Skip to main content
Download PDF

Environment influences the genetic structure and genetic differentiation of Sassafras tzumu (Lauraceae)

BMC Ecology and Evolution volume 24, Article number: 80 (2024) Cite this article

Abstract

Background

Sassafras tzumu, an elegant deciduous arboreal species, belongs to the esteemed genus Sassafras within the distinguished family Lauraceae. With its immense commercial value, escalating market demands and unforeseen human activities within its natural habitat have emerged as new threats to S. tzumu in recent decades, so it is necessary to study its genetic diversity and influencing factors, to propose correlative conservation strategies.

Results

By utilizing genotyping-by-sequence (GBS) technology, we acquired a comprehensive database of single nucleotide polymorphisms (SNPs) from a cohort of 106 individuals sourced from 13 diverse Sassafras tzumu natural populations, scattered across various Chinese mountainous regions. Through our meticulous analysis, we aimed to unravel the intricate genetic diversity and structure within these S. tzumu populations, while simultaneously investigating the various factors that potentially shape genetic distance. Our preliminary findings unveiled a moderate level of genetic differentiation (FST = 0.103, p < 0.01), accompanied by a reasonably high genetic diversity among the S. tzumu populations. Encouragingly, our principal component analysis painted a vivid picture of two distinct genetic and geographical regions across China, where gene flow appeared to be somewhat restricted. Furthermore, employing the sophisticated multiple matrix regression with randomization (MMRR) analysis method, we successfully ascertained that environmental distance exerted a more pronounced impact on genetic distance when compared to geographical distance (βE = 0.46, p < 0.01; βD = 0.16, p < 0.01). This intriguing discovery underscores the potential significance of environmental factors in shaping the genetic landscape of S. tzumu populations.

Conclusions

The genetic variance among populations of S. tzumu in our investigation exhibited a moderate degree of differentiation, alongside a heightened level of genetic diversity. The environmental distance of S. tzumu had a greater impact on its genetic diversity than geographical distance. It is of utmost significance to formulate and implement meticulous management and conservation strategies to safeguard the invaluable genetic resources of S. tzumu.

Peer Review reports

Introduction

The genetic architecture and genetic variation serve as the underpinnings for plants to acclimate to their surroundings and ensure their survival and reproductive success [1, 2]. The greater the wealth of genetic diversity, the more adaptable a species becomes in navigating its environment, thus bestowing it with a heightened advantage in terms of survival and evolutionary potential [3]. Factors such as the geographical distribution range, growth patterns, and reproductive strategies exert influence on the genetic structure and diversity of plant species [4]. Species with a broader range of distribution may exhibit a greater tapestry of genetic variability [5]. Self-pollinating species, due to reproductive assurance, possess a more extensive geographical reach compared to their hybrid counterparts [6,7,8,9]. The duration of a species' generational growth profoundly impacts its genetic diversity. Species with shorter generations are anticipated to possess more restricted gene pools, hence fostering population isolation. Conversely, species with lengthier generation times are expected to experience a more gradual decline in genetic diversity [10], albeit this trend could also lead to genetic homogeneity. Furthermore, species with limited dispersal capabilities tend to exhibit greater differentiation, while those with long-distance dispersal mechanisms are more prone to population homogenization [10]. Thus, the genetic structure and diversity of species can, to a certain extent, serve as a reflection of their genetic evolutionary potential and adaptive capacity to their environment [11].

Sassafras tzumu, an arboreal species, pertains to the botanical family Lauraceae and falls under the genus Sassafras. It thrives abundantly across the southern region of the Yangtze River in China, flourishing at altitudes ranging from 100 to 1900 m amidst both sparse and dense woodland habitats [12]. Although the International Union for Conservation of Nature (IUCN) classifies S. tzumu as least concern (LC) and this species is not listed in the China Species Red List, in 2017, S. tzumu was included in the Reference List of Major Cultivated Precious Tree Species in China by the State Forestry Administration [13]. It usually begins to bloom from an early spring. With its vibrant crimson foliage in the autumn, ever-changing leaf patterns, and exceptional quality, S. tzumu not only served as a splendid ornamental tree but also boasted remarkable timber properties [14]. Moreover, the roots and bark possessed medicinal properties, known for their ability to enhance blood circulation, disperse blood stasis, alleviate wind and dampness, and treat contusions and lumbar muscle strains [13]. Regrettably, due to its immense commercial value, certain regions had suffered from rampant deforestation (http://qjwb.thehour.cn/html/2017-07/18/content_3547987.htm?div=-1) and theft of S. tzumu specimens (http://www.jiande.gov.cn/art/2018/6/27/art_1468690_18903167.html). In recent decades, escalating market demands and unforeseen human activities within its natural habitat had emerged as new threats to S. tzumu [15].

Presently, investigations pertaining to the genetic diversity and genetic structure of S. tzumu populations predominantly center around the analysis of genetic diversity utilizing isoenzymes and the development of microsatellite loci [14, 16,17,18]. Wang et al. [17] used 27 polymorphic nSSRs of S. tzumu to conduct genetic diversity, genetic structure analysis and mantel tests, thus providing corresponding theoretical basis for the protection and utilization of S. tzumu. A study conducted an analysis of the genetic structure of three diminutive natural populations of S. tzumu in Hubei Province, wherein the findings explicated that the proportion of polymorphic loci in the three populations stood at 49.5%. These populations were characterized by an inadequacy of heterozygotes and a surplus of homozygotes, thus signifying a state of disequilibrium [18]. Jiang et al. [14] found that five wild populations of S. tzumu at different altitudes had high genetic diversity (HE = 0.84) and moderate genetic differentiation with 13 polymorphic SSR markers from S. randaiense and Cinnamomum camphora. Employing ArcGIS 10.2 and MaxEnt 3.3.2, the distribution pattern of S. tzumu in different timeframes was simulated. The outcomes demonstrated that precipitation of driest month, precipitation of wettest month, temperature seasonality, and mean temperature of wettest quarter chiefly influenced the distribution. Furthermore, a comparison between the simulated outcomes of the distribution range during distinct periods revealed that the suitable habitat for S. tzumu contracted and shifted from the southern to the northern regions [19].

