High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice.

Martin Stervander,Helena Westerdahl,Jack Thorley,M De L Brooke,Elisa G Dierickx

doi:10.1111/mec.15471

Abstract

Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso lark Alauda razae, a species restricted to the 7km2 islet of Raso, Cape Verde, since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by cosegregation of multiple haplotypes comprising 2-8 linked MHC-I loci. Within-locus homozygosity is high, contributing to low population-wide diversity. Conversely, each individual had comparably many alleles, 6-16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species' adaptive potential.

Highlights

Islands have intrinsic geographic characteristics that underlie the exacerbated genetic threats to insular species
From a total of 130 samples, including eight technical replicates, we identified 22 major histocompatibility complex (MHC)-I alleles (Figure 1; Table S3; Supporting Information 3), many of which were present at high levels in the sampled population (Figure 1b), and several of which co-occurred within individuals (Figure 1c)
The explanation for the discrepancy between population and within-individual estimates is that the within-locus genetic diversity is low, as shown by a high degree of homozygosity, whereas the gene copy number is high

Summary

| Introduction

Islands have intrinsic geographic characteristics (isolation, small area) that underlie the exacerbated genetic threats to insular species. The maintenance of genetic diversity is crucial for fitness and survival, at the individual, population and species level (Richard Frankham, Ballou, & Briscoe, 2002). This suggests that confining species to small refugia reduces the rate of microevolution, which could limit the species’ ability to adapt to environmental changes (Tollington et al, 2013; Wright et al, 2009) It is on one of these small island refugia, the uninhabited 7 km islet of Raso (16° N 24° W), that the Critically Endangered Raso lark Alauda razae survives. Given the high risk of inbreeding that Raso larks face (Dierickx, Sin, et al, 2019), individuals are under strong selective pressure to develop a mating strategy that maximizes the genetic diversity of their future offspring. We test if there is an assortative MHC-I based mate choice and investigate whether MHC-I genetic diversity is associated with survival

| Material and Methods

| Evaluation and selection of primers

| Results

| Discussion

| Conclusions