Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus

Bridgett M Vonholdt,Thomas B Smith,Kristen Ruegg,Kirk E Lohmueller,Ying Zhen,Rebecca Y Kartzinel,Christian D Huber,Vinh Le Underwood

doi:10.1038/s41467-018-07374-9

Abstract

Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection. Morphs breed randomly with respect to bill size, and differ in diet and feeding performance relative to seed hardness. Previous breeding experiments are consistent with the polymorphism being controlled by a single genetic factor. Here, we use genome-wide pooled sequencing to explore the underlying genetic basis of bill morphology and identify a single candidate region. Targeted resequencing reveals extensive linkage disequilibrium across a 300 Kb region containing the insulin-like growth factor 1 (IGF1) gene, with a single 5-million-year-old haplotype associating with phenotypic dominance of the large-billed morph. We find no genetic similarities controlling bill size in the well-studied Darwin’s finches (Geospiza). Our results show how a single genetic factor may control bill size and provide a foundation for future studies to examine this phenomenon within and among avian species.

Highlights

Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection
We performed genome-wide Pool-seq on 20 small-billed, largebilled, and mega-billed P. ostrinus morphs to identify candidate regions associated with bill morphology
We investigated the region homologous to the P. ostrinus candidate region in three species of Darwin’s finches (Geospiza fuliginosa, G. fortis, and G. magnirostris) to determine whether alleles associated with bill morphology in P. ostrinus were segregating or fixed within the highly-studied Geospiza system

Summary

Introduction

Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection. Despite the ubiquity of phenotypic polymorphisms in natural populations[2], there are few instances in which the ecological and evolutionary factors that produce and maintain them are well understood, and still fewer where the genetic bases have been identified[3,4,5]. Resource polymorphisms, defined as intraspecific phenotypic variation associated with niche partitioning, can be under strong selection and are prime candidates for investigating the genetic, ecological, and evolutionary factors maintaining variation in natural populations and may represent important steps in speciation[6,7]. We identify a single candidate region underlying bill size differences in small and large morphs, confirming earlier work that suggested this trait is controlled by a single locus. Our results provide insights into how genetic variation contributes to discrete resource polymorphisms, and how they evolve and are maintained in natural populations

Methods

Results

Conclusion