Cell Lineage Trees in Mice Figure 1. Cell lineage analysis based on somatic MS mutations. A. The cell lineage tree of an organism is a rooted labeled binary tree representing its development from a single cell until present time. Nodes (circles) represent cells (dead cells are crossed), and edges (lines) connect parent and daughter cells (dashed lines represent several divisions). Uncrossed leaves (nodes with no daughters) represent extant cells. Lineage trees are a snapshot of a specific timepoint, which constantly grow throughout embryonic development and the adult life of the organism. Any cell sample (colored leaves) induces a partial subtree, called the cell sample lineage tree (panel B). B. The genomic composition of cells in the sample tree at three MS loci is shown. Spontaneous somatic mutations (marked by X) in these loci are sufficient to encode the lineage relations between these cells. Cells that are genetically similar tend to share a longer common developmental path, consequently enabling phylogenetic analysis to reconstruct the tree. Although idealized mutations are depicted, even potential hampering factors (such as coincident mutations) are not expected to disrupt analysis if a sufficient number of loci are analyzed [1]. C. Scheme of reconstruction procedure. DNA from isolated cells is amplified either by culture or whole genome amplification, after which each cell is analyzed over a large set of MS loci using PCR and capillary electrophoresis. Capillary histograms are automatically analyzed yielding cell identifiers, which represent the mutations each cell accumulated in the MS set. Phylogenetic analysis of cell identifiers yields a reconstructed tree, which is an estimation of the lineage relations between analyzed cells. doi:10.1371/journal.pone.0001939.g001 in a 7-month old wild-type mouse in the reconstruction of the lineage relations between about 50 cells (mainly hepatocytes) using fast-mutating MS [6]. Here we applied this method to the study of mouse cell lineage trees. We first aimed to get a glimpse of what mouse lineage trees look like, and to have a sense of their general features, structure and complexity. For this purpose we analyzed multiple cell types obtained from various sources in the mouse body. This analysis also allowed us to address for the first time three basic questions in developmental biology of higher organisms: 1. What is the correlation between lineage and function? (we use the terms cell type and function interchangeably in this paper) 2. What is the correlation between lineage and physical proximity among cells? 3. What is the correlation between lineage and anatomical proximity among cells? Caenorhabditis elegans offers the best point of reference for the first question, since its entire lineage tree (including 959 somatic cells, all with known function) has been reconstructed [2,3]. Even in C. PLoS ONE | www.plosone.org 2 April 2008 | Volume 3 | Issue 4 | e1939