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Stéphane Boyer's Research

Molecular diet analyses

Using modern genomics to decipher species interactions

Diet Analyses
One  of my main interest is to use molecular methods to analyse trophic interactions. My research projects in molecular diet analyses include the study of the diet of seabird (westland black petrels, black backed sea gulls and gannets), invertebrates (snails, wētā, scarabs and cephalopods), as well the multi-trophic interactions between aphids, parasitoids and hyperparasitoids. Many of these projects are on-going, below is the list of the papers I have co-authored on this subject.
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  • Nboyine J.A., Boyer S., Saville D., Cruickshank R.H., Wratten S.D. (2019) Identifying plant DNA in the faeces of a generalist insect pest to inform trap cropping strategy. Agronomy for Sustainable Development, 39(6), 39-57. URL PDF

  • Lefort M.-C., Wratten S.D.; Cusumano A., Varennes Y.-D. Boyer S. (2017) Disentangling higher trophic level interactions in the cabbage aphid food web using high-throughput DNA sequencing. Metabarcoding & Metagenomics, 1: e13709.

  • Olmos-Pérez L., Roura A., Pierce G.J., Boyer S., Gonzàlez A.F. (2017) Diet composition and variability of wild Octopus vulgaris and Alloteuthis media (Cephalopoda) paralarvae through a metagenomic lens. Frontiers in Physiology, 8: 321.

  • Boyer S., Snyder W.E., Wratten S.D. (2016) Editorial: Molecular and isotopic approaches to food webs in agroecosystems. Food Webs, 9, 1-3.

  • Gonzales-Chang M.A.G, Wratten S.D., Lefort M.-C., Boyer S. (2016) Food webs and biological control. A review of molecular tools used to reveal trophic interactions in agricultural systems. Food Webs, 9, 4-11.

  • Boyer S., Cruickshank R.H., Wratten S.D. (2015) Faeces of generalist predators as ‘biodiversity capsules’: a new tool for biodiversity assessment in remote and inaccessible habitats. Food Webs, 3, 1-6.

  • Waterhouse B., Boyer S., Wratten S.D. (2014) Pyrosequencing of prey DNA in faeces of carnivorous land snails to facilitate ecological restoration and relocation programmes. Oecologia. 175 (2), 737-746.

  • Varennes Y.-D., Boyer S., Wratten S.D. (2014) Un-nesting DNA Russian dolls – The potential for rapid construction of food webs using residual DNA in empty aphid mummies. Molecular Ecology, 23 (15), 3925–3933.

  • Boyer S., Wratten S.D., Holyoake A., Abdelkrim J., Cruickshank R.H. (2013) Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms. PLoS One, 8(9), e75962.

  • Boyer S., Brown, S.D.J. Collins R.A., Cruickshank R.H., Lefort M.-C.D., Malumbres-Olarte J., Wratten S.D. (2012) Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA. PLOS One, 7(5), e38215. 

  • Boyer S., Yeates G.W., Wratten S.D., Holyoake A., Cruickshank R.H. (2011) Molecular and morphological analyses of faeces to investigate the diet of earthworm predators: example of a carnivorous landsnail endemic to New Zealand. Pedobiologia, 54S, S153–S158.

Powelliphanta is a genus of giant carnivorous snails endemic to New Zealand

Snail Conservation
I have worked on the conservation of Powelliphanta snails since 2007. In particular, I was involved in the conservation efforts to save Powelliphanta augusta, a rare species, whose natural habitat was located in the footprint of an opencast coal mine in New Zealand.
In collaboration with colleagues from Lincoln University, including postgraduate students, I have informed the conservation plans for that species in particular with respect to its diet and its husbandry conditions.
Our work is available in the following references.
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  • Waterhouse B., Boyer S., Wratten S.D. (2014) Pyrosequencing of prey DNA in faeces of carnivorous land snails to facilitate ecological restoration and relocation programmes. Oecologia. 175 (2), 737-746.

  • Boyer S., Wratten S.D., Holyoake A., Abdelkrim J., Cruickshank R.H. (2013) Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms. PLoS One, 8(9), e75962.

