Leong JCK et al. (2022), Distinguishing Evolutionary Conservation from D...

ECB-ART-50417

Life (Basel) 2022 Mar 17;123:. doi: 10.3390/life12030440.

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Distinguishing Evolutionary Conservation from Derivedness.

Leong JCK , Uesaka M , Irie N .

Abstract
While the concept of "evolutionary conservation" has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or "derivedness". We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, "conservation" mainly considers genes or traits which species have in common, while "derivedness" additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, "transcriptomic derivedness index", for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.

PubMed ID: 35330191
PMC ID: PMC8954198
Article link: Life (Basel)
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Article Images: [+] show captions

	Figure 1. Conservation-oriented versus derivedness-oriented gene comparisons. (a) Conservation-oriented methods tend to compare commonly shared genes (e.g., 1:1 orthologs). (b) Derivedness-oriented methods additionally cover evolutionary changes of nonshared genes, such as 1-to-many orthologs, paralogs, and species-specific acquired or potentially lost genes. Rectangles: genes. Red: homologous genes inherited from the common ancestor of species A and B [27]. Blue: genes duplicated after the speciation event leading to species A and B (additionally marked by ’ and ” signs). Green and purple: orphan genes (genes without recognizable homologs in the other species).
	Figure 2. Typical methods of molecular and morphological phylogenetics. (a) A derivedness-oriented method, which compares not only commonly shared traits (morphological trait 3) but also those that are not shared among all species (morphological traits 1 and 2), is often used in morphological phylogenetics. For phylogenetic reconstruction, the traits of different species are encoded as different states (for example, “-” represents the absence of a trait here, “0” represents ancestral state, and “1” and “2” represent derived states). (b) A conservation-oriented method, which compares only commonly shared genes, is often used in molecular phylogenetics. Only the alignable sequences of the commonly shared 1:1 orthologs tend to be used to infer phylogeny.
	Figure 3. Quantification of phenotypic derivedness of embryos. The whole-embryonic transcriptome was utilized as a phenotype, and we developed a method to estimate the transcriptomic derivedness of each developmental stage from the common ancestor of echinoderms and chordates. In addition to 1:1 orthologs, expression levels of paralogs and potentially lost genes were also considered when calculating the evolutionary distances between embryonic transcriptomes. Transcriptomic derivedness of each developmental stage was then plotted as the total branch length from the common ancestral node on the inferred tree (modified from [26]).

References [+] :

Albalat, Evolution by gene loss. 2016, Pubmed