Geographic isolation and environmental heterogeneity contribute to genetic differentiation in <i>Cephalotaxus oliveri</i>

Liu, Hanjing; Wang, Zhen; Zhang, Yuli; Li, Minghui; Wang, Ting; Su, Yingjuan

doi:10.1002/ece3.9869

Cited by 7 publications

(6 citation statements)

References 128 publications

(116 reference statements)

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“…In addition, we found a significant pattern of IBD for gene expression ( r = 0.657). Similarly, strong correlations between genetic distance and geographical distance were observed for EST‐SSR data ( r = 0.738; Liu et al, 2023) and SNP data ( r = 0.792). These results showed that studying expression variation patterns using transcriptome data is an important complementary approach to investigating population divergence.…”

Section: Discussionmentioning

confidence: 68%

Local adaptation and demographic history of vulnerable conifer Cephalotaxus oliveri in southern China

Liu

Wang

et al. 2023

J of Sytematics Evolution

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Having a comprehensive understanding of genetic differentiation, responses to environmental change and demographic history is critical for genetic improvement and conservation efforts. Forest trees are an excellent resource for understanding population differentiation and adaptive genetic variation due to their ability to adapt to different climates and environments. Cephalotaxus oliveri is a relict conifer endemic to China. In this study, we generated transcriptome data and identified 17 728 high‐quality single‐nucleotide polymorphisms (SNPs) from 18 populations. We found significant negative correlations between expression diversity and nucleotide diversity within and among populations, suggesting that gene expression and nucleotide diversity have a reciprocal relationship when the species adapts to the environment. The analyses of population structure showed that C. oliveri displayed a striking genetic structure with four groups. BayeScEnv and RDA methods detected the signatures of local adaptation, and identified that 738 outlier SNPs were associated with precipitation, temperature and soil conditions across heterogeneous environmental conditions. Approximate Bayesian computation analyses showed that the first and second divergence occurred in the late Miocene (c. 10.075 million years ago [Ma]) and the middle Pleistocene transition (c. 0.815 Ma), respectively. Ecological niche modeling of C. oliveri revealed signs of westward expansion after the last glacial maximum, while it was predicted to experience significant range contractions in future climate change scenarios. Geographical factors and environmental factors in southern China have played a critical role in establishing the current genetic diversity and population structure of C. oliveri. This study provides an important reference for forest resource management and conservation for C. oliveri.

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Section: Discussionmentioning

confidence: 68%

Local adaptation and demographic history of vulnerable conifer Cephalotaxus oliveri in southern China

Liu

Wang

et al. 2023

J of Sytematics Evolution

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“…pringlei appears to be susceptible to the influence of environmental conditions, spatial autocorrelation, and even the interplay between both factors. Demographic history and gene flow processes might have been molded by distinct variations in their immediate environment, as has been suggested in other plants (Liu et al., 2023). Additionally, both neutral and adaptive data indicated the existence of induced spatial dependence, suggesting that geographical proximity may align with large‐scale environmental similarities (Borcard et al., 2011).…”

Section: Discussionmentioning

confidence: 82%

“…Finally, substantial variation remains unexplained, which is common in genetic studies using these methods (Gibson & Moyle, 2020; Liu et al., 2023). This could be attributed, in part, to the population structure that may not be fully explained by spatial variables of the MEM, potentially due to geographic heterogeneity present in the Mexican Transition Zone.…”

Section: Discussionmentioning

confidence: 99%

Genomic diversity and structure of a Neotropical microendemic fig tree

Rojas‐Cortés,

Gasca‐Pineda,

González‐Rodríguez

et al. 2024

Ecology and Evolution

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Genetic diversity is a key component of evolution, and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is Ficus (Moraceae). It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of Ficus species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5311 SNPs) derived from low‐coverage whole genomes and 17 populations, we analyzed the population genomics of Ficus pringlei to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans‐Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. Ficus pringlei populations from the north and south of the Trans‐Mexican Volcanic Belt also exhibited minimal genetic differentiation (FST = 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as F. pringlei.

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“…The isolation-by‐distance (IBD) reveals that genetic differentiation among populations increases with geographic distance, while the isolation‐by‐environment (IBE) assumes a linear relationship between genetic variation and environmental differences among populations [ 77 ]. To explore the existence of IBD and IBE, we applied Mantel test to assess the relationships between genetic distance and geographic or environmental distance with R v4.3.2 ( https://www.r-project.org/ ).…”

Section: Methodsmentioning

confidence: 99%

Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

Jin,

Zhao,

Chen

et al. 2024

BMC Plant Biol

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Background Relict species are important for enhancing the understanding of modern biogeographic distribution patterns. Although both geological and climatic changes since the Cenozoic have affected the relict flora in East Asia, the contributions of geographical processes remain unclear. In this study, we employed restriction-site associated DNA sequencing (RAD-seq) and shallow genome sequencing data, in conjunction with ecological niche modeling (ENM), to investigate the spatial genetic patterns and population differentiation history of the relict species Rehderodendron kwangtungense Chun. Results A total of 138 individuals from 16 populations were collected, largely covering the natural distribution of R. kwangtungense. The genetic diversity within the R. kwangtungense populations was extremely low (HO = 0.048 ± 0.019; HE = 0.033 ± 0.011). Mantel tests revealed isolation-by-distance pattern (R2 = 0.38, P < 0.001), and AMOVA analysis showed that the genetic variation of R. kwangtungense occurs mainly between populations (86.88%, K = 7). Between 23 and 21 Ma, R. kwangtungense underwent a period of rapid differentiation that coincided with the rise of the Himalayas and the establishment of the East Asian monsoon. According to ENM and population demographic history, the suitable area and effective population size of R. kwangtungense decreased sharply during the glacial period and expanded after the last glacial maximum (LGM). Conclusion Our study shows that the distribution pattern of southern China mountain relict flora may have developed during the panplain stage between the middle Oligocene and the early Miocene. Then, the flora later fragmented under the force of orogenesis, including intermittent uplift during the Cenozoic Himalayan orogeny and the formation of abundant rainfall associated with the East Asian monsoon. The findings emphasized the predominant role of geographical processes in shaping relict plant distribution patterns.

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Geographic isolation and environmental heterogeneity contribute to genetic differentiation in Cephalotaxus oliveri

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 7 publications

References 128 publications

Local adaptation and demographic history of vulnerable conifer Cephalotaxus oliveri in southern China

Local adaptation and demographic history of vulnerable conifer Cephalotaxus oliveri in southern China

Genomic diversity and structure of a Neotropical microendemic fig tree

Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

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