JOURNAL PUBLICATIONS

Published

1. Arroyo, J. I., Hoffmann, F. G., & Opazo, J. C. (2012). Gene duplication and positive selection explain unusual physiological roles of the relaxin gene in the European rabbit. Journal of molecular evolution, 74(1), 52-60. https://doi: 10.1007/s00239-012-9487-2.

2. Arroyo, J. I., Hoffmann, F. G., & Opazo, J. C. (2012). Gene turnover and differential retention in the relaxin/insulin-like gene family in primates. Molecular Phylogenetics and Evolution, 63(3), 768-776. https://doi: 10.1016/j.ympev.2012.02.011. Selected by Global Medical Discovery.

3. Arroyo, J. I., Hoffmann, F. G., Good, S., & Opazo, J. C. (2012). INSL4 pseudogenes help define the relaxin family repertoire in the common ancestor of placental mammals. Journal of molecular evolution, 75(1), 73-78. https://doi: 10.1007/s00239-012-9517-0.

4. Nery, M.F., Arroyo, J.I., Opazo, J.C.(2013). Accelerated evolutionary rate of myoglobin gene in cetaceans with better diving capacities. Journal of molecular evolution, 76: 380-387. https://doi: 10.1007/s00239-013-9572-1.

5. Nery, M.F., Arroyo, J.I., Opazo, J.C.(2013) Genomic organization and differential signature of positive selection in the alpha and beta globin gene clusters in two cetacean species. Genome biology and evolution, 5: 2359-2367. https://doi: 10.1093/gbe/evt176.

6. Arroyo, J.I., Hoffmann, F.G., Opazo, J.C. (2014) Evolution of the relaxin/insulin-like gene family in anthropoid primates. Genome biology and evolution, 6: 491-499. https://doi: 10.1093/gbe/evu023.

7. Toloza, J., Arroyo, J.I., Opazo, J.C. (2015). Circadian clock in teleost fish: comparative analysis reveals different fates of duplicated genes. Journal of molecular evolution, 80: 57-64. https://doi: 10.1007/s00239-014-9660-x.

8. Nery, M.F., Arroyo, J.I. & Opazo, J.C. (2014). Increased rate of keratin gene loss in the cetacean lineage. BMC genomics, 15:869. https://doi: 10.1186/1471-2164-15-869.

9. Strelin, M., Arroyo, J.I., Fliesswasser, S., Ackermann, M. (2017) Diversification of Caiophora (Loasaceae subfam. Loasoideae) during the uplift of the Central Andes. Organisms diversity and evolution, 17: 29. https://doi.org/10.1007/s13127-016-0312-4

10. Fuentes, S., Arroyo, J.I., Rodríguez-Marconi, S., Masotti, I., Polz, M.F., Trefault, N., De la Iglesia, R., Díez, B. (2019) Summer phyto- and bacterioplankton communities during low and high productivity scenarios in the Western Antarctic Peninsula. Polar biology, 42(1): 159-169. https://doi.org/10.1007/s00300-018-2411-5

11. Arroyo JI, Nery MF (2018) Gene fusion of heterophyletic gamma-globin genes in platyrrhine primates. Journal of Genetics 97(5):1473-1478. https://doi.org/10.1007/s12041-018-1039-0

12. Fernández-Gómez, B., Díez, B., Polz, M.F., Arroyo, J.I., Alfaro, F.D., Marchandon, G., Sanhueza, C., Farías L., Trefault, N., Marquet, P.A., Molina-Montenegro, M.A., Sylvander, P., Snoeijs-Leijonmalm, P. (2019) Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N. The ISME J, 13(2):316-333. https://doi: 10.1038/s41396-018-0268-9.

13. Gemmell, N.J., Rutherford, K., Prost, S.,…Arroyo, J.I.,… et al. The tuatara genome reveals ancient features of amniote evolution. Nature, 584, 403–409 (2020). https://doi.org/10.1038/s41586-020-2561-9

14. Tamayo-Leiva J, Cifuentes-Anticevic J, Aparicio-Rizzo P, Arroyo JI, Masotti I and Díez B (2021) Influence of Estuarine Water on the Microbial Community Structure of Patagonian Fjords. Frontiers in marine sciences, 8:611981. https://doi.org/10.3389/fmars.2021.611981

15. Arroyo, J. I., Díez, B., Kempes, C. P., West, G. B., & Marquet, P. A. (2022). A general theory for temperature dependence in biology. Proceedings of the National Academy of Sciences, 119(30), e2119872119. https://doi.org/10.1073/pnas.2119872119

16. Tamayo-Leiva, J., Alcorta, J., Sepúlveda, F., Fuentes-Alburquenque, S., Arroyo, J. I., González-Pastor, J. E., & Díez, B. (2024). Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton. ISME communications, 4(1), ycae059. https://doi.org/10.1093/ismeco/ycae059

17. Byun E, Müller C, Parisse B, Napoli R, Zhang JB, Rezanezhad F, Van Cappellen P, Moser G, Jansen-Willems AB, Yang WH, Urakawa R, Arroyo JI, Neri U, Elrys AS, Nardi P (2024)  A global dataset of gross nitrogen transformation rates across terrestrial ecosystems. Scientific Data, 11(1):1022. https://doi.org/10.1038/s41597-024-03871-3

18. Saavedra, S., Arroyo, J. I., Deng, J., Marquet, P. A., & Kempes, C. P. (2023). Integrating metabolic scaling and coexistence theories. Ecology, 106(8):e70173. https://doi.org/10.1002/ecy.70173

In Review

19. Brüning-González, M., Arroyo, J. I., Marquet, P. A., & Samaniego, H. (2025). The Science of Urban Metabolism and Sustainability. arXiv preprint arXiv:2501.09141.
https://doi.org/10.48550/arXiv.2501.09141. Under Review in Cities.

