The brine shrimp Artemia is a small crustacean that lives in hypersaline habitats such as salt lakes and coastal salt pans worldwide. In addition to being a major part of the food chain and a biological regulator of brine ecosystems (Triantaphyllidis et al., 1998; Sánchez et al., 2006; Georgiev et al., 2007), Artemia, especially Artemia nauplii obtained by hatching Artemia cysts, are crucial live food items in fish and shrimp larviculture (Sorgeloos et al., 2001). As a natural resource, the yield and quality of Artemia cysts are greatly influenced by environmental factors, such as salinity, temperature, food availability, and harvesting management (Wurtsbaugh and Maciej Gliwicz, 2001; Torrentera and Dodson, 2004; Van Stappen et al., 2020). In recent years, global warming has led to an increase in surface evaporation and changes in the spatiotemporal pattern of precipitation (Li et al., 2018), resulting in changes in the spatiotemporal distribution and biological diversity. Compared with marine and freshwater environments, the diversity and number of species in high-salinity habitat systems are often limited, making them more vulnerable and posing greater threats to biodiversity within these ecosystems. Salinity is the main environmental factor for the survival and reproduction of Artemia (Torrentera and Dodson, 2004). Artemia can survive in a salinity range of 15–300 g/L (Sung et al., 2008). However, the Artemia population suffers from significant salinity fluctuations in salt lakes. For example, the gradual drying of Lake Urmia in Iran has led to near-saturation levels of lake salinity and the loss of more than 90% of the Artemia population over the past two decades (Asem et al., 2019). In contrast, the Qinghai-Tibet Plateau (QTP) is experiencing warming and changing precipitation patterns, with a steady flow of freshwater from glaciers and snowmelt on the QTP into the plateau salt lakes, leading to salinity reduction and further triggering the survival crisis of Artemia in these salt lakes (Song et al., 2017). For instance, Qixiang Co, the most productive salt lake for Artemia cysts on the QTP, has gradually approached a salinity limit of 40 g/L in recent years.

Climate fluctuations are important drivers of changes in the current distribution, genetic diversity, and abundance of many species and communities (Hewitt, 2004). Species distribution models (SDMs) are among the primary tools used to infer the habitats of past species (Gavin et al., 2014). Combining SDMs with genetic analyses can reveal population differences across distributional ranges as well as population expansion and contraction. Moreover, SDMs can help explain the adaptive responses of different geographic populations to current and future environmental conditions and provide more accurate range estimates for the conservation management of threatened populations. Although climate change has threatened the sustainable production of Artemia cysts in recent years, currently there have been no reports that have combined SDMs and population genetics to study the responses of Artemia species to global warming.

Genetic diversity is the core of conservation research on species and a prerequisite for survival, adaptation, and evolution. The study of the diversity and population structure between and within populations is essential for the effective management of genetic resources. In recent years, molecular markers such as SSR, COI, and ITS1 (Han et al., 2019; Li et al., 2024) have been used to study the population genetic structure and genetic diversity of Artemia. The results showed that the genetic structure was clear between the Tibetan, Xinjiang, and Shanxi populations but was more complex within the Tibetan populations. Compared to these molecular markers, single-nucleotide polymorphisms (SNPs) have recently been recognized as some of the most popular molecular markers for genetic research because of their abundance, high stability, high polymorphism, etc (You et al., 2020). The emergence of multiple high-throughput sequencing technologies such as Rad-Seq, GBS, and SLAF-Seq has made it possible to obtain a large number of markers for population genetic analysis, germplasm resource evaluation, and phylogenetic evolution studies in many animals and plants. More recently, the SLAF-seq method was used to develop SNP markers and construct the first high-density genetic linkage map for Artemia franciscana (Han et al., 2021). However, there are few reports on the application of SNP in Artemia population genetics and molecular phylogeny (Li et al., 2024).

