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Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica

Yves Bawin, Tom Ruttink (UGent) , Ariane Staelens, Annelies Haegeman, Piet Stoffelen, Jean‐Claude ItheMwanga Mwanga, Isabel Roldán-Ruiz (UGent) , Olivier Honnay and Steven B. Janssens
(2021) JOURNAL OF SYSTEMATICS AND EVOLUTION. 59(5). p.953-963
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Abstract
Interspecific hybridization events have played a major role in plant speciation, yet the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to estimate the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also inferred to shed new light on the evolution of self-compatibility in Coffea. Coffea canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 000 years ago, coinciding with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.
Keywords
allopolyploidy, Coffea arabica (Arabica coffee), genotyping&#8208, by&#8208, sequencing, hybridization, molecular dating, self&#8208, compatibility, MITOCHONDRIAL-DNA, HYBRIDIZATION, ALLOPOLYPLOIDY, CHLOROPLAST, SPECIATION, TREES, DIVERSIFICATION, INTROGRESSION, HETEROCALYX, EUGENIOIDES

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MLA
Bawin, Yves, et al. “Phylogenomic Analysis Clarifies the Evolutionary Origin of Coffea Arabica.” JOURNAL OF SYSTEMATICS AND EVOLUTION, vol. 59, no. 5, 2021, pp. 953–63, doi:10.1111/jse.12694.
APA
Bawin, Y., Ruttink, T., Staelens, A., Haegeman, A., Stoffelen, P., ItheMwanga Mwanga, J., … Janssens, S. B. (2021). Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica. JOURNAL OF SYSTEMATICS AND EVOLUTION, 59(5), 953–963. https://doi.org/10.1111/jse.12694
Chicago author-date
Bawin, Yves, Tom Ruttink, Ariane Staelens, Annelies Haegeman, Piet Stoffelen, Jean‐Claude ItheMwanga Mwanga, Isabel Roldán-Ruiz, Olivier Honnay, and Steven B. Janssens. 2021. “Phylogenomic Analysis Clarifies the Evolutionary Origin of Coffea Arabica.” JOURNAL OF SYSTEMATICS AND EVOLUTION 59 (5): 953–63. https://doi.org/10.1111/jse.12694.
Chicago author-date (all authors)
Bawin, Yves, Tom Ruttink, Ariane Staelens, Annelies Haegeman, Piet Stoffelen, Jean‐Claude ItheMwanga Mwanga, Isabel Roldán-Ruiz, Olivier Honnay, and Steven B. Janssens. 2021. “Phylogenomic Analysis Clarifies the Evolutionary Origin of Coffea Arabica.” JOURNAL OF SYSTEMATICS AND EVOLUTION 59 (5): 953–963. doi:10.1111/jse.12694.
Vancouver
1.
Bawin Y, Ruttink T, Staelens A, Haegeman A, Stoffelen P, ItheMwanga Mwanga J, et al. Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica. JOURNAL OF SYSTEMATICS AND EVOLUTION. 2021;59(5):953–63.
IEEE
[1]
Y. Bawin et al., “Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica,” JOURNAL OF SYSTEMATICS AND EVOLUTION, vol. 59, no. 5, pp. 953–963, 2021.
@article{8736742,
  abstract     = {{Interspecific hybridization events have played a major role in plant speciation, yet the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to estimate the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also inferred to shed new light on the evolution of self-compatibility in Coffea. Coffea canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 000 years ago, coinciding with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.}},
  author       = {{Bawin, Yves and Ruttink, Tom and Staelens, Ariane and Haegeman, Annelies and Stoffelen, Piet and ItheMwanga Mwanga, Jean‐Claude and Roldán-Ruiz, Isabel and Honnay, Olivier and Janssens, Steven B.}},
  issn         = {{1674-4918}},
  journal      = {{JOURNAL OF SYSTEMATICS AND EVOLUTION}},
  keywords     = {{allopolyploidy,Coffea arabica (Arabica coffee),genotyping&#8208,by&#8208,sequencing,hybridization,molecular dating,self&#8208,compatibility,MITOCHONDRIAL-DNA,HYBRIDIZATION,ALLOPOLYPLOIDY,CHLOROPLAST,SPECIATION,TREES,DIVERSIFICATION,INTROGRESSION,HETEROCALYX,EUGENIOIDES}},
  language     = {{eng}},
  number       = {{5}},
  pages        = {{953--963}},
  title        = {{Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica}},
  url          = {{http://doi.org/10.1111/jse.12694}},
  volume       = {{59}},
  year         = {{2021}},
}
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