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Koçillari L, Cattelan S, Rasotto MB, Seno F, Maritan A, Pilastro A. Tetrapod sperm length evolution in relation to body mass is shaped by multiple trade-offs. Nat Commun 2024; 15:6160. [PMID: 39039080 PMCID: PMC11263692 DOI: 10.1038/s41467-024-50391-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 07/04/2024] [Indexed: 07/24/2024] Open
Abstract
Sperm length is highly variable across species and many questions about its variation remain open. Although variation in body mass may affect sperm length evolution through its influence on multiple factors, the extent to which sperm length variation is linked to body mass remains elusive. Here, we use the Pareto multi-task evolution framework to investigate the relationship between sperm length and body mass across tetrapods. We find that tetrapods occupy a triangular Pareto front, indicating that trade-offs shape the evolution of sperm length in relation to body mass. By exploring the factors predicted to influence sperm length evolution, we find that sperm length evolution is mainly driven by sperm competition and clutch size, rather than by genome size. Moreover, the triangular Pareto front is maintained within endotherms, internal fertilizers, mammals and birds, suggesting similar evolutionary trade-offs within tetrapods. Finally, we demonstrate that the Pareto front is robust to phylogenetic dependencies and finite sampling bias. Our findings provide insights into the evolutionary mechanisms driving interspecific sperm length variation and highlight the importance of considering multiple trade-offs in optimizing reproductive traits.
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Affiliation(s)
- Loren Koçillari
- Istituto Italiano di Tecnologia, 38068, Rovereto, Italy
- Department of Physics and Astronomy, Section INFN, University of Padova, 35131, Padova, Italy
- Institute for Neural Information Processing, Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), D-20251, Hamburg, Germany
| | - Silvia Cattelan
- Department of Biology, University of Padova, 35121, Padova, Italy.
- Fritz Lipmann Institute-Leibniz Institute on Aging, 07745, Jena, Germany.
| | | | - Flavio Seno
- Department of Physics and Astronomy, Section INFN, University of Padova, 35131, Padova, Italy
| | - Amos Maritan
- Department of Physics and Astronomy, Section INFN, University of Padova, 35131, Padova, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Andrea Pilastro
- Department of Biology, University of Padova, 35121, Padova, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
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Weistuch C, Murgas KA, Zhu J, Norton L, Dill KA, Tannenbaum AR, Deasy JO. Functional transcriptional signatures for tumor-type-agnostic phenotype prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.12.536595. [PMID: 37090606 PMCID: PMC10120658 DOI: 10.1101/2023.04.12.536595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cancer transcriptional patterns exhibit both shared and unique features across diverse cancer types, but whether these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that cancer transcriptional diversity mirrors patterns in normal tissues optimized for distinct functional tasks. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.
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Affiliation(s)
- Corey Weistuch
- Memorial Sloan Kettering Cancer Center, Department of Medical
Physics
| | - Kevin A. Murgas
- Stony Brook University, Department of Biomedical
Informatics
| | - Jiening Zhu
- Stony Brook University, Department of Applied Mathematics and
Statistics
| | - Larry Norton
- Memorial Sloan Kettering Cancer Center, Department of
Medicine
| | - Ken A. Dill
- Stony Brook University, Laufer Center for Physical and
Quantitative Biology
| | - Allen R. Tannenbaum
- Stony Brook University, Department of Applied Mathematics and
Statistics
- Stony Brook University, Department of Computer Science
| | - Joseph O. Deasy
- Memorial Sloan Kettering Cancer Center, Department of Medical
Physics
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Zilkha N, Chuartzman SG, Sofer Y, Pen Y, Cum M, Mayo A, Alon U, Kimchi T. Sex-dependent control of pheromones on social organization within groups of wild house mice. Curr Biol 2023; 33:1407-1420.e4. [PMID: 36917976 PMCID: PMC10132349 DOI: 10.1016/j.cub.2023.02.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023]
Abstract
Dominance hierarchy is a fundamental social phenomenon in a wide range of mammalian species, critically affecting fitness and health. Here, we investigate the role of pheromone signals in the control of social hierarchies and individual personalities within groups of wild mice. For this purpose, we combine high-throughput behavioral phenotyping with computational tools in freely interacting groups of wild house mice, males and females, in an automated, semi-natural system. We show that wild mice form dominance hierarchies in both sexes but use sex-specific strategies, displaying distinct male-typical and female-typical behavioral personalities that were also associated with social ranking. Genetic disabling of VNO-mediated pheromone detection generated opposite behavioral effects within groups, enhancing social interactions in males and reducing them in females. Behavioral personalities in the mutated mice displayed mixtures of male-typical and female-typical behaviors, thus blurring sex differences. In addition, rank-associated personalities were abolished despite the fact that both sexes of mutant mice formed stable hierarchies. These findings suggest that group organization is governed by pheromone-mediated sex-specific neural circuits and pave the way to investigate the mechanisms underlying sexual dimorphism in dominance hierarchies under naturalistic settings.
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Affiliation(s)
- Noga Zilkha
- Department of Brain Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | | | - Yizhak Sofer
- Department of Brain Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yefim Pen
- Department of Brain Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Meghan Cum
- Department of Brain Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tali Kimchi
- Department of Brain Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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Jedlicka P, Bird AD, Cuntz H. Pareto optimality, economy-effectiveness trade-offs and ion channel degeneracy: improving population modelling for single neurons. Open Biol 2022; 12:220073. [PMID: 35857898 PMCID: PMC9277232 DOI: 10.1098/rsob.220073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Neurons encounter unavoidable evolutionary trade-offs between multiple tasks. They must consume as little energy as possible while effectively fulfilling their functions. Cells displaying the best performance for such multi-task trade-offs are said to be Pareto optimal, with their ion channel configurations underpinning their functionality. Ion channel degeneracy, however, implies that multiple ion channel configurations can lead to functionally similar behaviour. Therefore, instead of a single model, neuroscientists often use populations of models with distinct combinations of ionic conductances. This approach is called population (database or ensemble) modelling. It remains unclear, which ion channel parameters in the vast population of functional models are more likely to be found in the brain. Here we argue that Pareto optimality can serve as a guiding principle for addressing this issue by helping to identify the subpopulations of conductance-based models that perform best for the trade-off between economy and functionality. In this way, the high-dimensional parameter space of neuronal models might be reduced to geometrically simple low-dimensional manifolds, potentially explaining experimentally observed ion channel correlations. Conversely, Pareto inference might also help deduce neuronal functions from high-dimensional Patch-seq data. In summary, Pareto optimality is a promising framework for improving population modelling of neurons and their circuits.
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Affiliation(s)
- Peter Jedlicka
- ICAR3R - Interdisciplinary Centre for 3Rs in Animal Research, Faculty of Medicine, Justus-Liebig-University, Giessen, Germany,Institute of Clinical Neuroanatomy, Neuroscience Center, Goethe University, Frankfurt/Main, Germany,Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
| | - Alexander D. Bird
- ICAR3R - Interdisciplinary Centre for 3Rs in Animal Research, Faculty of Medicine, Justus-Liebig-University, Giessen, Germany,Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany,Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, Frankfurt am Main, Germany
| | - Hermann Cuntz
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany,Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, Frankfurt am Main, Germany
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