A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes.

Alain Vignal,Valentine Yapi‐Gnaore,Wesley C Warren,Simon Boitard,Guiguigbaza‐Kossigan Dayo,Daniel Guémené,Francoise Thibaud‐Nissen,Xavier Rognon,Nóra Pálinkás‐Bodzsár,Issaka Youssao Abdou Karim,Noémie Thébault,Michèle Tixier‐Boichard,Cécile Berthouly‐Salazar

doi:10.1111/1755-0998.13017

Abstract

The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub‐Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first‐generation whole‐genome sequence draft assembly used as a reference for a study by a Pool‐seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB2, possibly explaining losses in plumage coloration phenotypes in domesticated populations.

Highlights

The helmeted guinea fowl, Numida meleagris, belongs to the Galliformes order and the Numididae family
After running pool‐hmm within each pool, we focused on three specific types of sweep regions: (a) potential domestication sweeps, which were detected in at least six domestic populations while showing no significant signal in any of the three wild populations; (b) potential European sweeps, which were detected in at least four European populations while showing no significant signal in any of the five wild and domesticated African populations; and (c) potential ‘production’ sweeps, which were detected in the three populations managed with strong artificial selection criteria, while showing no significant signal in any of the seven other populations
To assemble the scaffolds at the chromosome level, we took advantage of the high degree of karyotype conservation observed between gallo‐anseriformes including microchromosomes (Fillon et al, 2007) and used prior knowledge on the major rearrangements observed between chicken and guinea fowl macrochromosomes (Shibusawa et al, 2002)

Summary

| INTRODUCTION

The helmeted guinea fowl, Numida meleagris, belongs to the Galliformes order and the Numididae family. In the USA an attempt to use guinea fowl to control ticks on cervids (Duffy, Downer, & Brinkley, 1992) was later shown to be ineffective against tick‐borne zoonoses (Ostfeld, Price, Hornbostel, Benjamin, & Keesing, 2006) These uses and the attraction for human settlements (water and food) could be the source of domestication via a process of commensal association (Crawford, 1990; Gifford‐Gonzalez & Hanotte, 2011) as defined by Zeder (2012). Today short‐read sequencing technology (Illumina) allows for the automa ted pr oduction of deep sequence coverage at low cost, and as a result, there has been a rapid increase of the number of bird whole‐genome assemblies available, with at least one representat ive pe r bird order These 48 avian genomes were used for in‐depth analyses of bird evolution (Jarvis et al, 2014; Zhang et al, 2014).

| METHODS

Findings

| DISCUSSION