The genus Artemia has six sexually dimorphic species (Artemia. franciscana, Artemia. persimilis, Artemia. salina, Artemia. sinica, Artemia. urmiana, and Artemia. tibetiana) and many parthenogenetic Artemia populations. Recently, three new species (Artemia. murae, Artemia. frameshifta, and Artemia. sorgeloosi) were identified in the salt lakes in Mongolia and China (Naganawa and Mura, 2017; Asem et al., 2023). A. tibetiana and A. sinica are indigenous to China. The traditional view is that all Artemia species in Tibet belong to A. tibetiana. While salt lakes in Tibet are geographically close, they are relatively isolated, showing a fragmented distribution that may result in a certain degree of genetic differentiation of Artemia in Tibet. In recent years, people have introduced A. sinica and colonized successfully in Tibet, which, combined with the fact that Artemia cysts can be transmitted by waterfowls (Vest and Conover, 2011; Reynolds et al., 2015), necessitates studies into gene flows between salt lakes. There is evidence that Artemia populations in Tibet do not all belong to A. tibetiana (Abatzopoulos et al., 1998; Asem et al., 2023). Therefore, further research is needed to better understand the population genetic structure of Artemia in this region.

Artemia has a short reproductive cycle, viviparous and ovoviviparous reproduction modes, high level of genetic variability, and easy handling in the laboratory; thus, it is an ideal experimental organism in genetics, developmental biology, and molecular biology studies (Baxevanis et al., 2006; Duan et al., 2014, 2022). This study aimed to (1) determine the genetic diversity of Artemia in central and western China to guide the rational exploitation of Artemia resources, (2) explore the genetic structure to provide a reasonable reference for taxonomy (especially Tibetan Artemia), and (3) elucidate the relationship between geographic isolation and genetic differentiation using IBD (isolation by distance). This was the first time that Treemix and Maxent were used to study gene flow and species distribution to explore the historical dynamics of Artemia populations.

Genetic diversity is the basis of species diversity and an important prerequisite for the study of any species, affecting the evolutionary and reproductive potential of the species or population (Reusch, 2014; Schrieber and Lachmuth, 2017). In this study, ten individuals from each salt lake were used to develop SNP and the genetic diversity of the Tibetan populations was found to be higher than that of the other populations, while the Shanxi population had the lowest genetic diversity. This result was inconsistent with our previous findings in these populations (Han et al., 2019), in which the Shanxi population had the highest genetic diversity and the Tibetan population had the lowest. This may be due to the differences in the types and numbers of molecular markers, evaluation methods, and populations. In addition, salt lakes with higher Artemia cyst production (YC, QXC, and ABL) had lower genetic diversity. This is likely due to human activities, such as cyst collection and mineral extraction, which may also cause a decrease in the biomass of Artemia and changes in the chemical characteristics of the lake. Interestingly, within Tibetan Artemia populations, genetic diversity tended to be higher in the west and lower in the east. There are several possible explanations for this. One reason for this may be that the complex geographical environment and evolutionary history of the QTP have a long-lasting impact on species survival and promote species adaptation to local conditions (Mao et al., 2021; Shen et al., 2021). Studies have indicated that local adaptations may affect the genetic diversity of populations (Escalante et al., 2020; Zhao et al., 2020). For commercially exploited salt lakes (ABL, YC, and QXC) that have low genetic diversity, exploiters must consider rational exploitation. Research on Artemia has shown that some morphological features could differ significantly not only in different species (Zheng and Sun, 2008) but also in different salt lakes with different hydro chemical characteristics (Zheng and Liu, 2009; Qi et al., 2021), suggesting that Artemia populations could develop local adaptation and exhibit different adaptive characteristics and that local adaptation may further affect the genetic diversity of Artemia populations in different lakes. Studies have also found that some invasive species of Artemia show decreased genetic diversity when they enter new habitats (Kappas et al., 2004). Thus, the relatively low genetic diversity in the DQC may be due to an introduction event nearly 20 years ago (Jia et al., 2015).

