I have a diverse interest in ecological topics and have outlined my main research projects below. For a full list of my publications please click here. I have had a good track record of securing funding – as well as being listed as a key person securing NZ$150,000 for lab-in-a-box, a mobile educational lab facility, I also secured a further c. NZ$100,000 for research costs during my research career to date (for a full list of funding awarded please click here). I have acted as a reviewer for Wildlife Society Bulletin, Wildlife Biology in Practice, Amphibia-Reptilia and for Molecular Ecology Resources multiple times.
As an undergraduate (Natural Science and Botany, Trinity College Dublin) I worked on mosses as part of the much larger Bioforest project (funded by COFORD and the EPA) under the supervision of Dr. Daniel Kelly. The focus of the research was to investigate how varying timber harvesting strategies affect moss diversity in plantation forests, in particular allowing dead logs and tree stumps to remain in place for a number of years when selectively harvesting trees. My project was a relatively small one, but I did come across a rare moss Daltonia splachnoides (listed as Near Threatened in Europe). Bringing this specimen to the attention of the Bioforest group sparked a host of further investigations into the distribution of the species and as a result the known range has since been extended. For more see Bosanquet et al. 2010 and Coote et al. 2008.
During my postgraduate diploma (Wildlife Management, Otago University) I researched the potential for translocating two endangered frog species to a new site. These were Hochstetter’s frog and Maud Island frog. The project included recording numerous habitat variables in optimal and suboptimal frog habitats and comparing those with potential target sites within a larger chosen translocation area. A number of suitable sites for each species were identified, with the conclusion that the area in general appears to be more suitable for Hochstetter’s frogs rather than Maud Island frogs.
These species are listed at No. 39 (Hochstetter’s frog) and No. 59 (Maud Island frog) on the amphibian Evolutionarily Distinct and Globally Endangered (EDGE) list. You can find the full report here. This project has since been furthered by a master’s student as part of Professor Phil Bishop’s frog lab.
Predators of endangered frogs
During my PhD (University of Otago) I investigated the usefulness of DNA diet analysis in assessing the impact of introduced mammals on New Zealand’s native endangered frogs, under the supervision of Professor Phil Bishop. These strange frogs, which form a sister group to all other frogs, are threatened by introduced mammals, but the extent to which they are being predated is largely unknown.
Following a few feeding trials involving dead introduced frogs and very much alive wild rats and hedgehogs, we quickly realised that simple kill-trapping and subsequent visual stomach analysis would not be enough to inform us further. This was because rats tended to avoid frog bones and preferred to only consume flesh. How then could we reliably detect whether a small mammal we trapped in the wild had recently eaten a frog, let alone determine which species of frog he had eaten?
We found the answer in DNA. This is where Dr. Bruce Roberston, conservation biologist and molecular ecologist, came on board as a co-supervisor. We designed primers to target frog DNA, while ‘ignoring’ all other DNA that may be present in gastrointestinal samples, increasing the prey detection rate from 2% to 70% in stomachs and from 0% to 53% in faeces.
In the field we found that ship rats are consuming both Hochstetter’s frog and Archey’s frogs, the latter is listed as No. 1 on the global amphibian EDGE list and appears to be getting consumed by rats at an alarming rate. This was the first study to measure prey DNA detection periods in mammalian stomachs, and the first to compare prey DNA detection periods in the stomachs and faeces of any vertebrates. Along with all the recent proliferation of research in this area, the study also goes some way toward finding the ‘holy grail’ of diet analysis – accurately estimating predation rates from diet data. There is a more complete story of this research here. The full PhD thesis is here.
Using a few samples from our colleagues in Australia, we also found that rats are predating frogs and lizards in urban areas – again it was only possible to pick this up using DNA-based diet analyses.
Following my PhD I worked with Professor David Wharton on nematodes sourced from Antarctica Panagrolaimus davidi, the only organism that can survive extensive intracellular freezing throughout its tissues, showing high survival even after exposure to -80 °C. DNA sequence from the lab culture strain, which has been in culture for over 2o years, yielded very different results when compared to DNA from individuals extracted from frozen antarctic soil samples. The two strains appear morphologically identical, although only females are present in the lab culture (reproducing parthenogenetically). It is possible that the culture strain is present at very low abundance in the field, but is selected during culture. An alternative is that the lab strain colonized Antarctica very recently, and this is somewhat supported by the fact that the culture strain is genetically more closely related to Panagrolaimus spp. from California (perhaps even arriving with early Antarctic explorers) , than to the Antarctic field strain – but this would not fully explain the striking morphological similarities.
We successfully reisolated both the field strain and the culture strain from old frozen soil samples, confirming that both are indeed present in the field. However, we were not able to directly detect the culture strain from soil extractions, despite assaying over 150 individual nematodes, perhaps suggesting that the culture strain is indeed very rare. The question on the culture strain’s origin remains and this work is ongoing in Prof. David Wharton’s lab.
Phytophthora spp. (Oomycetes) have long been recognised as major pathogens of agricultural crops, including having caused the failure of potato crops resulting in the Irish famine of the 1840s. In New Zealand Phytophthora agathidicida is infecting an iconic large tree species, the kauri. Forest Phytophthora species are generally not able to be removed from contaminated sites, and kauri dieback disease is currently incurably fatal. Animals are known to spread plant pathogens and feral pigs are one of the main species of large vertebrates present in kauri forests. I worked with Auckland Council, The New Zealand Institute for Plant & Food Research and several academic institutions to assess the potential for feral pigs to act as a vector for P. agathidicida through ingestion of infected plant material and subsequent defecation leading to infection of new hosts. Although we didn’t detect P. agathidicida, we did detect 5 other species of Phytophthora in feral pig gut samples, some of which are known to remain viable after passing through pig gastrointestinal tracts.
Phytophthora is also responsible for catastrophic effects in a diverse range of ecosystems, including sudden oak death, alder dieback, apple collar rot, strawberry root rot, beech mortality, chestnut ink disease, cypress root rot, yew dieback and many more. Recent work has highlighted the prevalence of Phytophthora in Ireland and its potential for serious biodiversity and economic harm. This is a taxon I continue to be interested in and I hope to be involved in research on Phytophthora in the future.
In 2014 I set up a long-term lizard monitoring programme at Orokonui Ecosanctuary, NZ. The aim of the project is to assess the degree to which lizard populations benefit from the absence of introduced mammalian predators, and also to use the programme as an education tool for visitors to the sanctuary. This project currently involves approximately 30 personnel, including volunteers, site staff, education staff and myself as an advisor.
After consultation with many experts in this area, as well as with site staff and the Department of Conservation I developed a research plan that currently has a 10-year permit, but hopefully will continue for a number of decades. The project design incorporates 20 transects of artificial cover objects (ACOs). Each transect is comprised of either ground ACOs (double-layers of onduline) or arboreal ACOs (closed-cell foam wraps). ACOs are checked fortnightly by volunteers over 5 months each year. We had a half-season in 2014/15 and two full seasons since and the results are encouraging with over lizards observations going from 14, to 57 to 136 of three lizard species. Hopefully over the coming years we will establish a baseline for the resident lizard population and from a conservation point of view it would be great to see a rise in abundance over time and possibly a few other species turning up.