The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Author:

Martinez Barrio Alvaro12ORCID,Lamichhaney Sangeet1ORCID,Fan Guangyi34,Rafati Nima1ORCID,Pettersson Mats1,Zhang He45,Dainat Jacques16,Ekman Diana7,Höppner Marc16,Jern Patric1,Martin Marcel7ORCID,Nystedt Björn2,Liu Xin4,Chen Wenbin4,Liang Xinming4,Shi Chengcheng4,Fu Yuanyuan48,Ma Kailong4,Zhan Xiao4,Feng Chungang1,Gustafson Ulla9,Rubin Carl-Johan1,Sällman Almén Markus1,Blass Martina10,Casini Michele11,Folkvord Arild121314,Laikre Linda15,Ryman Nils15,Ming-Yuen Lee Simon3,Xu Xun4,Andersson Leif1916ORCID

Affiliation:

1. 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 Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden

12. Department of Biology, University of Bergen, Bergen, Norway

13. Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway

14. Institute of Marine Research, Bergen, Norway

15. Department of Zoology, Stockholm University, Stockholm, Sweden

16. Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, United States

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.

Funder

European Research Council

Swedish Research Council Formas

Knut och Alice Wallenbergs Stiftelse

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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