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Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

View Article: PubMed Central - PubMed

ABSTRACT

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick‐billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick‐billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome‐wide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non‐breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.

No MeSH data available.


Map showing colony locations
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ece32819-fig-0001: Map showing colony locations

Mentions: Among the colonies distributed along the Canadian Atlantic coast, we selected five colonies along a latitudinal cline that includes birds from the extremes of the distribution (Gannet and Prince Leopold, ~20° latitudinal difference), known migratory behavior (Gannet, Coats, Minarets, Prince Leopold), and morphometric distinctiveness (Akpatok; Figure 1). We used previously collected blood samples from breeding adults from each colony (Birt‐Friesen et al., 1992; Tigano et al., 2015; Environment and Climate Change Tissue Archive; Figure 1, Table 1). Samples were collected from breeding adults from each colony during June‐July in 1987 (Akpatok), 1996 (Coats and Gannet), and 2008 (Minarets and Prince Leopold) and stored in ethanol at −80°C. We also included samples of four common murres (Uria aalgae), the sister species of the thick‐billed murre, as an out group to test for the presence of hybrids (Taylor, Patirana, Birt, Piatt, & Friesen, 2012). We purified DNA for library preparation using standard protease k/phenol–chloroform extraction protocols and ethanol precipitation with resuspension in DNase‐free water (Sambrook, Fritsch, & Maniatis, 1989).


Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird
Map showing colony locations
© Copyright Policy - creativeCommonsBy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383466&req=5

ece32819-fig-0001: Map showing colony locations
Mentions: Among the colonies distributed along the Canadian Atlantic coast, we selected five colonies along a latitudinal cline that includes birds from the extremes of the distribution (Gannet and Prince Leopold, ~20° latitudinal difference), known migratory behavior (Gannet, Coats, Minarets, Prince Leopold), and morphometric distinctiveness (Akpatok; Figure 1). We used previously collected blood samples from breeding adults from each colony (Birt‐Friesen et al., 1992; Tigano et al., 2015; Environment and Climate Change Tissue Archive; Figure 1, Table 1). Samples were collected from breeding adults from each colony during June‐July in 1987 (Akpatok), 1996 (Coats and Gannet), and 2008 (Minarets and Prince Leopold) and stored in ethanol at −80°C. We also included samples of four common murres (Uria aalgae), the sister species of the thick‐billed murre, as an out group to test for the presence of hybrids (Taylor, Patirana, Birt, Piatt, & Friesen, 2012). We purified DNA for library preparation using standard protease k/phenol–chloroform extraction protocols and ethanol precipitation with resuspension in DNase‐free water (Sambrook, Fritsch, & Maniatis, 1989).

View Article: PubMed Central - PubMed

ABSTRACT

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick‐billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick‐billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome‐wide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non‐breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.

No MeSH data available.