The Daurian Partridge (Perdix dauuricae) is a kind of hunting bird with high economic value. Genetic diversity and structure in the Daurian Partridge were studied by analyzing eight microsatellite loci in 23 populations found throughout the range of the species in China. The objectives were to evaluate the consequences on genetic diversity and differentiation of Daurian Partridge populations and to obtain a profound genetic insight for future management decisions and for effective measures to protect and exploit Daurian Partridges. The results showed that microsatellites were polymorphic in all Daurian Partridge populations, with a high level of genetic diversity over all the loci, especially in the Qaidam Basin populations which have the highest level of diversity. Significant genetic divergence was observed among different groups as well as between populations within the same group; most pairwise FST values were highly significant. Both phylogenetic trees and Bayesian clustering analyses revealed clear differentiation among the 23 populations of the Daurian Partridge, which were classified into two genetically differentiated groups. A bottleneck analysis indicated that Daurian Partridge populations have experienced a recent bottleneck. Our study argues that the Qaidam populations, North China populations, JN population, ZJC population, and Liupan Mountain populations should be paid special attention in order to retain adequate population sizes for maintaining genetic diversity.
Dispersal is a central topic in ecology and evolution, because it is a fundamental life history trait that has important effects on both dynamics and genetic structures of populations (Clobert et al., 2001). If animals are less active, their genetic structure will be strong because of divergence and inbreeding in local populations. In contrast, in animals which show high dispersal patterns, few spatial genetic structures should be expected. Because of cost/benefit asymmetries of dispersal in animals, the sexes often show different dispersal tendencies. One special case is sex-biased dispersal, in which individuals of one sex tend to disperse and breed at a greater distance from their natal site than individuals of the opposite sex (Wolff and Plissner, 1998). Several hypotheses are put forward to explain this phenomenon. A prior mechanism expected to affect dispersal patterns is the mating system (Greenwood, 1980), with male-biased dispersal in mate-defense systems associated with most polygynous species and female-biased dispersal in resource-defense systems linked to most monogamous species. Intrasexual competition would also lead to differences in dispersal between the two sexes which mostly involves intense competition (Dobson, 1982). Waser and Jones (1983) emphasized the importance of inbreeding avoidance and parent-offspring competition in addition to the mating system. Moreover, recent studies have suggested that kin selection and social interaction may play an important role in sex-biased dispersal (Devillard et al., 2004). Physiologically, hormone levels may also exert an effect (Smale et al., 1997). There is no consensus on the evolutionary origins of sex differences in dispersal.
Elliot's Pheasant (Syrmaticus ellioti) is a vulnerable species endemic to China, found in Jiangxi, southern Anhui, Zhejiang, Fujian, Guangdong, Guangxi, Hunan, Guizhou and Hubei provinces (Delacour, 1977; Cheng et al., 1978; Li, 1996; Ding, 1998; BirdLife International, 2009). It is a bird of the Galliformes which has a polygynous mating system with the male typically having two or three mates (Ding et al., 1990). Many kinds of forests, e.g. broadleaf forest (both evergreen and deciduous), evergreen and deciduous broadleaf mixed forests, as well as coniferous and broadleaf mixed forests are used by Elliot's Pheasants as their habitat (Ding and Zhuge, 1988, 1989). Given present day clearing of forests and their replacement with single species plantations, deforestation, slash and burn systems, collection of firewood and other forest products, loss, fragmentation and degradation of habitats have become major threats for this species (Ding et al., 2000; BirdLife International, 2009). Since Elliot's Pheasant is a land-dwelling bird and its flight capacity relatively weak, an understanding of its dispersal behavior and pattern in the fragmented habitats is particularly important for its conservation and habitat management. Several studies have indicated that Elliot's Pheasant has a pre-nuptial dispersal between wintering sites and breeding sites during the early breeding season (Shi and Zheng, 1995; Peng and Ding, 2005). However, little is known about the sex differences in dispersal.