This study revealed the genetic structure of ten geographical populations of Artemia in inland salt lakes in China. Unlike previous studies on Asian Artemia (Kappas et al., 2011; Eimanifar et al., 2015), our results suggest that the genetic structure of Artemia in Tibet is more complex. The selection of the best K value for cross-validation must be performed carefully, and multiple datasets, such as phylogenetic trees and PCA, should be combined to determine the final genetic structure of the species (Liu et al., 2022; Mamat et al., 2023). Population structure analyses showed that ten 10 populations from different regions of China could be classified into four geographically and genetically distinct groups. Notably, clusters were more abundant in the Nagri region, suggesting the existence of a more refined population genetic structure. The combination of genetic structure and F _ST values further showed a high level of genetic differentiation among different Artemia groups. Geographical barriers and distances typically cause genetic differentiation (Goetze, 2003; Binks et al., 2019; Fu et al., 2022; Liang et al., 2022). The altitude of the Tibetan region is very high (above 4500 m), whereas Yuncheng Salt Lake (320 m), Aibi Lake (189 m), and Balikun Lake (3300 m) are relatively low. These low-elevation regions may act as barriers to geographic dispersal (Milá et al., 2013). In addition, the Kunlun, Qilian, Tianshan, and Qinlian Mountains separate Artemia populations and impede genetic flow between the populations in these three regions (Funk et al., 2005; Chen et al., 2006; Von Oheimb et al., 2013). The Mantel test revealed that the genetic differentiation among Artemia populations likely stemmed from the geographical distance between clades. Given the high correlation between geographical distance and genetic distance in 10 populations (R² = 0.857; P<0.0001), we can speculate that geographic distance and geographic barriers are major contributors to genetic differentiation among Artemia populations. In the Tibetan Nagri region, these Artemia populations can be divided into eastern Nagri populations (BGC, QXC, DDC, and DQC) and western Nagri populations (DC, LGC, and NEC), with a moderate correlation between geographical distance and genetic distance (R^{2 =} 0.5052; P<0.01). The climate of Tibet is unique and complex, with overall characteristics of severe cold in the northwest and humid in the southeast, and a variety of regional climates and obvious vertical climate zones due to the complex topography (Deng et al., 2019; Shi et al., 2022), which may explain the divergence of populations in the eastern and western Nagri regions.

Geological events occurring at certain times in history, such as the uplift of a mountain range, downcutting of rivers, and formation of deep valleys, disrupt the original balance of genetic exchange and cause genetic differentiation of species. These genetic divergences often appear as divisions between clades and usually coincide with geological events (Lemmon et al., 2007; Akın et al., 2010; Pickrell and Pritchard, 2012; Yan et al., 2013; Favre et al., 2015). Undoubtedly, the uplift of the QTP is one of the most prominent recent geological events on a global scale. The current mainstream view is that the QTP originated from the collision of the Indian and Eurasian plates at approximately 55–40 Mya (Hu et al., 2016), which began in the middle to late Eocene and ended in the late Miocene, with some areas reaching altitudes of 4,000 m (Li, 2008; Du, 2021). Previous studies on the timing of Artemia differentiation (Eimanifar et al., 2015) indicated that A. sinica separated from other populations at 19.99 Mya (95% HPD 9.37–36.69 Mya), a period corresponding to the second accelerated uplift of the QTP. This was mainly due to the change in landform. Gene flow between the Shanxi population in central China and the western population was hindered, resulting in genetic differentiation. Similarly, the differentiation of parthenogenetic Artemia and A. tibetiana occurred at 5.41 Mya (95% HPD 2.19–9.99), a period corresponding to the third accelerated uplift of the QTP. Therefore, it is likely that the differentiation of Artemia was related to successive geological events (three accelerated uplifts of the QTP). Each stage of these movements may produce fragmented habitats that limit the dispersal of previously contiguous populations owing to geographical isolation, thus promoting the formation of allopatry patterns (Liao et al., 2015; Scotti-Saintagne et al., 2019). Considering that Artemia is distributed in inland salt lakes with a relatively weak diffusion ability, this genetic differentiation effect is more obvious. Populations living in different regions have developed local adaptations that increase their genetic differentiation (Orsini et al., 2013; Colautti and Lau, 2015; Zhang et al., 2022).

