Unraveling the Evolutionary Secrets of Elaeocarpus in China: Fresh Perspectives on Phylogeny, Biogeography, and the Enigmatic 'Acronodia' Group
Imagine discovering that a seemingly ordinary tree family holds the key to understanding how plants have migrated and adapted across continents over millions of years. But here's where it gets controversial: this isn't just about trees—it's about challenging long-held beliefs on plant classification and sparking debates on biodiversity conservation. Keep reading, because the details might just change how you see the green world around you.
Research
Open Access
Published: November 7, 2025
Authors
- Yihui Wang¹² (Lead contributor)
- Yifei Xie¹ (Co-first author)
- Jiayi Jin¹³
- Jinyue Li⁴
- Xueping Lai¹
- Xiangdong Qiu¹⁵
- Yang Tong¹
- Zhixiang Zhang⁶
¹ School of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, P. R. China
² Key Laboratory of Ornamental Germplasm Innovation and Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, P. R. China
³ Key Laboratory of Plant Resources Conservation and Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, P. R. China
⁴ Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, P. R. China
⁵ School of Ecology and Environment, Tibet University, Lasa, Xizang, 850032, P. R. China
⁶ School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, P. R. China
Corresponding Author
Yifei Xie (yifeixie@gmu.edu.cn)
BMC Plant Biology
volume 25, Article number: 1524 (2025)
Cite this article
Abstract
Background
Elaeocarpus stands out as the most diverse genus within Elaeocarpaceae, a family in the Oxalidales order, boasting around 39 tree species that thrive in tropical and subtropical forests across China. Of these, 14 are unique to this region. Despite this richness, research on the evolutionary relationships of Elaeocarpus in China has been sparse. Existing studies suggest a close evolutionary link between Sect. Ganitrus and Sect. Dicera, yet the debate persists on whether the 'Acronodia' group deserves its own taxonomic status separate from Sect. Monocera. The reliability of the phylogenetic tree built from available chloroplast DNA fragments has not been thoroughly examined, leaving the classification of 'Acronodia' in Elaeocarpus uncertain.
Results
In our investigation, we aligned four complete chloroplast genomes using tools like mVISTA and KaKs_Calculator to assess their sequences. The findings showed strong bootstrap support for phylogenetic reconstruction using ycf1, ITS, and trnS-atpA markers. These markers helped classify 27 Elaeocarpus species—comprising 40 samples, including 3 not native to China—into two primary lineages: one encompassing Sect. Ganitrus and Sect. Dicera, and the other including Sect. Monocera alongside the ‘Acronodia’ group. Through BEAST analysis, we estimated that Elaeocarpus likely originated in southwest China around 40 million years ago (Ma) during the early Eocene, with diversification accelerating south of the Yangtze River in the early Miocene, about 15 Ma ago.
Conclusion
This work underscores the value of chloroplast genomes for taxonomic studies of Elaeocarpus and provides crucial timelines and geographic origins to guide future conservation efforts. For beginners in botany, phylogeny is like a family tree for plants, tracing how species evolved and related over time—think of it as uncovering the hidden connections in nature's vast network.
Peer Review Reports
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Introduction
Since the turn of the millennium, advancements in molecular marker technologies have revolutionized the use of DNA barcodes for classifying organisms, initially for animals but now extending to plants like those in Elaeocarpaceae. DNA barcodes, which are short genetic sequences easily amplified from plant chloroplast DNA, remain largely consistent across species, making them ideal for systematics. This is evident in how they've been applied to identify medicinal herbs and other plants in recent years. A phylogenetic tree constructed from DNA barcodes combined with fossil records can accurately estimate the divergence times of plant lineages. Studies have shown that employing a relaxed molecular clock model enhances precision, and these timelines often align with major geological events.
Elaeocarpus, the dominant genus in Elaeocarpaceae, includes 350–400 species worldwide that flourish in tropical and subtropical woodlands, with 39 species present in China. Many of these plants offer practical benefits; for instance, E. glabripetalus is prized for its glossy evergreen leaves and is commonly grown as an ornamental tree, while E. braceanus produces edible fruits sometimes used in brewing spirits. Morphological analyses in China's Flora Reipublicae Popularis Sinicae (FRPS) divided Elaeocarpus into three sections: Sect. Ganitrus, Sect. Dicera, and Sect. Monocera. However, Flora Yunnanica and Flora of China recognized Sect. Acronodia as distinct from Sect. Dicera. Sect. Acronodia was first defined by Master in 1875 and has been applied in classifications of Malaysian Elaeocarpus species.