Genotyping-by-sequence (GBS) technology represented one of the streamlined genome sequencing methodologies, aiming to reduce genome complexity through the application of restriction enzymes and the incorporation of single nucleotide polymorphisms (SNPs) [20]. This technique yielded a substantial number of SNPs, which were harnessed for exploring interspecies diversity, constructing haplotype maps, conducting genome-wide association studies, and facilitating genome selection [21]. Notably, GBS offered the advantage of requiring fewer steps for database construction and enabled the establishment of databases for a large number of samples [22]. In certain genomic studies, the utilization of genotyping-by-sequencing (GBS) technology allowed for the elucidation of species' genetic diversity and hybridization characteristics [23].

The fragmentation of habitats caused by anthropogenic activities and other contributing factors, coupled with the escalating effects of global climate change, has resulted in a significant decline in the genetic diversity of numerous indigenous plant species. Such diminishment in genetic diversity has profound implications for the long-term viability and survival of these plants [24, 25]. In order to establish a robust theoretical framework for future judicious development and utilization of germplasm resource collections, this study employed cutting-edge genotyping-by-sequencing technology to delve into the intricacies of genetic diversity and genetic structure across thirteen distinct populations. The primary objectives of this research endeavor encompass the following: (1) elucidating the genetic diversity and genetic structure within the species S. tzumu; (2) discerning the interplay between genetic distance, geographical distance, and environmental factors; (3) formulating pertinent conservation policies. The findings of this study hold the potential to enhance our understanding of the genetic diversity and structural dynamics within the thirteen populations of S. tzumu, thereby furnishing the necessary scientific foundation and conservation strategies.

Results

Genotyping and sequencing analysis results

In this study, GBS technology was used to genotype 106 S. tzumu samples collected from 13 different distributions in China, and a total of 134,935 SNPs were obtained. A total of 11,862 SNPs were obtained after Vcftools filtering. Meanwhile, clean reads ranged from 2,946,429 (TMS10) to 7,999,731 (GZS03), and the mean value of clean reads of 106 samples was 4,693,475. HighQ reads ranged from 2,436,391 (TMS10) to 6,541,952 (JHS06), and the mean value was 3,815,536. HighQ reads rates ranged from 77% (SS01) to 88% (LS05), and the mean value of the HighQ reads rates was 83.22%. HighQ bases ranged from 345,967,522 (TMS10) to 928,957,184 (JHS06), and its mean value was 541,806,161. HighQ bases rates were from 73% (SS01) to 84% (LS05), and its average value was 78.77%. HighQ Q20 bases rates were from 98.934% (SS01) to 99.4015% (GZS08), HighQ Q30 bases rates were from 95.742% (GZS17) to 97.654% (GZS08), and their average values were 99.19% and 96.83%, respectively. HighQ N content ranged from 13 (FD08)—1738 (LS05), HighQ GC content ranged from 43.554 (WYS01) to 49.0725 (JGS02), and their mean values were 630.55 and 45.0424 (Supplementary file 1), respectively.

Genetic diversity and genetic differentiation

The populations exhibited a number range of 2.020 (JGS) to 2.571 (SS) alleles (NA), with an average of 2.428. The effective number of alleles (NE) ranged from 1.912 (JGS) to 2.129 (SS), with an average of 2.057. The Shannon's information index (I) varied from 0.628 (JGS) to 0.779 (SS), with a mean of 0.734. Expected heterozygosity (HE) ranged from 0.426 (JGS) to 0.490 (SS), while observed heterozygosity (HO) ranged from 0.492 (JHS) to 0.595 (JGS). The average values of HE and HO for S. tzumu were 0.469 and 0.515, respectively. The polymorphism information content (PIC) ranged from 0.8396 (JGS) to 0.9676 (SS), with a mean of 0.9459 (Table 1). The results of AMOVA revealed that the genetic variation of different populations of S. tzumu was 10% (p < 0.01) among population, 19% (p < 0.01) among individual, and the primary variation in S. tzumu was attributed to differences within populations (71%, p < 0.01). Therefore, there was greater genetic differentiation within populations (Table 2). Moderate genetic differentiation was observed among the 13 populations of S. tzumu (FST = 0.103, p < 0.01). The inbreeding coefficient (FIS) was calculated to be 0.215 (p < 0.01). The number of migrants (Nm) between the 13 populations exceeded 1 (Nm = 2.172; Table 3). This indicated that the 13 S. tzumu populations had more gene exchange overall at the species level.

Table 1 Genetic diversity index of the 13 populations of Sassafras tzumu
Full size table
Table 2 The results of analyses of molecular variance (AMOVA) for Sassafras tzumu
Full size table
Table 3 The change in genetic differentiation (FST) (above diagonal) where p < 0.01, inbreeding coefficient (FIS), and number of migrants (Nm) among 13 populations of Sassafras tzumu
Full size table

Genetic structure analysis was conducted on the population data of 11,862 SNPs from the 13 populations. The results obtained from structure harvester indicated that the most suitable clustering was achieved when K = 4 (Fig. 1 a, b). When K = 2, 13 populations of S. tzumu could be divided into two genetic clusters, specifically, Hengshan Mountains (HS), Shaoshan Mountains (SS), Meiling Mountains (ML) and Lushan Mountains (LS) were divided into one cluster, and other populations were clustered into the other one. When K = 3, 13 populations of S. tzumu could be divided into three genetic clusters, in which HS, SS, ML and LS were still one cluster, Jiuhua Mountains (JHS), Longchi Mountains (LCS), Maoshan Mountains (MS) and Tianmu Mountains (TMS) were clustered into one cluster, Fuding Mountains (FD), Guanzhai Mountains (GZS), Jigong Mountains (JGS), Tiantai Mountains (TTS) and Wuyi Mountains (WYS) were clustered into one cluster. The findings of the genetic structure analyses revealed that the populations were organized into distinct clusters when K = 4. Cluster 1 consisted of samples from HS and SS, while cluster 2 comprised samples from ML and LS. Cluster 3 encompassed a significant number of samples from FD, GZS, JGS, MS, TMS, TTS and WYS. Additionally, a few specimens sourced from the JHS and LCS were consolidated within cluster 4 (Fig. 1c).

