I think mouse is the most complex organism with information on this, complexity measured by number of cell types. Try the Mouse Atlas at the HGU in Edinburgh: www.emouseatlas.org

Xenbase has all the cell fate information for Xenopus, Zfin has the info for zebrafish.

Thank you Julia and Dany for your answers. I think your information is helpful. But after reading those databases, I think these species either does not have the full tree (the whole lineage tree from zygote to all the terminal cells) or does not have the functional classification that is already mapped to the tree.

To be more specific:

For the mouse, there're static snapshots of the mouse embryo, with functional classifications on the cells, but these cells have not been organized into a lineage tree like that in C.elegans.

For zebrafish, I actually once tried to construct a complete developmental lineage from those 3D images of zebrafish. I failed back then, but I guess somebody have done it by now. However, I don't know any functional information that is directly mappable onto the lineage tree.

Please correct me if I'm wrong. But thank you again for your valuable information.

jianrong

C. elegans is an organism whose cell lineages are (largely) fully cell autonomous, so that you can make a tree. Most organisms, however, also have what is called regulative development. In those animals, many of the cell fates are determined by what cells they happen to end up next to, rather than by what they inherited from maternal cytoplasm. And cells crawl around during development, so who the neighbors will be can not be predicted. So you can not make a tree the same way. Maybe the answer to your question is no, you won't find anything exactly analogous to the C. elegans lineage chart, the fate maps. sorry.

Thank you Dany for your helpful explanations.

I guess the next question in turn is then whether it is possible to build a "consensus" or "reference" tree, allowing some statistical variance. But that's really too far from my original question to discuss here.

There are several "fate maps" available in the literature for zebrafish and medaka. Usually, these are focusing on a range of specific developmental stages. Also the technology is very variable, from single cell labeling and more recently transgene expression to label cell fates. There is no continuous fate map from zygote to, say, larval stages or even adults, because of the regulatory development Dany describes above. I suggest a literature search for "(cell) lineage" "cell fate" "fate map" on ZFIN to get you started.

Recently, several consortia capture 3D data and provide an atlas of embryo/larva gene expression and anatomy, but they are not 'continuous' in the sense that you can establish cell lineages from zygotes through any of these stages, or they focus on specific organs such as brain etc.

Concurring with some of the previous answers, I would say that there are very few species for which there is a definite lineage tree, with C. elegans and similar nematodes being extreme examples of fixed lineage. For a number of the major developmental model organisms there are fate maps that give (statistical) predictions of cell fate from cell positions at earlier stages of development. The prime examples of these are from amphibian (Xenopus) but there are others (zebrafish, chick, Drosophila). These fate maps are almost never represented as fate decision trees. This is partly because intermediate internal specification states of cells are usually unknown, but it is also because developmental biologists tend not to think this way and it is something you could probably extract from existing data (although there's a lot of work to be done to do it). Also, it is important to know that fate map starts at a given stage and this isn't necessarily the zygote - it is usually much later and sometimes very much later. Mouse is rather poorly fate mapped because it is relatively inaccessible at developmental stages but there are some parts that are better mapped, such as parts of the central nervous system (e.g. Cepko lab for retina) and the lungs (see the very nice work from the Krasnow lab). There is a good review of fate mapping technology by Margaret Buckingham (Buckingham ME, Meilhac SM., Dev Cell. 2011 Sep 13;21(3):394-409) that might be a good lead into other work in this area.

If I understand correctly, you are looking for eutelic organisms-animals with a fixed number of somatic cells in the adult, therefore often an invariant lineage from embryo to adult. In addition to C. elegans, other nematodes, rotifers, tartigrades, and dicyemida may be eutelic. I agree with Jeremy's points that particular tissues in mice may suit your needs, but fate maps in non-eutelic animals often have variance built in since environmental inputs can likely shape the final developmental outcome.

Cell lineage in ascidian is also well known. Recently we constructed the 3D atlas of the tailbud stage embryo. You can download the 3D PDF file from here. http://chordate.bpni.bio.keio.ac.jp/3DVMTE/3DVMTE_THratio1.86.pdf

Thanks Kohji ! Your work is beautiful and I really like the way you presented the data.

I think this is the data for the functional classification of the cells at the tailbud stage of C. intestinalis. But it seems that there is no developmental lineage tree that would connect the zygote to all the cells described in your 3D PDF. Please correct me and point me to such lineage tree if I'm wrong.

Thanks again !

Yang,

I once tried to construct the lineage tree from zygote to larva of C. intestinalis.

Please see the site below,

http://chordate.bpni.bio.keio.ac.jp/faba/cell_lineage2/

You can understand the temporal relationships of cells in different stages. However, there is no 3D spatial information. I think that 3D timelapse imaging of development will be a key to utilize both info. I'm interested in such approach.

Caenorhabditis elegans (C. elegans) is the best known example. However other studies on insects as Drosophila are well known on cell lineage. Furthermore ascidians are another example on invariant cleavage.

Jeremy, I think you could also be interested in Keller et al., 2008. They tracked a zebrafish embryo from zygote to 20000 cells stage, although they did not generate a lineage tree. I am very interested in the description of whole lineage trees in a vertebrate and in my opinion we should be able to generate what you called 'consensus trees'. I completely agree you in this. I have some ideas about how do it and now I am looking for a lab for my postdoc with this regarding. If I am finally successful I hope provide you a better answer.

By the way, I am very happy about this discussion.

http://www.sciencemag.org/content/322/5904/1065.abstract

Hi Jorge, actually I have looked into that data. Although as in their movies, the lineal relationship between cells (mother-daughter cells) seems quite obvious, I find it hard to connect all the appeared cells together. Eventually, what I got is many disconnected partial lineage trees.

However, I am guessing that there should be some software or algorithm out there available that could connect these trees. Or basically, connecting dots on images (in this case, 3 dimensional) taken in different time points. This task reminds me how next generation sequencing generate sequences from images.

Again, I'm no experts but I think this question at hand is solvable.

And by the way, I think the developmental lineage tree would be another great object to study with as quantitative traits.

Hi, there are a few other invertebrates for which the cell lineages have been done. certainly not as extensive as for c. elegans, but still quite complete.

The polychaete annelid C. teleta

http://www.evodevojournal.com/content/pdf/2041-9139-1-8.pdf

The acoel flatworm Neochildia fusca

http://www.sciencedirect.com/science/article/pii/S0012160600996283

The hemichordate P. flava

http://www.ncbi.nlm.nih.gov/pubmed/11806633

The sea urchin S. purpuratus

http://www.ncbi.nlm.nih.gov/pubmed/2448185

Those a just a few likns to papers and i am sure there are more up to date cell lineages for some species and there are certainly more cited in those papers.

Cheers,