TY - JOUR
T1 - Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos
T2 - A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
AU - Leong, Jason Cheok Kuan
AU - Li, Yongxin
AU - Uesaka, Masahiro
AU - Uchida, Yui
AU - Omori, Akihito
AU - Hao, Meng
AU - Wan, Wenting
AU - Dong, Yang
AU - Ren, Yandong
AU - Zhang, Si
AU - Zeng, Tao
AU - Wang, Fayou
AU - Chen, Luonan
AU - Wessel, Gary
AU - Livingston, Brian T.
AU - Bradham, Cynthia
AU - Wang, Wen
AU - Irie, Naoki
N1 - Publisher Copyright:
Copyright © 2021 Leong, Li, Uesaka, Uchida, Omori, Hao, Wan, Dong, Ren, Zhang, Zeng, Wang, Chen, Wessel, Livingston, Bradham, Wang and Irie.
PY - 2021/11/26
Y1 - 2021/11/26
N2 - 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.
AB - 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.
KW - chordates
KW - derivedness
KW - echinoderms
KW - evo-devo
KW - phenotypic evolution
KW - phylotypic period
UR - http://www.scopus.com/inward/record.url?scp=85120974539&partnerID=8YFLogxK
U2 - 10.3389/fcell.2021.749963
DO - 10.3389/fcell.2021.749963
M3 - 文章
AN - SCOPUS:85120974539
SN - 2296-634X
VL - 9
JO - Frontiers in Cell and Developmental Biology
JF - Frontiers in Cell and Developmental Biology
M1 - 749963
ER -