Population genomics of heterosporous lycophytes: allopatric speciation and historical persistence through paleoclimatic fluctuations
- 1State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- 2China National Botanical Garden Beijing 100093 China
- 3University of Chinese Academy of Sciences Beijing 101408 China
Abstract
SUMMARY: Speciation is the fundamental process driving the origin of earth biodiversity. While speciation mechanisms have been revealed in many plant taxa, the evolutionary dynamics of heterosporous lycophytes remain largely unexplored. Here, we used the Selaginella sanguinolenta group, comprising seven montane species in eastern Asia, as a model system. We generated a high‐quality, chromosome‐level reference genome for S. aitchisonii, conducted whole‐genome resequencing of 191 individuals across 49 populations, and integrated population genomic, phylogenomic, morphological, and ecological analyses. Our results revealed that strong geographic isolation, driven by Miocene paleogeographic events, led to high genetic differentiation and restricted interspecific gene flow. The unique combination of heterospory and independent gametophyte generations might exacerbate extreme inbreeding, further impeding the ability of these lineages to surmount geographical barriers. Ecological niche divergence indicated that these species experience heterogeneous selection pressures; moreover, evidence of selective sweeps, leaf arrangement variation, and functional gene divergence indicates that natural selection gives rise to new species with environmentally adaptive traits. Demographic reconstructions revealed a shared trajectory of expansion followed by contraction into bottlenecks from the late Miocene to the Pliocene. Montane refugia likely played a role in species persistence, preserving genetic diversity for the postglacial expansions observed in four species since the Last Interglacial. We conclude that the S. sanguinolenta group underwent allopatric speciation since the Miocene and successfully persisted through severe Quaternary climatic fluctuations, which provides novel insights based on population genomic analysis into the evolution of early‐diverging vascular plants.
Related
- Seasonal fluctuations in fitness result in severe reductions in effective population size
- Diurnal temperature fluctuations outweigh population origin in shaping thermal performance and range predictions in European Aedes albopictus
- Apparent sequential effects due to trial-to-trial fluctuations in decision criterion
- Rainfall and salinity-related landscapes shape cholera persistence in Haiti
- Landscape restoration strategies differ in their predicted benefits for species persistence
BibTeX
@article{ye2026population,
title = {{Population genomics of heterosporous lycophytes: allopatric speciation and historical persistence through paleoclimatic fluctuations}},
author = {TongXin Ye and Ran Wei and JiGao Yu and NingXin Wang and SiQi Liang and XianChun Zhang},
journal = {The Plant Journal},
year = {2026},
month = nov,
doi = {10.1111/tpj.71179},
url = {https://doi.org/10.1111/tpj.71179},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Population genomics of heterosporous lycophytes: allopatric speciation and historical persistence through paleoclimatic fluctuations
AU - TongXin Ye
AU - Ran Wei
AU - JiGao Yu
AU - NingXin Wang
AU - SiQi Liang
AU - XianChun Zhang
PY - 2026
DA - 2026/11/04
JO - The Plant Journal
DO - 10.1111/tpj.71179
UR - https://doi.org/10.1111/tpj.71179
AB - SUMMARY: Speciation is the fundamental process driving the origin of earth biodiversity. While speciation mechanisms have been revealed in many plant taxa, the evolutionary dynamics of heterosporous lycophytes remain largely unexplored. Here, we used the Selaginella sanguinolenta group, comprising seven montane species in eastern Asia, as a model system. We generated a high‐quality, chromosome‐level reference genome for S. aitchisonii, conducted whole‐genome resequencing of 191 individuals across 49 populations, and integrated population genomic, phylogenomic, morphological, and ecological analyses. Our results revealed that strong geographic isolation, driven by Miocene paleogeographic events, led to high genetic differentiation and restricted interspecific gene flow. The unique combination of heterospory and independent gametophyte generations might exacerbate extreme inbreeding, further impeding the ability of these lineages to surmount geographical barriers. Ecological niche divergence indicated that these species experience heterogeneous selection pressures; moreover, evidence of selective sweeps, leaf arrangement variation, and functional gene divergence indicates that natural selection gives rise to new species with environmentally adaptive traits. Demographic reconstructions revealed a shared trajectory of expansion followed by contraction into bottlenecks from the late Miocene to the Pliocene. Montane refugia likely played a role in species persistence, preserving genetic diversity for the postglacial expansions observed in four species since the Last Interglacial. We conclude that the S. sanguinolenta group underwent allopatric speciation since the Miocene and successfully persisted through severe Quaternary climatic fluctuations, which provides novel insights based on population genomic analysis into the evolution of early‐diverging vascular plants.
SN - 0960-7412
SN - 1365-313X
ER -