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Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos

View Article: PubMed Central - PubMed

ABSTRACT

Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Cionaintestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa. We compare both cell volume distributions and cell volume across developmental time within and between single species and assess differences between lineage tree and differentiation tree orderings. This enhances our understanding of the differentiation events in a model of pure mosaic embryogenesis and its relationship to evolutionary conservation. We also contribute several new techniques for assessing both differences between lineage trees and differentiation trees, and differences between differentiation trees of different species. The results suggest that at the level of differentiation trees, there are broad similarities between distantly related mosaic embryos that might be essential to understanding evolutionary change and phylogeny reconstruction. Differentiation trees may therefore provide a basis for an Evo-Devo Postmodern Synthesis.

No MeSH data available.


An isometric graph showing the Hamming distance of the differentiation tree from the lineage tree in Ciona (N = 213). The H abbreviation stands for Hamming distance. The position of a point representing a cell is based on the depth of its node in the differentiation tree. The positions of all points are rotated 45 degrees clockwise from a bottom-to-top differentiation tree ordering (where the 1-cell stage is at the bottom of the graph). Each cell is colored with its Hamming distance. Along a given line, the cells appear in their order, left to right, in the differentiation tree. For example, cells A.5.1 and A.5.1* at depth 4, where the total number of cells is 16 (ranging from 0 to 15), means cell A.5.1 is at the extreme left side of the differentiation tree, and cell A.5.1* is at the extreme right side of the differentiation tree. The other cells are spaced in between. The pattern of Hamming distances suggests that the relationship between the two orderings is nonrandom and therefore has some underlying anatomical importance.
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biology-05-00033-f011: An isometric graph showing the Hamming distance of the differentiation tree from the lineage tree in Ciona (N = 213). The H abbreviation stands for Hamming distance. The position of a point representing a cell is based on the depth of its node in the differentiation tree. The positions of all points are rotated 45 degrees clockwise from a bottom-to-top differentiation tree ordering (where the 1-cell stage is at the bottom of the graph). Each cell is colored with its Hamming distance. Along a given line, the cells appear in their order, left to right, in the differentiation tree. For example, cells A.5.1 and A.5.1* at depth 4, where the total number of cells is 16 (ranging from 0 to 15), means cell A.5.1 is at the extreme left side of the differentiation tree, and cell A.5.1* is at the extreme right side of the differentiation tree. The other cells are spaced in between. The pattern of Hamming distances suggests that the relationship between the two orderings is nonrandom and therefore has some underlying anatomical importance.

Mentions: One way we can compare the lineage tree order and the differentiation tree order is by calculating a numeric distance between the differentiation code and the lineage code. Since these binary codes provide specific addresses for each cell in the embryo, specific cells (and locations in the tree) can be compared between tree orderings, quantified using the Hamming distance. This distance between the lineage code and differentiation code is measured in bits (see Methods, Section 2.9). We use the lineage tree to root the lineage code/differentiation code comparison in Ciona and the differentiation tree to do the same in C. elegans, to demonstrate that both can be effectively used to determine the Hamming distance for individual cells. This makes no difference in terms of the Hamming distance for each cell nor the mother cell/descendant relationship. However, the lineage tree for Ciona is used because the Ciona differentiation tree potentially contains many more potential errors than the lineage tree. Measurable differences between the lineage code and differentiation code using the Hamming distance metric were visualized using an isometric graph (Figure 11 for Ciona and Figure 11 for C. elegans).


Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos
An isometric graph showing the Hamming distance of the differentiation tree from the lineage tree in Ciona (N = 213). The H abbreviation stands for Hamming distance. The position of a point representing a cell is based on the depth of its node in the differentiation tree. The positions of all points are rotated 45 degrees clockwise from a bottom-to-top differentiation tree ordering (where the 1-cell stage is at the bottom of the graph). Each cell is colored with its Hamming distance. Along a given line, the cells appear in their order, left to right, in the differentiation tree. For example, cells A.5.1 and A.5.1* at depth 4, where the total number of cells is 16 (ranging from 0 to 15), means cell A.5.1 is at the extreme left side of the differentiation tree, and cell A.5.1* is at the extreme right side of the differentiation tree. The other cells are spaced in between. The pattern of Hamming distances suggests that the relationship between the two orderings is nonrandom and therefore has some underlying anatomical importance.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037352&req=5

biology-05-00033-f011: An isometric graph showing the Hamming distance of the differentiation tree from the lineage tree in Ciona (N = 213). The H abbreviation stands for Hamming distance. The position of a point representing a cell is based on the depth of its node in the differentiation tree. The positions of all points are rotated 45 degrees clockwise from a bottom-to-top differentiation tree ordering (where the 1-cell stage is at the bottom of the graph). Each cell is colored with its Hamming distance. Along a given line, the cells appear in their order, left to right, in the differentiation tree. For example, cells A.5.1 and A.5.1* at depth 4, where the total number of cells is 16 (ranging from 0 to 15), means cell A.5.1 is at the extreme left side of the differentiation tree, and cell A.5.1* is at the extreme right side of the differentiation tree. The other cells are spaced in between. The pattern of Hamming distances suggests that the relationship between the two orderings is nonrandom and therefore has some underlying anatomical importance.
Mentions: One way we can compare the lineage tree order and the differentiation tree order is by calculating a numeric distance between the differentiation code and the lineage code. Since these binary codes provide specific addresses for each cell in the embryo, specific cells (and locations in the tree) can be compared between tree orderings, quantified using the Hamming distance. This distance between the lineage code and differentiation code is measured in bits (see Methods, Section 2.9). We use the lineage tree to root the lineage code/differentiation code comparison in Ciona and the differentiation tree to do the same in C. elegans, to demonstrate that both can be effectively used to determine the Hamming distance for individual cells. This makes no difference in terms of the Hamming distance for each cell nor the mother cell/descendant relationship. However, the lineage tree for Ciona is used because the Ciona differentiation tree potentially contains many more potential errors than the lineage tree. Measurable differences between the lineage code and differentiation code using the Hamming distance metric were visualized using an isometric graph (Figure 11 for Ciona and Figure 11 for C. elegans).

View Article: PubMed Central - PubMed

ABSTRACT

Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Cionaintestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa. We compare both cell volume distributions and cell volume across developmental time within and between single species and assess differences between lineage tree and differentiation tree orderings. This enhances our understanding of the differentiation events in a model of pure mosaic embryogenesis and its relationship to evolutionary conservation. We also contribute several new techniques for assessing both differences between lineage trees and differentiation trees, and differences between differentiation trees of different species. The results suggest that at the level of differentiation trees, there are broad similarities between distantly related mosaic embryos that might be essential to understanding evolutionary change and phylogeny reconstruction. Differentiation trees may therefore provide a basis for an Evo-Devo Postmodern Synthesis.

No MeSH data available.