title: Phylogeography, demography and recruitment in a widespread iconic Australian bird, Gymnorhina tibicen
Creators: name: McIntyre, Nathan D
Publisher: name: Griffith University
Year: 2022
Subjects: subject: Australian bird
subject: Gymnorhina tibicen
subject: environmental changes

description: With the advent of efficient and affordable sequencing technology, it has become increasingly viable to generate whole or reduced-representation genome sequence data for non-model organisms. The surfeit of genetic information contained in these datasets can be used in a wide range of studies. These include the assessment of genetic structure and diversity among contemporary populations, the investigation of past divergence events and demographic history, and the identification of variants or loci involved in adaptation. Not only do these insights afford us a greater understanding of the evolutionary history and likely future trajectory of a species, but they also allow us to inform conservation and wildlife management programs by identifying at-risk subpopulations and gauge the ability of a species to respond to environmental changes resulting from climate change or habitat loss. In this thesis, I investigate aspects of the population genetic structure and diversity of Gymnorhina tibicen, the Australian magpie, as well as phylogeographic relationships within the species and the impact that weather conditions have on the species’ ability to recruit new individuals. G. tibicen is an iconic member of the Australian avifauna, a medium-sized generalist passerine known for its characteristic ‘fluting’ call, stark black and white plumage, and aggressively territorial behaviour. Its distribution covers most of mainland Australia and Tasmania, as well as parts of Papua New Guinea, and has been recorded as an invasive species in New Zealand. Currently, the phylogeography &amp; demography of the Australian magpie has been examined using a single mitochondrial gene &amp; a small number of microsatellite loci. In Chapter 2, I use III genomic data to explore the structure, diversity, and biogeography of southern populations of Gymnorhina tibicen. I utilize restriction site-associated (RAD) sequencing to generate a dataset consisting of over 29,000 single nucleotide polymorphisms (SNPs) distributed over more than 15,000 loci. I detail the process of preparing the RADseq dataset, including the testing of parameters that influence the assembly of loci from raw reads. I then use the dataset to examine several hypotheses: that due to the influence of major biogeographic barriers across mainland Australia and Tasmania, reduced-representation genomic data would reveal clear structuring between eastern, western and Tasmanian populations of the Australian magpie, that the western group would be more structured and exhibit a more stable demographic history while the eastern would show signs of population expansion due to the more widespread temperate climate. I use ten populations of G. tibicen distributed across south-eastern and south-western Australia, including two populations from Tasmania. Tests for genetic clustering and fine-scale genetic structure among populations revealed a clear distinction between eastern, western and Tasmanian populations, with Tasmanian samples more closely related to the eastern mainland than western. Western populations also appear more differentiated from one another than those in the eastern cluster, supporting my initial hypothesis. Demographic analyses also suggested a greater rate of expansion in eastern mainland Australia, compared to the relatively stable western mainland. Previous phylogeographic studies of Gymnorhina tibicen made use of a single mitochondrial gene, but recent advances in sequencing technology make it possible to investigate phylogeographic relationships across entire mitogenomes to verify earlier results and increase the genetic resolution at which inferences are made. In Chapter 3, my goal was to assemble 60 whole mitochondrial genomes from specimens of G. tibicen across its distribution, and compare phylogenetic trees constructed from individual genes and complete + near-complete IV mitogenomes. Previously, a single attempt had been made to assemble a complete G. tibicen mitogenome from a museum eggshell specimen, which produced a near-complete sequence minus a repetitive area of the control region. In my study, five complete mitogenomes were assembled, with the remainder assembled into partial but near-complete sequences. Analysis of the mitogenomes assembled here revealed the same broad patterns of divergence between western and eastern halves of the Australian mainland, and closer relationship of the Tasmanian cluster to the eastern group than the western. This study incorporates new sampling locations into our understanding of the phylogeography of G. tibicen, and most notably suggests that the ‘eastern’ group may extend further west across the arid interior than previously identified. The results here also demonstrate the efficacy and improved resolution of phylogeographic analyses when whole mitogenomes are used in lieu of single genes. Long-term ecological datasets are often difficult to produce, but are invaluable when estimating the impact of changing environmental conditions on native wildlife. In Chapter 4, I analyse recruitment data collected over 25 years as part of a long-term territory monitoring study. Birds from over 200 territories were banded and monitored twice yearly, with a range of observations and biological samples taken. I have taken one aspect of the collected data, the number of new juveniles observed in each territory annually, and investigated how recruitment is influenced by variation in local weather conditions over the course of the year preceding the breeding season. I conclude that Gymnorhina tibicen appears relatively robust in the face of annual variation in weather and adverse conditions such as drought, though lower levels of precipitation in the leadup to the breeding season are linked to lower numbers of juveniles recruited per territory. I tentatively suggest that this is result of reduced 85 invertebrate abundance and therefore reduced foraging opportunities, impacting the reproductive health of individuals. Overall, genomic studies of the Australian magpie still have much to offer, particularly in the investigation of demographic history and the identification of regions under selection. Principal recommendations for building on the questions covered in this study are a more thorough sampling regime, both in total number of samples and their spatial resolution across G. tibicen’s distribution.