In our investigation, we have used both microsatellite DNA loci and mtDNA haplotype variation to detect the dispersal pattern of Elliot's Pheasant, to test whether this bird with its polygynous mating system has a male-biased dispersal pattern based on the significant impact of the mating system on the dispersal pattern of this species and to have a better understanding of the dispersal pattern to make action plans for future conservation and habitat management for this threatened species.
Materials and methods
Samples (Table 1) used in this study were obtained from Fujian, Hunan, Guizhou and Gutianshan areas and at adjacent areas of Zhejiang, Anhui and Jiangxi (Jiang et al., 2007). We used 105 samples (47 males, 39 females and 19 samples without sex information) for microsatellite analysis. A total of 63 samples (30 males, 29 females, 4 samples without sex information) were used for mtDNA analysis, in which 33 samples were from previous work by Jiang et al. (2007). These two sample sets were used for microsatellite and mtDNA analysis respectively.
Table
1.
Total number of genetically sampled birds (NT), number of females (NF) and number of males (NM) in each of the study area for microsatellite analysis
Protocol of DNA extraction and mtDNA amplification were used as described by Jiang et al. (2007).
Microsatellite
Seven polymorphic microsatellite loci (SE02, SE03, SE04, SE05, SE06, SE07 and SE08) were used as described by Jiang et al. (2006). PCR products were loaded on a 6.5% acrylamide gel and run on a LI-COR 4200 automatic sequencer of standard size (50–350 bp IRDye700, LI-COR). Gel images were analyzed using SAGA GT software. In order to minimize the errors of genetic typing, we repeated this six times to ensure consistent sizing of alleles.
Statistical analysis
mtDNA data
The program CLUSTAL X (Thompson et al., 1997) was used to align mtDNA control region sequences. The identification of variants and haplotypes was performed by MEGA4.0 (Kumar et al., 2008).
Microsatellite data
Microsatellite genotypes were tested for linkage disequilibrium (LD) within the whole population for each pair of loci using GENEPOP software (Raymond and Rousset, 1995). This program was also used to conduct tests for the Hardy-Weinberg equilibrium (HWE) employing the Markov chain method. Expected (HE) and observed (HO) heterozygosities were estimated with the program Cervus2.0 (Marshall et al., 1998). We used Weir and Cockerham's (1984) unbiased estimators for the calculation of F-statistics.
Sex-biased dispersal analyses
1) Microsatellites DNA
In order to test for possible differences in migration rates between males and females, five different tests, i.e., gene diversity (HS), differentiation among populations (FST), relatedness (r), mean assignment index (mAIc) and variance of the assignment index (vAIc) were carried out separately for both sexes over all populations. Whether these parameters differ significantly between the two sexes was determined using the approach of Goudet et al. (2002), as implemented by 10000 randomizations in FSTAT version 2.9.3 (Goudet, 2001).
Statistically significant dissimilarity in genetic parameters can be expected when sex-biased dispersal occurs. Allelic frequencies should be more homogeneous for individual birds of the dispersing sex, thus FST and r are expected to be higher for the more philopatric sex and for the within-group HS is expected to be lower (Goudet et al., 2002). The assignment values of individual birds (AIc) determine the probability of an individual genotype originating in the population from which it was sampled (Favre et al., 1997). The distribution of AIc is centered round a mean of 0. A positive value indicates a genotype more likely than average to occur in its sample and the bird is more likely a resident. In contrast, a negative value suggests that it is potentially a disperser. Because the AIc values for residents tend to be higher than for immigrants, under sex-biased dispersal, mAIc, for the more philopatric sex is expected to be higher than that for the sex that disperses most (Goudet et al., 2002). Because of the increased probability that members of the dispersing sex will include both residents and immigrants, vAIc for the sex dispersing is expected to be higher (Favre et al., 1997). Goudet et al. (2002) has pointed out that the efficiency and power of these indices, used to detect sex-biased dispersal, depend on dispersal rates, extent of the bias, sampling and markers used.