The infrageneric groupings of Elaeocarpus in China rely on traditional, intuitive methods and haven't been verified through modern phylogenetic analysis to confirm monophyly (where a group shares a common ancestor) or identify shared derived traits. Fossil evidence for Elaeocarpus dates back to Miocene sediments in Australia and India. Combining multiple genetic fragments has clarified Elaeocarpus's position within the Elaeocarpaceae alliance, which includes genera like Sericolea, Aceratium, and Elaeocarpus, and has illuminated the internal subdivisions. For example, using a penalized likelihood method on trnL-trnF and ITS sequences from just 13 Elaeocarpaceae species placed the common ancestor of Elaeocarpus around 46 Ma. Phoon proposed that this genus began in Australia during the Eocene, spreading to neighboring areas like Indonesia during the Oligocene and Miocene.
Yet, previous research mostly drew from Australian and Indonesian samples, omitting specimens from China and Indochina, which could compromise origin estimates. Moreover, low bootstrap values in some Elaeocarpus lineages suggested that fragments like trnL-trnF, trnV-ndhC, and ITS aren't ideal for resolving species relationships or identification. Integrating morphological data complicates the status of Sect. Acronodia further. To address this, we explored additional variable regions in Elaeocarpus to better understand its evolutionary connections with related genera.
Our study aimed to: (1) Identify effective genetic markers for building phylogenetic trees; (2) Determine the evolutionary placement of Sect. Acronodia and clarify relationships among sections within Chinese Elaeocarpus; (3) Estimate divergence times and historical distribution patterns for Elaeocarpus sections in China.
Materials and Methods
Plant Collection and DNA Isolation
Leaf samples from 27 Elaeocarpus species—totaling 40 specimens, plus 3 species not indigenous to China—were gathered from Chinese field sites and the Royal Botanic Gardens. Voucher specimens are stored at the Nanling Herbarium of Gannan Normal University (GNNU), the Museum of Beijing Forestry University (BJFC), and the Royal Botanic Gardens (K). Genomic DNA was extracted using the CTAB protocol and sequenced for four species (E. japonicus, E. angustifolius, E. hainanensis, and E. japonicus var. yunnanensis) via next-generation sequencing on the Illumina HiSeq 2000 platform in Beijing, China.
Chloroplast Genome Comparison and Phylogenetic Analysis
Focusing on the key lineages in Chinese Elaeocarpus—Sect. Ganitrus, Sect. Dicera, Sect. Monocera, and the ‘Acronodia’ group—we compared four published chloroplast genomes (E. japonicus MT683335, E. angustifolius MW242787, E. hainanensis MW602804, and E. japonicus var. yunnanensis MW242788) using the Shuffle-LAGAN mode in mVISTA software. To measure mutation rates, we calculated the ratio of nonsynonymous to synonymous substitutions (Ka/Ks) for protein-coding genes with the YN model in KaKs_Calculator 3.0. For non-coding regions, we estimated Kn/Ks ratios by comparing aligned sequences. This helped pinpoint hotspots of rapid change and highly variable areas. Primers for amplifying genes were designed with Primer Premier 6, and PCR products were purified and sequenced via Sanger method. Successful sequences are listed in Supplementary Table S1.
Phylogenetic trees were built for the 27 species plus outgroups (Sloanea sinensis, Vallea stipularis, Crinodendron patagua, and Aristotelia fruticosa) using ITS, trnS-atpA, and ycf1 regions. Bayesian inference ran in MrBayes 3.2.6 on 31 species' data, with the GTR+F+I model selected via jModelTest 2.1.10. MCMC chains ran for 10,000,000 generations, sampling every 1,000 steps, discarding the first 25% as burn-in. Maximum likelihood trees used RAxML v8.0.0 with the same model on CIPRES.
