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Alaei Kakhki N, Schweizer M, Lutgen D, Bowie RCK, Shirihai H, Suh A, Schielzeth H, Burri R. A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats. Mol Biol Evol 2023; 40:6964684. [PMID: 36578177 PMCID: PMC10161543 DOI: 10.1093/molbev/msac278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/01/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.
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Affiliation(s)
- Niloofar Alaei Kakhki
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany
| | - Manuel Schweizer
- Natural History Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Dave Lutgen
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Ornithological Institute, Sempach, Switzerland
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology - Systematic Biology (EBC), Science for Life Laboratory, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Holger Schielzeth
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Reto Burri
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Ornithological Institute, Sempach, Switzerland
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Lutgen D, Ritter R, Olsen R, Schielzeth H, Gruselius J, Ewels P, García JT, Shirihai H, Schweizer M, Suh A, Burri R. Linked‐read sequencing enables haplotype‐resolved resequencing at population scale. Mol Ecol Resour 2020; 20:1311-1322. [DOI: 10.1111/1755-0998.13192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Dave Lutgen
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Raphael Ritter
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Remi‐André Olsen
- Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna Sweden
| | - Holger Schielzeth
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Joel Gruselius
- Science for Life Laboratory Department of Biosciences and Nutrition Karolinska Institutet Stockholm Sweden
| | - Philip Ewels
- Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna Sweden
| | - Jesús T. García
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ciudad Real Spain
| | | | - Manuel Schweizer
- Natural History Museum Bern Bern Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Alexander Suh
- Department of Organismal Biology – Systematic Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Reto Burri
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
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