Review
Biochemistry & Molecular Biology
Andrei P. Kozlov
Summary: A theory called the carcino-evo-devo theory is being developed to explain the evolutionary role of hereditary tumors. The theory proposes that hereditary tumors played a role in the evolution of multicellular organisms by providing additional cell masses for the expression of novel genes. It has made several nontrivial predictions that have been confirmed in laboratory experiments and offers explanations for previously unexplained biological phenomena. By considering individual development, evolutionary development, and neoplastic development within one framework, the carcino-evo-devo theory has the potential to become a unifying biological theory.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
A. P. Kozlov
Summary: This paper introduces the theory of carcino-evo-devo, which explains the sources of additional cell masses in the evolution of multicellular organisms. Several non-trivial predictions are formulated and confirmed through experiments.
Editorial Material
Biochemistry & Molecular Biology
Alistair P. McGregor, Alexandra D. Buffry, Renske M. A. Vroomans
Summary: Evolutionary developmental biology is a broad field that aims to understand how developmental processes evolve and contribute to phenotypic change and organismal diversification. This special issue reviews key topics in the field, including advances in theory and methodology, as well as our latest knowledge about molecular, cellular, and organismal functionality and diversification.
ESSAYS IN BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Salem al-Mosleh, Gary P. T. Choi, Arhat Abzhanov, L. Mahadevan
Summary: The study analyzed the beak morphology of Darwin's finches, finding that the curvature increases linearly from the base to the tip of the beak and is related to dietary habits. By proposing an experimentally motivated growth law and utilizing a morphospace, the study shows how a combination of geometry and dynamics allows for the development and evolution of functional form in the finches.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biology
Daisuke Koyabu
Summary: Over the past decade, studies combining palaeontology, embryology, and experimental developmental biology have significantly changed our understanding of the homology of the mammalian skull. New evidence suggests the need to revisit and restructure the conventional anatomical terminology used for the components of the mammalian skull, which has been a longstanding unresolved issue since the nineteenth century. This review highlights the overlooked problems related to homology, development, and conservatism of the mammalian skull, with a call for future studies in these areas.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Plant Sciences
Beatrice Albert, Alexis Matamoro-Vidal, Charlotte Prieu, Sophie Nadot, Irene Till-Bottraud, Adrienne Ressayre, Pierre-Henri Gouyon
Summary: The diversity of pollen grain forms in flowering plants is determined by the developmental mechanisms involved in establishing pollen morphological features. Aperture pattern, characterized by aperture number, structure, and position, is determined during microsporogenesis, and plays a key role in plant reproduction. Advances in understanding aperture pattern development shed light on the evolution of aperture pattern in angiosperms.
Article
Cell Biology
Kai Ito, Vuong Tan Tu, Thomas P. Eiting, Taro Nojiri, Daisuke Koyabu
Summary: The homologies of bat nasal turbinals have been disputed, but tracing prenatal development may provide a solution. Bat turbinate structures are similar to laurasiatherians, indicating bats retain the ancestral condition, while the absence of certain structures in specific bat groups may have occurred through convergent evolution.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Alessandro Cavallo, Melody S. Clark, Lloyd S. Peck, Elizabeth M. Harper, Victoria A. Sleight
Summary: By studying shell development in the Antarctic clam, researchers found that the formation of the larval shell involves development-specific downstream effector genes, while the adult shell secretion processes use different genes. This suggests that the formation of the larval shell is a conserved and ancestral feature in molluscs.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Psychology, Multidisciplinary
Laura Nuno de la Rosa, Mihaela Pavlicev, Arantza Etxeberria
Summary: Critiques of the container model and the emergence of new perspectives have led to a reevaluation of the concept of pregnancy as an evolved relational novelty. The idea of historical individuality, as opposed to other views of biological individuality, offers a fresh insight into pregnancy and may help dispel misconceptions.
