Models in ecology increasingly rely on rich genomic data which has a complex correlation structure due to shared ancestry, spatial and environmental history.

Modelling these relationships accurately is core to progress in this area. The group generates genome scale data set and works with bioinformaticians and modellers to test key hypotheses in ecology and evolution. Our research also extends to phylogeography where we investigate phylogenetic inference for populations spreading in a continuous landscape, and to Bayesian total evidence analyses which incorporate diverse fossil, geological and morphological trait data to understand modern biodiversity.

Projects in this area include:

Exploring the adaptive potential of hihi (stitchbird, Notiomystis cincta)

Hihi collage1

Hihi are an endemic New Zealand forest bird last seen on the North Island mainland in 1882. As part of their conservation management program, the birds have been moved to predator-free islands and reserves including the Tiritiri Matangi Open sanctuary in the Hauraki Gulf just north of Auckland.

Our project is to create a genomics toolkit for the hihi, including designing a custom genotying array. We will carry out quantitative trait linkage and association analysis to identify regions of the genome that influence morphological and reproductive traits, based on data and samples collected from the Tiritiri Matangi population. We also hope to explore ways in which the genomic data we will generate might contribute to conservation management of these birds in the future, including managing the metapopulation across different sanctuaries and assessing their adaptive potential.

Researchers: Dr Anna Santure



Predator Free New Zealand seeks to eradicate invasive rats, possums and mustelids from New Zealand by 2050. Existing molecular tools can assist management of these species today, e.g. SNPs facilitate advanced wildlife forensics to monitor invasions, while a genomic understanding of these pest species may reveal hitherto unknown modes of action by which to eradicate these pest species, such as through siRNA or gene-editing. The pestGENOME project seeks to advance the genomic toolkit available to scientists and managers to facilitate the research and management of the invasive mammals targeted by Predator Free New Zealand. The project currently focuses on invasive rodents (rats and mice) and collaborates nationally and internationally with those research groups at the forefront of developing genomic resources for invasive mammal control, and applies these results to determining the phylogeography of invasive rodents in New Zealand and around the world.

Researcher: Dr James Russell



Evolution of cold tolerance in New Zealand stick insects

Fig 3 Heatmap 17genes DENNIS ET AL 2015

The acquisition of physiological strategies to tolerate novel thermal conditions allows organisms to exploit new environments. As a result, thermal tolerance is a key determinant of the global distribution of biodiversity, yet the constraints on its evolution are not well understood. Here we investigate parallel evolution of cold tolerance in New Zealand stick insects, an endemic radiation containing three montane (at or above the tree line)-occurring species. Using a phylogeny constructed from 274 orthologous genes, we show that stick insects have independently colonized montane environments at least twice. We compare supercooling point and survival of internal ice formation among ten species from eight genera, and identify both freeze tolerance and freeze avoidance in separate montane lineages.

Freeze tolerance is also verified in both lowland and montane populations of a single, geographically widespread, species. Transcriptome sequencing following cold shock identifies a set of structural cuticular genes that are both differentially regulated and under positive sequence selection in each species. However, while cuticular proteins in general are associated with cold shock across the phylogeny, the specific genes at play differ among species. Thus, while processes related to cuticular structure are consistently associated with adaptation for cold, this may not be the consequence of shared ancestral genetic constraints.

Paper: Dennis, A. B., Dunning, L. T., Sinclair, B. J., Buckley, T. R. (2015) Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects  Scientific Reports, 5:13965 doi: 10.1038/srep13965

Researcher: Associate Professor Thomas Buckley


Biodiversity assessment of Little Barrier Island

New Zealand Genomic Observatory project aims to produce a comprehensive phylogenetic and environmental characterization of the terrestrial species in a well-defined New Zealand model ecosystem using modern sequencing, informatics, niche modelling and field ecology approaches. The project is a collaboration between several universities and research centres in New Zealand and Australia, the Department of ConservationAuckland Council, and iwi, and internationally as part of the Network of Genomic Observatories. It also aims to provide a long-term research program structure for collaborative, interdisciplinary research projects at the intersection of ecology, evolutionary biology and genomics. 

In this study, samples of an elevated series of soils were taken from 5 regions of Little Great Barrier Island. We evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient.

From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures.

Using a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods.

Paper: Drummond, A.J., Newcomb, R. D., Buckley, T. R., Xie, D., Dopheide, A., Potter, B. C. M., Heled, J., Ross, H. A., Tooman, L., Grosser, S., Park, D., Demetras, N. J., Stevens, M. I., Russell, J. C., Anderson, S. H., Carter, C., Nelson, N. (2015) Evaluating a multigene environmental DNA approach for biodiversity assessment GigaScience 4:46 doi: 10.1186/s13742-015-0086-1

Researchers: Professor Alexei Drummond, Professor Richard Newcomb, Associate Professor Thomas Buckley, Dr Walter Xie, Andrew Dopheide

Our more projects about eDNA can be seen here