Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Genetic Adaptation and Speciation in Darwin’s Finches and Atlantic Herring
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Description
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 [en]
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: urn:nbn:se:uu:diva-397886ISBN: 978-91-513-0826-5 (print)OAI: oai:DiVA.org:uu-397886DiVA, id: diva2:1373998
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
List of papers
1. A beak size locus in Darwin’s finches facilitated character displacement during a drought
Open this publication in new window or tab >>A beak size locus in Darwin’s finches facilitated character displacement during a drought
Show others...
2016 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6284, p. 470-474Article in journal (Refereed) Published
Abstract [en]

Ecological character displacement is a process of morphological divergence that reducescompetition for limited resources. We used genomic analysis to investigate the geneticbasis of a documented character displacement event in Darwin’s finches on Daphne Majorin the Galápagos Islands: The medium ground finch diverged from its competitor, the largeground finch, during a severe drought. We discovered a genomic region containing theHMGA2gene that varies systematically among Darwin’s finch species with different beaksizes. Two haplotypes that diverged early in the radiation were involved in the characterdisplacement event: Genotypes associated with large beak size were at a strong selectivedisadvantage in medium ground finches (selection coefficients= 0.59). Thus, a majorlocus has apparently facilitated a rapid ecological diversification in the adaptive radiationof Darwin’s finches.

National Category
Genetics and Breeding
Identifiers
urn:nbn:se:uu:diva-279968 (URN)10.1126/science.aad8786 (DOI)000374479700050 ()27102486 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2019-11-28Bibliographically approved
2. Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Open this publication in new window or tab >>Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Show others...
2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 6, p. 1004-1015Article in journal (Refereed) Published
Abstract [en]

Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-340985 (URN)10.1101/gr.212522.116 (DOI)000402521400011 ()28442558 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation
Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2019-11-28Bibliographically approved
3. Rapid hybrid speciation in Darwin's finches
Open this publication in new window or tab >>Rapid hybrid speciation in Darwin's finches
Show others...
2018 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, no 6372, p. 224-228Article in journal (Refereed) Published
Abstract [en]

Homoploid hybrid speciation in animals has been inferred frequently from patterns of variation, but few examples have withstood critical scrutiny. Here we report a directly documented example, from its origin to reproductive isolation. An immigrant Darwin's finch to Daphne Major in the Galápagos archipelago initiated a new genetic lineage by breeding with a resident finch (Geospiza fortis). Genome sequencing of the immigrant identified it as a G. conirostris male that originated on Española >100 kilometers from Daphne Major. From the second generation onward, the lineage bred endogamously and, despite intense inbreeding, was ecologically successful and showed transgressive segregation of bill morphology. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-340986 (URN)10.1126/science.aao4593 (DOI)000419816600048 ()29170277 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2019-11-28
4. Female-biased gene flow between two species of Darwin’s finches
Open this publication in new window or tab >>Female-biased gene flow between two species of Darwin’s finches
Show others...
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.

Keywords
Darwin's finches, introgression, hybridisation
National Category
Ecology Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-396776 (URN)
Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28
5. A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
Open this publication in new window or tab >>A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
Show others...
2019 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 29, no 11, p. 1919-1928Article in journal (Refereed) Published
Abstract [en]

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.

Place, publisher, year, edition, pages
Cold Spring Harbor Laboratory Press (CSHL), 2019
Keywords
Atlantic herring, assembly, ecological adaptation, supergene
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-396775 (URN)10.1101/gr.253435.119 (DOI)000493952800015 ()31649060 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Research Council of Norway, 254774Wellcome trust, WT108749/Z/15/Z
Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28Bibliographically approved

Open Access in DiVA

fulltext(1415 kB)23 downloads
File information
File name FULLTEXT01.pdfFile size 1415 kBChecksum SHA-512
7552cd6d8a2637da4a29a4b45145a84aa74179371b77c8e5418d02afa15ae84234037c1ca57be8fd27902ceb281bcc7978ce6bfe96d6105445a4920dc7171935
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Han, Fan
By organisation
Department of Medical Biochemistry and Microbiology
EcologyEvolutionary BiologyGenetics

Search outside of DiVA

GoogleGoogle Scholar
Total: 23 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 162 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf