Papers by Takahiro Kohsokabe
PLOS computational biology/PLoS computational biology, Feb 29, 2024
Determining the general laws between evolution and development is a fundamental biological challe... more Determining the general laws between evolution and development is a fundamental biological challenge. Developmental hourglasses have attracted increased attention as candidates for such laws, but the necessity of their emergence remains elusive. We conducted evolutionary simulations of developmental processes to confirm the emergence of the developmental hourglass and unveiled its establishment. We considered organisms consisting of cells containing identical gene networks that control morphogenesis and evolved them under selection pressure to induce more cell types. By computing the similarity between the spatial patterns of gene expression of two species that evolved from a common ancestor, a developmental hourglass was observed, that is, there was a correlation peak in the intermediate stage of development. The fraction of pleiotropic genes increased, whereas the variance in individuals decreased, consistent with previous experimental reports. Reduction of the unavoidable variance by initial or developmental noise, essential for survival, was achieved up to the hourglass bottleneck stage, followed by diversification in developmental processes, whose timing is controlled by the slow expression dynamics conserved among organisms sharing the hourglass. This study suggests why developmental hourglasses are observed within a certain phylogenetic range of species.
Author response for "Dynamical systems approach to evolution–development congruence: Revisiting Haeckel's recapitulation theory
21pAE-4 Mechanism and Evolution of Aperiodic Pattern Formation by Gene Regulation Network II
Meeting abstracts of the Physical Society of Japan, Aug 24, 2012
arXiv (Cornell University), Feb 21, 2014
Search for possible relationships between phylogeny and ontogeny is one of the most important iss... more Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, evolved are gene regulation networks under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most of thousands of numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Here, both the pattern dynamics consist of several epochs to form successive stripe formations between quasi-stationary regimes. In evolution, the regimes are generations needed to hit relevant mutations, while in development, they are due to the emergence of slowly varying expression that controls the pattern change. Successive pattern changes are thus generated, which are regulated by successive combinations of feedback or feedforward regulations under the upstream feedforward network that reads the morphogen gradient. By using a pattern generated by the upstream feedforward network as a boundary condition, downstream networks form later stripe patterns. These epochal changes in development and evolution are represented as same bifurcations in dynamical-systems theory, and this agreement of bifurcations lead to the evolution-development congruences. Violation of the evolution-development congruence, observed exceptionally, is shown to be originated in alteration of the boundary due to mutation at the upstream feedforward network. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis.
EPL, Nov 1, 2016
Boundary-induced pattern formation from a spatially uniform state is investigated using onedimens... more Boundary-induced pattern formation from a spatially uniform state is investigated using onedimensional reaction-diffusion equations. The temporal oscillation is successively transformed into a spatially periodic pattern, triggered by diffusion from the fixed boundary. We introduced a spatial map, whose temporal sequence, under selection criteria from multiple stationary solutions, can completely reproduce the emergent pattern, by replacing the time with space. The relationship of the pattern wavelength with the period of oscillation is also obtained. The generality of the pattern selection process and algorithm is discussed with possible relevance to biological morphogenesis.
EPL, Apr 1, 2017
Time development of the reaction diffusion dynamics. The fixed boundary condition at x = 0 transf... more Time development of the reaction diffusion dynamics. The fixed boundary condition at x = 0 transforms a uniform temporal oscillation to a stationary periodic pattern.
Journal Of Experimental Zoology Part B: Molecular And Developmental Evolution, Feb 18, 2021
It is acknowledged that embryonic development has a tendency to proceed from common toward specif... more It is acknowledged that embryonic development has a tendency to proceed from common toward specific. Ernst Haeckel raised the question of why that tendency prevailed through evolution, and the question remains unsolved. Here, we revisit Haeckel's recapitulation theory, that is, the parallelism between evolution and development through numerical evolution and dynamical systems theory. By using intracellular gene expression dynamics with cell-to-cell interaction over spatially aligned cells to represent the developmental process, gene regulation networks (GRN) that govern these dynamics evolve under the selection pressure to achieve a prescribed spatial gene expression pattern. For most numerical evolutionary experiments, the evolutionary pattern changes over generations, as well as the developmental pattern changes governed by the evolved GRN exhibit remarkable similarity. Changes in both patterns consisted of several epochs where stripes are formed in a short time, whereas for other temporal regimes, the pattern hardly changes. In evolution, these quasi-stationary generations are needed to achieve relevant mutations, whereas, in development, they are due to some gene expressions that vary slowly and control the pattern change. These successive epochal changes in development and evolution are represented as common bifurcations in dynamical systems theory, regulating working network structure from feedforward subnetwork to those containing feedback loops. The congruence is the correspondence between successive acquisitions of subnetworks through evolution and changes in working subnetworks in development. Consistency of the theory with the segmentation gene-expression dynamics is discussed. Novel outlook on recapitulation and heterochrony are provided, testable experimentally by the transcriptome and network analysis.
