Animal cell types across evolutionary timescales: from regulatory characters to cell phylogenies

Introduction

Cell types are the basic constituents of animal multicellularity, with each type defined by a gene regulatory program that specifies cell function and structure. Thus, understanding cell type diversity is key to explaining animal adaptation and evolution. However, despite recent advances in the molecular characterization of cell types, the phylogenetic relationships between animal cell types remain obscure, mainly because we do not understand how the different elements of a cell type identity program (e.g., transcription factors and regulatory sequences) change over time and how these changes translate into cellular novelties.

Project Overview

This project will bridge the gap between cell type micro- and macroevolution, focusing on Cnidaria as a model to study cell type evolutionary processes. We will measure and compare cell identity characters across divergent timescales:

1. Intraspecies variation between sea anemone populations
2. Cross-species comparisons within Cnidaria
3. Cross-phyla cell phylogenies

Methodology

By combining single-cell and functional genomics experiments with advanced computational methods, we will:

1. Build whole-organism genotype-phenotype maps at cellular resolution to explain the genetic basis of cell type evolution.
2. Model the evolutionary processes underlying the diversification, novelty, and functional adaptation of cell types across the cnidarian phylum.
3. Study the evolutionary conservation and divergence rates of cell type regulatory characters to resolve the phylogenetic relationships between animal cell types (e.g., neurons, gland, epidermal, and sensory cells).

Expected Results

The expected results will offer a multi-level, quantitative, and phylogenetic perspective on animal cell types, allowing us to test long-standing hypotheses about cell type evolution. Our novel comparative framework will lay the foundations of cell systematics and provide transformative insights into a fundamental question in biology: how do cell types originate and diversify?