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

Zach G Gayk,Jeffrey Horn,Diana Le Duc,Alec R Lindsay

doi:10.1186/s12862-018-1181-6

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsSignatures 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.

Highlights

The common loon (Gavia immer) is one of five species that comprise the avian order Gaviiformes
ABySS assemblies of the common loon genome with eight different k-mer sizes ranging from k25—k64 yielded contig N50 values from 641 to 814 bp in length
That candidate positively selected genes are available, future work could examine the expression of these genes through RNA-sequencing [21]; in particular the mechanisms through which osmoregulation is balanced in salt and freshwater environments, low-light phototransduction is achieved, and oxygen saturation is maximized in flight and diving should be elucidated

Summary

Introduction

The common loon (Gavia immer) is one of five species that comprise the avian order Gaviiformes. Order Gaviiformes, are a small extant group of five species, all of which are specialized for diving in freshwater and marine-coastal aquatic habitats. They exhibit a number of specialized morphological traits used for diving and piscivory, including posteriorly-positioned feet for foot-propelled diving, dense bones [1], and compressible feathers to reduce buoyancy forces [2]. Adaptation to freshwater aquatic habitats such as those occupied by loons during nesting, likely presents different selection pressures to saltwater aquatic divers such as penguins.

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