Conservation genetics of granivorous birds in a heterogeneous landscape: the case of the black-throated finch (Poephila cincta)

More than a third of granivorous birds have declined in Australia as a result of substantial landscape changes through grazing, altered fire regimes and land clearing for agricultural purposes. Understanding the genetic impact of the granivore decline is important to determine appropriate conservation management strategies because declining populations are vulnerable to negative genetic processes such as inbreeding depression, genetic bottlenecks and genetic drift, all of which could lead to decreased genetic diversity and reduced evolutionary potential. This thesis uses the threatened Black-throated Finch as a case study to investigate the importance of applying genetic information in the conservation of declining granivorous birds in Australia. Specifically, I developed 18 novel microsatellite markers using next generation sequencing technology for the Black-throated Finch and tested these for cross-species amplification success in two other co-occurring grass finch species, the Double-barred Finch (Taeniopygia bichenovii) and the Chestnut-breasted Mannikin (Lonchura castaneothorax) (Chapter III). Using these microsatellite markers, I then examined the genetic diversity and population structure of four major surviving populations of the Black-throated Finch in northern Queensland, Australia (Chapter IV). Fine-scale spatial genetic structuring was also analysed among individuals around a man-made dam in northern Queensland to determine the relationship between local heterogeneous landscapes that birds occupy and the genetic distance between individuals within tens of square kilometres (Chapter V). Last, I evaluated conservation values of the Black-throated Finch in captivity by comparing the genetic diversity, effective population sizes, inbreeding and relatedness between in situ and ex situ populations (Chapter VI). The sampled four, widely-dispersed wild populations of the Black-throated Finch had similar levels of genetic diversity. There was a significant separation between northern and southern subspecies based on genetic structuring analysis (between subspecies FCT = 0.034, p < 0.001). At the local scale, individual birds demonstrated strong spatial genetic structuring separated by the Ross River Dam in the Townsville region. Environmental Niche Modelling identified local landscape features such as vegetation structure and the presence of water as having a strong association with the occurrence of the Black-throated Finch. The individual genetic distance was weakly, but significantly correlated with the geographical distance (Mantel R = 0.081, p < 0.001) and the landscape resistance distance (Mantel R = 0.083, p < 0.001). Samples from captive birds showed significant differentiation from wild birds. Birds in captivity had significantly lower levels of genetic diversity (average H(O) = 0.35 among captive populations versus average HO = 0.45 in the wild; average r = 2.34 in captivity versus r = 3.08 in the wild); smaller effective population sizes; higher levels of inbreeding (F = 0.114 in the wild versus F = 0.216 in captivity) and more admixed genetic structuring compared with their wild counterparts. Results of my thesis have provided evidence that the northern and southern subspecies of the Black-throated Finch are genetically differentiated, but the differentiation is weak. The similar level of genetic diversity across all wild populations suggested that the genetic exchange was historically high among sampled populations despite demonstrated low levels of demographic connectivity and recent population declines. Fine-scale genetic analysis of birds around the Ross River Dam from the Townsville population demonstrated that current landscape features (an open lake in particular) and spatial separation had a combined effect on the genetic structure of the local Black-throated Finch population. In addition, birds in captivity have lost genetic variability to some degree and increased levels of inbreeding potentially may reduce the viability. However, birds descended from extinct wild populations are still maintained in captivity, providing potential genetic sources for future captive breeding programmes. Conservation management strategies should therefore 1) prioritise in situ approaches, such as frequent monitoring of population trends, identifying and maintaining existing suitable habitats, increasing the connectivity between suitable habitats by minimising dispersal barriers (large open waters, dense invasive plants and heavily grazed landscapes); and 2) consider the conservation values of captive birds (particularly birds with known origins) in establishing possible in situ breeding stocks if ex situ conservation strategies fail to increase the population viability.