Ecology research

Ecology models increasingly rely on rich genomic data, which has a complicated correlation structure due to shared ancestry, spatial and environmental history.

Hihi (stitchbirds)
Hihi (stitchbirds)

Modelling relationships accurately is core to progress in this area. The group generates genome-scale data sets and works with bioinformaticians and modellers to test hypotheses in ecology and evolution. 

Our research also extends to phylogeography, where we investigate phylogenetic inference for populations in a continuous landscape, and to Bayesian total evidence analyses, which incorporate diverse fossil, geological and morphological trait data to understand modern biodiversity.

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

New Zealand's endemic hihi (stitchbird) has been missing from the North Island mainland since 1882. However, conservation efforts have preserved the birds on predator-free islands and reserves such as Tiritiri Matangi Island in the Hauraki Gulf.

The project team are using data from this island population to create a genomics toolkit for the hihi; including designing a custom genotyping array. By carrying out quantitative trait linkage and association analysis, they hope to identify regions within the genome that influence morphological and reproductive traits.

They hope the genomic data might contribute to the conservation management of these birds in the future.

About the researchers

Dr Anna Santure
School of Biological Sciences

pestGENOME

Predator Free New Zealand aims to eradicate invasive rats, possums and mustelids from New Zealand by 2050.

Many existing molecular tools can assist in the management of these species. With the pestGENOME project, researchers are developing a genomic toolkit to aid scientists and managers in the research and management of these invasive mammals.

With a focus on invasive rodents (rats and mice), the team are collaborating nationally and internationally with research groups at the forefront of genomic resource development. They have applied the results to determine the phylogeography of invasive rodents in New Zealand and around the world.

About the researcher

Associate Professor James Russell
School of Biological Sciences

Evolution of cold tolerance in New Zealand stick insects

Thermal tolerance is a key determinant in the global distribution of biodiversity, yet the constraints on its evolution are not well understood.

This project investigates the parallel evolution of cold tolerance in New Zealand stick insects, across three montane-occurring (at or above the tree line) species.

Using a phylogeny constructed from 274 orthologous genes, the project team found that stick insects have independently colonized montane environments at least twice. The team compared supercooling point and survival of internal ice formation among ten species, from eight genera and were able to identify both freeze tolerance and freeze avoidance in separate montane lineages.

About the researcher

Associate Professor Thomas Buckley
School of Biological Sciences

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 Conservation, Auckland 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-metre elevational gradient.

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.

About the researchers

Professor Alexei Drummond
School of Biological Sciences

Associate Professor Thomas Buckley
School of Biological Sciences

Dr Walter Xie
Faculty of Science

Dr Andrew Dopheide 
Landcare Research

Dr Joseph Heled 
Max Planck Institute