Treemix analysis revealed that A. sinica underwent unidirectional gene flow in four salt lakes: QXC, BGC, DQC, and DDC. Despite the large environmental differences between habitats, the relatively small ecological niche overlap between Artemia populations makes invasion and successful colonization possible. As an aquatic invertebrate, the dispersal capacity of Artemia is limited and geographic isolation caused by geologic events contributes significantly to differentiation among Artemia populations; however, gene flow among Artemia populations can still be detected based on SLAF-seq data. We suggest that this is passive dispersal, mainly from anthropogenic introductions and birds (Vest and Conover, 2011; Reynolds et al., 2015). The genetic structure of Tibetan Artemia is complex and its taxonomic status remains controversial (Sainz-Escudero et al., 2021). The Treemix results demonstrated that a certain amount of gene flow exists between Artemia populations and that geological events and gene flow promote interspecies hybridization, leading to hybrid polyploidization and the formation of isoploid hybrid species (Wu et al., 2022), which may have contributed to the current complex genetic structure of Tibetan Artemia. Considering the effects of climate change on bird migration routes, the genetic structure of the Tibetan Artemia populations may undergo further changes in the future.

Pleistocene climate fluctuations and periodic glaciations have contributed to the current patterns of genetic variation in biological species (Shepard and Burbrink, 2009; Neaves et al., 2012; Evans and Jacquemyn, 2020). During glaciation, especially during LGM, which had a dry climate, low temperatures, and massive glacial coverage globally (Gasse, 2000; Clark et al., 2009), many species experienced severe habitat range contractions and survived only in restricted geographic range refuges (Hewitt, 2004). The present study found that the distribution of the Tibetan and Shanxi populations shrank during the LGM and the Xinjiang populations experienced range expansion but a significant decrease in the proportion of suitable habitats. During warm interglacial periods, the retreating ice cap created new suitable habitats and species began to expand away from their refuges (Hewitt, 2000; Jenkins et al., 2018). Our SDM results were consistent with this phenomenon, with all populations having optimal suitable areas during the LIG, except for the western Nagri populations, which had almost no suitable areas during the LIG. The Pleistocene has experienced many alternating glacial and interglacial periods and is one of the most volatile periods in history. Climatic fluctuations had a strong impact on Artemia suitable areas, especially in Shanxi, where populations experienced strong contraction and expansion. We hypothesize that the influence of Pleistocene climate fluctuations on the distribution patterns of Artemia may be common in the aquatic life of inland salt lakes in China. In the future (2070 RCP8.5), the suitable area of Tibetan populations will shrink, while Shanxi and Xinjiang populations will expand. Today, the world’s glaciers are retreating and speeding up due to relatively rapid global warming. Given the importance of salinity to Artemia (Abatzopoulos et al., 2003), it is not difficult to understand that the lake expansion and salinity reduction in QTP salt lakes will pose a serious threat to the survival of Artemia in these plateau salt lakes. Thus, efforts should be made to establish and improve corresponding monitoring, assessment, and protection systems for Artemia resources.

A large number of SNPs were identified in 10 Artemia populations. These populations can be classified into four groups (Shanxi, Xinjiang, eastern Nagri, and western Nagri), with both Nagri groups exhibiting the highest levels of genetic diversity. The Shanxi population showed unidirectional gene flow to the eastern Nagri population. SDMs were established for Artemia populations for the first time, which will help us understand the impact of climate change on Artemia distribution worldwide. The genetic diversity results and declining trend of Tibetan populations indicate that Artemia germplasm resources require protection to ensure the sustainable development of Artemia resources.

The datasets generated during the current study are available in the NCBI repository, PRJNA1014179.

The animal study was approved by Tianjin University of Science and Technology. The study was conducted in accordance with the local legislation and institutional requirements.

KL: Conceptualization, Data curation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing. RZ: Data curation, Formal analysis, Writing – original draft. L-YS: Conceptualization, Funding acquisition, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing. CZ: Conceptualization, Funding acquisition, Writing – review & editing. X-KH: Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing.