San Diego’s Mission Bay has a new kind of local: a newly identified hybrid eelgrass that appears wired to survive in low light, and scientists say that quirk could make future restoration plantings a lot tougher. The team, writing in Nature Plants, argues that this find points toward genomically informed coastal restoration that might cut down the stubbornly high failure rates of traditional replanting projects. Local researchers say the hybrid borrows clock genes from its deeper water parent that help it keep photosynthesizing when things get dim.
According to UC San Diego Today, Scripps scientists first suspected something unusual was growing in Mission Bay’s Mariner’s Basin in fall 2022, after a colleague snorkeling in the area noticed eelgrass with noticeably thicker leaves. In a press release from the Salk Institute, the authors report that the bed holds plants that are a first generation cross between shallow water Zostera marina and deep water Zostera pacifica, and that genomic sequencing revealed which parental genes the hybrid leans on when it is living in shade.
Genome Work Confirms an F1 Hybrid
In the Nature Plants study, the researchers built haplotype resolved genomes and concluded that the Mission Bay population is an F1 hybrid, with distinct Z. marina and Z. pacifica subgenomes sitting side by side. When they compared the plants’ transcriptomes in low light mesocosms, they found the hybrid cranked up photosystem and chlorophyll biosynthesis genes and shifted expression of circadian regulators such as LATE ELONGATED HYPOCOTYL and WNK kinases under shaded conditions.
Lab ‘Extreme Gardening’ and Low Light Trials
To see how this plays out in practice, the team grew the hybrid and Z. marina side by side in tanks set to reduced light, an approach the authors jokingly dubbed “extreme gardening”. A Salk Institute release notes that the hybrid kept photosynthesis related genes switched on even as light dropped, a response the researchers trace to circadian clock genes inherited from Z. pacifica.
Why This Matters for Mission Bay Restoration
Past mitigation planting projects and routine dredging in Mission Bay have pushed Z. pacifica and Z. marina into close quarters, which the researchers say created the opportunity for hybridization in the first place. Those same restoration efforts often struggle, with failure rates around half the time and in some reports up to roughly 60 percent, so the team argues that matching plant genotypes to specific light and depth conditions could matter a lot. Lead author Malia Moore described the work as the first functional study of this kind of hybrid in San Diego waters and highlighted the potential for genome aware selection to improve restoration outcomes.
Next Steps and Open Questions
The researchers stress that these lab results are an early step and that field trials will be needed to see how well the hybrid actually survives, reproduces and fits into the broader ecosystem. The paper reports that the hybrid produced flowers and seeds in summer 2025, which points to sexual reproduction but not to widespread recombination. The Nature Plants article also discloses a conflict of interest: senior author Todd P. Michael is listed as a founder of the carbon sequestration company CQuesta, and the team pairs that disclosure with calls for transparent ecological testing before the hybrid is used in any restoration program…