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Safian D, Ahmed M, van Kruistum H, Furness AI, Reznick DN, Wiegertjes GF, Pollux BJ. Repeated independent origins of the placenta reveal convergent and divergent organ evolution within a single fish family (Poeciliidae). SCIENCE ADVANCES 2023; 9:eadf3915. [PMID: 37611099 PMCID: PMC10446500 DOI: 10.1126/sciadv.adf3915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
An outstanding question in biology is to what extent convergent evolution produces similar, but not necessarily identical, complex phenotypic solutions. The placenta is a complex organ that repeatedly evolved in the livebearing fish family Poeciliidae. Here, we apply comparative approaches to test whether evolution has produced similar or different placental phenotypes in the Poeciliidae and to what extent these phenotypes correlate with convergence at the molecular level. We show the existence of two placental phenotypes characterized by distinctly different anatomical adaptations (divergent evolution). Furthermore, each placental phenotype independently evolved multiple times across the family, providing evidence for repeated convergence. Moreover, our comparative genomic analysis revealed that the genomes of species with different placentas are evolving at a different pace. Last, we show that the two placental phenotypes correlate with two previously described contrasting life-history optima. Our results argue for high evolvability (both divergent and convergent) of the placenta within a group of closely related species in a single family.
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Affiliation(s)
- Diego Safian
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Evolutionary Developmental Biology Laboratory, The Francis Crick Institute, London, UK
| | - Marwa Ahmed
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Henri van Kruistum
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Animal Breeding and Genomics, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrew I. Furness
- U.S. Fish and Wildlife Service, Maryland Fish and Wildlife Conservation Office, Annapolis, MD, USA
| | - David N. Reznick
- Department of Biology, University of California, Riverside, Riverside, CA, USA
| | - Geert F. Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Bart J.A. Pollux
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
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Moura Gama J, Ludwig A, Gazolla CB, Guizelini D, Recco-Pimentel SM, Bruschi DP. A genomic survey of LINE elements in Pipidae aquatic frogs shed light on Rex-elements evolution in these genomes. Mol Phylogenet Evol 2022; 168:107393. [PMID: 35051593 DOI: 10.1016/j.ympev.2022.107393] [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: 08/12/2021] [Revised: 11/09/2021] [Accepted: 12/25/2021] [Indexed: 11/19/2022]
Abstract
The transposable elements (TE) represent a large portion of anuran genomes that act as components of genetic diversification. The LINE order of retrotransposons is among the most representative and diverse TEs and is poorly investigated in anurans. Here we explored the LINE diversity with an emphasis on the elements generically called Rex in Pipidae species, more specifically, in the genomes ofXenopus tropicalis, used as a model genome in the study of anurans,the allotetraploid sister species Xenopus laevis and theAmerican species Pipa carvalhoi. We were able to identify a great diversity of LINEs from five clades, Rex1, L2, CR1, L1 and Tx1, in these three species, and the RTE clade was lost in X. tropicalis. It is clear that elements classified as Rex are distributed in distinct clades. The evolutionary pattern of Rex1 elements denote a complex evolution with independent losses of families and some horizontal transfer events between fishes and amphibians which were supported not only by the phylogenetic inconsistencies but also by the very low Ks values found for the TE sequences. The data obtained here update the knowledge of the LINEs diversity in X. laevis and represent the first study of TEs in P. carvalhoi.
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Affiliation(s)
- Joana Moura Gama
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil; Laboratório de Citogenética evolutiva e Conservação Animal (LabCeca), Departamento de Genética, Universidade Federal do Paraná (UFPR), Brazil
| | - Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas, Fiocruz-PR, Brazil.
| | - Camilla Borges Gazolla
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil; Laboratório de Citogenética evolutiva e Conservação Animal (LabCeca), Departamento de Genética, Universidade Federal do Paraná (UFPR), Brazil
| | - Dieval Guizelini
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Daniel Pacheco Bruschi
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil; Laboratório de Citogenética evolutiva e Conservação Animal (LabCeca), Departamento de Genética, Universidade Federal do Paraná (UFPR), Brazil.
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