Developmental hourglass: Confirmation by numerical evolution and elucidation by dynamical-systems theory
Determining the general laws between evolution and development is a fundamental biological challe... more Determining the general laws between evolution and development is a fundamental biological challenge. Developmental hourglasses have attracted increased attention as candidates for such laws, but the necessity of their emergence remains elusive. We conducted evolutionary simulations of developmental processes to confirm the emergence of the developmental hourglass and unveiled its establishment. We considered organisms consisting of cells containing identical gene networks that control morphogenesis and evolved them under selection pressure to induce more cell types. By computing the similarity between the spatial patterns of gene expression of two species that evolved from a common ancestor, a developmental hourglass was observed, that is, there was a correlation peak in the middle stage of development. The fraction of pleiotropic genes increased, whereas the variance in individuals decreased, consistent with previous experimental reports. Reduction of the unavoidable variance by i...
27pXZD-11 遺伝子制御ネットワークによる非周期パターン形成の仕組み及びその進化III(27pXZD 領域12,領域11合同 生物合同セッション(ネットワーク系など),領域12(ソフトマター物理,化学物理,生物物理))
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2013
21pAE-4 遺伝子制御ネットワークによる非周期空間パターン形成の仕組み及びその進化II(21pAE 生物・生態系2/ネットワーク一般2,領域11(統計力学,物性基礎論,応用数学,力学,流体物理))
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2012
24pAR-4 パターン形成力学系に基づく進化-発生対応
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2015
16aCX-8 固定端境界条件に誘起される周期空間パターン
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2015
19aBS-4 発生で遅く変化する変数と進化可能性
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2016
27pAR-1 分岐から見る進化-発生対応とその崩れ(27pAR 領域11,領域12合同 生物合同セッション2,領域11(物性基礎論・統計力学・流体物理・応用数学・社会経済物理))
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2014
24aBD-13 遺伝子制御ネットワークによる非周期パターン形成の仕組み及びその進化(24aBD 生物・生態系1,領域11(統計力学,物性基礎論,応用数学,力学,流体物理))
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2012
Deciphering and understanding potential relationships between evolution and development has been ... more Deciphering and understanding potential relationships between evolution and development has been an important research goal for over a century. Recent advancements in quantitative analyses based on comparative genomics and massive gene expression data suggest that the time is ripe to uncover new re-lationships on phylogeny and ontogeny. By representing the developmental dynamics of spatially located cells with gene expression dynamics involving cell-to-cell interactions, under an external morphogenic gradient, we numerically evolved gene regulation networks, subject to mutation and selection, as they approach a prescribed spatial pattern of expressed genes. From analyses of hundreds of numerical evolu-tion experiments, remarkable congruence was observed between generational change in patterns through evolution along a single chain phylogeny and that through developmental process of the evolved descen-dant. Here, both of the pattern dynamics consisted of several epochs capable of pro...
25aKL-7 パターン形成力学系の進化に於ける遅い変数の持つ役割(生物合同1,領域11,領域12合同,領域11(統計力学,物性基礎論,応用数学,力学,流体物理))
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2013
Author response for "Dynamical systems approach to evolution–development congruence: Revisiting Haeckel's recapitulation theory
21pAE-4 Mechanism and Evolution of Aperiodic Pattern Formation by Gene Regulation Network II
It is acknowledged that embryonic development has tendency to proceed from common toward specific... more It is acknowledged that embryonic development has tendency to proceed from common toward specific. Ernst Haeckel raised the question of why that tendency prevailed through evolution, and the question remains unsolved. Here, we revisit Haeckel’s recapitulation theory, i.e., the parallelism between evolution and development through numerical evolution and dynamical systems theory. By using intracellular gene-expression dynamics with cell-to-cell interaction over spatially aligned cells to represent the developmental process, gene regulation networks (GRN) that govern these dynamics evolve under the selection pressure to achieve a prescribed spatial gene expression pattern. For most numerical evolutionary experiments, the evolutionary pattern changes over generations, as well as the developmental pattern changes governed by the evolved GRN exhibit remarkable similarity. Both pattern changes consisted of several epochs where stripes are formed in a short time, whereas for other temporal...
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Papers by Takahiro Kohsokabe