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Endemic to Madagascar, their small and highly fragmented populations make them particularly vulnerable to both genetic disease and anthropogenic environmental changes. Over the past decade, conservation genomic efforts have largely focused on inferring and monitoring population structure based on single nucleotide variants to identify and protect critical areas of genetic diversity. However, the recent release of a highly contiguous genome assembly allows, for the first time, for the study of structural genomic variation (deletions, duplications, insertions, and inversions) which are likely to impact a substantial proportion of the species\u2019 genome. Based on whole-genome data from 14 individuals, &amp;gt;1,000 autosomal structural variants were detected, affecting \u223c240\u2005kb of the aye-aye genome. The majority of these variants (&amp;gt;85%) were deletions shorter than 200\u2005bp, consistent with the notion that longer structural mutations are often associated with strongly deleterious fitness effects. For example, two deletions longer than 850\u2005bp located within disease-linked genes were predicted to impose substantial fitness deficits owing to a resulting frameshift and gene fusion, respectively; whereas several other major effect variants outside of coding regions are likely to impact gene regulatory landscapes. Taken together, this first glimpse into the landscape of structural variation in aye-ayes will enable future opportunities to advance our understanding of the traits impacting the fitness of this endangered species, as well as allow for enhanced evolutionary comparisons across the full primate clade.<\/jats:p>","DOI":"10.1093\/gbe\/evaf167","type":"journal-article","created":{"date-parts":[[2025,8,27]],"date-time":"2025-08-27T11:44:29Z","timestamp":1756295069000},"source":"Crossref","is-referenced-by-count":5,"title":["The Landscape of Structural Variation in Aye-Ayes (<i>Daubentonia madagascariensis<\/i>)"],"prefix":"10.1093","volume":"17","author":[{"given":"Cyril J","family":"Versoza","sequence":"first","affiliation":[{"name":"Center for Evolution and Medicine, School of Life Sciences, Arizona State University , Tempe, AZ 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