2) Mitochondrial DNA
Since mtDNA is maternally inherited, males do not transmit their mtDNA haplotypes to their offspring. If a male animal dies or migrates to a different population, his haplotype will not be available. In contrast, females can contribute their haplotype to the next generation. When female animals or their female offspring disperse to different populations, they will leave a copy of their haplotypes. Compared with males, females have a greater potential power to homogenize mtDNA genetic structures through dispersal (Escorza-Trevino and Dizon, 2000). If the mtDNA genetic structure in females is stronger than in males, it would probably be assumed that the result provides compelling evidence for male-biased dispersal (O'Corry-Crowe et al., 1997). Many studies have used mtDNA to infer patterns of sex-differential dispersal (O'Corry-Crowe et al., 1997; Escorza-Trevino and Dizon, 2000; Lukoschek et al., 2008).
Gender-specific hierarchical AMOVA were conducted for mtDNA, performed in the software package Arlequin3.11 (Excoffier et al., 2005).
3) Comparison between microsatellites DNA and mtDNA
When sex-biased dispersal occurs in animals with relatively complex social behavior the patterns of population structure, based on uniparentally inherited markers, e.g. mtDNA, may differ from those based on biparentally inherited nuclear markers. The rationale is as follows: for uni-parentally inherited markers, only one sex contributes to a part of the genome of its offspring. In contrast, for bi-parental markers, both sexes make contributions (Prugnolle and de Meeus, 2002).
For species with male-biased dispersal, population differentiation based on microsatellites will be weaker than that based on mtDNA. This approach has been successfully used in several studies (e.g. Gibbs et al., 2000; Hoarau et al., 2004; Maki-Petays et al., 2007).
A comparison of the differentiation level of the genetic structure in microsatellite and mtDNA can infer patterns of sex-biased dispersal. The overall differentiation for microsatellites and mtDNA was estimated by AMOVA, implemented in program Alequin 3.11.
Results
There was substantial variation at each locus as shown by the number of alleles and the observed and expected heterozygosity (Table 2). For the seven microsatellite loci, the number of alleles per locus ranged from 6 to 11 (average of 8.86), with a total of 62 alleles across 7 loci. HO was generally low, ranging from 0.261 for SE02 up to 0.782 for SE06.
Table
2.
Genetic diversity of Elliot's Pheasant (Syrmaticus ellioti) at seven microsatellite loci
Locus ID
Range of allele sizes
Na
HE
HO
SE02
202–230
7
0.618
0.261
SE03
266–276
6
0.641
0.269
SE04
168–185
9
0.856
0.411
SE05
263–287
11
0.767
0.461
SE06
299–327
11
0.878
0.782
SE07
196–225
8
0.719
0.607
SE08
300–345
10
0.767
0.737
Na, number of alleles; HE, expected heterozygosity; HO, observed heterozygosity.
A total of 47 males and 39 females were included in the microsatellite analysis, where genetic parameters of the population were estimated separately for each sex. FST and r were significantly higher for females than males (female FST = 0.142, male FST = 0.059, p = 0.020; female r = 0.198, male r = 0.092, p = 0.040). mAIc was negative in males (–0.593), but not statistically significantly different (p = 0.060) from the positive mean assignment index in females (0.715). Neither was the difference in the variance of assignment index significant, although the level in males was on average higher (Table 3). Furthermore, males displayed significantly higher gene diversity, HS (males = 0.724, females = 0.654, p = 0.025).
Table
3.
Differentiation among populations (FST), gene diversity (HS), relatedness (r), mean assignment index (mAIc) and variance of the assignment index (vAIc) for male and female Elliot's Pheasant (Syrmaticus ellioti) based on microsatellite analyses
FST
HS
r
mAIc
vAIc
Males
0.059
0.724
0.092
–0.593
10.024
Females
0.142
0.654
0.198
0.715
8.979
pa
0.020*
0.025*
0.040*
0.060
0.682
ap-values are from two-sided tests where * indicates significance at p < 0.05.
