Is the Sunda-Sahul floristic exchange ongoing? A study of distributions, functional traits, climate and landscape genomics to investigate the invasion in Australian rainforests By Jia-Yee Samantha Yap Bachelor of Biotechnology Hons. A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 Queensland Alliance for Agriculture and Food Innovation i Abstract Australian rainforests are of mixed biogeographical histories, resulting from the collision between Sahul (Australia) and Sunda shelves that led to extensive immigration of rainforest lineages with Sunda ancestry to Australia. Although comprehensive fossil records and molecular phylogenies distinguish between the Sunda and Sahul floristic elements, species distributions, functional traits or landscape dynamics have not been used to distinguish between the two elements in the Australian rainforest flora. The overall aim of this study was to investigate both Sunda and Sahul components in the Australian rainforest flora by (1) exploring their continental-wide distributional patterns and observing how functional characteristics and environmental preferences determine these patterns, (2) investigating continental-wide genomic diversities and distances of multiple species and measuring local species accumulation rates across multiple sites to observe whether past biotic exchange left detectable and consistent patterns in the rainforest flora, (3) coupling genomic data and species distribution models of lineages of known Sunda and Sahul ancestry to examine landscape-level dynamics and habitat preferences to relate to the impact of historical processes. First, the continental distributions of rainforest woody representatives that could be ascribed to Sahul (795 species) and Sunda origins (604 species) and their dispersal and persistence characteristics and key functional characteristics (leaf size, fruit size, wood density and maximum height at maturity) of were compared. Sunda species richness decreased with increasing latitude but maintained high levels of endemism, including in the south, and comparative functional analyses suggest that Sunda-derived lineages are on average more skewed towards more efficient dispersal and faster growth than Sahul- derived lineages. Studying distributional patterns at finer scale also revealed the influence of two highly correlated environmental factors on both ancestries: temperature and altitude, and the local distribution of invading lineages was shown to be resisted in stable, saturated communities of Sahul lineages. Next, whole-chloroplast genome sequencing was used to measure diversities and distances across multiple, common rainforest species of differing ancestry in the Tropics and Subtropics, and from within, a smaller sample of species was investigated across both regions to study landscape connectivity. A recent framework that explores the timing and rate of accumulation of co-occurring species at each study site was applied to the genetic data to study how species of distinct biogeographic histories accumulate locally. Also, floristic composition within Tropics and Subtropics plots were included in the study to investigate the role of biogeographical and ecological processes ii and landscape characteristics in determining Sunda and Sahul species distributions. Species of Sunda ancestry displayed consistently lower chloroplast genomic diversity than Sahul ancestry, with recent accumulation rates for Sunda species being measured across all sites, confirming recent arrival and expansion across eastern Australia. Sunda-derived species with continuous distributions exhibited the highest diversity at the most northerly sampled site, suggesting a north to south colonisation process. The same species however, differed in the levels of genomic divergence between the Tropics and Subtropics, suggesting that continental expansion occurs at different temporal scales, with some species experiencing a northern time lag before a southern expansion along the east coast of Australia. Genome-wide nuclear markers wer used to study the landscape-level genetic patterns of Doryphora sassafras of Sahul ancestry and Toona ciliata of Sunda ancestry across their shared distributional range in New South Wales. Population genomic patterns were supported by predicting availability of habitat during the Last Glacial Maximum (LGM), mid-Holocene (MH) and current periods using environmental niche modelling (ENM). Future (2070) habitat models were also developed to make predictions on the impact of anthropogenic climate change. D. sassafras exhibited high levels of north / south genomic divergence and higher genomic diversity at higher latitudes, whereas T. ciliata showed landscape-level homogeneity of genomic diversity, indicating differential responses to past climate involving long-term persistence vs. recent invasion. Habitat suitability models provided independent support for species differences across landscape, and further predicted T. ciliata had a recent rapid expansion that took place in the mid-Holocene, 6,000 ybp suggesting the species may not have adjusted its distributional range to current climatic conditions yet. These findings show biogeographic history, together with functional attributes and local habitat are important determinants of Australian rainforest species’ distribution and assembly at local as well as continental scales. Additionally, the genomic patterns confirm the recent and rapid expansion of Sunda-derived lineages across the Australian landscape, revealing insights into the timing, mode and pace of the expansion. This study demonstrates how the study of species distributions, functional characteristics and genetic variation can provide insights into the current distribution and assembly of flora at a specific biogeographic region of floristic exchange. It is anticipated that the outcomes of this study will lead to (1) reciprocal studies across Southeast Asia to investigate floristic origins and drivers of intercontinental exchange, (2) distribution-wide investigations to better understand the factors (e.g. environmental factors, biotic interactions, species attributes) that drive invasion, range expansion and long-term persistence, (3) a new set of conservation priorities for Australian rainforests that considers species’ biogeographic history. iii Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. iv Publications included in this thesis Yap, J. S., Rossetto, M., Costion, C., Crayn, D., Kooyman, R. M., Richardson, J., & Henry, R. J. (2018). Filters of floristic exchange: How traits and climate shape the rain forest invasion of Sahul from Sunda. Journal of Biogeography, 45, 838-847. – Incorporated as Chapter 2 Contributor Statement of contribution Conception and design (75%) Data collection (20%) Yap, J. S. (Candidate) Analysis and interpretation (75%) Wrote the paper (90%) Edited the paper (40%) Conception and design (20%) Rossetto, M. (Supervisor) Analysis and interpretation (20%) Wrote the paper (10%) Edited the paper (10%) Costion, C. Data collection (20%) Edited the paper (10%) Crayn, D. Data collection (20%) Edited the paper (10%) Conception and design (5%) Kooyman, R. M. Data collection (20%) Analysis and interpretation (5%) Edited the paper (10%) Richardson, J. Data collection (20%) Edited the paper (10%) Henry, R. J. Edited the paper (10%) v Submitted manuscripts included in this thesis Yap, J. S., van der Merwe, M., Ford, A., Rossetto, M., & Henry, R. J. (Under review) Biotic exchange leaves detectable patterns in the Australian rainforest flora. Biotropica. – Incorporated as Chapter 3 Contributor Statement of contribution Conception and design (65%) Field work (50%) Yap, J. S. (Candidate) Lab work (100%) Analysis and interpretation (80%) Wrote the