Fig. 1
figure 1

Genetic structure analyses of 13 populations of Sassafras tzumu. a Relationship between mean LnK and K value. b Relationship between Delta K and K value. c Genetic structure plots based on SNPs data (K = 2, 3 and 4)

Full size image

The first principal component (PC1) and the second principal component (PC2) of the PCA captured 7.68% and 11.94% of the total variance, respectively. The proportions of inertia associated with PC1 and PC2 were statistically significant (p < 0.01). The results showed that HS, SS, ML and LS clustered, and others segregated from them (Figs. 2 and 3).

Fig. 2
figure 2

Principal component analyses (PCA) among 13 populations. PCA axis 1 explained 7.68% of the variance, whereas PCA axis 2 explained 11.94%. Different colors represented 13 populations

Full size image
Fig. 3
figure 3

Red points were sampling locations of S. tzumu used in this study. The map was obtained from the National Geomatics Center of China (NGCC, https://www.ngcc.cn/ngcc/html/1/391/392/16114.html)

Full size image

The multiple matrix regression with randomization (MMRR) analysis

The utilization of MMRR analysis had unveiled a noteworthy positive correlation between genetic and geographical distances amongst the 13 populations (r = 0.58, p < 0.01; Fig. 4a). Within the 13 S. tzumu populations, the regression coefficient of environmental distance (βE = 0.46, p < 0.01) exceeded that of geographical distance (βD = 0.16, p < 0.01) by approximately threefold, implying that IBE predominantly accounted for the genetic distance. However, IBD also made a considerable contribution (Fig. 4b). Additionally, a significant association between genetic and environmental distances was observed (r = 0.56, p < 0.01; Fig. 4c). Furthermore, the outcomes of MMRR analyses demonstrated a significant association between environmental distances and geographical distances (r = 0.97, p < 0.01; Fig. 4d). In conclusion, the genetic distance among the 13 S. tzumu populations was jointly influenced by environmental and geographical distances (Table 4). Notably, environmental distance exhibited a more pronounced impact on genetic distance.

Fig. 4
figure 4

a Correlations between genetic distance and geographical distance. b Geographical distance and environmental distance effects on genetic distance. c Correlations between genetic distance and environmental distance. d Correlations between environmental distance and geographical distance

Full size image
Table 4 The results of multiple matrix regression with randomization (MMRR) analyses of among genetic distance and different factors
Full size table

Discussion

Genetic diversity is the main factor leading to population survival and evolution. It determines the coping ability of natural populations under the stress of various biotic and abiotic factors, which is crucial for the long-term survival of populations [26]. Genetic diversity is directly affected by species' own factors, including mating system, meiotic behavior, gene flow, mutation and natural selection [27,28,29]. In addition, human activities and environmental factors can also affect the level of genetic diversity of species, such as temperature, water, light, wind, soil salinity and nutrients, and the surrounding biological communities may exert different selective pressures on plant populations, thereby determining the evolution process of the population and shaping the genetic diversity and structure of populations [30, 31]. The greater the genetic variation of a species, the stronger its capacity to adapt to intricate and ever-changing environments [32]. We can quantify the genetic diversity of a species by calculating its expected heterozygosity (HE) [33]. The mean HE value of the 13 S. tzumu populations stood at 0.469, surpassing that of 39 Cinnamomum camphora populations distributed in China (HE = 0.322) [34]. Moreover, the HE and HO values of the 13 S. tzumu populations were lower than those of other arboreal species, such as Xanthoceras sorbifolium (HE = 0.53 and HO = 0.72) [35] and Olea europaea L. (HE = 0.60 and HO = 0.75) [36]. In contrast to the extensive genetic diversity observed in the aforementioned studies, it can be inferred that the level of genetic diversity of the S. tzumu populations examined in this study is inherently high.

Wright [37] believed that genetic differentiation coefficient (FST) among populations was between 0 and 0.05, indicating that there was no genetic differentiation, and the FST value between 0.05 and 0.15 was moderately differentiated, then the FST value between 0.15 and 0.25 was highly differentiated. Furthermore, the mean FST value in our study was calculated to be 0.103, suggesting a moderate level of differentiation among 13 S. tzumu populations Compared with other Lauraceae plants, it was much lower than and Cryptocarya chinensis (FST = 0.141) [38] and Litsea szemaois (GST = 0.37) [39], and had a similar value with Cinnamomun camphora (FST = 0.109) [40]. The predominant distribution of genetic variation within 13 S. tzumu populations was observed to be within populations (71%, p < 0.01), whereas the genetic variation among populations was minimal (10%, p < 0.01). These findings aligned with the outcomes of previous studies on perennial plants [41] and further supported the notion that the genetic differentiation of S. tzumu primarily occurred within populations (93.6%, p < 0.001) [14]. Similar to Zhang's investigation, which focused on genus Phoebe, the primary source of variation in this species was within population (about 75.5%) rather than between populations (about 24.5%) [42]. Genetic diversity played a crucial role in adapting to extreme environments, and insufficient diversity could impede survival advantages in the face of environmental changes. Despite the current wide distribution of S. tzumu, it may lack sufficient genetic diversity to adapt to climate change. The inbreeding coefficient (FIS) was calculated to be 0.215. It was worth noting that a high inbreeding coefficient might result in a decrease in genetic diversity and an increase in genetic structure within the 13 S. tzumu populations [43].