AMOVA, based on mtDNA, showed stronger genetic structure and hierarchical partitioning of genetic variation in females (FST = 0.350) than in males (FST = 0.290).
Simple comparisons between differentiation based on haplotype and based on allele frequencies are feasible, although the two markers of mtDNA and microsatellite represent two different genetic data. The result showed that the overall differentiation based on mtDNA was almost six times higher (mtDNA: overall FST = 0.320; microsatellite overall FST = 0.058).
Discussion
As our results show, we have used indirect methods to examine dispersal in Elliot's Pheasant by 1) comparing different genetic indices and genetic differentiation patterns estimated separately for both sexes by microsatellite and mtDNA; 2) comparing the level of genetic structures obtained from two markers with different inherited modes: microsatellite and mtDNA. All indices estimated suggest that males have a higher dispersal rate than females in Elliot's Pheasant. The indications given by the differences in relatedness and gene diversity show statistically significant differences. Assignment tests show that the mean of AIc (mAIc) and the variance in AIc (vAIc) are consistent with the prediction of male-biased dispersal, although there are no statistically significant differences. This may due to the relatively low efficiency and power of the assignment tests (Goudet et al., 2002). Also, no significant differences in vAIc were expected from the fact that both sexes disperse in the spring (Peng and Ding, 2005), so distributions of both male and female AIc values include immigrants, resulting in more overlaps. The result from the assignment index test is supported by F-statistics, given that the male FST is significantly smaller than the female FST. In contrast to the result from the variation in the mtDNA control region, the level of overall genetic differentiation is much lower in microsatellite variation. In addition, gender-specific hierarchical AMOVA shows a higher partition of genetic variation in females than in males for mtDNA. Lower levels of the mtDNA genetic structure in males than in females probably suggests a strong dispersal pattern of male-biased dispersal (O'Corry-Crowe et al., 1997).
Seielstad et al. (1998) stressed that the results from the comparison between two classes of genetic markers should be interpreted carefully. The disparity in the level of genetic differentiation may be due to their different effective population sizes and rates of mutation (Chesser and Baker, 1996). Gibbs et al. (2000) used the approach suggested by Seielstad et al. (1998) to assess the effect of these genetic differences on levels of differentiation in the yellow warbler and found that the expected level of divergence, based on haploid mtDNA, was almost four times higher than that based on diploid microsatellite markers. Similarly, in our study, the differentiation based on mtDNA is almost six times higher than that of microsatellite loci. In addition to the genetic characteristics of the two types of markers, there must be another reason to explain the difference. Combining with the outcomes from the other two methods we used in this study, it is difficult to explain the result from the comparison between mtDNA and microsatellites as anything but a biased dispersal between male and female Elliot's Pheasants.