Molecular Dating and Diversification Rate Analysis
In BEAST 1.10.4, we used a lognormal relaxed clock and Yule process tree prior, calibrated with fossils: 40±30 Ma for Vallea-Aristotelia split, 25±2 Ma for E. angustifolius from Australia, and 13±3 Ma for Sloanea-Vallea divergence from Germany. MCMC ran for 500 million generations, sampling every 50,000, ensuring ESS >200. Diversification rates were calculated with GEIGER in R.
Biogeographic Analysis
Ancestral ranges were reconstructed using RASP with the DEC model, defining eight areas: southern Yunnan, Hainan, India, Indochina Peninsula (a); Yunnan, Guangxi, Hainan, Indochina Peninsula (b); southern Yangtze River, Indochina Peninsula (c); Japan, southern Yangtze River, northern Vietnam (d); South America (e); Australia (f); Indonesia (g); India (h).
Results
Chloroplast Genome Comparison
To spot variations among species, we examined protein-coding genes, finding that rpl16 and ycf1 had high Ka/Ks ratios (>0.7), indicating possible adaptive evolution, while others (<0.7) suggested purifying selection. Elevated Kn/Ks ratios (>6) in non-coding areas like ndhF-trnL, psbE-petL, psbZ-trnG, rbcL-psaI, trnS-atpA, and ycf3-trnS pointed to rapid change under positive selection, making them good for DNA barcodes.
Identity plots showed conserved genomes, with more variation in non-coding regions and introns of rpl16 and ycf1.
Phylogenetic Analysis of Elaeocarpus
Testing eight fragments, we found strong support for ycf1, ITS, and trnS-atpA. The tree grouped Elaeocarpus into two clades: one with Sect. Ganitrus and Sect. Dicera, the other with Sect. Monocera and ‘Acronodia’. Bayesian analysis strongly supported four lineages.
Age Estimates, Ancestral Distributions, and Diversification
Diversification began ~31.5 Ma in Elaeocarpaceae. Elaeocarpus split ~28.8 Ma from Indochina Peninsula/southwest China, with Sect. Ganitrus/Dicera diverging at 24.8 Ma and Sect. Monocera/‘Acronodia’ at 15.9 Ma. Ancestral ranges expanded from Indochina/southwest China to south Yangtze/Japan. Diversification peaked 4–20 Ma.
Discussion
DNA Markers and Evolutionary Relationships
Positive selection on genetic regions often correlates with rapid evolution, aiding in dating. Traditional barcodes like ITS fail for many plants, but ycf1 and trnS-atpA work well here, aligning with broader findings.
Our tree, using cpDNA and ITS, contrasts prior studies, robustly resolving East Asian Elaeocarpus phylogeny.
Major Lineages in Elaeocarpus
Split into two clades: I (Sect. Ganitrus/Dicera) and II (Sect. Monocera/‘Acronodia’). Morphological differences include petal shapes and fruit shine.
Within clades, Sect. Dicera (12 species) is monophyletic, as is Sect. Monocera with two subclades based on fruit shape. ‘Acronodia’ relates more to Monocera, challenging morphological classifications.
Timing, Origins, and Environmental Influences
Ancestral reconstructions point to Oligocene origins in Indochina, driven by humid climates. Miocene diversification south of Yangtze linked to monsoon changes from Tibetan uplift. Quaternary glaciations created refugia, promoting speciation—echoing patterns in plants like Taxus and Taiwania.
Animal dispersal (birds, primates) and fruit morphology likely aided spread. But here's the part most people miss: climate shifts and human-like migrations might have shaped this, raising questions about modern conservation.
Data Availability
Raw data and sequences are in the article/supplementary files; GenBank IDs in Table S1. Contact authors for more.
References
[Full list of references from the original article, with citations intact.]
Funding
Supported by National Natural Science Foundation of China (31110103911, J1310002) and Jiangxi Province Education Department (190781).
Acknowledgments
Thanks to Prof. Ren-Lin Liu.
Author Contributions
Yihui Wang: Analysis, curation, drafting. Yifei Xie: Conceptualization, editing. Others as listed.
Ethics
No animal/human involvement.
Competing Interests
None declared.
What do you think—does reclassifying 'Acronodia' change our understanding of plant evolution? Is biogeography more about continents or climate? Share your views in the comments; let's discuss!
