For example, one of the ancestral duplications (between A1 and A5, illustrated in purple) involves orthologous/paralogous modern chromosomes 1 5, 3-6-8, 3-9, and 1-3, respectinely, in rice, maize, sorghum, and the Triticeae.
For example, the active site of the ancestral MDH could have certain residues that the modern MDH lacks, residues that interact with the insertion and allow it to preferentially bind pyruvate.
The past 5 years have seen an interesting controversy as to whether mimetic forms in the L. arthemis complex have evolved once (monophyletic mimicry hypothesis (MMH); Figure 1b), or whether the non-mimetic arthemis phenotype might constitute an example of the reversion to an ancestral phenotype from a mimetic one (reversion hypothesis (RH); Figure 1a).
In genetic association studies, for example, the ancestral background of human subjects can have a strong confounding effect [for example, [ 2- 5]].
For example, the ancestral states of the maximal reported organism size and genome size (supplementary files 2 and 3, Supplementary Material online) suggest secondary reductions along the lineages leading to the different unicellular algae under study here.
For example, the ancestral genome of vertebrates is thought to have undergone two consecutive rounds (1R/2R) of WGD (Dehal and Boore 2005), with a third round (3R) in the lineage leading to teleost fish (Taylor et al. 2003; Jaillon et al. 2004).
For example, the ancestral gene order of the Leotiomycetes was most closely related to the two ancestral gene orders of the Sordariomycetes and Eurotiomycetes based on the parsimonious rearrangement scenarios reconstructed by crex reflecting an intermediate position of the Leotiomycetes (see Additional File 4).
Perhaps the best studied example of this are the ancestral tetraploid salmonids, who possess a single classical MHIIβ gene [ 25].
For example, Basidiomycetes may have lost most of the ancestral PL1 genes whereas Sordariomycetes have retained most of them.