FRONTIERS IN PSYCHOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Christine Hirschberger, Victoria A. Sleight, Katharine E. Criswell, Stephen J. Clark, J. Andrew Gillis
Summary: The study reveals broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid, and gill arches of a cartilaginous fish, the skate. It also highlights differences in notch signaling between mandibular and gill arches in skate. Comparative transcriptomic analyses show additional genes differentially expressed along the DV axis of the pharyngeal arches.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Sebastian S. James, Mackenzie Englund, Riley Bottom, Roberto Perez, Kathleen E. Connor, Kelly J. Huffman, Stuart P. Wilson, Leah A. Krubitzer
Summary: Advances in sequencing techniques have allowed for comparative studies of gene expression, but spatial expression has remained limited due to a lack of robust methodology. In this study, methods and software tools were developed to quantify and compare tissue-wide spatial patterns of gene expression within and between species. The expression patterns of RZR beta and Id2 mRNA in the cortex were compared across early postnatal development in mice and voles. The results showed that RZR beta expression patterns were highly conserved between species, while Id2 expression patterns emerged in a consistent manner across layers in both species. These differences in neocortical patterning development were suggested to reflect the independent evolution of brains, bodies, and sensory systems since their common ancestor 35 million years ago.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Melanie J. Hopkins, Rebecca To
Summary: This study analyzes over 1500 species of trilobites and reveals long-term shifts in segment number and allocation, which cannot be explained by taxonomic turnover or trends in functionally relevant behavior.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Plant Sciences
Shilpi Singh, John L. Bowman
Summary: Ricciocarpos natans is an aquatic liverwort that transitions from an aquatic growth form to a terrestrial growth form, making it a model for studying genomic consequences, evolution of sexual systems, and population genomics.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biology
Ethan Ozment, Arianna N. Tamvacakis, Jianhong Zhou, Pablo Yamild Rosiles-Loeza, Esteban Elias Escobar-Hernandez, Selene L. Fernandez-Valverde, Nagayasu Nakanishi
Summary: A class IV POU homeodomain transcription factor, POU-IV, has been identified as crucial for the development of hair cells in the sea anemone Nematostella vectensis. This transcription factor is postmitotically expressed in tentacular hair cells and regulates the expression of a unique set of effector genes, including polycystin 1, specifically in hair cells. These findings suggest a distinct gene regulatory mechanism for hair cell development controlled by POU-IV in cnidarians.
Review
Biology
Long Zhao, Feng Gao, Shan Gao, Yujun Liang, Hongan Long, Zhiyi Lv, Ying Su, Naihao Ye, Liusuo Zhang, Chengtian Zhao, Xiaoyu Wang, Weibo Song, Shicui Zhang, Bo Dong
Summary: Evo-Devo seeks to understand how developmental changes impact organismal evolution, but current model organisms may not be sufficient to cover the vast biodiversity on Earth.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Fabrice Darbellay, Celia Bochaton, Lucille Lopez-Delisle, Benedicte Mascrez, Patrick Tschopp, Saskia Delpretti, Jozsef Zakany, Denis Duboule
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Editorial Material
Developmental Biology
Denis Duboule
DEVELOPMENTAL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Cedric Le Caignec, Olivier Pichon, Annaig Briand, Benoit de Courtivron, Christian Bonnard, Pierre Lindenbaum, Richard Redon, Caroline Schluth-Bolard, Flavie Diguet, Pierre-Antoine Rollat-Farnier, Marta Sanchez-Castro, Marie-Laure Vuillaume, Damien Sanlaville, Denis Duboule, Andre Megarbane, Annick Toutain
EUROPEAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Developmental Biology
Christopher Chase Bolt, Denis Duboule
Article
Biology
Ana Rita Amandio, Lucille Lopez-Delisle, Christopher Chase Bolt, Benedicte Mascrez, Denis Duboule
Article
Anatomy & Morphology
Leonardo Beccari, Gabriel Jaquier, Lucille Lopez-Delisle, Eddie Rodriguez-Carballo, Benedicte Mascrez, Sandra Gitto, Joost Woltering, Denis Duboule
Summary: HOXA13 and HOXD13 transcription factors cooperatively activate Dbx2 gene expression by binding to mammalian specific regulatory sequences in the Dbx2 neighborhood during digit development. Enhancers near Dbx2 can overcome TAD boundaries in order to co-regulate a set of genes located in distinct chromatin domains.
