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General Relationships Between Development and Evolution?

Diverse multi-cellular animals originally evolved from a simple unicellular organism. Similarly, animal development generally proceeds from a single-celled zygote to a complex multi-cellular organism. This tendency has inspired scientists to propose a relationship between development and evolution so far (e.g., Haeckel's recapitulation theory and developmental hourglass model).

What are the general relationships, if any, between development and evolution? 

This question has long been central to the fields of evolutionary developmental biology. A better understanding of the relationships between development and evolution not only helps to infer the ancestral state of the common ancestor, but also provides insights into how animals have diversified by modifying their developmental programs. Nonetheless, there are still many related questions left unanswered.

Focusing mainly on the evolution of vertebrates, my collaborators and I tackle this theme from the molecular perspective using bioinformatics and molecular experiment approaches. 

Three of my main research topics to date are as follows:

  • Recapitulation patterns in chromatin accessibility during embryogenesis and the underlying mechanisms of it.
  • Why has the organogenesis period been conserved through vertebrate evolution?
  • Integration of the recapitulation pattern and the developmental hourglass model.

Masahiro Uesaka, PhD

Research Scientist
Laboratory for Evolutionary Morphology (Kuratani Lab.)
RIKEN Center for Biosystems Dynamics Research

2-2-3 Minatojima-minami, Chuo-ku, Kobe
Hyogo 650-0047, JAPAN


Lab Homepage (Kuratani Lab.)

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*corresponding author, #equal contributions

Distinguishing Evolutionary Conservation from Derivedness.
Jason Cheok Kuan Leong*, Masahiro Uesaka, Naoki Irie*. 
Life. (2022). 12(3), 440. doi:10.3390/life12030440.

Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms.
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*. 
Frontiers in Cell and Developmental Biology. (2021). 9:749963. doi: 10.3389/fcell.2021.749963.

MeCP2 controls neural stem cell fate specification through miR-199a-mediated inhibition of BMP–Smad signaling.
Hideyuki Nakashima, Keita Tsujimura*, Koichiro Irie, Takuya Imamura, Cleber A. Trujillo, Masataka Ishizu, Masahiro Uesaka, Miao Pan, Hirofumi Noguchi, Kanako Okada, Kei Aoyagi, Tomoko Andoh-Noda, Hideyuki Okano, Alysson R. Muotri, Kinichi Nakashima*. 
Cell Reports. (2021).18;35(7):109124. doi: 10.1016/j.celrep.2021.109124.

The developmental hourglass model and recapitulation: An attempt to integrate the two models.
Masahiro Uesaka*, Shigeru Kuratani, Naoki Irie.
Journal of Experimental Zoology Part B. (2021). 1– 11. https://doi.org/10.1002/jez.b.23027

How can recapitulation be reconciled with modern concepts of evolution?
Shigeru Kuratani*, Masahiro Uesaka, Naoki Irie. 
Journal of Experimental Zoology Part B. (2020). 1– 8. https://doi.org/10.1002/jez.b.23020

Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. 
Yongxin Li, Akihito Omori, Rachel L. Flores, Sheri Satterfield, Christine Nguyen, Tatsuya Ota, Toko Tsurugaya, Tetsuro Ikuta, Kazuho Ikeo, Mani Kikuchi, Jason C. K. Leong, Adrian Reich, Meng Hao, Wenting Wan, Yang Dong, Yaondong Ren, Si Zhang, Tao Zeng, Masahiro Uesaka, Yui Uchida, Xueyan Li, Tomoko F. Shibata, Takahiro Bino, Kota Ogawa, Shuji Shigenobu, Mariko Kondo, Fayou Wang, Luonan Chen, Gary Wessel, Hidetoshi Saiga, R. Andrew Cameron, Brian Livingston, Cynthia Bradham, Wen Wang*, Naoki Irie*. 
Communications Biology. (2020). 3, 371. https://doi.org/10.1038/s42003-020-1091-1

Recapitulation-like developmental transitions of chromatin accessibility in vertebrates.
Masahiro Uesaka*
, Shigeru Kuratani, Hiroyuki Takeda, Naoki Irie. 
Zoological Letters. (2019). 5, 33. doi:10.1186/s40851-019-0148-9.

Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos.
Yui Uchida*, Masahiro Uesaka, Takayoshi Yamamoto, Hiroyuki Takeda, Naoki Irie*. 
EvoDevo. (2018). 9:7. https://doi.org/10.1186/s13227-018-0095-0

Constrained vertebrate evolution by pleiotropic genes.
Haiyang Hu#, Masahiro Uesaka#, Song Guo#, Kotaro Shimai, Tsai-Ming Lu, Fang Li, Satoko Fujimoto, Masato Ishikawa, Shiping Liu, Yohei Sasagawa, Guojie Zhang, Shigeru Kuratani, Jr-Kai Yu, Takehiro G. Kusakabe, Philipp Khaitovich, Naoki Irie*. 
Nature Ecology & Evolution. (2017). Nov;1(11):1722-1730.

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals. 
Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura*.
BMC Genomics. (2017). 18, 285.

miR-199a Links MeCP2 with mTOR Signaling and Its Dysregulation Leads to Rett Syndrome Phenotypes.
Keita Tsujimura, Koichiro Irie, Hideyuki Nakashima, Yoshihiro Egashira, Yoichiro Fukao, Masayuki Fujiwara, Masayuki Itoh, Masahiro Uesaka, Takuya Imamura, Yasukazu Nakahata, Yui Yamashita, Takaya Abe, Shigeo Takamori, Kinichi Nakashima*. 
Cell Reports. (2015). 12, 1-15.

Gene activation-associated long noncoding RNAs function in mouse preimplantation development.
Nobuhiko Hamazaki, Masahiro Uesaka, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura*.
Development. (2015). 140, 910-920.

Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals.
Masahiro Uesaka
, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura*. 
BMC Genomics. (2014) 15, 35.

Epigenetic setting and reprogramming for neural cell fate determination and differentiation.
Takuya Imamura, Masahiro Uesaka, Kinichi Nakashima*.
Philosophical Transactions of The Royal Society B. (2014). 369, 20130511

Cell- to Species-Level Diversity of Epigenetic Setting for Androgen Receptor Expression in Mammals.
Masahiro Uesaka, Takuya Imamura*.
Journal of Steroids & Hormonal Science. (2012). Sci S2:004. doi:10.4172/2157-7536.S2-004

Single-stranded noncoding RNAs mediate local epigenetic alterations at genepromoters in rat cell lines.
Junko Tomikawa, Hiroko Shimokawa, Masahiro Uesaka, Naoki Yamamoto, Yuji Mori, Hiroko Tsukamura, Kei-ichiro Maeda, Takuya Imamura*.
Journal of Biological Chemistry. (2011). 286, 34788–34799.


Chapter 4 - Roles of Epigenetics in the Neural Stem Cell and Neuron. 
Naoki Yamamoto, Masahiro Uesaka, Takuya Imamura, Kinichi Nakashima*.
In Epigenetics in Psychiatry (2nd edition). Edited by: Jacob Peedicayil, Dennis Grayson, Dimitri Avramopoulos. 
Elsevier Academic Press. (2021). Pages 53-84, ISBN: 9780128235775

Chapter 4 - Roles of Epigenetics in the Neural Stem Cell and Neuron. 
Naoki Yamamoto, Masahiro Uesaka, Takuya Imamura, Kinichi Nakashima*.
In Epigenetics in Psychiatry. Edited by: Jacob Peedicayil, Dennis Grayson, Dimitri Avramopoulos. 
Elsevier Academic Press. (2014). Pages 51-78, ISBN: 9780124171145


Beyond recapitulation: Past, present, and future.
Masahiro Uesaka*, Naoki Irie*.
Journal of Experimental Zoology Part B. (2022). 9– 12. https://doi.org/10.1002/jez.b.23116

In the Spotlight–Postdoc.
Masahiro Uesaka

Journal of Experimental Zoology Part B. (2020). 1– 2. https://doi.org/10.1002/jez.b.23003


  • March 2022: New paper out in Life.
  • January 2022: Our special issue “Beyond recapitulation: Past, present, and future” has been published in Journal of Experimental Zoology Part B.
  • November 2021: New paper out in Front. Cell Dev. Biol.
  • August 2021: Talk at The 2nd AsiaEvo Conference.
  • May 2021: New paper out in Cell Report.