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

Citation

Duntsch, Laura et al. (2020), Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi (Notiomystis cincta), Dryad, Dataset, https://doi.org/10.5061/dryad.98sf7m0g1

Abstract

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.

Methods

Information on data collection and processing can be found in the Methods section of the article.

Usage Notes

.phen

Phenotypic data in RepeatABEL format for the individuals used in the article. More info in the README.txt file.

.tfam

Family data in a standard PLINK format for the individuals used in the article. More info in the README.txt file.

.tped

Genotype data in a standard PLINK format for the individuals used in the article. More info in the README.txt file.

.R

R scipt with main settings used to retrieve heritability from MCMCglmm output (including partitioning among chromosomes) and full R code to perform a GWAS in RepeatABEL, including the model.

Funding

New Zealand National Science Challenge Biological Heritage Project, Award: Project 1.4

Royal Society of New Zealand, Award: Marsden Fund UOA1408

University of Auckland, Award: University of Auckland Doctoral Scholarship

Zoological Society of London, Award: ZSL Fellowship

New Zealand National Science Challenge Biological Heritage Project, Award: Project 1.4