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Large-amplitude internal solitary waves were recently observed in a coastal plain estuary and were hypothesized to evolve from an internal lee wave generated at the channel–shoal interface. To test this mechanism, a 3D nonhydrostatic model with nested domains and adaptive grids was used to investigate the generation of the internal solitary waves and their subsequent nonlinear evolution. A complex sequence of wave propagation and transformation was documented and interpreted using the nonlinear wave theory based on the Korteweg–de Vries equation. During the ebb tide a mode-2 internal lee wave is generated by the interaction between lateral flows and channel–shoal topography. This mode-2 lee wave subsequently propagates onto the shallow shoal and transforms into a mode-1 wave of elevation as strong mixing on the flood tide erases stratification in the bottom boundary layer and the lower branch of the mode-2 wave. The mode-1 wave of elevation evolves into an internal solitary wave due to nonlinear steepening and spatial changes in the wave phase speed. As the solitary wave of elevation continues to propagate over the shoaling bottom, the leading edge moves ahead as a rarefaction wave while the trailing edge steepens and disintegrates into a train of rank-ordered internal solitary waves, due to the combined effects of shoaling and dispersion. Strong turbulence in the bottom boundary layer dissipates wave energy and causes the eventual destruction of the solitary waves. In the meantime, the internal solitary waves can generate elevated shear and dissipation rate in local regions.

In the coastal ocean nonlinear internal solitary waves are widely recognized to play an important role in generating turbulent mixing, modulating short-term variability of nearshore ecosystem, and transporting sediment and biochemical materials. However, their effects on shallow and stratified estuaries are poorly known and have been rarely studied. The nonhydrostatic model simulations presented in this paper shed new light into the generation, propagation, and transformation of the internal solitary waves in a coastal plain estuary.

 

High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.

 

The impacts of pulsed nutrient injections or extreme runoff events on marine ecosystems are far less studied than those associated with long‐term eutrophication, particularly in regard to mechanisms regulating the response of plankton community structure. Over 800 million liters of nutrient‐rich water from a fertilizer mine were discharged over a 2‐week period into Tampa Bay, Florida, in 2021, providing a unique opportunity to document the plankton response. A 3D‐coupled hydrodynamic biogeochemical model was developed to investigate this response and to understand the observed succession of a large, short diatom bloom followed by a secondaryKarenia brevisbloom that lasted through the summer. The model reproduced the observed changes in nutrient concentration, total chlorophylla, and diatom andK. brevisbiomass in Tampa Bay. With a faster growth rate and spring temperature close to the optimal window of growth, diatoms had an initial competitive advantage, with 2/3 of the nutrient uptake due to ammonium and 1/3 due to nitrate. However, exhaustion of external nutrients led to the rapid decline of the diatom bloom, and the associated particular organic nitrogen sank onto the bay sediment. Enhanced sediment release of ammonium during the weeks following, and summer remineralization of dissolved organic nitrogen provided sufficient regenerated nitrogen to support slow‐growingK. brevisthat could capitalize on low nutrient conditions. Modeling analysis largely confirmed Margalef's conceptual model ofrtoK‐selected species succession and provided additional insights into nutrient cycling supporting the initial diatom bloom and the subsequent bloom of a slow‐growing harmful algal species.

 

The impacts of pulsed nutrient injections or extreme runoff events on marine ecosystems are far less studied than those associated with long-term eutrophication, particularly in regard to mechanisms regulating the response of plankton community structure. Over 800 million liters of nutrient-rich water from a fertilizer mine were discharged over a 2-week period into Tampa Bay, Florida, in 2021, providing a unique opportunity to document the plankton response. A 3D-coupled hydrodynamic biogeochemical model was developed to investigate this response and to understand the observed succession of a large, short diatom bloom followed by a secondary Karenia brevis bloom that lasted through the summer. The model reproduced the observed changes in nutrient concentration, total chlorophyll a, and diatom and K. brevis biomass in Tampa Bay. With a faster growth rate and spring temperature close to the optimal window of growth, diatoms had an initial competitive advantage, with 2/3 of the nutrient uptake due to ammonium and 1/3 due to nitrate. However, exhaustion of external nutrients led to the rapid decline of the diatom bloom, and the associated particular organic nitrogen sank onto the bay sediment. Enhanced sediment release of ammonium during the weeks following, and summer remineralization of dissolved organic nitrogen provided sufficient regenerated nitrogen to support slow-growing K. brevis that could capitalize on low nutrient conditions. Modeling analysis largely confirmed Margalef's conceptual model of r to K-selected species succession and provided additional insights into nutrient cycling supporting the initial diatom bloom and the subsequent bloom of a slow-growing harmful algal species.