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We want to improve evolutionary theory since it is the main way by which we humans can explain why organisms are the way they are. Essentially, improving evolutionary theory means improving our understanding of life. Also theory is the way to understand nature that with the least information explains the most.
Although evolutionary theory has been quite successful over the years there are still some important gaps in it. Current evolutionary theory explains evolution as resulting from mutation and natural selection (in addition to drift and some other minor processes). Mutation is classically described as being random and, thus, the direction in which phenotypes change from one generation to the next is understood to be determined mostly by natural selection (i.e. ecological factors determine which phenotypic variants will pass to the next generation). Although mutation can be seen as random at the genetic level (with some caveats), it has long been known that it is not random at the phenotypic level (Alberch, 1982). Phenotypic variations comes, ultimately, from genetic and environmental variation, but this does not explain which phenotypic variation would arise from genetic variation in a given population and generation. This instead depends on the inner workings of the mechanisms by which the phenotype is constructed. In the case of morphology (i.e. the distribution of cells and cell types in space), this mechanism is development. In other words, the way (or network of) genes and cells interact to construct morphology from the zygote (or equivalent early structures), determines how that morphology change when there is mutations. This implies that the direction of phenotypic evolution does not only depend on natural selection but also on development. Development determines which directions of phenotypic variation are possible and natural selection chooses among them in each generation. In that sense both development and natural selection determine the direction of evolution.
Classical evolutionary theory does not consider the role of development in the direction of evolution. Some developmental evolutionary biology (or evo-devo) does. However, we do not understand very well how development works and, most importantly, how it determines which phenotypic variation will arise from genetic variation.
Our research focuses in three aims. The first one is to better understand development to better understand which phenotypic variation, and thus, evolution is possible. This implies trying to understand pattern formation and morphogenesis during development. This is how is it possible that a simple zygote transforms itself into a complex functional organisms with a specific distribution of cells and cell types in space. This is understanding how this spatial information arises from networks of molecular and cell interactions and how it will vary when there are mutations in these networks.
The second aim is to see how our improved understanding of development and the phenotypic variation it generates can be used to better understand phenotypic evolution.
The third aim is to understand how development itself evolves. This is important even to just understand the evolution of the phenotype because the improved understanding of phenotypic evolution obtained in aims 1 and 2 only lasts as long as development itself does not evolve. However, if we can understand some aspects of how development evolves, then we should be able to understand phenotypic evolution better and over larger periods of time.
1. Understanding development and the phenotypic variation it produces
For this aim we take two complementary approaches.
1.1 Study as many specific developmental systems as possible to extract general principles about how gene and cell networks lead to pattern formation and morphogenesis. We do not study specific genes or specific interactions. Instead we build mathematical models of how genetic interactions, cell behaviors (cell division, cell contraction, cell death, etc.) and mechanical interactions can be wired to lead to the development of specific organs. We have done that for teeth (Salazar-Ciudad and Jernvall, 2002, 2010; Salazar-Ciudad, 2012; Marin-Riera et al., 2018, etc.), Drosophila segmentation (Salazar-Ciudad et al., 2001b), Drosophila wing (Ray, et al. 2015; Matamoro-Vidal et al., 2018), spiral cleavage (Brun-Usan et al., 2017) and turtle carapace (Moustakas-Verho et al., 2014). This research is performed in close collaboration with experimental developmental biologists (for example Jukka Jernvall).
Simulation of turtle carapace (Moustakas-Verho et al., 2014)
1.2 Build general models of development and explore what is logically required for development to lead to pattern formation and morphogenesis. By general models of development we mean models that can implement arbitrary gene networks, cell mechanical interactions, cell behaviors (cell division, cell contraction, cell adhesion, cell death, cell growth, cell polarization, etc.), cell signaling, the diffusion of signals in the extracellular space of an embryo and the regulation of all these things by each other. With these models we build large numbers of random networks and simulate which morphologies they can lead to from very simple initial morphologies (i.e. this is a process of pattern formation and morphogenesis).
By studying which of these networks can lead to pattern formation and morphogenesis and which ones cannot, we extract general theoretical principles that developmental networks should fulfill for the production of complex morphologies. These models are mostly EmbryoMaker (Marin-Riera et al, 2016; see software section; Hagolani et al., 2019, 2021).
We also have a set of early models in which we identify that there is a mathematical constraint on the possible range of gene network topologies that can lead to pattern formation in cells that are communicating by extracellular signals (e.g. growth factors) (Salazar-Ciudad et al., 2000, 2001a,2001b).
2. Understanding how development affects morphological evolution
The models of development in the previous section are combined with populational models with mutation, reproduction and natural selection on the morphologies produced by the developmental model. This way we simulate phenotypic evolution but not from the unrealistic perspective of classical evolutionary theory and population genetics where genes directly determine the phenotype but from a more updated and realistic approach. This approach has lead to many deep insights on phenotypic evolution, on how development affects it and on how the classical approach fails to capture important aspects of it. See (Salazar-Ciudad et al., 2001a, 2004, 2005, 2010; Marin-Riera et al., 2013; Milocco and Salazar-Ciudad, 2020, 2022).
3. Models on the evolution of development
To study the evolution of development we take a similar approach to the study of the evolution of the phenotype. Development can vary between individuals (i.e. different individuals can have slightly different developmental networks with different genes, different interactions,etc.). Then, there is two questions one needs to address to understand the direction of developmental evolution. 1) Which developments can transform into other by mutations (and how likely this is in each case) 2) Which developments are more likely to produce adaptive morphologies (that would of course depend on the environment). Question 1 determines which developments arise while question 2 determines which of them would be selected. Through our general models of development we have been able to implement this approach in practice to study the ways in which development itself can evolve (Salazar-Ciudad et al., 2001a, 2004; Salazar-Ciudad 2010) and how it may evolved in specific sets of species (Salazar-Ciudad et al., 2001b).
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