uu.seUppsala universitets publikasjoner
Endre søk
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.ORCID-id: 0000-0002-7570-6847
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
Vise andre og tillknytning
2019 (engelsk)Inngår i: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 29, nr 11, s. 1919-1928Artikkel i tidsskrift (Fagfellevurdert) 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.

sted, utgiver, år, opplag, sider
Cold Spring Harbor Laboratory Press (CSHL), 2019. Vol. 29, nr 11, s. 1919-1928
Emneord [en]
Atlantic herring, assembly, ecological adaptation, supergene
HSV kategori
Identifikatorer
URN: urn:nbn:se:uu:diva-396775DOI: 10.1101/gr.253435.119ISI: 000493952800015PubMedID: 31649060OAI: oai:DiVA.org:uu-396775DiVA, id: diva2:1368969
Forskningsfinansiär
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Research Council of Norway, 254774Wellcome trust, WT108749/Z/15/ZTilgjengelig fra: 2019-11-09 Laget: 2019-11-09 Sist oppdatert: 2019-11-28bibliografisk kontrollert
Inngår i avhandling
1. Genetic Adaptation and Speciation in Darwin’s Finches and Atlantic Herring
Åpne denne publikasjonen i ny fane eller vindu >>Genetic Adaptation and Speciation in Darwin’s Finches and Atlantic Herring
2020 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
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.

sted, utgiver, år, opplag, sider
Uppsala: Acta Universitatis Upsaliensis, 2020. s. 49
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1620
Emneord
Darwin's finches, Atlantic herring, Population genetics, Evolution, Ecological adaptation, Speciation
HSV kategori
Forskningsprogram
Biologi med inriktning mot zooekologi; Bioinformatik
Identifikatorer
urn:nbn:se:uu:diva-397886 (URN)978-91-513-0826-5 (ISBN)
Disputas
2020-02-28, Room C8:305, BMC, Husargatan 3, Uppsala, 13:15 (engelsk)
Opponent
Veileder
Tilgjengelig fra: 2020-01-13 Laget: 2019-11-28 Sist oppdatert: 2020-03-05

Open Access i DiVA

fulltext(5084 kB)39 nedlastinger
Filinformasjon
Fil FULLTEXT01.pdfFilstørrelse 5084 kBChecksum SHA-512
99884e7446f121be5c555e6d85ff926233acd9bd5cc9dfb2796f481df4acd83ce90a7407aba13e2a243d1b1c8412b42a49829c7ad085429759cc0adbc5fd0854
Type fulltextMimetype application/pdf

Andre lenker

Forlagets fulltekstPubMed

Personposter BETA

Pettersson, MatsRochus, Christina MarieHan, FanHill, JasonWallerman, OlaBunikis, IgnasAndersson, Leif

Søk i DiVA

Av forfatter/redaktør
Pettersson, MatsRochus, Christina MarieHan, FanHill, JasonWallerman, OlaBunikis, IgnasAndersson, Leif
Av organisasjonen
I samme tidsskrift
Genome Research

Søk utenfor DiVA

GoogleGoogle Scholar
Totalt: 39 nedlastinger
Antall nedlastinger er summen av alle nedlastinger av alle fulltekster. Det kan for eksempel være tidligere versjoner som er ikke lenger tilgjengelige

doi
pubmed
urn-nbn

Altmetric

doi
pubmed
urn-nbn
Totalt: 137 treff
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf