| Abstrakt: |
The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses. Author summary: Reconstructing the deep evolutionary history of viruses presents significant challenges, particularly due to a common decline in their evolutionary rate estimates over time. This decline can lead to substantial underestimations of their evolutionary history when divergence time since the most recent common ancestor are estimated based on extrapolations of the short-term evolutionary rates. Our study revisited the evolutionary timeline of the Sobemovirus genus, which was previously thought to have originated about 10,000 years ago based on short-term rate extrapolations. By employing the Prisoner of War model, which accounts for changes in virus rate estimates over time, and by analyzing updated datasets of sobemoviruses including metagenomic samples, we found that the Sobemovirus genus likely originated over four million years ago. This timeline significantly extends beyond prior estimates, challenging the conventional view of the origins of sobemoviruses and suggesting that they may have ancient beginnings. Furthermore, our study revealed that these viruses have undergone considerable diversification, influenced by agricultural development and environmental changes, particularly over the last 5,000 years. This study paves the way for new insights into the deep evolutionary history of plant viruses and the implications of their long-term interactions with hosts in the context of agriculture. [ABSTRACT FROM AUTHOR] |