  • Boyer S., Yeates G.W., Wratten S.D., Holyoake A., Cruickshank R.H. (2011) Molecular and morphological analyses of faeces to investigate the diet of earthworm predators: example of a carnivorous landsnail endemic to New Zealand. Pedobiologia, 54S, S153–S158.

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Also see Mark Hamilton's Master thesis: Monitoring Powelliphanta land snails: an assessment of the current technique and the development of a new mark-recapture technique
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REstoration
of native ecosystems

To conserve endangered species, sometimes we first need to re-create their ecosystems

Restoration
I have worked with a number of mining companies in New Zealand including Solid Energy New Zealand Limited, Rio Tinto Limited and Bathurst Buller Coal. The aim of my work was to better understand the impact of opencast mining on native ecosystems, particularly on invertebrates, and how can we minimise or repair the damage caused by mining and other human activities. Most of this work was conducted with colleagues and students from Lincoln University.
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  • Boyer S., Case B.S., Lefort M.-C. Waterhouse B.R., Wratten S.D. (2016) Can ecosystem-scale translocations mitigate the impact of climate change on terrestrial biodiversity? Promises, pitfalls, and possibilities [version 1; referees: 2 approved]. F1000Research 2016, 5:146.

  • Bowie M.H., Black L., Boyer S., Dickinson N.M., Hodge S. (2016) Vulnerability and resilience of a natural vegetation remnant within an intensive dairy farm landscape in New Zealand. New Zealand Journal of Ecology, 40(1), 121-130.

  • Smith C., Bowie M.H., Hahner J.L., Boyer S., Kim Y.-N., Zhong H.-T., Abbott M., Rhodes S.H., Sharp D., Dickinson N. (2016) Punakaiki Coastal Restoration Project: a case study for a consultative and multidisciplinary approach in selecting indicators of restoration success for a sand mining closure site, West Coast, New Zealand. CATENA, 136, 91–103.

  • Boyer S. (2014) Fauna in decline: The community way. Science, 346, 821–821.

  • Waterhouse B., Adair K.L., Boyer S., Wratten S.D. (2014) Advanced mine restoration protocols facilitate early recovery of soil microbial biomass, activity and functional diversity. Basic and Applied Ecology. 15(7), 599-606.

  • Waterhouse B., Boyer S., Adair K.L. Wratten S.D. (2014) Using municipal biosolids in ecological restoration: what is good for plants and soil may not be good for endemic earthworms. Ecological Engineering, 70, 414-421.

  • Waterhouse B., Boyer S., Wratten S.D. (2014) Pyrosequencing of prey DNA in faeces of carnivorous land snails to facilitate ecological restoration and relocation programmes. Oecologia. 175 (2), 737-746.

  • Impact of mining rehabilitation on soil fauna: example of endemic earthworms in a New Zealand coal mine. Pedobiologia, 54S, S99–S102.

  • Boyer S., Wratten S.D. (2010) The potential of earthworms to restore ecosystem services after opencast mining - A review. Basic and Applied Ecology, 11: 196–203.

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Also see Benjamin Waterhouse's PhD thesis: Conserving New Zealand’s endemic carnivorous land snail Powelliphanta patrickensis through restoration of a functioning ecosystem

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NZ endemic earthworms

A poorly known group, yet very rich and essential to NZ ecosystems

NZ earthworms
Despite what we usually picture, biodiversity does not stop on the surface of the ground. Earthworm diversity for example is comparable to bird diversity in New Zealand with about 200 species described of which 179 are endemic. These very diverse communities find food and shelter beneath our feet, where they have a fundamental role in the recycling of organic matter, the formation of soils and the foodweb of New Zealand ecosystems. Despite these essential ecological functions little is known about endemic earthworms in New Zealand. I have been studying earthworms since 2007 and have dug tons of soil particularly across New Zealand's South Island to learn about them. With the help of many colleagues and students, we have published a number of papers, which provide some insight into their ecology.
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  • Kim Y.-N., Dickinson N., Bowies M., Robinson B., Boyer S. (2017) Molecular identification and distribution of native and exotic earthworms in New Zealand human-modified Soils. New Zealand Journal of Ecology, 41(2): 218-225.

