The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.

Oksung Chung,Hyunho Kim,Yun Sung Cho,Stephen J O’Brien,Jeongheui Lim,Hyejin Lee,Jessica A Weber,Seondeok Jin,Sungwoong Jho,Jeremy Edwards,Jehoon Jun,Hak-Min Kim,Kyudong Han,Junsu Ko,Andrea Manica,Alvin Chon,Woon Kee Paek,Jong Bhak

doi:10.1186/s13059-015-0780-4

Abstract

BackgroundThe cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.ResultsWe sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene.ConclusionsWe present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0780-4) contains supplementary material, which is available to authorized users.

Highlights

The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, preventing the spread of diseases
In order to identify the genetic adaptations and possible convergent evolution linked to obligate scavenging, we provide a whole genome and transcriptome analysis of the cinereous vulture which we compared to other avian genomes; including other birds of prey belonging to the family Accipitridae, as well as New World vultures from the family Cathartidae
The comparative analyses revealed likely signatures of selection in cinereous vulture genes associated with the immune response and gastric acid secretion

Summary

Introduction

The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, preventing the spread of diseases. The presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging. The term vulture refers to two independently evolved groups of birds of prey, namely the Old World (16 species) and New World (7 species) vultures. While the two vulture groups are members of different avian families (Accipitridae and Cathartidae), they are phenotypically similar and are both obligate scavengers. Over the past two centuries, its numbers have declined across most of its range leading to this species being classified as ‘near threatened’ on the International Union for Conservation of Nature (IUCN) Red List [5]. Several protection and conservation efforts for this species have been developed at a national [6] and international level [7, 8]

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