Genetic diversity, inbreeding and mean kinship
Consistent with our predictions, observed levels of genetic diversity
were significantly lower in King Island scrubits than in all Tasmanian
scrubtit subpopulations apart from the Tasman Peninsula. Interestingly,
the samples from the Tasman Peninsula exhibit the similar
within-population mean kinship values as those on King Island.
Relatively lower levels of genomic diversity are observed in many island
vertebrate populations, particularly on small islands as shown in
northern quolls Dasyurus hallucatus (von Takach et al. 2022) and
black-footed tree rats (Djintamoonga) Mesembriomys gouldii (von
Takach et al. 2023). Individual inbreeding coefficients and mean kinship
measures were also higher in the King Island scrubtit than in the
Tasmanian scrubtit but, against our predictions, inbreeding measures
(FIS) were lower for the Colliers Swamp and Nook Swamps
subpopulations than for all Tasmanian scrubtit subpopulations.
FIS detects non-random mating in the most recent
generation (Waples, 2015), so our lower-than-expected estimates for
these two King Island subpopulations could simply mean that these
individuals are not mating with close relatives. However, other results
— notably the reasonably high individual inbreeding coefficients
calculated from the modified Visscher’s method (Figure 5) — suggest
these unusually low FIS values may be explained by small
and / or sex-biased sampling and therefore requires further study.
Phenotypic evidence of defective traits in small, inbred populations is
likely to occur but not always noticed in wild systems (but see e.g.
Roelke et al. 1993 and Harrisson et al. 2019). Although unknown at this
time if it is a defective trait or not, over 50 % of King Island
scrubtits we sampled exhibited crown baldness (Figures 5 & S3).
Baldness was present in both sexes and all three King Island
subpopulations, but was not recorded in any Tasmanian scrubtits. The
probability of baldness was negatively associated with multi-locus
heterozygosity, but the relationship disappeared when we restricted the
analysis to the King Island population. It is possible that baldness may
be due to non-genetic effects such as endemic parasitism, disease,
inter/intraspecific aggression linked to low habitat availability or an
ageing population (Lachish et al. 2012; Thys et al. 2017; van Velden et
al. 2017). However, baldness was similar in all affected individuals
(Figure S3) and we found six candidate SNPs that may play a role in the
development or expression of this trait. One of these SNPs is associated
with the DOCK11 gene, a gene that has been linked to early feather
development in chickens (Figure S10; Table S7; Cheng et al. 2018).
Further investigation into the phenotype-genotype associations may be
able to determine the genetic and physiological pathways leading to
baldness.