  • Kim Y.-N., Robinson B., Horswell J., Boyer S., Dickinson N. (2017) Biochemical impacts of endemic Maoridrilus earthworms (Megascolecidae) in biosolids-amended soil. Journal of Environmental Quality, 46, 177-184.

  • Kim Y.-N., Robinson B., Lee K.-A., Boyer S., Dickinson N. (2017) Interactions between earthworm burrowing, growth of a leguminous shrub and nitrogen cycling in a former agricultural soil. Applied Soil Ecology,  110, 79–87.

  • Boyer S., Kim Y.-N., Bowie M.H., Lefort M.-C., Dickinson N.M. (2016) Response of endemic and exotic earthworm communities to ecological restoration. Restoration Ecology, 24 (6), 717-721.

  • Kim Y.-N., Robinson B., Boyer S., Zhong H.-T., Dickinson N. (2015) Native, exotic and novel: earthworms, soils and plants in New Zealand’s production landscapes. Applied Soil Ecology, 96, 141-150.

  • Boyer S., Blakemore R.J. Wratten S.D. (2011) An integrative taxonomic approach to the identification of three new New Zealand endemic earthworm species (Acanthodrilidae, Octochaetidae: Oligochaeta). Zootaxa, 2994, 21–32.

  • Boyer S., Wratten S.D., Pizey M., Weber P. (2011) Impact of mining rehabilitation on soil fauna: example of endemic earthworms in a New Zealand coal mine. Pedobiologia, 54S, S99–S102.

  • Boyer S., Wratten S.D. (2010) The potential of earthworms to restore ecosystem services after opencast mining - A review. Basic and Applied Ecology, 11: 196–203.

  • Boyer S., Wratten S.D. (2010) Using molecular tools to identify New Zealand endemic earthworms in a mine restoration project. Zoology in the Middle East 49: S31–S40. 

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Also see Young-Nam Kim's PhD thesis: Interactions between soil biogeochemistry and native earthworms in New Zealand

Invasive insect species

Invasive insects are still mainly controlled with pesticides

Invasive species
Invasive insects can cause millions of dollars of loss to our economy. Despite the progress in biological control and other sustainable pest control strategies, we still rely heavily on pesticides to control agricultural pests around the world. In New Zealand, the move towards more sustainable pest management is driven not only by our concern for the environment, but also by the fact that some of these pest species are actually native (e.g. ground wētā, grass grub beetle). So we sometimes need to strike a balance between controlling populations of these species in agroecosystems without threatening the survival of the species. This singularity provides a unique system to study insect invasiveness and better understand why some species have become invasive after the conversion of their native habitat into agricultural land, while others have not. In collaboration with a number of colleagues and students, particularly from the Bio-Protection Research Centre, we have been actively investigating these issues as indicated in the following list of publications on the subject.
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  • Lefort M-C., Boyer S., Glare T. (2017) A response to Pennisi - “How do gut microbiomes help herbivores”, a hint into next-generation biocontrol solutions. Rethinking Ecology, 1: 9-13.

  • Nboyine J.A., Boyer S., Saville D., Smith M.J., Wratten S.D. (2016) Ground weta in vines of the Awatere Valley, Marlborough: biology, density and distribution. New Zealand Journal of Zoology, 43 (4), 336-350.

  • Varennes Y.-D., Chang M., Boyer S., Wratten S.D. (2016) Nectar feeding increases exploratory behaviour in the aphid parasitoid Diaeretiella rapae (McIntosh). Journal of Applied Entomology, 140, 479–483

  • Varennes Y.-D., Boyer S., Wratten S.D. (2016) Nectar from oilseed rape and floral subsidies enhances longevity of an aphid parasitoid more than does host honeydew. Biocontrol, 61(6), 631-638.

  • Lefort M.-C., Boyer S., Vereijssen J., Sprague R., Glare T.R., Worner S.P.A (2015) Preference of a native beetle for "exoticism", characteristics that contribute to invasive success of Costelytra zealandica (Scarabaeidae: Melolonthinae). PeerJ, 3, e1454.

