CASE partner with Cardiff University, a 3 year Phd study utilising DNA and scent technology started in January 2016. What drives change in population structure? Dispersal, home range, and landscape barriers to the otter Lutra lutra, across the UK.
January 2021 Update
Below is an update from Nia Thomas with some basic pie charts showing the progress of the analysis of samples the Somerset Otter Group collected for the Cardiff project.
Without mapping and more detail, which will hopefully eventually follow, the data so far tells us there are male and female otters in Somerset!
A message from Nia Thomas, Cardiff University Otter Project
As with everyone else, this year brought great changes and challenges to the way in which I could work on my PhD due to the ongoing pandemic. In March we left the labs at Cardiff University to work from home and after 5 months of no access we had to take the hard decision to restructure my PhD to avoid any further lab work so that I could complete the thesis by May 2021.
This unfortunately means that the final genetic work to get individual identities from the spraint samples collected by all the SOG volunteers has been put on hold. We have however, spoken with the external funder for that section of the project and they have agreed to let us continue the work after I’ve handed in my PhD thesis – so I will keep you updated on this. We have already managed to use the DNA extracted from the samples to check for a species ID and to sex type the samples which has given us a good idea of the quality of DNA in the samples. See the graphs below for a summary of what we have learnt so far from those two steps.
One area of the research that has continued to progress under lockdown/general pandemic restrictions is working with a Statistician at Canterbury University in Kent to use the fresh spraint counts and locations from the two-day event data to model the otter population size across both the Tone and the Brue. This work is still fairly preliminary, but the models are running successfully for the Tone catchment and we are continuing to tweak some of the parameters to make the estimates a reliable as possible. My hope is that we can produce a model that can be used by SOG with future two-day event day to estimate population size each year and thus detect any significant changes.
Thank you once again for all your time and help in collecting otter spraint over the three years and I will continue to send updates via the SOG Newslotter and other SOG channels as and when I have them – Nia
*This number is likely to increase / proportions of males and females might change when we are able to re-run some of the samples a second time that gave ambiguous/incomplete results the first time round.
June 2018 Update from the Somerset Otter Group
The Somerset Otter Group (SOG) made its last collection of fresh spraint during the April two day event 2018. This week Nia Thomas, the Cardiff University Phd student, collected the last of the spraints from Rob Williams freezer and took them to Cardiff to start on their analysis.
A huge effort was put into the project by the SOG. Two main catchments were selected; the Tone and the Brue. Both these catchments were subject to the DNA study conducted by Karen Coxon in 1999.
Nia collected 38 samples across both catchments and SOG surveyors contributed another 455; collected between April 2016 and April 2018. A total of 493 spraint samples. 268 were from the River Brue and River Axe and 225 from the Tone which included sampling from the Blackdown hills as a possible dispersal route from the Tone.
Through the 3 years at least 60 SOG surveyors contributed their time doing either consecutive surveys and/or the usual 2 day annual survey, to obtain fresh samples. With the mobility and range of the otters a lot of that effort was not always rewarded. But 42 people successfully contributed fresh spraint samples. 17 surveyors from the Brue and 25 from the Tone. This does not count those people assisting and accompanying others during the surveys. So a massive and sustained effort by many.
At least 281 sites were checked multiple times over the 3 years, 146 sites on the Brue catchment and 135 sites on the Tone. Fresh spraint was collected from 79 sites on the Tone and 94 sites on the Brue, a total of 173 sites. 33 patches on the Tone, 26 on the Brue and Axe and 4 on the Blackdowns.
The map below, produced by the Somerset Otter Group, illustrates the coverage achieved by everyone. The darker dots are where multiple samples were obtained through the years. Six sites had double figure samples, 4 sites on the Tone and 2 sites on the Brue.
Thank you to everyone who took part.
January 2018 Update.
A message from Nia Thomas, Cardiff University Otter Project
Thanks to all the SOG volunteers this year for their hard work hunting out fresh spraints across both the Tone and Brue catchments – as of this November we have 315 samples collected and transported back to the otter archive freezers in Cardiff. There will be two more sampling periods in 2018: a 6 week winter period from mid-January until the end of February and the 2 day event on the 28th and 29th April – it would be great if as many of you as possible could help with this last push in finding as many fresh spraints as possible.
During this year CUOP applied for (and received) two grants to help fund the otter population genetic work on the Tone and Brue catchments. The first was from the People’s Trust for Endangered Species who awarded us nearly £15,000 towards the enhancement of our methods. This includes improvement of a genotyping method which we hope will improve success rates using spraint as a DNA source, as well as volatile organic compound analysis (‘smell’!) on spraint samples to determine otter age class. The second was from the NERC Biomolecular Analysis Facility in Sheffeld who have awarded us the equivalent of £15,000 in Next Generation Sequencing runs and associated bioinformatic training. With the funding from both of these grants we will now be able to genotype all of the spraint collected across both catchments (subject to DNA quality)!
