title: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.
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.
authors.affiliation: 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.
authors.forename: Alvaro
authors.identifier: 0000-0001-5064-2093
authors.initials: A
authors.lastname: Martinez Barrio
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Sangeet
authors.identifier: 0000-0003-4826-0349
authors.initials: S
authors.lastname: Lamichhaney
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.|BGI-Shenzhen, Shenzen, China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Fan
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Nima
authors.identifier: 0000-0002-3687-9745
authors.initials: N
authors.lastname: Rafati
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Mats
authors.initials: M
authors.lastname: Pettersson
authors.affiliation: BGI-Shenzhen, Shenzen, China.|College of Physics, Qingdao University, Qingdao, China.
authors.forename: He
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden.
authors.forename: Jacques
authors.initials: J
authors.lastname: Dainat
authors.affiliation: Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
authors.forename: Diana
authors.initials: D
authors.lastname: Ekman
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden.
authors.forename: Marc
authors.initials: M
authors.lastname: Höppner
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Patric
authors.initials: P
authors.lastname: Jern
authors.affiliation: Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
authors.forename: Marcel
authors.identifier: 0000-0002-0680-200X
authors.initials: M
authors.lastname: Martin
authors.affiliation: Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
authors.forename: Björn
authors.initials: B
authors.lastname: Nystedt
authors.affiliation: BGI-Shenzhen, Shenzen, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzen, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzen, China.
authors.forename: Xinming
authors.initials: X
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzen, China.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Shi
authors.affiliation: BGI-Shenzhen, Shenzen, China.|School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Fu
authors.affiliation: BGI-Shenzhen, Shenzen, China.
authors.forename: Kailong
authors.initials: K
authors.lastname: Ma
authors.affiliation: BGI-Shenzhen, Shenzen, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Zhan
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Chungang
authors.initials: C
authors.lastname: Feng
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Ulla
authors.initials: U
authors.lastname: Gustafson
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Carl-Johan
authors.initials: CJ
authors.lastname: Rubin
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Markus
authors.initials: M
authors.lastname: Sällman Almén
authors.affiliation: Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden.
authors.forename: Martina
authors.initials: M
authors.lastname: Blass
authors.affiliation: Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden.
authors.forename: Michele
authors.initials: M
authors.lastname: Casini
authors.affiliation: Department of Biology, University of Bergen, Bergen, Norway.|Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway.|Institute of Marine Research, Bergen, Norway.
authors.forename: Arild
authors.initials: A
authors.lastname: Folkvord
authors.affiliation: Department of Zoology, Stockholm University, Stockholm, Sweden.
authors.forename: Linda
authors.initials: L
authors.lastname: Laikre
authors.affiliation: Department of Zoology, Stockholm University, Stockholm, Sweden.
authors.forename: Nils
authors.initials: N
authors.lastname: Ryman
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
authors.forename: Simon
authors.initials: S
authors.lastname: Ming-Yuen Lee
authors.affiliation: BGI-Shenzhen, Shenzen, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: 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.
authors.forename: Leif
authors.identifier: 0000-0002-4085-6968
authors.initials: L
authors.lastname: Andersson
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D001267:Atlantic Ocean; D005399:Fishes / Q000145:classification / Q000235:genetics* / Q000502:physiology; D014644:Genetic Variation; D005828:Genetics, Population; D023281:Genomics; D000068357:Saline Waters; D012623:Seawater
keywords: Atlantic herring; evolutionary biology; genetic adaptation; genomics; natural selection