The reproductive strategy of S. tzumu entails cross-pollination, facilitated by its amphimerotic flowers. Insects act as the primary agents for pollen dispersal, while birds play a role in fruit dispersion [44]. These two mechanisms of transmission are the key drivers of gene flow among populations. The transfer of genetic information occurs through the fruits, thereby contributing to gene flow [16]. This study revealed a certain degree of gene exchange (Nm = 2.172) among the 13 S. tzumu populations. This could be attributed to the prolonged presence of frugivorous birds within the same population, who consumed the fruit seeds of S. tzumu and facilitated gene exchange within populations. Additionally, it was determined that the genetic differentiation level among the 13 natural S. tzumu populations was a moderate significance.

Based on the genetic structure analysis results of 13 populations of S. tzumu, S. tzumu could be divided into four clusters: cluster 1 was distributed in Hunan Province (HS and SS populations), cluster 2 was distributed in Jiangxi Province (ML and LS populations), cluster 3 (FD, GZS, JGS, MS, TMS, TTS and WYS) was mostly located in the eastern part of the populations, and cluster·4 included JHS and LCS populations (Fig. 1c). However, the results of PCA supported the HS, SS, ML and LS groups were cluster 1 and other groups were cluster 2 (Figs. 2 and 3). And the results of IBD analysis showed that the spatial distribution pattern of gene clusters and geographical distance of S. tzumu populations were extremely significant correlation (r = 0.58, p < 0.01, see Fig. 4a). Based on the study of major peaks and mountains in China by Wang et al. [45], the divergence of cluster 1 and cluster 2 was related to the geographical boundaries of Wuyi Mountains. The four populations in this study, HS, SS, ML and LS formed one cluster, which was consistent with cluster 2 in Zhou's research results [46]. A total of 9 populations of S. tzumu, FD, GZS, JGS, JHS, LCS, MS, TMS, TTS and WYS constituted another cluster, which was consistent with cluster 1 in Zhou's study. Finally, we are more supportive of the grouping of genetic structures in PCA.

Woody plants have a similar life history. Tapiscia sinensis (Tapisciaceae), whose life history is defined as outcrossing, and its seeds and pollen also spread over short distances [47]. In addition, other species with dioecious or morphologically dioecious but functionally dioecious breeding systems tend to maintain high genetic structure [48, 49]. Meanwhile, some potential factors may affect genetic structure, such as habitat fragmentation, breeding system and life forms of plants [50, 51].

The Multiple Matrix Regression with Randomization (MMRR) analysis is a linear regression model that aims to quantify the impact of multiple explanatory variables. A portion of the genetic variation could be accounted for geographical distance (r = 0.58, p < 0.01; Fig. 4a). The S. tzumu populations in cluster 1 and cluster 2 were distinct due to geographical distance. This could explain the results of the previous principal component analysis. Moreover, the results of MMRR analyses demonstrated that genetic distance was influenced by both geographical distance and environmental distance (r = 0.57, p < 0.01; Fig. 4b). But environmental distance of S. tzumu in this study had a greater and profounder impact on its genetic diversity than geographical distance (βE = 0.46, p < 0.01; βD = 0.16, p < 0.01; Fig. 4b), which could be attributed to its preference for warm and humid habitats based on its biological characteristics [52]. IBD and IBE (βD = 0.404, p < 0.001; βE = 0.382, p < 0.001) were the major and equal contributor to genetic differentiation among 61 populations of Neolitsea sericea (Lauraceae) in the study of Cao et al. [53]. Notably, IBE (r = 0.56, p < 0.01; Fig. 4c) exerted a significant influence on genetic distance. In the event of unfavorable environmental conditions, such as cold frosts or inclement weather during the pollination period, the pollination success of S. tzumu could be easily compromised [16], resulting in blooming without fruiting. Meanwhile, the distribution pattern of S. tzumu populations was found to be associated with elevation, slope direction, slope position, and humus thickness [54]. Research indicated that relative humidity (accounting for 26.2% of permutation importance), mean temperature of coldest quarter (16.6%), annual precipitation (12.6%), and temperature annual range (10.3%) were the primary factors influencing the distribution of S. tzumu in China [15].

In the research, 13 populations of S. tzumu exhibited a moderate degree of genetic diversity, rendering them less resilient to diverse habitats and intricate climate fluctuations, thereby posing a potential threat to the species' survival [55]. Consequently, it is imperative to implement protective measures. Firstly, there is a need to enhance the promotion of plant preservation and cultivate public consciousness regarding this matter. This can be achieved by implementing localized protective measures in economically underdeveloped and remote areas with limited transportation and inadequate awareness, as well as intensifying the dissemination of information regarding the conservation of S. tzumu to curb deforestation. Secondly, it is advisable to establish a nationwide network for ex situ conservation of plants, with National Botanical gardens playing a pivotal role. This network should encompass the creation of ecological corridors to facilitate gene flow among S. tzumu populations. Thirdly, in regions highly susceptible to climate change, it is recommended to introduce tree species that are known to adapt well to specific climatic conditions, instead of further expanding the cultivation of S. tzumu. Lastly, it is suggested to prioritize single plant selection and asexual propagation, while developing a comprehensive and scientifically guided breeding strategy for the development and utilization of S. tzumu.

