Phylogenetic analysis of developmental and postnatal mouse cell lineages

Abstract

Fate maps depict how cells relate together through past lineage relationships, and are useful tools for studying developmental and somatic processes. However, with existing technologies, it has not been possible to generate detailed fate maps of complex organisms such as the mouse. We and others have therefore proposed a novel approach, "phylogenetic fate mapping," where patterns of somatic mutation carried by the individual cells of an animal are used to retrospectively deduce lineage relationships through phylogenetic inference. Here, we have cataloged genomic polymorphisms at 324 mutation-prone polyguanine tracts for nearly 300 cells isolated from a single mouse, and have explored the cells' lineage relationships both phylogenetically and through a network-based approach. We present a model of mouse embryogenesis, where an early period of substantial cell mixing is followed by more coherent growth of clones later. We find that cells from certain tissues have greater numbers of close relatives in other specific tissues than expected from chance, suggesting that those populations arise from a similar pool of ancestral lineages. Finally, we have investigated the dynamics of cell turnover (the frequency of cell loss and replacement) in postnatal tissues. This work offers a longitudinal study of developmental lineages, from conception to adulthood, and provides insight into basic questions of mouse embryology as well as the somatic processes that occur after birth.

Fig. 1

Examples of and statistics for somatic variation in polyguanine markers. (A) Electropherograms of a polyclonal mixture of cells used to estimate the genotype of the mouse zygote aligned with those of various somatic cells. X-axis indicates product length (bp), Y-axis represents signal intensity. Allele lengths are indicated, with mutations from the zygote noted. (B) Histogram for the number of markers that demonstrate different numbers of distinguishable mutant genotypes, across all cells. (C) Histogram for the quantity of cells displaying particular numbers mutations from the zygote.

Fig. 2

Lineage reconstruction. (A) The Bayesian phylogenetic fate map is displayed as a circular phylogram rooted at the estimated zygote. Scale bar reflects the number of changes per allele along branches. Each terminal circle represents a single cell, color coding indicates the cell's origin. (B) Fraction of the branch length from the zygote to the most recent common ancestor of cells from the same tissue or two different tissues. Internal controls, which are known to share a very recent common ancestor, are shown for comparison. Error bars indicate standard error of the mean. *P<0.05, **P<0.001. (C) Depiction of results from B. Recent mitoses, with the greatest distance from the common ancestor (“A,” in circle) to the zygote, tend to produce cells from the same tissue (top). Older common ancestors, falling closer to the zygote, tend to produce cells of different tissues (bottom).

Fig. 3

Network-based fate map of mouse tissues. The degree of similarity between tissues’ founding lineages is depicted. Nodes represent various tissues, and the lines connecting them depict the specific pairwise comparisons used to construct the network. The distance between nodes (or along lines) is inversely proportional to the degree of association between two tissues. Black lines indicate highly significant (P<0.05) relationships, gray lines represent suggestive relationships (P<0.25), and less significant relationships are not shown. It is possible for connections to extend unidirectionally from one node, thus, arrowheads represent the polarity of association.

Fig. 4

Mitotic distance from the zygote to tissues. The average number of mutations differentiating cells from the estimated zygote are displayed for each tissue. Error bars indicate standard error of the mean.

Fig. 5

Model of embryogenesis. Fertilization establishes the genotype of the diploid zygote. As mitosis occurs, lineages become distinguishable from one another based on their pattern of somatic mutations. Cell divisions during cleavage are thought to result in contiguous daughter cells (Zernicka-Goetz 2005). Extensive cell mixing occurs before gastrulation, homogenizing lineages. Cell motility becomes restricted sometime after gastrulation. During organogenesis, patches of contiguous cells, derived from dissimilar lineages, are induced to form particular tissues. Tissues increase in size through relatively coherent clonal growth of various lineages in the induced patches.