Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi (Notiomystis cincta)

To predict if a threatened species can adapt to changing selective
pressures, it is crucial to understand the genetic basis of adaptive
traits, especially in species historically affected by severe bottlenecks.
We estimated the heritability of three hihi (Notiomystis cincta)
morphological traits known to be under selection: nestling tarsus length,
body mass and head-bill length, using 523 individuals and 39,699 single
nucleotide polymorphisms (SNPs) from a 50K Affymetrix SNP chip. We then
examined the genetic architecture of the traits via chromosome
partitioning analyses and genome-wide association scans (GWAS).
Heritabilities estimated using pedigree relatedness or genomic relatedness
were low. For tarsus length, the proportion of genetic variance explained
by each chromosome was positively correlated with its size, and more than
one chromosome explained significant variation for body mass and head-bill
length. Finally, GWAS analyses suggested many loci of small effect
contributing to trait variation for all three traits, although one locus
(a SNP within an intron of the transcription factor HEY2) was tentatively
associated with tarsus length. Our findings suggest a polygenic nature for
the morphological traits, with many small effect size loci contributing to
the majority of the variation, similar to results from many other wild
populations. However, the small effective population size, polygenic
architecture and already low heritabilities suggest that both the total
response and rate of response to selection are likely to be limited in
hihi.