Demographic modeling reveals simultaneous radiation and genetic-morphological discordance in Asian eggplant (Solanum melongena L.) landraces: evolutionary insights into geography and anthropogenic selection
6 affiliations
- 1Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804 Taiwan
- 2Kaohsiung District Agricultural Research and Extension Station, Ministry of Agriculture, Pingtung, 908 Taiwan
- 3Department of Nursing, Meiho University, Pingtung, 912 Taiwan
- 4Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
- 5Research Laboratory Section, Offices of Health Science Research, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400 Thailand
- 6Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, 807 Taiwan
Abstract
Background: The domestication history and spatial expansion of the cultivated eggplant (Solanum melongena L.) in Asia have been debated due to conflicting hypotheses regarding a monocentric versus polycentric origin. Furthermore, relying on morphology to reconstruct this history is problematic given the species’ extensive phenotypic plasticity. To resolve these evolutionary uncertainties, we integrated phenotypic and microsatellite data from 373 landraces (855 individuals) across 12 Asian countries to evaluate the respective roles of neutral genetic drift, geographic isolation, and anthropogenic selection.
Results: Our analysis supported South Asia as the primary center of origin and identified Thailand and China as secondary diversity hubs. We observed a clear discordance between neutral genetic structure and morphological differentiation. Genetic clusters reflect geographic isolation, whereas phenotypic variation is primarily driven by divergent anthropogenic selection for regional cultural preferences. Through demographic model testing based on approximate Bayesian computation, we rejected a simple linear stepping-stone dispersal scenario. The modeling supported a simultaneous radiation framework, indicating a rapid and concurrent divergence of East and Southeast Asian lineages from a South Asian ancestral population approximately 2,800 years ago. Additionally, historical gene flow estimates indicated an ancient Pan-Asian metapopulation connected by early trade networks. This historical connectivity contrasts sharply with the low contemporary migration rates that characterize modern isolated gene pools.
Conclusions: This simultaneous radiation model provides a demographic framework that helps reconcile previous conflicting findings on eggplant domestication. The study suggests human-mediated dispersal and cultural selection have acted as major forces shaping rapid spatial radiation and phenotype-genotype decoupling, offering a quantitative basis for understanding the evolutionary dynamics of cultivated species.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13062-026-00935-9.
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BibTeX
@article{chu2026demographic,
title = {{Demographic modeling reveals simultaneous radiation and genetic-morphological discordance in Asian eggplant (Solanum melongena L.) landraces: evolutionary insights into geography and anthropogenic selection}},
author = {Ya-Ling Chu and Ya-Zhu Ko and Huie-Chuan Shih and Annamalai Muthusamy and Meng-Shin Shiao and Yu-Chung Chiang},
journal = {Biology Direct},
year = {2026},
month = aug,
doi = {10.1186/s13062-026-00935-9},
url = {https://doi.org/10.1186/s13062-026-00935-9},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Demographic modeling reveals simultaneous radiation and genetic-morphological discordance in Asian eggplant (Solanum melongena L.) landraces: evolutionary insights into geography and anthropogenic selection
AU - Ya-Ling Chu
AU - Ya-Zhu Ko
AU - Huie-Chuan Shih
AU - Annamalai Muthusamy
AU - Meng-Shin Shiao
AU - Yu-Chung Chiang
PY - 2026
DA - 2026/08/06
JO - Biology Direct
DO - 10.1186/s13062-026-00935-9
UR - https://doi.org/10.1186/s13062-026-00935-9
AB - Background: The domestication history and spatial expansion of the cultivated eggplant (Solanum melongena L.) in Asia have been debated due to conflicting hypotheses regarding a monocentric versus polycentric origin. Furthermore, relying on morphology to reconstruct this history is problematic given the species’ extensive phenotypic plasticity. To resolve these evolutionary uncertainties, we integrated phenotypic and microsatellite data from 373 landraces (855 individuals) across 12 Asian countries to evaluate the respective roles of neutral genetic drift, geographic isolation, and anthropogenic selection. Results: Our analysis supported South Asia as the primary center of origin and identified Thailand and China as secondary diversity hubs. We observed a clear discordance between neutral genetic structure and morphological differentiation. Genetic clusters reflect geographic isolation, whereas phenotypic variation is primarily driven by divergent anthropogenic selection for regional cultural preferences. Through demographic model testing based on approximate Bayesian computation, we rejected a simple linear stepping-stone dispersal scenario. The modeling supported a simultaneous radiation framework, indicating a rapid and concurrent divergence of East and Southeast Asian lineages from a South Asian ancestral population approximately 2,800 years ago. Additionally, historical gene flow estimates indicated an ancient Pan-Asian metapopulation connected by early trade networks. This historical connectivity contrasts sharply with the low contemporary migration rates that characterize modern isolated gene pools. Conclusions: This simultaneous radiation model provides a demographic framework that helps reconcile previous conflicting findings on eggplant domestication. The study suggests human-mediated dispersal and cultural selection have acted as major forces shaping rapid spatial radiation and phenotype-genotype decoupling, offering a quantitative basis for understanding the evolutionary dynamics of cultivated species. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13062-026-00935-9.
SN - 1745-6150
ER -