Development and optimisation of genetic tools for monitoring and managing the European otter (Lutra...

Post summary

Background

Lough Carra, a marl lake in Co. Mayo is a site of national importance due to its high ecological and biodiversity value, and the National Parks and Wildlife Service (NPWS) were recently awarded EU LIFE funding to help conserve, protect and restore the site. Some of the key objectives for this work include the protection and enhancement of key species of conservation concern e.g. European otter (Lutra lutra), and the control of invasive species including the American mink (Neovision vision) (https://loughcarra.org/catchment-association/life-project/ ).

The conservation of European otters in Ireland requires detailed demographic information to inform future population management schemes. This project aims to integrate genetic data (such as microsatellites) to provide more descriptive and detailed information to assess the population size, structure, health and ecology of European otters. DNA sequencing technology has advanced enough to obtain high quality DNA from non-invasively collected samples (i.e. collecting samples without disturbing the animal) such as hair or faeces. The primary source of non-invasive DNA obtained from otters in Ireland and elsewhere in Europe has been faeces, but previous studies commonly show a low success rate from this sample type. There is an urgent necessity for developing and refining a non-invasive sampling methodology that is cost and labour effective, generates high resolution data and can be standardised for future monitoring of otter populations in Ireland and Europe. In addition, these optimised methods will be applied to monitor the non-native populations of American mink. No genetic studies have taken place on the American mink in Ireland, but these are now required to help inform future management schemes of non-native species.

The candidate will be based in WIT with a team of researchers highly experienced in genetic techniques and surveying mammals in Europe, specialising in Irish ecology. They will work in conjunction with the NPWS’s Scientific Unit and their work will be used to inform the Lough Carra LIFE restoration project. The candidate will also collaborate with researchers in the UK specialising in eDNA techniques, with the opportunity to build further collaborations. The project will provide the opportunity to develop skills in field based surveys of mammals, lab skills in various genetic techniques, subsequent computational analyses and writing reports directly applicable to conservation practice and papers for publication in peer-reviewed journals.

Project Aims/Goals

The overall aim of this project, based in the Lough Carra Catchment, is to provide genetic data regarding the conservation, management and population status of the native European otter and the invasive American mink. The successful PhD candidate will be responsible for the following objectives:

Project Objectives

• Develop an optimised non-invasive sampling protocol for otters (that can be applied to other mustelids such as mink) to collect samples that will yield high quality DNA for both population genetic data and dietary assessments. Optimisation will include a critical evaluation of each step from survey method, sample storage, DNA extraction and sequencing technique.

• Design and or optimise species, sex and individual identification markers for both mink and otter.

• Develop and optimise DNA based dietary methods for the overall dietary assessment of otters and mink via DNA metabarcoding and/or design and optimise species-specific real-time PCR tests for the rapid detection of species of interest.

• Compare environmental DNA (eDNA) protocols for the detection of otters and mink with standard surveillance methods.

• Once methods have been optimised, protocols will be applied to Lough Carra and other sites within Ireland to estimate otter and mink populations.