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. 2018 Apr 27;18(1):64.
doi: 10.1186/s12862-018-1181-6.

Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation

Zach G Gayk  1   2 , Diana Le Duc  3   4 , Jeffrey Horn  5 , Alec R Lindsay  6
Affiliations

Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation

Zach G Gayk et al. BMC Evol Biol. .

Abstract

Background: The common loon (Gavia immer) is one of five species that comprise the avian order Gaviiformes. Loons are specialized divers, reaching depths up to 60 m while staying submerged for intervals up to three minutes. In this study we used comparative genomics to investigate the genetic basis of the common loon adaptations to its ecological niche. We used Illumina short read DNA sequence data from a female bird to produce a draft assembly of the common loon (Gavia immer) genome.

Results: We identified 14,169 common loon genes, which based on well-resolved avian genomes, represent approximately 80.7% of common loon genes. Evolutionary analyses between common loon and Adelie penguin (Pygoscelis adeliae), red-throated loon (Gavia stellata), chicken (Gallus gallus), northern fulmar (Fulmarus glacialis), and rock pigeon (Columba livia) show 164 positively selected genes in common and red-throated loons. These genes were enriched for a number of protein classes, including those involved in muscle tissue development, immunoglobulin function, hemoglobin iron binding, G-protein coupled receptors, and ATP metabolism.

Conclusions: Signatures of positive selection in these areas suggest the genus Gavia may have adapted for underwater diving by modulating their oxidative and metabolic pathways. While more research is required, these adaptations likely result in (1) compensations in oxygen respiration and energetic metabolism, (2) low-light visual acuity, and (3) elevated solute exchange. This work represents the first effort to understand the genomic adaptations of the common loon as well as other Gavia and may have implications for subsequent studies that target particular genes for loon population genetic, ecological or conservation studies.

Keywords: Comparative genomics; Diving; Freshwater adaptation; Migration; Positive selection.

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Competing interests

The authors declare they have no competing interests.

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Figures

Fig. 1
Fig. 1
Percent GC content of the common loon k = 30 genome assembly. Variation in the percentage of bases composed of paired G (guanine) and C (cytosine) is shown across assembled bases from 1 to 767,326,331 base pairs in the total assembly length. Individual values of GC across the genome assembly were plotted using a sliding window analysis set to examine every 10 Kbp. Regions with no GC content, shown as white spaces, likely represent sequencing gaps
Fig. 2
Fig. 2
Cladogram representation of common loon (Gavia immer), red-throated-loon (Gavia stellata), northern fulmar (Fulmarus glacialis), Adelie penguin (Pygoscelis adelie), rock pigeon, (Columba livia), and chicken (Gallus gallus). The aquatic diving lineages are highlighted in blue
See this image and copyright information in PMC

References

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