Genetic diversity and genetic structure of red deer in the Ebinur Lake Wetland National Nature Reserve

doi:10.17520/biods.2025233

Abstract

Abstract:

Aims: In the context of global biodiversity facing threats, protecting the genetic diversity of wildlife is of critical importance for maintaining ecological balance and enhancing the adaptive capacity of ecosystems.

Methods: This study focused on red deer (Cervus elaphus) in the Ebinur Lake Wetland National Nature Reserve (Ebinur Lake Reserve), employing non-invasive sampling methods to collect fecal samples. Genetic diversity and structure were analyzed using microsatellite and mitochondrial markers (Cytb, D-loop).

Results: The results showed that the overall observed heterozygosity (Ho) for microsatellites was 0.662, the expected heterozygosity (He) was 0.777, the polymorphic information content (PIC) was 0.712, and the inbreeding coefficient (Fis) was 0.165, indicating a deviation from Hardy-Weinberg equilibrium. The haplotype diversity (Hd) of mitochondrial markers Cytb and D-loop was 0.447 and 0.605, respectively, and the nucleotide diversity (Pi) was 0.00463 and 0.00334, respectively. Compared to other subspecies of red deer, the genetic diversity of red deer in Ebinur Lake Reserve is moderately high. No bottleneck effect was detected, although a certain degree of inbreeding was observed. Microsatellite structure analysis and principal coordinates analysis indicated that red deer in Ebinur Lake Reserve formed two distinct genetic clusters, suggesting genetic differentiation has occurred. Phylogenetic and genetic distance analyses suggested that the red deer in the Ebinur Lake Reserve was closely related to both the Tianshan red deer and the Altai red deer.

Conclusion: As one of the large ungulate species within the reserve, its genetic diversity is of significant importance for maintaining the ecosystem. Therefore, to preserve the genetic diversity of the red deer in the Ebinur Lake Reserve, it is recommended to strengthen the protection of red deer habitats, establish ecological corridors to facilitate gene exchange, and prevent inbreeding.

Key words: Ebinur Lake Reserve, red deer, genetic diversity, non-invasive sampling, microsatellites, mitochondrial DNA

Jinshan Wu, Changle Yang, Yufeng Ma, Yaxuan Li, Wenjia Gao, Ye Kusili, Lianghong Ye, Yujiao Yang, Mengqi Xu, Tingqiong Liao, Linqiang Zhong, Wenjuan Shan. Genetic diversity and genetic structure of red deer in the Ebinur Lake Wetland National Nature Reserve[J]. Biodiv Sci, 2025, 33(12): 25233.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2025233

https://www.biodiversity-science.net/EN/Y2025/V33/I12/25233

Figures/Tables 10

Fig. 1 Results of cumulative gene locus identity consistency resolution testing for the protection of red deer in Ebinur Lake Wetland National Nature Reserve. PIDsib, Probability of identity for siblings; PID, Probability of identity for individuals.

Table 1 Genetic diversity parameters of 10 pairs of microsatellite loci

Locus	N	Na	Ne	I	Ho	He	PIC	Fis	P
BM4208	73	16	6.952	2.154	0.589	0.856	0.799	0.312	0.000^***
BM5004	73	7	2.100	0.972	0.110	0.524	0.416	0.791	0.000^***
T530	73	16	9.716	2.439	0.767	0.897	0.871	0.145	0.000^***
T507	73	11	6.741	2.048	0.822	0.852	0.823	0.035	0.013^*
CSSM19	73	12	7.506	2.166	0.890	0.867	0.855	-0.027	0.000^***
T123	73	14	4.320	1.872	0.808	0.769	0.685	-0.052	0.000^***
T501	73	23	4.860	2.192	0.589	0.794	0.662	0.258	0.000^***
BM1225	73	19	7.706	2.342	0.671	0.870	0.849	0.229	0.000^***
BM848	73	13	2.771	1.339	0.603	0.639	0.536	0.057	0.000^***
BM6506	73	10	3.332	1.554	0.767	0.700	0.619	-0.096	0.000^***
平均值 Mean	73	14.1	5.600	1.908	0.662	0.777	0.712	0.165

Fig. 2 Comparative analysis of genetic diversity in red deer from in the Ebinur Lake Wetland National Nature Reserve (Ebinur Lake Reserve) and other red deer populations. (a) Microsatellite genetic diversity; (b) Cytb genetic diversity (c) D-loop genetic diversity. Ho, Observed heterozygosity; He, Expected heterozygosity; Pi, Nucleotide diversity; Hd, Haplotype diversity.

