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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
Barrio A.M.1,2; Lamichhaney S.1; Fan G.3,4; Rafati N.1; Pettersson M.1; Zhang H.4,5; Dainat J.1,6; Ekman D.7; Höppner M.1,6; Jern P.1; Martin M.7; Nystedt B.2; Liu X.4; Chen W.4; Liang X.4; Shi C.4; Fu Y.4,8; Ma K.4; Zhan X.4; Feng C.1; Gustafson U.9; Rubin C.-J.1; Almén M.1; Blass M.10; Casini M.10; Folkvord A.11,12,13; Laikre L.14; Ryman N.14; Lee S.-Y.3; Xu X.4; Andersson L.1,9,15
2016
Source PublicationeLife
ISSN2050084X
Volume5Issue:2016-05-01
Abstract

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring-and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

DOI10.7554/eLife.12081
URLView the original
Indexed BySCIE
Language英语
WOS Research AreaLife Sciences & Biomedicine - Other Topics
WOS SubjectBiology
WOS IDWOS:000387459700001
The Source to ArticleScopus
Fulltext Access
Citation statistics
Cited Times [WOS]:54   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionInstitute of Chinese Medical Sciences
Affiliation1.Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
2.Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
3.State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
4.BGI-Shenzhen, Shenzen, China
5.College of Physics, Qingdao University, Qingdao, China
6.Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden
7.Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
8.School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
9.Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
10.Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden
11.Department of Biology, University of Bergen, Bergen, Norway
12.Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway
13.Institute of Marine Research, Bergen, Norway
14.Department of Zoology, Stockholm University, Stockholm, Sweden
15.Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, United States
Recommended Citation
GB/T 7714
Barrio A.M.,Lamichhaney S.,Fan G.,et al. The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing[J]. eLife,2016,5(2016-05-01).
APA Barrio A.M..,Lamichhaney S..,Fan G..,Rafati N..,Pettersson M..,...&Andersson L..(2016).The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.eLife,5(2016-05-01).
MLA Barrio A.M.,et al."The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing".eLife 5.2016-05-01(2016).
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