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, 9 (4), 2004-2017
eCollection

Characterizing Neutral and Adaptive Genomic Differentiation in a Changing Climate: The Most Northerly Freshwater Fish as a Model

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Characterizing Neutral and Adaptive Genomic Differentiation in a Changing Climate: The Most Northerly Freshwater Fish as a Model

Kathleen G O'Malley et al. Ecol Evol.

Abstract

Arctic freshwater ecosystems have been profoundly affected by climate change. Given that the Arctic charr (Salvelinus alpinus) is often the only fish species inhabiting these ecosystems, it represents a valuable model for studying the impacts of climate change on species life-history diversity and adaptability. Using a genotyping-by-sequencing approach, we identified 5,976 neutral single nucleotide polymorphisms and found evidence for reduced gene flow between allopatric morphs from two high Arctic lakes, Linne'vatn (Anadromous, Normal, and Dwarf) and Ellasjøen (Littoral and Pelagic). Within each lake, the degree of genetic differentiation ranged from low (Pelagic vs. Littoral) to moderate (Anadromous and Normal vs. Dwarf). We identified 17 highly diagnostic, putatively adaptive SNPs that differentiated the allopatric morphs. Although we found no evidence for adaptive differences between morphs within Ellasjøen, we found evidence for moderate (Anadromous vs. Normal) to high genetic differentiation (Anadromous and Normal vs. Dwarf) among morphs within Linne'vatn based on two adaptive loci. As these freshwater ecosystems become more productive, the frequency of sympatric morphs in Ellasjøen will likely shift based on foraging opportunities, whereas the propensity to migrate may decrease in Linne'vatn, increasing the frequency of the Normal morph. The Dwarf charr was the most genetically distinct group. Identifying the biological basis for small body size should elucidate the potential for increased growth and subsequent interbreeding with sympatric morphs. Overall, neutral and adaptive genomic differentiation between allopatric and some sympatric morphs suggests that the response of Arctic charr to climate change will be variable across freshwater ecosystems.

Keywords: Arctic charr; Svalbard; climate change; genotyping‐by‐sequencing; population genomics; salmonids.

Figures

Figure 1
Figure 1
Location of the two lakes, Linne'vatn and Ellasjøen in the Svalbard archipelago. Anadromous Arctic charr were sampled in the Linne'vatn River, and both resident Normal and resident Dwarf charr were sampled from Lake Linne'vatn. Littoral and Pelagic Arctic charr samples were collected from Lake Ellasjøen. The inset map for the Svalbard archipelago was generated using the R package maps (Becker & Wilks, 2008)
Figure 2
Figure 2
Cluster analyses of 5,076 neutral loci among five different Arctic charr morphs from lakes Ellasjøen and Linne'vatn: (a) first two axes from a discriminant analysis of principal components with points corresponding to individuals. Shape of points is based upon actual phenotypic group, with color corresponding to inferred group; (b) barplot of inferred group membership probability (k = 3 clusters) from k‐means clustering; and (c) k = 3 also identified by admixture as best describing the structure in the data

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