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Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi

Published in: Molecular Ecology

Authors: Laura Duntsch, Annabel Whibley, Patricia Brekke, John G. Ewen & Anna W. Santure


Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.

You can access the paper here

Written by Dr John Ewen

I have been interested and working with hihi since I was involved with establishing the Tiritiri Matangi island population through translocation in 1995. I am now employed as a Research Fellow at the Zoological Society of London and have been here since 2004. My research is multi-disciplinary and focusses on small population biology and management. I use decision science to assist in planning hihi management and drive our applied research with this species and have experience in molecular and behavioural ecology, wildlife health and nutrition and reintroduction biology.


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