A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic

Abstract

Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer-like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.

Keywords: genetic structure; hybridization; introgression; microsatellite variability; sika-red deer hybrid.

Figure 1

A map of the Czech Republic showing the sampling locations in the red and sika deer.

Figure 2

The NeighborNet dendrogram constructed from the Nei´s DA distances between the seven red and sika deer sampling populations (n = 123). Population codes: RD-D (Red deer Doupovské hory), RD-S (Red deer Slavkovský les), SD-D (Sika deer Doupovské hory), SD-S (Sika deer Slavkovský les), SD-K (Sika deer Kladská), SD-L (Sika deer Lány), and SD-Z (Sika deer Žlutice).

Figure 3

The Bayesian model-based clustering rendered with the STRUCTURE software: (a) the evolution of the mean ln of likelihood (ln P(K)) according to K, based on the five runs of the 50,000 burn–ins and 150,000 MCMCs (standard deviations indicated); (b) STRUCTURE clustering results at K = 2 (the admixture model and 11-locus dataset). Each vertical line represents one individual. The thin black lines separate individuals from different sampling sites (groups). Population codes: RD-D (Red deer Doupovské hory), RD-S (Red deer Slavkovský les), SD-D (Sika deer Doupovské hory), SD-S (Sika deer Slavkovský les), SD-K (Sika deer Kladská), SD-L (Sika deer Lány), and SD-Z (Sika deer Žlutice).

Figure 3

The Bayesian model-based clustering rendered with the STRUCTURE software: (a) the evolution of the mean ln of likelihood (ln P(K)) according to K, based on the five runs of the 50,000 burn–ins and 150,000 MCMCs (standard deviations indicated); (b) STRUCTURE clustering results at K = 2 (the admixture model and 11-locus dataset). Each vertical line represents one individual. The thin black lines separate individuals from different sampling sites (groups). Population codes: RD-D (Red deer Doupovské hory), RD-S (Red deer Slavkovský les), SD-D (Sika deer Doupovské hory), SD-S (Sika deer Slavkovský les), SD-K (Sika deer Kladská), SD-L (Sika deer Lány), and SD-Z (Sika deer Žlutice).

Figure 4

The Circos-like plot displaying the interspecies variation based on the nDNA data. Population codes: SD-K (Sika deer Kladská), SD-L (Sika deer Lány), and SD-Z (Sika deer Žlutice).

Figure 5

The estimated proportion of interspecific hybridization ancestry (Q) between the sika and red deer (n = 123), and the threshold values of 0.01 < Q < 0.99 used to detect the hybrid individuals in the western parts of the Czech Republic. We detected more red-like hybrids (n = 9) exhibiting a recent sika ancestry (0.50 < Q < 0.99) than sika-like ones (n = 4) having a recent red deer ancestry (0.01 < Q < 0.50).