Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms

Abstract

Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named “derivedness index” to quantify the degree of derivedness. In contrast to the conservation-based approach, which deals with expressions of commonly shared genes among species being compared, the derivedness index also considers those that were potentially lost or duplicated during evolution. By applying our method, we found that the gene expression profiles of penta-radial phases in echinoderm tended to be more highly derived than those of the bilateral phase. However, our results suggest that echinoderms may not have experienced much larger modifications to their developmental systems than chordates, at least at the transcriptomic level. In vertebrates, we found that the mid-embryonic and organogenesis stages were generally less derived than the earlier or later stages, indicating that the conserved phylotypic period is also less derived. We also found genes that potentially explain less derivedness, such as Hox genes. Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through future studies. We anticipate that this index will serve as a quantitative guide in the search for constrained developmental phases or processes.

Distinguishing Evolutionary Conservation from Derivedness

“…To be specific, due to the strict definition of 1:1 orthologs, these genes often cover only a small part of the entire gene repertoire in the genome, especially when a large number of species are compared. For example, in our recent analysis comparing 13 species of chordates and echinoderms [ 26 ], we identified only 271 1:1 orthologous genes, which covered only ~1.5% of all the genes in a typical deuterostome genome (~20,000 genes). While these 1:1 orthologs would still be sufficient for reconstructing phylogeny [ 38 ] or estimating the evolutionary rate of each species, their analysis may not be sufficient for evaluating derived features, or changes that accumulated during evolution, as it ignores changes that took place in the remaining ~98.5% of the gene repertoire.…”

“…In this respect, we recently attempted to develop a method to quantify the degree of phenotypic evolution of embryos, or degree of their derivedness, by incorporating the expression profiles of paralogous genes (where we utilized the transcriptome as a phenotype of an embryo) [ 26 ]. We focused on echinoderms, a group of animals that are generally considered as highly derived species on the basis of their unique anatomical features, such as pentameral symmetry in the adult stage [ 61 , 62 ].…”

“…Similarly, although the evolutionary conservation of the mid-embryonic period has been clarified in a wide variety of animals (including vertebrates [ 5 , 6 , 12 , 63 , 64 , 65 ], Drosophila species [ 66 , 67 ], nematodes [ 68 ], and mollusks [ 69 ]), this does not necessarily mean that this embryonic period remains less derived than the earlier and the later stages because the nonshared genes have not been considered. In our recent study [ 26 ], we compared the expression profiles of not only 1:1 orthologs, but also paralogs and potentially lost genes of various echinoderm and chordate species to quantify the evolutionary derivedness of their developmental stages ( Figure 3 ). Data were previously collected from wild-type embryos, with biological replicates from independent parents in order to represent the statistical population of interest by incorporating phenotypic variations among the wild-type embryos.…”

“…However, the tree covering orphan genes (genes that have no homologs in the other species) violated the second criterion. Therefore, to be conservative, in further analyses in the study, we adhered to the method and the tree that showed a topology consistent with the phylogeny estimated from genomic sequences, where only 1:1 orthologs, paralogs and potentially lost genes were considered in the calculation (discussed in detail in [ 26 ]). We note that it is also possible that the derivedness tree does not strictly match the phylogenetic relationship estimated from genomic sequences, compromising the second criterion.…”

“…We will then discuss the technical limitations and challenges of current conservation-oriented and derivedness-oriented molecular methods. Finally, as an application of the concept of derivedness, we will briefly describe our recently developed method, “transcriptomic derivedness index” [ 26 ], to estimate the evolutionary derivedness of transcriptomes of various echinoderm and chordate embryos from their common ancestor.…”