In conclusion, we screened and developed 11,862 SNPs to effectively elucidate the genetic structure of S. tzumu populations. The findings revealed that S. tzumu populations exhibited a high level of genetic diversity. Simultaneously, it had come to our attention that the existing S. tzumu resources had suffered significant damage due to deforestation. In remote areas characterized by relatively underdeveloped economies, limited transportation, and insufficient protection and public awareness, it became imperative to implement in situ conservation measures and bolstered the dissemination of information regarding the protection of S. tzumu to deter indiscriminate deforestation. As for the development and utilization of S. tzumu resources, we propose placing emphasis on selective breeding of individual camphor trees, complemented by asexual reproduction. Additionally, it is crucial to formulate scientifical and comprehensive breeding strategies, manage S. tzumu genetic resources in a scientific manner, and enhance the sustainable utilization of these resources.

Methods

Collection and preservation of plant materials

During the summer of 2017, we gathered fresh leaves without pests or diseases as plant material samples from 13 naturally existing populations of S. tzumu across its range in China (Fig. 3). We made sure to collect individuals that were at least 50 m apart, with a collection of 2–10 individuals from each population. Ultimately, we carefully selected a total of 106 samples of S. tzumu for analysis (Table 5). To maintain the plant leaves' integrity, we carefully dried the leaves in sealed plastic bags with silica gel and stored them in a freezer at -20℃.

Table 5 The sampling locations of Sassafras tzumu
Full size table

DNA extraction and genotyping-by-sequencing data set

For DNA extraction, dried floral leaves were subjected to the Plant Genomic DNA kit (Tiangen, Beijing, China) following the manufacturer's instructions. The extracted DNA from all samples was quantified using a Qubit spectrophotometer. To facilitate genotyping by sequencing, all samples were sent to the esteemed Institute of Shanghai OE Biotech. Co., Ltd. In brief, the DNAs from the 106 individuals were digested with EcoRI-HF and MspI to reduce the complexity of the genome. Subsequently, a 106-plex GBS library, comprising 105 DNA samples and a negative control (no DNA), was meticulously prepared by ligating the digested DNA to unique barcode nucleotide adapters, followed by standard PCR amplification. Finally, the resulting 106-plex library was sequenced on a single lane of an HiSeq X Ten platform. Sequence data obtained from the Hiseq X Ten platform were processed for SNPs identification using the GBS pipeline integrated within Stacks 3.0.166 [56]. In brief, variants were filtered using Vcftools 0.1.14 [57] based on criteria such as a minimum depth of coverage (> 5), quality score (> 30), and an initial maximum missingness of 50% [58]. Subsequently, the dataset was examined to ensure that no samples exhibited high levels of missingness (all samples were found to have less than 30% missing data). The final set of SNPs was further filtered to retain those with a maximum of 20% missing values and a minor allele frequency below 0.05.

Genetic diversity and genetic structure analysis

The resulting vcf file in our GBS data set was converted into compatible formats using PGDspider 2.0.9.0 [59] Genetic differentiation (FST) was calculated for each SNP using GenAlEx 6.501 [60], and these values were utilized for analyses of molecular variance (AMOVA) among populations. To determine the number of genetic clusters across populations, the STRUCTURE 2.3.4 [61] was employed. The genetic structure analysis was conducted with three independent replicates, ranging from K = 2 to K = 13. Each run consisted of 5.0 × 104 burn-in iterations and 3.0 × 104 MCMC replications under the admixture model. The resulting output was submitted to the Structure Harvester [62] website for further analysis. The best K value was determined to represent the best number of clusters. The Q-matrix data, including Kx. indfile (individuals) and Kx. popfile (populations), obtained from multiple runs were downloaded. These data were then analyzed using CLUMPP [63] and visualized using DISTRUCT [64] and Adobe Illustrator 2021. To explore the clustering patterns between populations, principal components analysis (PCA) was performed using GenAlEx 6.501 [60].

The multiple matrix regression with randomization analysis

Geographical distance and environmental distance affect gene flow and genetic differentiation between populations [65], and isolation by distance (IBD) and isolation by environment (IBE) are important ways to reflect that the complex landscapes affect the genetic structure of natural populations [66,67,68,69,70]. When gene flow may be affected by geographical and environmental variables, multiple matrix regression analysis (MMRR) [71] provides a valuable approach to quantify the impact of geographical and environmental isolation on genetic distance. In contrast to the many methods used to analyze distance matrices in landscape genetics [72,73,74], MMRR can ask not only whether variables are correlated but also how the dependent variable changes with respect to multiple independent variables, contributing to a comprehensive understanding of how landscape influences gene flow patterns.

In the study, the geosphere package in R software [75] was utilized to compute the euclidean distance of the latitude and longitude information from 13 populations. Additionally, MEGA 11 [76] was employed to determine the genetic distance among these populations. In this study, we used climate variables, soil pH and elevation as environmental factors. The climate variables (1970–2000) and elevation layer were downloaded from WorldClim website (https://worldclim.org), and soil pH was downloaded from ISRIC — World Soil Information (https://www.isric.org/). Then, we used Maxent 3.3.1 [77] to simulate the suitable layer in the species distribution model. SDM Tools in ArcMap 10.8 was used for converting from environment suitability layer to migration resistance layer. The value of the environmental layer in sampling locations was extracted from the matrix format utilizing ArcMap 10.8 [78], and the specifical operation was “Spatial Analyst Tools—Extract by points”.

The isolation by distance (IBD) and isolation by environment (IBE) were quantified using the "MMRR" function in R software [79]. We used genetic information as the response variable, with geographical and environmental distances serving as explanatory variables to describe the patterns of IBD and IBE, the correlation between the three matrices was computed to assess the impact of geographical distance and environmental distance on genetic distance.

Availability of data and materials

The datasets generated and/or analyzed during the current study are available in the Figshare repository under persistent web link “https://figshare.com/articles/dataset/Data_in_VCF_format_for_single_nucleotide_polymorphisms_SNPs_of_13_i_Sassafras_tzumu_i_Lauraceae_populations_with_106_individuals/24899328”.