DEVELOPMENTAL DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Marc Fernandez-Guerrero, Nayuta Yakushiji-Kaminatsui, Lucille Lopez-Delisle, Sofia Zdral, Fabrice Darbellay, Rocio Perez-Gomez, Christopher Chase Bolt, Manuel A. Sanchez-Martin, Denis Duboule, Marian A. Ros
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Eddie Rodriguez-Carballo, Lucille Lopez-Delisle, Andrea Willemin, Leonardo Beccari, Sandra Gitto, Benedicte Mascrez, Denis Duboule
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Anatomy & Morphology
Marc Fernandez-Guerrero, Sofia Zdral, Alejandro Castilla-Ibeas, Lucille Lopez-Delisle, Denis Duboule, Marian A. Ros
Summary: This study analyzed the transcriptomes of distal limb mesenchymal progenitors and ectodermal cells, revealing specific transcriptional signatures for different developmental stages. Genes with previously unnoticed roles in limb development were identified, along with signaling pathways enriched between different layers.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Christopher Chase Bolt, Lucille Lopez-Delisle, Benedicte Mascrez, Denis Duboule
Summary: This study explores the link between rearrangements in the HoxD cluster and mesomelic dysplasia in both humans and mice, providing a mechanistic framework to understand the molecular origins of this condition associated with 2q31. By engineering a 1 Mb inversion including the HoxD gene cluster, the authors demonstrate the role of ectopic HOXD13 in inducing mesomelic dysplasia and show that this bone anomaly can be rescued by a secondary Hoxd13 null mutation. Single-cell expression analysis and evaluation of HOXD13 binding sites suggest that the phenotype primarily arises through genes controlled by HOXD13 in distal limb cells.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Andrea Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodriguez-Carballo
Summary: This study investigates the function of boundaries in regulating gene expression during development, particularly focusing on the ability of certain boundary sequences to act independently of their genomic context. The researchers found that a boundary sequence from the HoxD gene cluster can split a topological domain and affect gene expression levels, even when introduced into a different genomic context. This suggests that topological boundaries can function autonomously, providing important insights into gene regulation processes in mammalian genomes.
Article
Cell Biology
Ana Rita Amandio, Leonardo Beccari, Lucille Lopez-Delisle, Benedicte Mascrez, Jozsef Zakany, Sandra Gitto, Denis Duboule
Summary: Understanding the diverse functions of CTCF sites within the Hox gene clusters is crucial for the formation of TAD borders and maintaining gene expression, showing significant evolutionary conservation.
GENES & DEVELOPMENT
(2021)
Article
Developmental Biology
Aurelie Hintermann, Isabel Guerreiro, Lucille Lopez-Delisle, Christopher Chase Bolt, Sandra Gitto, Denis Duboule, Leonardo Beccari
Summary: Modifications in gene regulation are important for the evolution of organisms. This study focuses on cis-regulatory elements (CREs), which interact with target genes through higher-order chromatin structures. The researchers analyzed the regulation of Hoxd genes in murine vibrissae and chicken feather primordia, and compared it with the regulation in the elongation of the posterior trunk. They found that different subsets of Hoxd genes were regulated by lineage-specific enhancers in the two structures, while the regulation in the embryonic trunk relied on conserved CREs. These non-coding sequences in the trunk have functionally diverged between species, but transcriptional robustness is maintained.
Article
Multidisciplinary Sciences
Christopher Chase Bolt, Lucille Lopez-Delisle, Aurelie Hintermann, Benedicte Mascrez, Antonella Rauseo, Guillaume Andrey, Denis Duboule
Summary: The study demonstrates that a strong enhancer sequence can be regulated by the chromatin environment provided by a nearby topologically associated domain (TAD). Furthermore, the results indicate that the functioning of enhancer elements is subordinated to the host chromatin context.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Hocine Rekaik, Lucille Lopez-Delisle, Aurelie Hintermann, Benedicte Mascrez, Celia Bochaton, Alexandre Mayran, Denis Duboule
Summary: In mouse pseudo-embryos in vitro, the temporal activation of Hox genes starts from the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Afterwards, posterior CTCF sites act as transient insulators, regulating the timed transcription of more posterior genes. This temporal activation contributes to the proper identities of structures along the rostrocaudal axis.
