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 endemic 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 genomics study of the King Island and Tasmanian scrubtit 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 separately. 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 effective size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.

TITLE : Genomic insights into a critically endangered island endemic songbird provide a roadmap for preventing extinction.RUNNING TITLE: King Island Scrubtit conservation genetics.AUTHORS : Ross Crates1¶, Brenton von Takach2, Catherine M Young1, Dejan Stojanovic1, Linda Neaves1, Liam Murphy1, Daniel Gautschi1, Carolyn J. Hogg3,4, Robert Heinsohn1, Phil Bell5, Katherine A. Farquharson3,4.1. Fenner School of Environment and Society, Australian National University, Linnaeus Way, Acton, Canberra 2601.2. School of Molecular and Life Sciences, Curtin University, Bentley, Perth, Western Australia 6102.3. The University of Sydney, School of Life and Environmental Sciences, NSW 2006, Australia4. Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW 2006, Australia5. Biological Sciences, School of Natural Sciences, University of Tasmania, Hobart, Tasmania, 7005, Australia¶Corresponding Author: ross.crates@anu.edu.auABSTRACT: 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 endemic subspecies of the nominate Tasmanian scrubtit Acanthornis magna 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 genomics study of the King Island and Tasmanian scrubtit 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 separately. 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 effective size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.

Giselle Owens1,4, Ana Gracanin2, Joanne Potts3, Catherine M. Young1, Robert Heinsohn1, Philip Gibbons1, Dejan Stojanovic1Fenner School of Environment and Society, Australian National University, Canberra, AustraliaCentre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong Australia, New South Wales, AustraliaThe Analytical Edge Statistical Consulting, Hobart, AustraliaCorresponding author: giselle.owens@anu.edu.auRunning Head: Detection and density estimation for a cryptic speciesKey Words: detection probability, spatially explicit capture-recapture, SECR, meta-analysis, literature review, bait, lure, Petaurus notatus , sugar glider, density

IntroductionCaptive animal phenotypes can diverge from the ideal ‘wild type’, and these changes can affect behavior, morphology and physiology (Crates et al. 2022). However, the specific nature and combination of ‘captive phenotypes’ can vary widely between species (Crates et al. 2022). Whether changes are important depends on the intended use of captive-bred animals. For display animals, phenotypic changes may be inconsequential. Conversely, conservation breeding programs – a globally popular tool to combat species extinctions (Conde et al.2011) – should ideally produce animals optimized for life in the wild after release, but this more easily said than done (Taylor et al.2017). If altered captive phenotypes incur a fitness cost in the wild, conservation breeding may be less effective than hoped (Crates et al. 2022). Thus, it is important that conservation breeding programs quantify optimal wild phenotypes, and be vigilant of changes arising from life in captivity that might jeopardize survival after release (Shier 2016; Berger-Tal et al. 2020).Phenotypic changes to traits involved in strenuous or high-risk phases of life history may be disproportionately important for fitness post release from captivity. For example, migration is a high-risk behavior that strongly selects for the most capable individuals (Dingle 2014; Rotics et al. 2016). Captive-born animals are often less successful migrants than wild-born conspecifics (Crates et al.2022). This is sometimes attributable to behavioral differences. For example, some captive-born birds depart later and travel shorter distances than wild conspecifics (Burnside et al. 2017), and captive-bred butterflies fail to orient themselves or even attempt migration (Tenger-Trolander et al. 2019). Morphological changes also likely contribute to poor migration outcomes post release, but evidence for their effects on fitness is surprisingly limited. Davis et al. (2020) recently showed that captive-bred monarch butterflies Danaus plexippus have differently shaped wings and lower migration success than wild conspecifics. Wing shape strongly predicts flight efficiency (Lockwood et al. 1998; Sheard et al.2020). Given that migratory birds are commonly bred in captivity for reintroduction (Davis 2010; Burnside et al. 2017; Hutchins et al. 2018; Stojanovic et al. 2020b; Tripovich et al. 2021), quantifying the ubiquity of deleterious captive wing shape phenotypes and their post-release fitness consequences is critical information.I aimed first to compare captive/wild wings of 16 species representing three commonly captive-bred bird families (Phasianidae, Psittacidae, Estrildidae) to evaluate the ubiquity of captive wing shape phenotypes. Then, using a critically endangered migratory bird as a model, I aimed to demonstrate that a captive wing shape phenotype incurs a fitness cost post release.