References

  1. Buzhdygan OY, Meyer ST, Weisser WWG, Eisenhauer N, Ebeling A, Borrett SR, et al. Biodiversity increases multitrophic energy use efficiency, flow and storage in grasslands. Nat Ecol Evol. 2020;4:393–405.

    Article  PubMed  Google Scholar 

  2. Isbell F, Craven D, Connolly J, Loreau M, Schmid B, Beierkuhnlein C, et al. Biodiversity increases the resistance of ecosystem productivity to climate extremes. Nature. 2015;526:574–89.

    Article  CAS  PubMed  Google Scholar 

  3. Agashe D, Falk JJ, Bolnick DI. Effects of founding genetic variation on adaptation to a novel resource. Evolution. 2011;65:2481–91.

    Article  PubMed  Google Scholar 

  4. Hu XQ, Wu S, Wang YG, Zhao HB, Zhang YY. Genetic diversity and genetic structure of different types of natural populations in Osmanthus fragrans Lour. and the relationships with sex ratio, population structure, and geographic isolation. Sci World J. 2014;2014:817080.

    Article  Google Scholar 

  5. Hamrick JL, Godt MJW. Allozyme diversity in plant species. Crop Sci. 1997;37:26–30.

    Article  CAS  Google Scholar 

  6. Baker HG. Self-compatibility and establishment after “long-distance” dispersal. Evolution. 1955;9:347–9.

    Google Scholar 

  7. Grossenbacher D, Runquist RB, Goldberg EE, Brandvain Y. Geographic range size is predicted by plant mating system. Ecol Lett. 2015;18:706–13.

    Article  PubMed  Google Scholar 

  8. Pannell JR. Evolution of the mating system in colonizing plants. Mol Ecol. 2015;24:2018–37.

    Article  PubMed  Google Scholar 

  9. Stebbins GL. Self-fertilization and population variability in the higher plants. Am Nat. 1957;91:337–54.

    Article  Google Scholar 

  10. Loveless MD, Hamrick JL. Ecological determinants of genetic structure in plant populations. Annu Rev Ecol Evol Syst. 1984;15:65–95.

    Article  Google Scholar 

  11. Yan JW, Bai WF, Li JH, Yu L, Nie DL, Xiong Y, Wu SZ. Genetic structure and diversity of Cerasus conradinae in Hunan Province. J Plant Genet Resour. 2022;23:376–84.

    Google Scholar 

  12. Li XW, Li J, van der Werff H. Sassafras J. Presl in Berchtold & J. Presl Prir. Rostlin 2(2): 30. 1825. Flora of China. Beijing: Science Press; St. Louis: Missouri Botanical Garden Press; 2008:159–161.

  13. Chen HZ, Liu J, Jiang JM, Sun Y, Dong X, Fu AP. A study on flowering and fruit development of Sassafras tzumu. For Res. 2020;33:148–54.

    Google Scholar 

  14. Jiang AP, Jiang JM, Liu J. Genetic diversity and genetic structure in Sassafras tzumu populations along altitudinal gradients in Tianmushan Mountain. China J Appl Ecol. 2016;27:1829–36.

    Google Scholar 

  15. Zhang KL, Zhang Y, Jia DW, Tao J. Species distribution modeling of Sassafras tzumu and implications for forest management. Sustainability. 2020;12:4132.

    Article  Google Scholar 

  16. Chung KF, van der Werff H, Peng CI. Observations on the floral morphology of Sassafras randaiense (Lauraceae). Ann Mo Bot Gard. 2010;97:1–10.

    Article  Google Scholar 

  17. Wang S, Wang Y, Zhou JB, Li P, Lin HW, Peng Y, et al. Genetic diversity and population structure of an arctic tertiary relict tree endemic to China (Sassafras tzumu) revealed by novel nuclear microsatellite (nSSR) markers. Plants. 2022;11:2706.18.

    Article  Google Scholar 

  18. Ding XF, Chen HL, Cao J, Koozo K, Masatosi U, Masanori O. Preliminary study on genetic structure of three natural populations in Sassafrass Tzumu. Hubei Forestry Science and Technology. 2006;5:1–2.

  19. Liu X, Gong X, Chen SS, Guan BC. Simulation of the distribution pattern of Sassafras tzumu and changes in habitat based on ArcGIS and MaxEnt. Plant Sci J. 2018;36:320–6.

    Google Scholar 

  20. Wu ZY, Zong D, Gan PH, Liu ZT, Zhu MC, He CZ. Genetic analysis on different stem forms of Pinus yunnanensis by reduced-representation genome sequencing. J Yunnan Agric Univ (Nat Sci). 2022;37:285–93.

    Google Scholar 

  21. Poland JA, Rife TW. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome. 2012;5:92–102.

    CAS  Google Scholar 

  22. Rowe HC, Renaut S, Guggisberg A. RAD in the realm of next-generation sequencing technologies. Mol Ecol. 2011;20:3499–502.

    CAS  PubMed  Google Scholar 

  23. Alipour H, Bihamta MR, Mohammadi V, Peyghambari SA, Bai GH, Zhang GR. Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat Landraces and cultivars. Front Plant Sci. 2017;8:1293.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Wang J, Li ZJ, Guo QH, Ren GP, Wu YX. Genetic variation within and between populations of a desert poplar (Populus euphratica) revealed by SSR markers. Ann For Sci. 2011;68:1143–9.

    Article  Google Scholar 

  25. Zhao Y, Li GY, Yang J. Conservation and utilization of wild relatives of cultivated plants. Biodiversity Science. 2018;26:414–26.