Suggestions have been made explaining that males and females differ in their movement patterns. The more common mechanism to explain the pattern is that sex-biased dispersal may be associated with their type of mating system (Greenwood, 1980). In polygynous mating systems, local mate competition is dominant and often observed on male-biased dispersal species. In contrast, female-biased dispersal is highly correlated with a monogamous mating system due to competition for local resources (Greenwood, 1980; Dobson, 1982; Favre et al., 1997). The dispersal pattern of Elliot's Pheasant conforms to the expected result based on the polygynous mating system of this species. Elliot's Pheasant has a polygynous breeding system in which the male has two or three mates (Ding et al., 1990). In successful breeding attempts of Elliot's Pheasant, females nest and hatch on their own and males take no part in nest construction, incubation or care of the chicks. In this context, males make little contribution to parental investment but invest more in male-male competition for females. Males are therefore more likely to exhibit strong local mate competition. Because getting more mates is more important than being familiar with local resources for male reproductive success, dispersing males can increase their breeding opportunities and fitness (Hamilton and May, 1977). On the other hand, females who invest highly in their offspring show competition for local resources. They benefit from being philopatric due to their familiarity with the food resources for successful breeding. Another important mechanism may be related to avoid inbreeding. In Elliot's Pheasant, females typically reproduce only once per breeding season. The opposite is that males may copulate repeatedly, so males can avoid mating with related individuals and hence lower the negative impact of inbreeding by dispersing. The males can sometimes be somewhat aggressive towards hens, so female philopatry in Elliot's Pheasant may also be advantageous for defending themselves against males. However, the dispersal pattern of male-bias is not applicable to all polygynous birds. Most grouse and pheasant species also have polygynous mating systems. Lekking behavior is common in grouse species, e.g. Sage Grouse (Centrocercus urophasianus) (Dunn and Braun, 1985), in which several males display in a ground where females come and choose mates. In this case, defending resources is important for males to attract females, hence it is advantageous to be more philopatric for males. In contrast, females have more choices to get the best mates by dispersing (Wolff and Plissner, 1998). All five grouse species listed by Clarke et al. (1997) show female-biased dispersal, although examples of no sex-biased dispersal exit (Maki-Petays et al., 2007). The lek mating system was not found in Elliot's Pheasant from field observations (Ding et al., 1990). Local mate competition among males may be stronger than local resource competition among females, as is the case in the male-biased dispersal pattern in Elliot's Pheasant. We are of the opinion that polygynous birds of Galliformes without lekking behavior are more likely to exhibit a male-biased dispersal pattern.
Our field study has shown that the movement routes of Elliot's Pheasant are selective when dispersal occurs in the spring. The major factors affecting dispersal are the number of shrub species, canopy height of shrubs, slope and abundance of shrubs (Peng and Ding, 2005). This suggests that the dispersal behavior of this pheasant is affected by habitat characteristics and availability. Hence, the increasingly serious problems of habitat loss, fragmentation and degradation are bound to limit the dispersal of Elliot's Pheasant and then cause the recession of population fitness. To some extent, the dispersal behavior can weaken the negative effect of habitat fragmentation, for it will expand the distribution area of the species. How to reduce the impact of habitat fragmentation on the dispersal of Elliot's Pheasant by improving the suitability of habitat and decreasing the level of fragmentation is vital for the sustained survival of this species. Since males need a larger range of activities than females, their reactions to habitat fragmentation are much more sensitive. Combined with the male-biased dispersal pattern of Elliot's Pheasant, it is particularly important to create favorable conditions for male Elliot's Pheasants to enhance their dispersal capacity in habitat management, such as habitat recreation and corridors establishment. Specific measures should be explored further in future studies.
Although our genetic evidence has shown strong male-biased dispersal in Elliot's Pheasant, more research should be carried out to support our argument that polygynous birds without lekking behavior are more likely to exhibit male-biased dispersal patterns in Galliformes. As well, ultimate mechanisms, the adaptive significance and the evolutionary implications of male-biased dispersal patterns should be detected more in future studies, which is vital for the conservation and management of Elliot's Pheasant.
Acknowledgements
Our research was supported by grants from the National Natural Science Foundation of China (30470232). We thank Wei Liang, Li Li and others for their great assistance in collecting samples.
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Table
1.
Total number of genetically sampled birds (NT), number of females (NF) and number of males (NM) in each of the study area for microsatellite analysis
Table
3.
Differentiation among populations (FST), gene diversity (HS), relatedness (r), mean assignment index (mAIc) and variance of the assignment index (vAIc) for male and female Elliot's Pheasant (Syrmaticus ellioti) based on microsatellite analyses
FST
HS
r
mAIc
vAIc
Males
0.059
0.724
0.092
–0.593
10.024
Females
0.142
0.654
0.198
0.715
8.979
pa
0.020*
0.025*
0.040*
0.060
0.682
ap-values are from two-sided tests where * indicates significance at p < 0.05.
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