- Evolutionary ecology research
- Australian rainforest - evolutionary ecology
- Australian rainforest through time
- Biodiversity adaptation transect
- Botany of Botany Bay
- Ceratopetalum - Phylogenetic relationships
- Conservation genetics
- Ecology of Cumberland Plain Woodland
- Eucalypts: adaptive variation vs vicariance
- Floristic Lists of NSW
- Habitat fragmentation
- Isopogon prostratus - ecology
- Liverpool Plains grasslands
- Native plants of Sydney Harbour NP
- Newnes Plateau Shrub Swamps
- Plants of the Newnes Plateau
- Plants, vegetation, landscape, country
- Podocarpus elatus - rainforest conifer
- Post-glacial range shift
- Proteaceae - natural hybridisation
- Proteaceae - shifting species boundaries
- Proteaceae - speciation
- Rainforest diversity
- Testing speciation models
- Horticultural research
- Plant diversity research
- Plant pathology research
- Herbarium & resources
- Scientific publications
- Restore & Renew NSW
Australian rainforest - evolutionary ecology
Bicentenary Rainforest project
Hannah McPherson & Marlien van der Merwe - Post Doctoral Fellows
A multispecies landscape-level study of population dynamics among diverse functional groups can reveal contrasting responses to environmental change. Chloroplast DNA provides useful information to investigate phylogeographic patterns across plants, particularly when traditional approaches cannot always identify sufficient levels of variation for interpretation.
Next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies by providing high quantity and quality data at low cost. We developed a simple bioinformatic method of extracting whole chloroplast DNA and identifying variable sites that provide information to investigate how plants have responded to environmental change in the past (McPherson et al. 2013). We completed a pilot study in which we applied our method to 13 Australian rainforest species (see picture at right). Samples were collected from two regions representing northern and southern NSW.
Most species tested (with the exception of two low-diversity trees) displayed considerably greater diversity in the northern region than in the southern Sydney region (76.3% vs. 23.7% average diversity respectively). This confirms the Nightcap / Border Ranges rainforests as important long-term refugial areas, even for species found in cooler rainforest types. Our findings suggest that southern rainforests have been less stable and have endured periods when their distribution has been reduced followed by recurrent re-colonisation from the north.
This pilot study demonstrated that it is possible to considerably reduce costs of sequencing, and its success encouraged us to expand our studies. Further collections were made from over 100 Australian rainforest tree species from five regions representing the eastern distribution of Australian rainforests. DNA was extracted from 84 species (representing 64 genera and 36 families), and prepared for whole genome sequencing was conducted at the Ramaciotti Sequencing Centre (UNSW) and was financially supported by Bioplatforms Australia Ltd.
Bio-informatic analyses aimed at studying the evolutionary ecology of the Australian rainforest are currently underway. A combination of genetic and functional trait data of multiple species will enable a critical understanding of what are the major factors impacting on the distribution and assemblage of Australian rainforest trees, and recognise differences in susceptibility to threats and change occurring now and into the future.
A summary of the whole choloroplast DNA variation results of nine rainforest species obtained from whole genome shotgun sequencing. The number of variable SNPs within a population is indicated by the numbers in red circles while between region SNP variation is indicated in the yellow boxes (McPherson et al. in prep).