Avian MHC Evolution in the Era of Genomics: Phase 1.0

Abstract

Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.

Keywords: MHC genes; birds; concerted evolution; disease resistance; ecology; gene duplication; high-throughput sequencing; life history; long-read sequencing; orthology.

Figure 1

Evidence for the impact of high-throughput sequencing on the number of bird species genotyped for MHC, as demonstrated by the increase in the number of bird species genotyped for MHC each year since 2010 (red dashed line) when the first studies using high-throughput sequencing for avian MHC genotyping were published. Figure prepared using data from Minias et al. 2018 [103] with updated information added for studies until the end of 2018 using identical methods to those described within Minias et al 2018 [103].

Figure 2

Ancestral character estimation of gene copy number at MHC class I genes along the branches and nodes of a tree for birds. Bars associated with each terminal node indicate the estimated number of MHC gene copies. Figure modified from Minias et al. 2018 [103]. Key to species names is supplied in Supplementary Table S1.

Figure 3

Ancestral character estimation of gene copy number at MHC class IIB genes along the branches and nodes of a tree for birds. Bars associated with each terminal node indicate the estimated number of MHC gene copies. Figure modified from Minias et al. 2018 [103]. Key to species names is supplied in Supplementary Table S1.