Performance summary of all the methods on all the datasets of mice and humans.

<p>Upper panels – Mouse, Lower panels- Human. Each column presents a different clustering measure (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003297#s4" target="_blank">Materials and Methods</a> for details), and each bar represents a different distance measure, where the colors specify the distance measures as noted in the legend. The first and the second group of bars (from left to right) present the results using the NJ algorithm and the QMC algorithm respectively. Rows description: (A) The average score of all the methods, where higher values (that are transformations of the real scores) indicate better performance. (B) The number of times every method received the highest rank (for the mouse panel the highest rank is 20 since we compared 20 methods, and for the human panel the highest rank is 12).</p

Depth quality of the different methods.

<p>Each column presents a different depth quality measure (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003297#s4" target="_blank">Materials and Methods</a> for details), and each bar represents a different distance measure, where the colors specify the distance measures as noted in the legend. Rows description: (A) The average depth score of all the methods, where lower values for the KS test, lower values for the overlap percentage and higher values for the normalized distance test mean better performance. (B)The number of times every method received the highest rank (in this case it is 10 since we compared 10 methods).</p

Cells from different organisms are clustered separately in the lineage tree.

<p>Two reconstructed lineage trees are shown: (A) A lineage tree containing cells from three mice, M3 (blue), M5 (pink) and M6 (green). (B) A lineage tree containing cells from seven humans, H1 (blue), H2 (red), H3 (orange), H4 (pink), H5 (green), H6 (purple) and H7 (turquoise). The root of the trees (colored in black) is the weighted mean of the organisms' putative zygotes. The trees were reconstructed using the NJ algorithm along with the Normalized-Absolute distance measure.</p

Performance summary of all the methods for datasets composed of cells of same depth only.

<p>Each column presents a different clustering measure (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003297#s4" target="_blank">Materials and Methods</a> for details), and each bar represents a different distance measure, where the colors specify the distance measures as noted in the legend. The first group of bars (from left to right) presents the results using the NJ algorithm, the second group of bars presents the results using the QMC algorithm, the third presents the results using the UPGMA algorithm, and the last one presents the results using the BATWING tool. Rows description: (A) The average score of all the methods, where higher values (that are transformations of the real scores) indicate better performance. (B) The number of times every method received the highest rank (in this case it is 31 since we compared 31 methods).</p

Accelerated increase in GV oocyte from large antral follicles depth following unilateral ovariectomy.

<p>a–c) Reconstructed lineage trees of oocytes from both ovaries of unilaterally ovariectomized mice. Blue circles are oocytes extracted from the ovary removed at a young age – 23 days (a) 29 days (b) and 26 days (c). Green circles are oocytes extracted from the contralateral ovary removed at an older age – 139 days (a) 161 days (b) and 150 days in which the ovulated oocytes were marked with blue dots (c). Horizontal lines are the average depths of young oocytes (blue) and old oocytes (green). d) Increase in depth with age following ovariectomy is accelerated relative to the increase observed for non-ovariectomized mice. Last two boxes include pooled data from the indicated mice. * p<0.05, ** p<0.01.</p

Microsatellite mutations are replication dependent.

<p>a) Shown are two scenarios for microsatellite mutations – replication dependent mutations that occur during mitotic divisions at a cell stage with two chromosomal copies (left), and spontaneous, replication independent mutations occurring at the quiescent oocyte stage with four chromosomal copies (right). While replication dependent mutations would result in two alleles, spontaneous mutations would mostly result in more than two alleles. The bottom plots show representative capillary signals. b) The increase with age in fraction of alleles with spontaneous mutations is significantly smaller than the increase in fraction of alleles with replication dependent mutations. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002477#s2" target="_blank">Results</a> are for the three longitudinal experiments.</p

Oocytes form a cluster distinct from bone marrow cells.

<p>Reconstructed cell lineage tree of mice in several ages, each showing that GV oocytes from large antral follicles (red) form a cluster that is distinct from cells of bone marrow origin (mesenchymal stem cells- yellow and lymphocytes-blue). Ovarian cumulus cells are in green. Shaded boxes denote subtrees that are statistically enriched for cells of a certain cell population, using a hyper-geometric enrichment test. Mouse names represent their age in days. Y axis is depth (number of divisions since the zygote). One cell in M278 was cropped for visual clarity.</p