    Article  Google Scholar 

  26. Khan MK, Pandey A, Thomas G, Akkaya MS, Kayis SA, Ozsensoy Y, et al. Genetic diversity and population structure of wheat in India and Turkey. AoB Plants. 2015;7:plv083.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Levin DA, Kerster HW. Gene flow in seed plants. Evol Biol. 1974;7:139–220.

    Google Scholar 

  28. Linhart YB, Grant MC. Evolutionary significance of local genetic differentiation in plants. Annu Rev Ecol Evol Syst. 1996;27:237–77.

    Article  Google Scholar 

  29. Gutiérrez-Ortega JS, Molina-Freaner F, Martínez JF, Pérez-Farrera MA, Vovides AP, Hernández-López A, et al. Speciation along a latitudinal gradient: The origin of the Neotropical cycad sister pair Dioon sonorense –D. vovidesii (Zamiaceae). Ecol Evol. 2021;11:6962–76.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Peleg Z, Saranga Y, Krugman T, Abbo S, Nevo E, Fahima T. Allelic diversity associated with aridity gradient in wild emmer wheat populations. Plant Cell Environ. 2008;31:39–49.

    Article  PubMed  Google Scholar 

  31. Castilla AR, Méndez-Vigo B, Marcer A, Martínez-Minaya J, Conesa D, Picó FX, et al. Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana. BMC Evol Biol. 2020;20:71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Du QZ, Wang BW, Wei ZZ, Zhang DQ, Li BL. Genetic diversity and population structure of Chinese white poplar (Populus tomentosa) revealed by SSR markers. J Hered. 2012;103:853–62.

    Article  PubMed  Google Scholar 

  33. Li CH, Zheng YQ, Liu Y, Lin FR, Huang P. Development of genomic SSR for the subtropical hardwood tree Dalbergia hupeana and assessment of their transferability to other related species. Forests. 2021;12:804.

    Article  Google Scholar 

  34. Gong X, Yang A, Wu Z, Chen C, Li H, Liu Q, et al. Employing genome-wide SNP discovery to characterize the genetic diversity in Cinnamomum camphora using genotyping by sequencing. Forests. 2021;12(11):1511.

    Article  Google Scholar 

  35. Shen Z, Zhang KQ, Ma LY, Duan J, Ao Y. Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data. Electron J Biotechnol. 2017;26:33–9.

    Article  Google Scholar 

  36. Dervishi A, Jakše J, Ismaili H, Javornik B, Štajner N. Comparative assessment of genetic diversity in Albanian olive (Olea europaea L) using SSRs from anonymous and transcribed genomic regions. Tree Genet Genomes. 2018;14:53.

    Article  Google Scholar 

  37. Wright S. Evolution and the genetic of population, variability within and among natural populations. Chicago: University of Chicago Press; 1978;4:213–20.

  38. Gao SH, Wang ZF, Zhang JL, Tian SN. Genetic diversity of Cryptocarya chinensis life stages in heishiding Guangdong Province. J Plant Genet Resour. 2005;6:300–3.

    Google Scholar 

  39. Chen JQ, Ci XQ, Li QM, Li J. Genetic diversity of Litsea szemaois, an endangered species endemic to China, detected by inter-simple sequence repeat (ISSR). Biodivers Sci. 2006;14:410–20.

    Article  CAS  Google Scholar 

  40. Liu S. Population genetic structure of Cinnamomum camphora in China [D]. Master Dissertation, Jiangxi Agricultural University, Nanchang, China. 2019.

  41. Xing C, Tian Y, Guan FC, Meng FJ. Evaluation of genetic diversity in Amygdalus mira (Koehne) Ricker using SSR and ISSR markers. Plant Syst Evol. 2015;301:1055–64.

    Article  Google Scholar 

  42. Zhang R, Zhou ZC, Jin GQ, Wang SH, Wang XH. Genetic diversity and differentiation within three species of the family Lauraceae in southeast China. Biochem Syst Ecol. 2012;44:317–24.

    Article  CAS  Google Scholar 

  43. Cole CT. Genetic variation in rare and common plants. Annu Rev Ecol Evol Syst. 2003;34:213–37.

    Article  Google Scholar 

  44. Yang Z, Tan C, Wei YM, Rohwer JG, Liu B, Yang Y. Floral morphology and phenology of Sassafras tzumu (Lauraceae). BMC Plant Biol. 2022;22:327.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Wang XP, Wang ZH, Fang JY. Mountain ranges and peaks in China. Biodiversity Science. 2004;01:206–12.

    Google Scholar 

  46. Zhou JB. The population genetics of Sassafras tzumu based on nuclear microsatellite (nSSR) [D]. Master Dissertation, Nanjing University, Nanjing, China. 2021.

  47. Zhang JJ, Li ZZ, Fritsch PW, Tian H, Yang AH, Yao XH. Phylogeography and genetic structure of a Tertiary relict tree species, Tapiscia sinensis (Tapisciaceae): implications for conservation. Ann Bot. 2015;116:727–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Rendell S, Ennos RA. Chloroplast DNA diversity of the dioecious European tree Ilex aquifolium L. (English holly). Mol Ecol. 2003;12:2681–8.

    Article  CAS  PubMed  Google Scholar 

  49. Wang J, Gao P, Kang M, Lowe AJ, Huang H. Refugia within refugia: the case study of a canopy tree Eurycorymbus cavaleriei in subtropical China. J Biogeogr. 2009;36:2156–64.

    Article  Google Scholar 

  50. Wang HW, Ge S. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA. Mol Ecol. 2006;15:4109–22.

    Article  CAS  PubMed  Google Scholar 

  51. Vekemans X, Hardy OJ. New insights from fine-scale spatial genetic structure analyses in plant populations. Mol Ecol. 2004;13(4):921–35.

