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Overview

Human impacts have caused pervasive global biodiversity declines across ecosystems, leading to a reorganisation of global biodiversity patterns. Rapid and accurate biomonitoring techniques are essential to track the causes and consequences of global environmental change and assist with focussed conservation efforts. Weakness in our abilities to detect species and measure declines is often cited as a fundamental challenge by researchers and major international initiatives. My research program addresses critical questions in biodiversity discovery and loss by using large-scale genomics and bioinformatics tools which address the intractable challenge of biodiversity monitoring. I am a molecular ecologist who combines lab techniques and big data approaches alongside field ecology.

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Ecological monitoring of rapid biodiversity change

My research focuses on developing environmental DNA (eDNA) as a system for species monitoring and environmental assessment. I have developed next-generation sequencing approaches to biomonitoring by examining the spatial and temporal distribution of eDNA in freshwater ecosystems. More recently, I have applied these concepts to sequencing trace amounts of DNA from air (airDNA), to examine terrestrial eukaryotic diversity and human forensics. My research combines the latest molecular, bioinformatic and big data approaches with fieldwork. We are developing projects around measuring organism abundance with eDNA and the optimal design of eDNA field surveys. My major collaborators in this work are the Cristescu lab at McGill University, WSP Montreal, and NGO and industry partners such as the IISD Experimental Lakes Area.

Students: Samia Asvid (MSc) Ecology with molecules: modelling species abundance from DNA sequences, Imogen Hobbs (Summer undergraduate research programme), Michelle Chen (work-study placement).

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Bioinformatics methods development

How can we usefully define Molecular Operational Taxonomic Unit (MOTU) in eukaryotic metabarcoding, and how does this relate to species concepts? How do different bioinformatic and statistical pipelines used in post-sequencing cleaning and analysis affect our estimations of diversity from metabarcoding datasets? I’m exploring these questions in collaboration with Beth Clare at Queen Mary University of London. I am also collaborating with Sergio Hleap from the Cristescu lab to undertake a benchmark assessment of taxonomic assignment tools for amplicon sequencing data.

Students: Isaac Eckert (work-study placement)

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Trophic interactions along environmental gradients

Predator-prey interactions can be profoundly affected by gradients of natural and human-induced stressors which can have ecosystem level impacts. In collaboration with Beth Clare at Queen Mary University of London and John-James Wilson at the University of Malaya, I use metabarcoding to determine trophic relationships through dietary analysis, and to investigate the physical and environmental influences on predator-prey relationships.  We are examining rapid land use change, using the growth of SE Asian megacities and the surrounding modification of land as a study system. Molecular tools allow fine-scale resolution of dietary data from gut contents and faeces of vertebrates, which has previously been taxonomically difficult to identify.

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If you’re interested in collaboration on any of these themes, please get in touch.