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

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 degr...

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Autores principales:	Jason Cheok Kuan Leong, Yongxin Li, Masahiro Uesaka, Yui Uchida, Akihito Omori, Meng Hao, Wenting Wan, Yang Dong, Yandong Ren, Si Zhang, Tao Zeng, Fayou Wang, Luonan Chen, Gary Wessel, Brian T. Livingston, Cynthia Bradham, Wen Wang, Naoki Irie
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	derivedness evo-devo phenotypic evolution phylotypic period chordates echinoderms Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b79e0810810f4e63812ea630e4bb4930
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spelling	oai:doaj.org-article:b79e0810810f4e63812ea630e4bb49302021-12-01T06:01:29ZDerivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms2296-634X10.3389/fcell.2021.749963https://doaj.org/article/b79e0810810f4e63812ea630e4bb49302021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fcell.2021.749963/fullhttps://doaj.org/toc/2296-634XSpecies 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.Jason Cheok Kuan LeongYongxin LiMasahiro UesakaYui UchidaYui UchidaAkihito OmoriMeng HaoWenting WanYang DongYandong RenSi ZhangTao ZengFayou WangLuonan ChenLuonan ChenGary WesselBrian T. LivingstonCynthia BradhamWen WangWen WangNaoki IrieNaoki IrieFrontiers Media S.A.articlederivednessevo-devophenotypic evolutionphylotypic periodchordatesechinodermsBiology (General)QH301-705.5ENFrontiers in Cell and Developmental Biology, Vol 9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	derivedness evo-devo phenotypic evolution phylotypic period chordates echinoderms Biology (General) QH301-705.5
spellingShingle	derivedness evo-devo phenotypic evolution phylotypic period chordates echinoderms Biology (General) QH301-705.5 Jason Cheok Kuan Leong Yongxin Li Masahiro Uesaka Yui Uchida Yui Uchida Akihito Omori Meng Hao Wenting Wan Yang Dong Yandong Ren Si Zhang Tao Zeng Fayou Wang Luonan Chen Luonan Chen Gary Wessel Brian T. Livingston Cynthia Bradham Wen Wang Wen Wang Naoki Irie Naoki Irie Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
description	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.
format	article
author	Jason Cheok Kuan Leong Yongxin Li Masahiro Uesaka Yui Uchida Yui Uchida Akihito Omori Meng Hao Wenting Wan Yang Dong Yandong Ren Si Zhang Tao Zeng Fayou Wang Luonan Chen Luonan Chen Gary Wessel Brian T. Livingston Cynthia Bradham Wen Wang Wen Wang Naoki Irie Naoki Irie
author_facet	Jason Cheok Kuan Leong Yongxin Li Masahiro Uesaka Yui Uchida Yui Uchida Akihito Omori Meng Hao Wenting Wan Yang Dong Yandong Ren Si Zhang Tao Zeng Fayou Wang Luonan Chen Luonan Chen Gary Wessel Brian T. Livingston Cynthia Bradham Wen Wang Wen Wang Naoki Irie Naoki Irie
author_sort	Jason Cheok Kuan Leong
title	Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
title_short	Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
title_full	Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
title_fullStr	Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
title_full_unstemmed	Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
title_sort	derivedness index for estimating degree of phenotypic evolution of embryos: a study of comparative transcriptomic analyses of chordates and echinoderms
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/b79e0810810f4e63812ea630e4bb4930
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Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms

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