Population Genetic Structure and Climate Adaptation Analysis of Brachystachyum densiflorum

doi:10.11983/CBB24094

Abstract

Abstract: INTRODUCTION: Genetic diversity is considered as a crucial aspect in assessment and conservation of rare and endangered species. Brachystachyum densiflorum is a species endemic to eastern China. In recent years, with rapid economic development, accelerated urbanization, and escalating pollutant emissions, the habitat of B. densiflorum has been continuously degraded, habitat fragmentation has intensified, and its populations have shown a tendency to decline. RATIONALE: Genetic diversity endows species with abundant genetic resources and plays a pivotal role in shaping their capacity to adapt to new environments. To elucidate the genetic diversity of B. densiflorum and evaluate the influence of climate change on its genetic variation, reduced-representation genome sequencing technology was employed to obtain single nucleotide polymorphisms (SNPs), and subsequently population genetics and landscape genetics together with species distribution modelling were analyzed. RESULTS: B. densiflorum had a moderate level of genetic diversity. Six populations were divided into two groups, and there was moderate differentiation (F_ST=0.102) and high gene flow (Nm=2.442) between them. Genotype-environment association analysis indicated that the two groups were diverged attributable to local adaptation to the climate. Temperature differences and low-temperature regimes interacting together with precipitation gave rise to genetic variation of this species. In total, 544 adaptive loci were identified, which displayed significant correlations with temperature difference, low-temperature factors (Bio2, Bio6, Bio11, and Bio7), and precipitation factors (Bio19). B. densiflorum migrated evidently northward from the Last Glacial Maximum to the current, with its distribution area increased by 89.5%. However, during the period from 2061 to 2080, the extent of the suitable area for this species will be contracted, and there will be partial degradation and fragmentation occurring in highly suitable areas within Anhui Province. CONCLUSION: B. densiflorum showed a moderate level of genetic diversity and a moderate degree of genetic differentiation. Local adaptation drove the formation of the current genetic pattern of B. densiflorum, and temperature differences, low-temperature, and precipitation led to genetic variation. B. densiflorum has evidently migrated northward from the Last Glacial Maximum to the current with increase of distribution area. However, niche modelling indicated that during the period from 2061 to 2080, the suitable habitat area of B. densiflorum would be contracted, with partial degradation and fragmentation occurring in highly suitable areas within Anhui Province. These results provide the basis for conservation and utilization of B. densiflorum.

Population genetic structure analysis of Brachystachyum densiflorum

Key words: Brachystachyum densiflorum, reduced-representation genome sequencing, genetic diversity, genetic structure, species distribution model

Zhang Ruli, Li Dezhu, Zhang Yuxiao. Population Genetic Structure and Climate Adaptation Analysis of Brachystachyum densiflorum[J]. Chinese Bulletin of Botany, 2025, 60(3): 407-424.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24094

https://www.chinbullbotany.com/EN/Y2025/V60/I3/407

Figures/Tables 8

Table 1 Sampling information of Brachystachyum densiflorum populations

Population	Locality	Sample individuals	Longitude	Latitude
AHYX	Yuexi, Anhui	7	116°14′49″ E	30°55′27″ N
AHHS	Huoshan, Anhui	4	116°26′38″ E	31°24′01″ N
AHGD	Guangde, Anhui	9	119°14′10″ E	30°48′56″ N
JSLY	Liyang, Jiangsu	3	119°28′30″ E	31°14′39″ N
JSYX	Yixing, Jiangsu	10	119°47′54″ E	31°16′49″ N
ZJCX	Changxing, Zhejiang	3	119°52′31″ E	31°07′24″ N

Table 2 Genetic diversity indices of six populations

Population	PIC	Ho	He	π	Fis	Ne (95% CI)
AHYX	0.8102	0.0880	0.3051	0.3295	0.6466	5.4 (5.2, 5.7)
AHHS	0.6412	0.0863	0.2712	0.3099	0.4899	9.4 (8.4, 10.4)
AHGD	0.8802	0.0885	0.3148	0.3339	0.7123	3.8 (3.6, 4.0)
JSLY	0.5502	0.0841	0.2492	0.2990	0.4098	Inf (inf, inf)
JSYX	0.9069	0.0884	0.3183	0.3358	0.7385	4.0 (3.9, 4.2)
ZJCX	0.5462	0.0865	0.2474	0.2969	0.4017	4.8 (4.5, 5.1)
Mean	0.7225	0.0870	0.2843	0.3175	0.5665	5.6 (5.1, 5.9)

Figure 1 Population genetic structure analysis of Brachystachyum densiflorum (A) Phylogenetic tree and individual genetic components at K=2, 3, 4, the numbers above the branch are the bootstrap values; (B) Principal component analysis (PCA); (C) Discriminant analysis of principal components (DAPC). AHYX, AHHS, AHGD, JSLY, JSYX, and ZJCX are the same as shown in Table 1.

Figure 2 The cross-validation error rate of K value

Table 3 Genetic differentiation (FST, lower left triangle) and gene flow (Nm, upper right triangle) among six populations

Population	AHGD	AHYX	AHHS	JSLY	JSYX	ZJCX
AHGD	0.000	3.596	2.497	2.065	4.958	2.108
AHYX	0.065	0.000	2.382	1.869	3.848	1.887
AHHS	0.091	0.095	0.000	1.523	2.591	1.562
JSLY	0.108	0.118	0.141	0.000	2.154	1.406
JSYX	0.048	0.061	0.088	0.104	0.000	2.177
ZJCX	0.106	0.117	0.138	0.151	0.103	0.000

Figure 3 Redundancy analysis (RDA) and gradient forest (GF) analysis (A), (C), (E) Association analysis between climate, geography and genetic structure; (B) Gradient forest analysis; (D), (F) Bio2 and Bio6 response curves. Bio2: Average daily temperature range; Bio6: The lowest temperature in the coldest month; Bio7: Annual temperature range; Bio8: The average temperature of the wettest quarter; Bio11: The average temperature of the coldest quarter; Bio15: Seasonal variation of precipitation; Bio17: The wettest season precipitation; Bio19: The coldest season precipitation. AHYX, AHHS, AHGD, JSLY, JSYX, and ZJCX are the same as shown in Table 1.

Figure 4 Screening of outlier single nucleotide polymorphism (SNP) sites by three methods (A) Screening by BayeScan software; (B) Screening by redundancy analysis (RDA); (C) Screening by latent factor mixed modeling (LFMM). FST: Fixation index of subdivision. Bio2, Bio6, Bio7, Bio11, and Bio19 are the same as shown in Figure 3.

Figure 5 Distribution of suitable habitats for Brachystachyum densiflorum in different periods (A) Current (1970‒2000) climate scenarios; (B) Mid Holocene climate scenarios; (C) Last Glacial Maximum climate scenarios; (D), (G) 2021-2040 climate scenarios; (E), (H) 2041-2060 climate scenarios; (F), (I) 2061-2080 climate scenarios

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