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Female-biased gene flow between two species of Darwin’s finches
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0003-4826-0349
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0003-1141-2863
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
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2019 (English)In: Article in journal (Refereed) Submitted
Abstract [en]

The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Galápagos island of Daphne Major two species of Darwin’s finches, Geospiza fortis and G. scandens, hybridize rarely and backcross bidirectionally with little or no loss of fitness under conditions of plentiful food. We used whole genome sequences to compare genomes from periods before and after successful interbreeding followed by backcrossing. We inferred extensive introgression from G. fortis to G. scandens on autosomes and mitochondria but not on the Z chromosome. The unique combination of long-term field observations and genomic data shows that the reduction of gene flow for Z-linked loci reflects female-biased gene flow, arising from hybrid male disadvantage in competition for territories and mates, rather than from genetic incompatibilities at Z-linked loci.

Place, publisher, year, edition, pages
2019.
Keywords [en]
Darwin's finches, introgression, hybridisation
National Category
Ecology Evolutionary Biology Genetics
Identifiers
URN: urn:nbn:se:uu:diva-396776OAI: oai:DiVA.org:uu-396776DiVA, id: diva2:1368971
Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28
In thesis
1. Genetic Adaptation and Speciation in Darwin’s Finches and Atlantic Herring
Open this publication in new window or tab >>Genetic Adaptation and Speciation in Darwin’s Finches and Atlantic Herring
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Natural selection acts on existing genetic variation to drive genetic adaptation of organisms to various ecological niches. Interaction between closely related populations, through processes such as competition and hybridization, may either lead to their divergence or population fusion, which has consequences for adaptation and the formation of species. This thesis aims to use two natural populations, Darwin’s finches and Atlantic herring, as models to explore the genetic mechanisms underlying ecological adaptation and speciation.

The ecological adaptation of Darwin’s finches across the Galápagos Islands is primarily reflected by variation in beak morphology. Using whole-genome re-sequencing of all Darwin’s finch species, we discover that a locus, HMGA2, is highly associated with variation in beak size. Data collected before and after a severe drought show that this locus plays a critical role for ecological character displacement in large ground finches Geospiza magnirostris and medium ground finches G. fortis.

Genomic islands of divergence refer to genomic regions of elevated divergence when comparing the genomes of closely related taxa. Establishment of these genomic islands can reflect a role in reproductive isolation or be related to ecological adaptation or background selection. Investigating their properties can shed light on how new species evolve. We study the landscape of genomic islands in Darwin’s finches, and find that the most pronounced genomic islands are likely ancient balanced polymorphisms, which govern adaptive variation in beak morphology.

Hybridization is increasingly recognized as an important evolutionary process which may lead to speciation. We study two cases of hybridization in Darwin’s finches. In the first case, a new lineage of Darwin’s finches was founded through hybridization between a resident medium ground finch G. fortis and an immigrant Española cactus finch G. conirostris. In the second case, female-biased introgression occurred predominantly from medium ground finches G. fortis to common cactus finches G. scandens. Our genetic analysis on the mosaic genomes of hybrid finches show that non-random mating and natural selection primarily determine the outcome of hybridization.

We generate a chromosome-level assembly of the Atlantic herring with a total size of 726 Mb, which coincides with a high-resolution linkage map and an LD-based recombination map. This facilitates the identification of an ~8Mb inversion, which is likely to be associated with ecological adaptation in herring to differences in water temperature. The contiguity of the assembly sorts placement of loci under selection that were identified based on a previous, highly fragmented draft assembly of the herring genome.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2020. p. 49
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1620
Keywords
Darwin's finches, Atlantic herring, Population genetics, Evolution, Ecological adaptation, Speciation
National Category
Ecology Evolutionary Biology Genetics
Research subject
Biology with specialization in Animal Ecology; Bioinformatics
Identifiers
urn:nbn:se:uu:diva-397886 (URN)978-91-513-0826-5 (ISBN)
Public defence
2020-02-28, Room C8:305, BMC, Husargatan 3, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2020-01-13 Created: 2019-11-28 Last updated: 2020-01-13

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Lamichhaney, SangeetHan, FanWebster, Matthew ThomasAndersson, Leif

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