Genomic insights into the critically endangered King Island scrubtit

Small, fragmented or isolated populations are at risk of population
decline due to fitness costs associated with inbreeding and genetic drift.
The King Island scrubtit Acanthornis magna greeniana is a critically
endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with
an estimated population of < 100 individuals persisting in three
patches of swamp forest. The Tasmanian scrubtit is widespread in wet
forests on mainland Tasmania. We sequenced the scrubtit genome using
PacBio HiFi and undertook a population genomic study of the King Island
and Tasmanian scrubtits using a double-digest restriction site-associated
DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long,
comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits
formed one of four overall genetic clusters, but separated into three
distinct subpopulations when analysed independently of the Tasmanian
scrubtit. Pairwise FST values were greater among the King Island scrubtit
subpopulations than among most Tasmanian scrubtit subpopulations. Genetic
diversity was lower and inbreeding coefficients were higher in the King
Island scrubtit than all except one of the Tasmanian scrubtit
subpopulations. We observed crown baldness in 8/15 King Island scrubtits,
but 0/55 Tasmanian scrubtits. Six loci were significantly associated with
baldness, including one within the DOCK11 gene which is linked to early
feather development. Contemporary gene flow between King Island scrubtit
subpopulations is unlikely, with further field monitoring required to
quantify the fitness consequences of its small population size, low
genetic diversity and high inbreeding. Evidence-based conservation actions
can then be implemented before the taxon goes extinct.