  • Lefort M.-C., Worner S.P., Rostas M., Vereijsen J., Boyer S. (2015) Responding positively to plant defences, a candidate key trait for invasion success in phytophagous insects. New Zealand Journal of Ecology, 39(1), 128-132.

  • Lefort M.-C., Brown S.D.J., Boyer S., Worner S.P., Armstrong K. (2014) The PGI enzyme system and fitness response to temperature as a measure of environmental tolerance in an invasive species. PeerJ, 2, e676.

  • Lefort M.-C., Boyer S., De Romans S., Armstrong K. Glare T.R., Worner S.P. (2014) Was the invasion process in the scarab Costelytra zealandica (White) within its native range driven by a host range expansion or a host-shift? PeerJ, 2, e262.

  • Lefort M.-C., Barrat B., Marris J., Boyer S. (2013) Combining molecular and morphological approaches to differentiate the pest Costelytra zealandica (White) (Coleoptera: Scarabeidae: Melolonthinae) from the non-pest Costelytra brunneum (Broun) at the larval stage. New Zealand Entomologist 36, 15-21.

  • Lefort M.-C., Boyer S., Worner S.P., Armstrong K. (2012) Noninvasive molecular methods to identify live scarab larvae: an example of sympatric pest and nonpest species in New Zealand. Molecular Ecology Resources, 12(3), 389–395.

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Also see Marie-Caroline Lefort's PhD thesis: When natives go wild... Why do some insect species become invasive in their native range?
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Also see Mauricio Gonzáles-Chang's PhD thesis: Sustainable management of adult Costelytra zealandica (Coleoptera: Melolonthinae) damage in Marlborough vineyards
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Biological Control

Harnessing species interactions to control agricultural pests

Biological Control
By 2050, it is expected that the human population will reach over 9 billion people. This presents an extreme challenge to modern agriculture, and requires a significant shift towards sustainable practices to produce enough food without having major harmful effects on the environment. In particular, broad-range pesticides and chemical fertilisers need to be phased out in favour of better-targeted ecosystem services such as biological control.
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  • Nboyine J.A., Boyer S., Saville D., Cruickshank R.H., Wratten S.D. (2019) Identifying plant DNA in the faeces of a generalist insect pest to inform trap cropping strategy. Agronomy for Sustainable Development, 39(6), 39-57. URL PDF

  • Nboyine J.A., Boyer S., Saville D., Cruickshank R.H., Wratten S.D. (2017) Agro-ecological management of a soil-dwelling orthopteran pest in vineyards. Insect Science, In Press. DOI: 10.1111/1744-7917.12425

  • Nboyine J.A., Boyer S., Saville D., Smith M.J., Wratten S.D. (2016) Ground weta in vines of the Awatere Valley, Marlborough: biology, density and distribution. New Zealand Journal of Zoology, 43 (4), 336-350.

  • Varennes Y.-D., Chang M., Boyer S., Wratten S.D. (2016) Nectar feeding increases exploratory behaviour in the aphid parasitoid Diaeretiella rapae (McIntosh). Journal of Applied Entomology, 140, 479–483

  • Varennes Y.-D., Boyer S., Wratten S.D. (2016) Nectar from oilseed rape and floral subsidies enhances longevity of an aphid parasitoid more than does host honeydew. Biocontrol, 61(6), 631-638.

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Also see Yann-David Varennes' PhD thesis: Floral resource subsidies for the enhancement of the biological control of aphids in oilseed rape crops
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Also see Jerry Nboyine's PhD thesis: Integrated management of ground wētā (Orthoptera: Anostostomatidae) in Marlborough vineyards
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outreach and citizen science

Engaging and inspiring through the practice of science at all age

Science outreach
I have been involved in a number of other science outreach events and have been leading citizen science projects in collaboration with primary school students. Have look at my project on the conservation of little blue penguins. Other projects are described on the page Molecular Ecology in action.
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  • ​Boyer S. (2017) Outside the tower: Nature’s treasure hunt. Science, 356 (6336), 387-387. 

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