20. Hernandez, J., & Arroyo, J. I. (2024). A database of foraging guilds of seabirds. https://doi.org/10.32942/X29C9M. Under Review in Ornithology Research

21. Yang, V.C., Holehouse, J., Kempes, C.P., Youn, H., Arroyo, J.I., Redner, S., & West, G.B. (2022). Scaling Laws for Function Diversity and Specialization Across Socioeconomic and Biological Complex Systems.
https://doi.org/10.48550/arXiv.2208.06487. In Review in PNAS

22. Lee, E.D., Kempes, C.P., Laubichler, M.D., West, G.B., Evans, J., Lockhart, J.W., Arroyo, J.I., Neffke, F., Hamilton, M.J., Ortega, E., Trancik, J., Wang, D., Youn, H., Yin, Y., Servedio, V.D.P., and Yang, V.C. (2024) Synthesis of innovation and obsolescence. https://doi.org/10.48550/arXiv.2505.05182. In Review in Nature

23. Yang, V.C., Kempes, C.P., Redner, S., West, G., Arroyo, J.I., Youn, H. (2025) How much regulation do we need from cells to societies? https://doi.org/10.48550/arXiv.2409.02884. In Review in Nature Communications

24. Arroyo, J.I., Mackenzie, R., Pedros-Alio, C., Polz, M., Marquet, P., Diez, B. (2024) Fine-scale spatial patterns in hot springs bacterial mats. https://doi.org/10.1101/2025.03.11.642739. In Review in Microbiology Research

25. Saavedra, S., Arroyo, J. I., Deng, J., Marquet, P. A., & Kempes, C. P. (2023). Linking metabolic scaling and coexistence theories. bioRxiv, 2023-02. Accepted In Brian Enquist, Mary O´Connor, and Chris Kempes (Eds.) Synthesizing Biological Scaling: Towards a Universal Theory. https://doi.org/10.1101/2023.02.28.530509

26. Arroyo, J.I., Savage, V, Desai-Chowdhry, P, Kempes, C, & West, G. (2024). Scaling in Nervous Systems. In review In Brian Enquist, Mary O´Connor, and Chris Kempes (Eds.) Synthesizing Biological Scaling: Towards a Universal Theory. https://doi.org/10.32942/X2691Z

27. Arroyo, J.I., Marquet, P., Kempes, C. & West, G (2024). Toward a general theory for the scaling behavior in thermal responses in biology. In Review In Brian Enquist, Mary O´Connor, and Chris Kempes (Eds.) Synthesizing Biological Scaling: Towards a Universal Theory. https://doi.org/10.48550/arXiv.2503.05128

28. Arroyo, J.I., Okie, J., Muratore, D., Kempes, C. & West, G. (2024) Scaling in Cells. In Review In Brian Enquist, Mary O´Connor, and Chris Kempes (Eds.) Synthesizing Biological Scaling: Towards a Universal Theory. https://doi.org/10.20944/preprints202507.0976.v1

29. Ritchie, M., Arroyo, J.I. (2024). The physical and chemical basis for temperature effects on metabolic rate and biological processes–a brief history. In  Review In Brian Enquist, Mary O´Connor, and Chris Kempes (Eds.) Synthesizing Biological Scaling: Towards a Universal Theory. https://doi.org/10.32942/X2NK9S

30. Holehouse, J., Redner, S., Yang, V. C., Krapivsky, P. L., Arroyo, J. I., Kempes, C., West, G. B., Youn, H. (2025). A generative model of function growth explains hidden self-similarities across biological and social systems. arXiv preprint arXiv:2509.14468. In Review in Science Advances 

Preprints

31. Hernandez, J., & Arroyo, J. I. (2023). Foraging specialization and body size seabirds. bioRxiv, 2023-06. https://doi.org/10.1101/2023.06.25.546462

32. Hernandez, J., & Arroyo, J. I. (2023). Foraging guild structure of seabirds. bioRxiv, 2023-12. https://doi.org/10.1101/2023.12.09.570957

33. Arroyo, J.I., Kempes C (2024) An algorithm for predicting per-cell proteomic properties. bioRxiv 2024.12.03.626698. https://doi.org/10.1101/2024.12.03.626698

34. Arroyo, J. I., Diez, B., & Marquet, P. (2025). Global patterns of taxonomic and functional diversity in hot springs microbiomes. bioRxiv, 2025-08. https://doi.org/10.1101/2025.08.04.668570

35. Arroyo, J. I., Diez, B., & Marquet, P. (2025). Metabolic ecology, microbial community structure, and gen-centric metagenomics. bioRxiv 2025.08.05.668563. https://doi.org/10.1101/2025.08.05.668563