PhD Project - DECODES at University of Santiago de Compostela, listed on FindAPhD.com

Comparative embryology has revealed that early animal development is based on highly conserved genetic programs. Beyond embryogenesis however, animals undergo remarkably diverse post-embryonic developmental transitions such as metamorphosis. Whether these transitions are also organised into conserved genetic programs remains largely unexplored. To identify conserved genetic programs underlying post-embryonic development, we examine metamorphic remodelling in five teleost fishes, spanning 200 million years of evolution. By integrating comparative co-expression networks, evolutionary genomics, phylogenetic modelling, and functional data in zebrafish, we uncovered a conserved post-embryonic developmental network. This conserved network comprises components involved in core cellular processes, and involved in development and physiology, both of which are under the control of thyroid hormone during metamorphosis. Despite evolutionary conservation at the coding sequence level, this network exhibits significant turnover in gene family copy number following the teleost-specific whole-genome duplication as well as lineage-specific expansions and contractions. The variation in gene copy numbers is associated with macroevolutionary variation in a number of ecological and morphological traits, including swimming performance and trophic level. Cross-species tissue expression, zebrafish single-cell transcriptomics, and zebrafish perturbation phenotypes placed the implicated genes in biological contexts relevant to these traits. Together, our results provide evidence of an ancient, functionally partitioned post-embryonic developmental network that has diversified throughout teleost evolution. The heterochronic variation in network function, changes in endocrine activity, and gene-family turnover provide potential routes through which a shared developmental architecture contributed to the evolution of phenotypic diversity in teleosts. ### Competing Interest Statement The authors have declared no competing interest. International Human Frontier Science Program Organization, LT0063/2022-L

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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Certain genes, chromosomes, organelles, or entire sets of chromosomes can bias their transmission to the next generation, propagating themselves at the expense of the rest of the genome. Referred to …

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Letter to the Editor

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Teleosts are the most diverse group of vertebrates on earth. Their diversity is a testament to the combined effects of genetic, developmental, and evolutionary forces. However, disentangling the interactions between these forces is challenging due to the complexity of the genotype-phenotype relationship and the masking of adaptive genetic signals by genetic noise. Estimates of molecular convergence where changes in the sequence of protein-coding genes lead to identical amino acid substitution across multiple lineages provide strong evidence of adaptive evolution. In this study, we estimated signals for molecular convergence in protein-coding genes across 143 teleost genomes to identify genes and processes that experienced adaptive changes. We find that genes with signals of molecular convergence are implicated in diverse processes ranging from embryonic development, tissue morphogenesis, metabolism, to hormone and heat response. Some convergent substitutions are located on functionally important sites on proteins potentially providing the molecular basis for adaptations to hypoxia, salinity fluctuations, and varying skeletal morphologies. Additionally, single-cell RNA sequencing data from zebrafish showed that the convergent genes have dynamic expression across various cell types during embryonic development. These results highlight the functional importance of the convergent genes as well as their pleiotropic nature. Although traditionally considered a source of genetic constraint, we argue that adaptation via changes in pleiotropic genes are particularly advantageous during periods of ecological shifts. We present the pleiotropic release model which describes how adaptive variation on pleiotropic genes can have large fitness effects, allowing organisms to overcome selective pressures during periods of ecological shifts. ### Competing Interest Statement The authors have declared no competing interest.

Abstract. Dioecious plants are frequently sexually dimorphic. Such dimorphism, which reflects responses to selection acting in opposite directions for male

Pleiotropy (a single mutation altering many traits) has long been seen as hindering adaptation. A new study in PLOS Biology offers a striking counterexample, suggesting that regulatory networks may ev...

Based on phylogenomic and geometric morphometric analyses of 132 anglerfish species, the authors infer a Cretaceous origin of the clade and show that bathypelagic anglerfish are undergoing rapid pheno...

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Teleosts are the most diverse group of vertebrates on earth. Their diversity is a testament to the combined effects of genetic, developmental, and evolutionary forces. However, disentangling the inter...