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Genomic architecture and introgression shape a butterfly radiation

View ORCID ProfileNathaniel B. Edelman, View ORCID ProfilePaul B. Frandsen, Michael Miyagi, View ORCID ProfileBernardo Clavijo, View ORCID ProfileJohn Davey, View ORCID ProfileRebecca Dikow, View ORCID ProfileGonzalo García-Accinelli, View ORCID ProfileSteven van Belleghem, Nick Patterson, View ORCID ProfileDaniel E. Neafsey, Richard Challis, View ORCID ProfileSujai Kumar, Gilson Moreira, View ORCID ProfileCamilo Salazar, View ORCID ProfileMathieu Chouteau, View ORCID ProfileBrian Counterman, Riccardo Papa, View ORCID ProfileMark Blaxter, View ORCID ProfileRobert D. Reed, Kanchon Dasmahapatra, Marcus Kronforst, Mathieu Joron, View ORCID ProfileChris D. Jiggins, View ORCID ProfileW. Owen McMillan, View ORCID ProfileFederica Di Palma, Andrew J. Blumberg, John Wakeley, David Jaffe, View ORCID ProfileJames Mallet
doi: https://doi.org/10.1101/466292
Nathaniel B. Edelman
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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Paul B. Frandsen
2Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, 84602, USA
3Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, D.C., 20560, USA
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Michael Miyagi
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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Bernardo Clavijo
4Earlham Institute, Norwich Research Park, NR4 7UZ, UK
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John Davey
5Department of Biology, University of York, YO10 5DD, UK
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Rebecca Dikow
3Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, D.C., 20560, USA
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Gonzalo García-Accinelli
4Earlham Institute, Norwich Research Park, NR4 7UZ, UK
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  • ORCID record for Gonzalo García-Accinelli
Steven van Belleghem
6Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico
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Nick Patterson
7Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
8Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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Daniel E. Neafsey
8Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
9Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
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Richard Challis
10Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
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Sujai Kumar
10Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
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Gilson Moreira
11Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
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Camilo Salazar
12Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Carrera 24, No. 63C-69, Bogotá, D.C. 111221, Colombia
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Mathieu Chouteau
13Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens (LEEISA), USR 3456, Université De Guyane, CNRS Guyane, 275 Route de Montabo, 97334 Cayenne, French Guiana.
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Brian Counterman
14Department of Biological Sciences, Mississippi State University, Starkville, Mississippi 39762, USA
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Riccardo Papa
6Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico
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Mark Blaxter
10Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
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Robert D. Reed
15Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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Kanchon Dasmahapatra
5Department of Biology, University of York, YO10 5DD, UK
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Marcus Kronforst
16Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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Mathieu Joron
17CEFE, CNRS, Université Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
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Chris D. Jiggins
18Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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W. Owen McMillan
19Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panama
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Federica Di Palma
4Earlham Institute, Norwich Research Park, NR4 7UZ, UK
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Andrew J. Blumberg
20Department of Mathematics, University of Texas, Austin, TX, 78712, USA
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John Wakeley
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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David Jaffe
8Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
2110x Genomics, Pleasanton, California 94566, USA
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James Mallet
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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Abstract

We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 04, 2018.
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Genomic architecture and introgression shape a butterfly radiation
Nathaniel B. Edelman, Paul B. Frandsen, Michael Miyagi, Bernardo Clavijo, John Davey, Rebecca Dikow, Gonzalo García-Accinelli, Steven van Belleghem, Nick Patterson, Daniel E. Neafsey, Richard Challis, Sujai Kumar, Gilson Moreira, Camilo Salazar, Mathieu Chouteau, Brian Counterman, Riccardo Papa, Mark Blaxter, Robert D. Reed, Kanchon Dasmahapatra, Marcus Kronforst, Mathieu Joron, Chris D. Jiggins, W. Owen McMillan, Federica Di Palma, Andrew J. Blumberg, John Wakeley, David Jaffe, James Mallet
bioRxiv 466292; doi: https://doi.org/10.1101/466292
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Genomic architecture and introgression shape a butterfly radiation
Nathaniel B. Edelman, Paul B. Frandsen, Michael Miyagi, Bernardo Clavijo, John Davey, Rebecca Dikow, Gonzalo García-Accinelli, Steven van Belleghem, Nick Patterson, Daniel E. Neafsey, Richard Challis, Sujai Kumar, Gilson Moreira, Camilo Salazar, Mathieu Chouteau, Brian Counterman, Riccardo Papa, Mark Blaxter, Robert D. Reed, Kanchon Dasmahapatra, Marcus Kronforst, Mathieu Joron, Chris D. Jiggins, W. Owen McMillan, Federica Di Palma, Andrew J. Blumberg, John Wakeley, David Jaffe, James Mallet
bioRxiv 466292; doi: https://doi.org/10.1101/466292

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