Fig. 3 The ΔK results (a) and the corresponding internal genetic structure (b) of the red deer population in Ebinur Lake Wetland National Nature Reserve under different K values

Fig. 4 Principal coordinates analysis (PCoA) genetic structure analysis of red deer in Ebinur Lake Wetland National Nature Reserve based on microsatellites

Fig. 5 Genetic structure and phylogenetic relationship of red deer populations in Ebinur Lake Wetland National Nature Reserve. (a) Phylogenetic tree of Cytb haplotypes; (b) Haplotype network diagram of Cytb haplotypes; (c) Phylogenetic tree of Cytb haplotypes in red deer from Ebinur Lake Wetland National Nature Reserve and Chinese red deer subspecies; In Figure c, Clade I, Clade II, Subclade I, and Subclade II correspond sequentially to the red deer populations of the Tianshan-Altai-Northeast-Alashan- Sichuan-Gansu region and the Ebinur Lake Wetland National Nature Reserve, the Tarim red deer population, the Tianshan-Altai-Northeast-Alashan-Sichuan-Gansu region and the Ebinur Lake Wetland National Nature Reserve red deer population, and the Tianshan-Altai and Ebinur Lake Wetland National Nature Reserve red deer populations.

Table 2 Cytb genetic distance between red deer and Chinese red deer subspecies in Ebinur Lake Wetland National Nature Reserve

	ABH	ALT	TS	DB	ALS	GS	SC
ALT	0.010
TS	0.009	0.009
DB	0.010	0.011	0.008
ALS	0.014	0.014	0.010	0.011
GS	0.012	0.013	0.009	0.011	0.014
SC	0.012	0.012	0.009	0.010	0.014	0.002
TLM	0.054	0.051	0.052	0.053	0.053	0.052	0.052

Fig. 6 Genetic structure and phylogenetic relationships of the red deer population in the Ebinur Lake Wetland National Nature Reserve. (a) Phylogenetic tree of the D-loop haplotype system; (b) Network diagram of the D-loop haplotype system; (c) Phylogenetic tree of D-loop haplotype in red deer from Ebinur Lake Wetland National Nature Reserve and Chinese red deer subspecies; In Figure c, Clade I, Clade II, Subclade I, and Subclade II correspond sequentially to the red deer populations of the Tianshan-Altai-Gansu-Sichuan-Northeast-Alashan and Ebinur Lake Wetland National Nature Reserve, the Tarim red deer, the red deer populations of the Tianshan-Altai-Gansu-Sichuan-Northeast-Alashan and Ebinur Lake Wetland National Nature Reserve, and the red deer populations of the Tianshan-Altai and Ebinur Lake Wetland National Nature Reserve.

Table 3 D-loop genetic distance between red deer and Chinese red deer subspecies in Ebinur Lake Wetland National Nature Reserve

	ABH	ALT	TS	DB	ALS	GS	SC
ALT	0.013
TS	0.015	0.005
DB	0.032	0.018	0.014
ALS	0.046	0.018	0.022	0.007
GS	0.036	0.018	0.023	0.033	0.025
SC	0.039	0.019	0.025	0.031	0.022	-0.001
TLM	0.120	0.091	0.093	0.080	0.087	0.087	0.082

Table 4 Detection of population bottlenecks of red deer in the Ebinur Lake Wetland National Nature Reserve

位点 Locus	基因数 N	等位基因数 Na	期望杂合度 He	无限等位基因突变模型 I.A.M.		两阶段突变模型 T.P.M.		逐步突变模型 S.M.M.
位点 Locus	基因数 N	等位基因数 Na	期望杂合度 He	平均期望杂合度 Heq	P	平均期望杂合度 Heq	P	平均期望杂合度 Heq	P
BM4208	146	16	0.862	0.817	0.250	0.871	0.315	0.904	0.033^*
BM5004	146	7	0.527	0.600	0.259	0.687	0.066	0.762	0.007^*
T530	146	16	0.903	0.822	0.014^*	0.871	0.122	0.903	0.449
T507	146	11	0.858	0.735	0.039^*	0.803	0.142	0.854	0.465
CSSM19	146	12	0.873	0.749	0.020^*	0.821	0.090	0.868	0.494
T123	146	14	0.774	0.797	0.284	0.851	0.039^*	0.888	0.000^**
T501	146	23	0.800	0.885	0.035^*	0.919	0.002^*	0.936	0.002^*
BM1225	146	19	0.876	0.855	0.400	0.896	0.166	0.920	0.008^*
BM848	146	13	0.644	0.776	0.072	0.839	0.000^**	0.878	0.000^**
BM6506	146	10	0.705	0.715	0.368	0.783	0.097	0.839	0.003^*

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