Asymmetric Evolution without Neo-Darwinism

The study "Asymmetric Evolution of Protein Domains in the Leucine-Rich Repeat Receptor-Like Kinase Family of Plant Signaling Proteins" delves into the intricate evolutionary patterns of protein domains within the LRR-RLK family, a group of signaling proteins that play a pivotal role in plant development and defense. The research focuses on two distinct domains: the leucine-rich repeat (LRR) domain and the receptor-like kinase (RLK) domain.

Key Findings:

1. Asymmetric Evolutionary Rates: The LRR domains of LRR-RLK proteins exhibit a significantly faster evolutionary rate compared to their cognate RLK domains. This asymmetry is a consistent feature across eleven subfamilies of LRR-RLKs, despite their diverse functions in plant development and defense. This finding suggests that the LRR and RLK domains are subjected to distinct evolutionary pressures, with the LRR domain evolving more rapidly to accommodate recognition of diverse extracellular cues.

2. Shared Evolutionary Patterns: Despite their functional differences, all tested subfamilies of LRR-RLKs displayed remarkably similar patterns of molecular development. This observation suggests that the LRR and RLK domains may be constrained by shared structural or functional requirements, despite their divergent roles. Additionally, it implies that the functional divergence between developmental and defense LRR-RLKs may occur through mechanisms beyond NeoDarwinian protein sequence changes, such as alterations in gene regulation or protein interactions.

3. Contribution of Multiple Mechanisms: Heterologous transformation experiments revealed that multiple mechanisms, including escape from adaptive conflict, likely contribute to the development of the of LRR-RLK function. Adaptive conflict arises when a protein has multiple functions, and changes that improve one function may come at the expense of another. Escape from adaptive conflict can occur through various mechanisms, such as gene duplication or the development of tissue-specific isoforms. The study's findings suggest that escape from adaptive conflict may play a role in developing LRR-RLK function, allowing for specialization in different developmental or defense pathways.

Implications:

• The distinct development rates of LRR and RLK domains within LRR-RLK proteins suggest that they may be subjected to different development pressures. The LRR domain's faster change rate likely reflects its role in ligand recognition, while the RLK domain's slower rate may be due to its involvement in conserved signaling pathways.

• The shared development patterns across LRR-RLK subfamilies imply that the functional divergence between developmental and defense LRR-RLKs may occur through mechanisms beyond protein sequence changes. This suggests that regulatory mechanisms or protein interactions may play a more significant role in functional diversification than previously thought.

• The study highlights the complex interplay of factors that drive the change of gene and protein function. The findings demonstrate that multiple mechanisms, including adaptive conflict, can contribute to the evolution of LRR-RLK function, emphasizing the intricate nature of developmental processes.

Overall, the research provides valuable insights into the development dynamics of protein domains within the LRR-RLK family, shedding light on the mechanisms that shape plant signaling and adaptation. The study's findings have implications for understanding the evolution of protein function in other biological systems and for developing novel strategies for crop improvement and pest resistance.

The study's conclusions challenges neo-Darwinism in several ways.

1. The study suggests that protein domains can evolve independently of each other, which is not consistent with the neo-Darwinian view of evolution as a gradual process of random mutation and selection.

The study found that the LRR domains of LRR-RLK proteins change  faster than the RLK domains. This suggests that the two domains are under different  pressures and may have different functions. This is not consistent with the neo-Darwinian view of evolution as a gradual process of random mutation and selection, which would predict that all parts of a protein would evolve at the same rate.

2. The study suggests that the development  of protein function can be driven by factors other than natural selection, such as escape from adaptive conflict.

The study found that the change of LRR-RLK function is likely due to multiple mechanisms, including escape from adaptive conflict. Adaptive conflict occurs when a gene has multiple functions that are under conflicting pressures. In the case of LRR-RLKs, the LRR domain is responsible for binding ligands, while the RLK domain is responsible for signaling. These two functions may be under conflicting  pressures, which could lead to the development of independent  trajectories for the two domains.

3. The study suggests that the development  of protein function can be complex and involve multiple interacting mechanisms.

The study found that the change of LRR-RLK function is likely due to multiple mechanisms, including escape from adaptive conflict, changes to cis-regulation, and coding sequence evolution. This suggests that the development of protein function is a complex process that involves multiple interacting mechanisms. This is not consistent with the neo-Darwinian view of evolution as a simple process of random mutation and selection.

Overall, the study challenges neo-Darwinism by suggesting that protein domains can evolve independently of each other, that the development of protein function can be driven by factors other than natural selection, and that the development of protein function can be complex and involve multiple interacting mechanisms.