eLife (May 2016)
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
- Alvaro Martinez Barrio,
- Sangeet Lamichhaney,
- Guangyi Fan,
- Nima Rafati,
- Mats Pettersson,
- He Zhang,
- Jacques Dainat,
- Diana Ekman,
- Marc Höppner,
- Patric Jern,
- Marcel Martin,
- Björn Nystedt,
- Xin Liu,
- Wenbin Chen,
- Xinming Liang,
- Chengcheng Shi,
- Yuanyuan Fu,
- Kailong Ma,
- Xiao Zhan,
- Chungang Feng,
- Ulla Gustafson,
- Carl-Johan Rubin,
- Markus Sällman Almén,
- Martina Blass,
- Michele Casini,
- Arild Folkvord,
- Linda Laikre,
- Nils Ryman,
- Simon Ming-Yuen Lee,
- Xun Xu,
- Leif Andersson
Affiliations
- Alvaro Martinez Barrio
- ORCiD
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Sangeet Lamichhaney
- ORCiD
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Guangyi Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China; BGI-Shenzhen, Shenzen, China
- Nima Rafati
- ORCiD
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- He Zhang
- BGI-Shenzhen, Shenzen, China; College of Physics, Qingdao University, Qingdao, China
- Jacques Dainat
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden
- Diana Ekman
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Marc Höppner
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden
- Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Marcel Martin
- ORCiD
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Björn Nystedt
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Xin Liu
- BGI-Shenzhen, Shenzen, China
- Wenbin Chen
- BGI-Shenzhen, Shenzen, China
- Xinming Liang
- BGI-Shenzhen, Shenzen, China
- Chengcheng Shi
- BGI-Shenzhen, Shenzen, China
- Yuanyuan Fu
- BGI-Shenzhen, Shenzen, China; School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- Kailong Ma
- BGI-Shenzhen, Shenzen, China
- Xiao Zhan
- BGI-Shenzhen, Shenzen, China
- Chungang Feng
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Ulla Gustafson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Markus Sällman Almén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Martina Blass
- Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden
- Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden
- Arild Folkvord
- Department of Biology, University of Bergen, Bergen, Norway; Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway; Institute of Marine Research, Bergen, Norway
- Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Nils Ryman
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
- Xun Xu
- BGI-Shenzhen, Shenzen, China
- Leif Andersson
- ORCiD
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, United States
- DOI
- https://doi.org/10.7554/eLife.12081
- Journal volume & issue
-
Vol. 5
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.
Keywords
