population had genotypes of MU. In contrast, only a small percentage of the ME and MU populations exhibited genotypes of VI (Figure 2). The correspondence analysis (CA) was performed using 186 allelic frequencies to summarize population relationships (Figure 3). The first three dimensions of the CA account for a total of 60% of the variance. Consistent with the other analyses used in this study, four well-differentiated ‘‘groups’’ were observed: AG, PZ, VI, and a fourth one consisting of the possible source population FL and the populations ME, MU, OE, PR, and UE (Figure 3). In the third dimension, the 140 MU population does not match the remaining group members (Figure 3). The fuzzy grouping based on the Cavalli-Sforza chord distance between the populations and the population structuring derived by assigning individuals to groups using the STRUCTURE program (Pritchard et al. 2000) showed generally the same results (Table 3). Again, four different groups were observed. With the fuzzy grouping, a clear and significant (P , 0.05) clustering was obtained. In the case of the clustering based on the individual classification, however, the results were somewhat ambiguous. Yet regarding the significance level, the same classification is evident. Discussion Genetic Variability and Differentiation By applying 18 microsatellites we were able to detect rather high heterozygosity values (He) ranging from 0.64 to 0.69, as well as great variation between individuals within red deer populations. The amount of heterozygosity examined in this study is consistent with previous studies on ungulate species (Barker et al. 1997; Forbes et al. 1995; Kuehn et al. 2003). However, comparison of the genetic variability of Swiss red deer with that of several endangered, bottlenecked, founded, Kuehn et al. Red Deer in Switzerland with a large amount of immigration from one or more source populations is very likely to have caused the current genetic structure of the red deer population in eastern Switzerland. To further examine the foundation of the red deer population in eastern Switzerland, we calculated pairwise population differentiation. This analysis revealed that the possible founders (AG and VI) have higher FST values compared to the founded ones than the other possible source population, FL. Particularly noteworthy is that there is a lower differentiation between FL and MU than between VI and MU, although the geographical distance between FL and MU is about 3.5 times higher than that between VI and MU. The genetic differentiation between the Engadin valley populations (ME, OE, and UE) is negligible. The FST values suggest a high gene flow from FL to the Engadin valley and to MU. Regarding FST values, a genetic connectivity between MU and VI is likely to exist. These results are consistent with theories deduced from historical and demographic data mentioned before. Population Assignment and Relationships Figure 3. Correspondence analysis based on frequencies of 18 microsatellite loci showing the first three components. The cube shows the populations with the lowest variation between populations in all three dimensions. or isolated populations (Goodman et al. 2001; Houlden et al. 1996; Kuehn et al. 2003; Menotti-Raymond and O’Brien 1995) with respect to the examined levels of He did not allow any conclusions on founder or bottleneck effects. Similarly the founded populations showed no differences in variability in the number of polymorphic alleles when compared to the possible founders. In addition, no allele shifts by changes in population size were detectable using the test for heterozygosity excess (Cornuet and Luikart 1996). No founder or bottleneck effects were detectable, therefore colonization Further investigations to detect possible source populations or a genetic admixture of red deer in eastern Switzerland are based on population assignment tests. The exclusionsimulation tests revealed that 13–15% of the populations of the Engadin valley (ME, OE, and UE) and the PR and MU populations exhibit genotypes of the FL population. The probability values of genotypes for the other possible founders, VI and AG, are low in all Swiss populations. Gene flow originating from FL through PR to the Engadin populations and MU is supported by the assignment test. An interesting result is that 13% and 11% of the VI genotype belongs to MU and ME, respectively. This supports the historical and demographic data (Haller 2002), according to which an increasing population in MU led to the dispersal of animals to VI. However, due to the small geographic distance, a former gene flow originating from VI to MU is likely to have taken place, but this was not clearly Table 3. Probability of belonging of analyzed red deer populations to different classes based on (1) the fuzzy grouping algorithm using the chord distance (Ohmayer 1982, 1985; Medjugorac 1995) and (2) the Markov chain Monte Carlo algorithm using the individual classification (STRUCTURE; Pritchard et al. 2000) Fuzzy grouping Structure Population OA 1 Class I Class II Class III Class IV OA 2 Class I Class II Class III Class IV Ammergebirge (AG) Fuerst. Liechtenstein (FL) Mittelengadin (ME) Muestair (MU) Oberengadin (OE) Praettigau (PR) Paznaun (PZ) Unterengadin (UE) Vinschgau (VI) 2* 1 1 1 1 1 3* 1 4* 0.000 0.389 0.487 0.320 0.396 0.375 0.000 0.407 0.000 1.000 0.200 0.160 0.184 0.208 0.234 0.002 0.173 0.024 0.000 0.204 0.166 0.212 0.191 0.193 0.998 0.201 0.027 0.000 0.207 0.188 0.284 0.205 0.198 0.000 0.220 0.949 2* 1* 1* 1 1* 1* 1 1* 1 0.003 0.954 0.960 0.862 0.989 0.973 0.790 0.991 0.650 0.993 0.003 0.002 0.002 0.003 0.002 0.004 0.002 0.003 0.002 0.007 0.014 0.011 0.003 0.014 0.008 0.002 0.003 0.002 0.036 0.024 0.125 0.005 0.011 0.199 0.005 0.344 Columns OA 1 and OA 2 show the object allocation into the most likely class using the different methods. * Significant P , 0.05. 141 Journal of Heredity 2004:95(2) deducible by this analysis. Eight percent of MU exhibits genotypes of VI. The classification with the fuzzy grouping as well as the Structure analysis identify the FL population as the source population of the red deer in PR, MU, and the Engadin valley. The AG and VI populations group into significantly different classes and can therefore be excluded as possible founders of the red deer population in eastern Switzerland. The CA analysis clearly supports the theories mentioned earlier. According to all investigations, PZ emerges as an isolated population with no connectivity to the Engadin valley and AG, but with minor gene flow from FL (Figures 2 and 3; third dimension). Management Implications Animal populations with a long history of anthropogenically caused change most often show a complex spatial structure coupled with a mixed genetic history. Demographic and short-term changes in population growth give rise to largescale changes in genetic variability. Understanding the historical sequence of population movement across landscapes—long ago fragmented by human development activities—is difficult and can be helped by appropriate studies involving conservation genetics. These studies should envisage endangered species as well as obvious problems caused by overhunting and habitat fragmentation to assist wildlife managers in making their decisions for sustainable conservation. In the present study, the genetic roots of eastern Swiss red deer were clearly demonstrated. The results confirm historical and demographic data by revealing that the red deer population in eastern Switzerland was founded by the population in Liechtenstein (FL). Long distance gene flow and high genetic admixture, coupled with high genetic variability, were detectable, showing that red deer are capable of long-distance recolonization, provided that a migration corridor and a suitable habitat exist. 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Volume 4: Variability within and among natural populations. Chicago: University of Chicago Press. Received March 23, 2003 Accepted November 11, 2003 Corresponding Editor: Oliver A. Ryder 143
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