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Inbreeding may be negatively associated with fitness traits like survival and reproduction, that is, inbreeding depression, and is therefore detrimental to population persistence and adaptive potential. Realised genetic load\u2014the count of homozygous deleterious alleles\u2014is increasingly used as a proxy for fitness when investigating inbreeding depression. However, assessing the limitations of genetic load in predicting fitness, and comparisons with other homozygosity and inbreeding metrics, are needed. Our study system is the hihi\/stitchbird (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Notiomystis cincta<\/jats:italic>\n                    <\/jats:styled-content>\n                    ), a forest bird endemic to Aotearoa, New Zealand. The hihi was extirpated from the North Island in the late 1800s and underwent a prolonged bottleneck on an island before reintroduction efforts began in 1980. In this study, we used imputed whole\u2010genome resequencing data of over 400 individuals spanning two decades from Tiritiri Matangi, the largest reintroduced population. We quantified inbreeding using runs of homozygosity (ROH), annotated variants using variant effect predictor, and detected variants related to lifetime reproductive success (LRS) through a genome\u2010wide association study (GWAS). We then tested for inbreeding depression by modelling LRS against genome\u2010wide homozygosity, homozygosity in coding regions, inbreeding (F\n                    <jats:sub>ROH<\/jats:sub>\n                    ) and realised load. We found moderately high inbreeding levels in the hihi (mean F\n                    <jats:sub>ROH<\/jats:sub>\n                    = 0.27). GWAS revealed two variants associated with LRS that are in or near genes associated with laying performance and yolk weight in other birds. We found genome\u2010wide homozygosity to best predict fitness, although F\n                    <jats:sub>ROH<\/jats:sub>\n                    may be more useful at lower SNP densities. A relationship between realised genetic load and fitness likely reflects genome\u2010wide homozygosity levels, and high\u2010impact SNPs may present a misleading proxy for fitness. Our study provides support for genetic exchange to reduce inbreeding levels and contributes to a greater understanding of small population genetics and measures of inbreeding depression.\n                  <\/jats:p>","DOI":"10.1111\/eva.70252","type":"journal-article","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T08:03:08Z","timestamp":1779350588000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome\u2010Wide Homozygosity Predicts Inbreeding Depression in the Hihi\/Stitchbird (\n                    <i>Notiomystis cincta<\/i>\n                    ) Better Than Realised Load"],"prefix":"10.1111","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6750-7506","authenticated-orcid":false,"given":"Hui Zhen","family":"Tan","sequence":"first","affiliation":[{"name":"School of Biological Sciences University of Auckland  Auckland New Zealand"},{"name":"Centre for Computational Evolution 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