Biology subjects

Zaremba, B.

Publications and source records attributed to Zaremba, B..

3 recordsLinked to original sources

bioRxiv2025

A dual genetic constraint underlies the conservation of early brains in vertebrates.

As the body plan, the embryonic brain bauplan reflects the shared features of vertebrate brains. Yet, disagreements among sparse histogenetic frameworks have undermined the bauplans power to trace homologies. Here, we generate and integrate five vertebrate single-cell multi-omic atlases of early embryonic brains, revealing a conserved cellular blueprint that defines equivalent progenitor domains across species. Our cellular neuromeric model provides an unified and unbiased framework for the vertebrate brain bauplan and revises the regionalisation of the prosencephalon, refining its molecular boundaries and developmental relationships. Furthermore, cross-species gene-network analyses expose regulatory complexity beyond classical neuromeric patterning, resolving networks into modules aligned with regional cell types or cell class (progenitor/neuron). Evolutionarily, two main developmental constraints emerge: brain bauplan genes, early essential for regional identity, and pleiotropic stemness gene modules, indispensable across all proliferating cells. In turn, later development displays tissue-specific and less essential modules, explaining its rapid divergence into species-specific features. Together, these findings reveal a dual evolutionary constraint--neuromeric identity and pleiotropic stemness--that underlies the conservation of early vertebrate brains. This duality explains how deeply conserved regulatory architectures coexist with evolutionary flexibility to develop into the immense diversity of vertebrate nervous systems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/684766v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@a337a2org.highwire.dtl.DTLVardef@19987adorg.highwire.dtl.DTLVardef@9a9394org.highwire.dtl.DTLVardef@4ef279_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2025

The origin and molecular evolution of the mammalian liver cell architecture

The liver is a central organ with essential roles in processes such as nutritional metabolism, detoxification, and immune defense1-6. It has been instrumental in the adaptation of mammalian species to diverse environments, as reflected by its rapid molecular evolution7,8. However, the origins and evolutionary dynamics of liver cell types and their structural organization remain largely unexplored. Here we report evolutionary analyses of transcriptome and chromatin accessibility data for liver cells from 17 species, spanning all major feeding strategies (herbivory, omnivory, carnivory, insectivory), great apes (including humans), placental clades (Afrotheria, Xenarthra, Laurasiatheria, Euarchontoglires), major mammalian lineages (placentals, marsupials, monotremes), and a bird as outgroup. Integrated with spatial transcriptomics, our data reveal that liver zonation--the compartmentalization of hepatocyte functions along the lobule, the livers fundamental anatomical and functional unit--is conserved across mammals but absent in other vertebrates. We find that zonation originated in the mammalian ancestor, driven by the emergence of WNT and R-spondin signaling from central vein endothelial cells, which activate central hepatocyte gene expression via the transcription factor TCF7L2. Despite this conserved architecture and signaling, genes with zonated expression exhibit rapid evolutionary turnover. Consistently, hepatocytes evolve fast, likely due to reduced selective constraints, enabling adaptive changes under positive selection. Alongside immune cells, hepatocytes are therefore key drivers of the livers rapid evolution and functional innovations. In great apes, we identify human-specific shifts in zonation and cell-type-specific expression linked to recent cis-regulatory changes, particularly in genes involved in lipid metabolism, likely contributing to human-specific metabolic traits. Our study uncovers the origins of a mammal-specific liver cell architecture, within which reduced constraints facilitated molecular changes underlying ecological adaptations.

evolutionary biology↗

bioRxiv2024

Developmental origins and evolution of pallial cell types and structures in birds

The advanced cognitive abilities of birds rival those of mammals and have been attributed to evolutionary innovations in the pallium. However, a comprehensive cellular characterization of this brain region in birds has been lacking. We scrutinized the structures, cell types and evolutionary origins of the avian pallium based on single-cell and spatial transcriptomics atlases for the adult and developing chicken, and comparisons to corresponding data from mammals and non-avian reptiles. We found that the avian pallium shares most inhibitory neuron types with other amniotes. While excitatory neuron repertoires in the (medial) hippocampal formation show high conservation, they substantially diverged in other pallial regions during avian evolution, defining novel structures like the avian-specific (dorsal) hyperpallium, whose neuronal gene expression identities partly converge during late development with those of the (ventral) nidopallium. Our work also unveils the evolutionary relationships of pallial structures across amniotes, like the previously unknown homology between avian (lateral) mesopallial and mammalian deep layer cortical neurons. One-Sentence SummaryAn avian neural cell type atlas illuminates the developmental origins and evolution of the amniote pallium.

evolutionary biology↗