    Article  CAS  PubMed  Google Scholar 

  52. Sun JJ, Jiang B, Wu CP, Yuan WG, Zhu JR, Huang YJ, et al. Study on the habitat and niche of Sassafras tzumu (Hemsl.) Hemsl. in Zhejiang Province. Acta Ecologica Sinica. 2019;39:884–94.

    Google Scholar 

  53. Cao YN, Wang IJ, Chen LY, Ding YQ, Liu LX, Qiu YX. Inferring spatial patterns and drivers of population divergence of Neolitsea sericea (Lauraceae), based on molecular phylogeography and landscape genomics. Mol Phylogenet Evol. 2018;126:162–72.

    Article  PubMed  Google Scholar 

  54. Sun JJ, Guo JH, Shen AH, Xu X, Feng HL, Zhang S, et al. Composition and environmental interpretation of the communities of Sassafras tzumu, a protected species, at Zhejiang Province in eastern China. Glob Ecol Conserv. 2020;24:e01218.

    Google Scholar 

  55. Zhou PY, Hui LX, Huang SJ, Ni ZX, Yu FX, Xu LA. Study on the genetic structure based on geographic populations of the endangered tree species: Liriodendron chinense. Forests. 2021;12:917.

    Article  Google Scholar 

  56. Catchen JL, Hohenlohe PA, Bassham SS, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol. 2013;22:3124–40.

    Article  PubMed  PubMed Central  Google Scholar 

  57. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics. 2011;27:2156–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. da Cunha NL, Xue HR, Wright SI, Barrett SCH. Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range. Mol Ecol. 2022;31(20):5307–25.

    Article  PubMed  Google Scholar 

  59. Lischer HEL, Excoffier L. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics. 2012;28:298–9.

    Article  CAS  PubMed  Google Scholar 

  60. Smouse PE, Whitehead MR, Peakall R. An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation. Mol Ecol Resour. 2015;15:1375–84.

    Article  PubMed  Google Scholar 

  61. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Earl DA, VonHoldt BM. Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Cons Genet Res. 2012;4:359–61.

    Article  Google Scholar 

  63. Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007;23:1801–6.

    Article  CAS  PubMed  Google Scholar 

  64. Rosenberg NA. DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes. 2003;4:137–8.

    Article  Google Scholar 

  65. Wright S. Isolation by distance. Genetics. 1943;28:114–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Nosil P. Reproductive isolation caused by visual predation on migrants between divergent environments. Proc Biol Sci. 2004;271:1521–8.

    Article  PubMed  PubMed Central  Google Scholar 

  67. Nosil P, Vines TH, Funk DJ. Perspective: Reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution. 2005;59:705–19.

    PubMed  Google Scholar 

  68. Wang IJ, Summers K. Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog. Mol Ecol. 2010;19:447–58.

    Article  PubMed  Google Scholar 

  69. Lee-Yaw JA, Davidson A, Mcrae BH, Green DM. Do landscape processes predict phylogeographic patterns in the wood frog? Mol Ecol. 2009;8:1863–74.

    Article  Google Scholar 

  70. Zellmer AJ, Hanes MM, Hird SM, Carstens BC. Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata. Syst Biol. 2012;61:763–77.

    Article  PubMed  Google Scholar 

  71. Wang IJ. Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation. Evolution. 2013;67:3403–11.

    Article  PubMed  Google Scholar 

  72. Holderegger R, Wagner HH. Landscape genetics. Bioscience. 2008;58:199–207.

    Article  Google Scholar 

  73. Balkenhol N, Waits LP, Dezzani RJ. Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography. 2009;32:818–30.

    Article  Google Scholar 

  74. Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP. Landscape genetics: where are we now? Mol Ecol. 2010;19:3496–514.

    Article  PubMed  Google Scholar 

  75. Karney CFF. Algorithms for geodesics. J Geod. 2013;87:43–55.

    Article  Google Scholar 

  76. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol. 2021;38:3022–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Phillips SJ, Anderson RP, Schapire RE. Maximum entropy modeling of species geographic distributions. Ecol Model. 2006;190:231–59.

    Article  Google Scholar 

  78. Brown JL. SDMtoolbox: a python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses. Methods Ecol Evol. 2014;5:694–700.

    Article  Google Scholar 

  79. Legendre P, Lapointe FJ, Casgrain P. Modeling brain evolution from behavior: a permutational regression approach. Evolution. 1994;48:1487–99.

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the other members of our research group from Laboratory of Landscape Genetics, Nanchang University for their assistance.

Funding

This work was supported by the Natural Science Foundation of Jiangxi Province (Grant No.20212BAB205030).

Author information

Authors and Affiliations

  1. School of Life Sciences, Nanchang University, Nanchang, 330031, China

    Bicai Guan, Qian Liu, Xiang Liu & Xi Gong

Authors
  1. Bicai Guan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qian Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xi Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization, Bc.G., Q.L., X.L., and X.G.; Data curation, X.L.; Formal analysis, Q.L.; Funding acquisition, X.G.; Investigation, X.L. and X.G.; Methodology, Q.L. and Bc.G.; Resources, Bc.G.; Visualization, Q.L.; Writing-original draft, Q.L. and X.L.; Writing-review and editing, Bc. G., Q.L., X.L., and X.G.; Supervision, X.G. and Bc.G.; All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Xi Gong.

Ethics declarations

Ethics approval and consent to participate

We ensure the collection of the plants used in the study (Sassafras tzumu) complies with Chinese guidelines. All methods were carried out in accordance with relevant guidelines and regulations.

Consent for publication

Not applicable to this study.

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guan, B., Liu, Q., Liu, X. et al. Environment influences the genetic structure and genetic differentiation of Sassafras tzumu (Lauraceae). BMC Ecol Evo 24, 80 (2024). https://doi.org/10.1186/s12862-024-02264-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12862-024-02264-9

Keywords

BMC Ecology and Evolution

ISSN: 2730-7182

Contact us