After a nasty bike crash in May, Nia was forced to take 4 months off work over the summer while on crutches. Although not completely healed yet, she’s very happy to be well on her way to recovery and back at work full time since October. The project has been set back slightly due to this but we’re hoping to catch up the lost time over the next 2 years.
Nia addresses the SOG members meeting Wellington – January 2018
January 2017 update.
Genetics Study on the Brue and the Tone.
The study of otter genetics on the rivers Tone and Brue in collaboration with Cardiff University Otter Project, started in 2016. PhD student Nia Thomas received 56 fresh spraint samples from the two-day event. The DNA has now been extracted and is frozen awaiting further analysis. In August, Nia returned and collected a further 12 fresh spraints from 45 surveyed sites on the Brue and 6 fresh spraint from 28 sites on the Tone. This is a great start to the project and early results look promising for the PhD being able to analyse a considerable number of spraints from Somerset. So in 2017 and 2018 we will be doing more intensive collections on the Brue and the Tone in 3 six-week periods each year. We will be contacting surveyors on those rivers to see if you are interested in helping.
Nia has sent a photo of extracted samples together with details of new methods and her other work.
Poo Pantone! Each spraint is unique – this is particularly easy to see half way through the extraction process.
New methods Nia and her colleagues are working on developing new methods to increase the genotyping success rate of spraint samples. For spraints collected in a British-type climate the success rate is usually between 20-50% meaning that it’s likely that less than half of our spraints will get a full genetic ID. The new method (based on human forensics techniques) hopes to increase this. A trial in the coming months should determine whether the new method will improve this. If it does (we really hope it will!), Nia will continue extracting the DNA as samples are collected, but the genotyping will all happen right at the end – Next Generation Sequencing methods require large batches of samples to be processed together and to help minimise costs.
Nia has also been ‘sniffing’ spraints for volatile organic compounds (VOCs). Eleanor Kean, a previous Otter Project PhD student (who some of you may have met) showed that in otter scent gland material such compounds differ between adults and juveniles. Nia is currently working if this can be used in the field by testing spraint material from known-age captive otters. If successful this will be applied to the spraints collected in the Tone and Brue catchments.
Nia has also been working on how the population structure of otters has changed across the UK over the last 20 years. She has genotyped 100 samples from otters sent into Cardi? University Otter Project in 2014 and analysed their population structure – preliminary results indicating that previous structure may be disappearing (good news – as this would mean otter populations are becoming more mixed). In 2017, she will genotype 100 samples from 2009, and analyse these alongside the genotyped samples from 1988-2007 to see how population structure has changed over time.
Summary: CASE Studentship with Cardiff University
What drives change in population structure? Dispersal, home range, and landscape barriers to the otter Lutra lutra, across the UK.
Keywords: Otter, genetics, landscape ecology, spatial analysis.
Duration of project: 3 years.
Start date of project: January 2016.
Names and affiliations of supervisors.
Dr Elizabeth A Chadwick (School of Biosciences, Cardiff University) (supervisor from a GW4 University),
Prof. Robbie Mcdonald (Exeter University) (Supervisor from a GW4 University)
Prof Mike Bruford ((School of Biosciences, Cardiff University) (supervisor from a GW4 University)
Description of project
Studies of genetic structure in natural populations of terrestrial species usually focus on assessments at a single time point, often failing to capture temporal population dynamics. The Eurasian otter (Lutra lutra) suffered continental scale declines during the 1950s-70s, from which it is now recovering. In the UK, previous research suggests considerable sub-structuring, with 4 major groupings, likely to have arisen from geographically separated remnant populations (Hobbs et al 2011; Stanton et al 2014). These subpopulations are now largely contiguous, and it is likely that the degree of admixture reflects (i) the permeability of landscape barriers, (ii) the otter’s home range, and (iii) dispersal distances from natal sites. Little is known about any of these elements.
This proposal aims to use molecular techniques to investigate recent changes in otter population structure over a twenty-year period of recolonisation, at a national scale. In analysing this recolonisation process, it aims to gain new and previously intractable information on otter range and dispersal, and in doing so, examine the permeability of landscape barriers to movement.
The PhD student will
Characterise population structure at 5 year intervals across a twenty year period, using geolocated muscle tissue samples collected across England and Wales
Assess and compare dispersal distances in three distinct regions (SW, E Anglia, and Wales) using genetic relatedness measures to identify parent-offspring and sibling pairs, from tissue samples collected across the same twenty year period.
Identify individual movements and characterise home range size over a three year period, using spraint samples collected from the River Tone in Somerset. In addition to molecular analyses, the student will use novel chemical analysis of volatiles in scent material (Kean et a xxx) to distinguish juveniles from adults.
Identify landscape barriers to otter movement, using data from (1) and (2).
Extensive sample and data collections are already available from Cardiff University’s long-term Otter Project (www.otterproject.cf.ac.uk). Specifically, the project holds an archive of muscle tissue samples collected from >2000 individual otters, collected from known place/time points across England and Wales since 1994. Microsatellite data are already held for previously collected samples. In addition, partnership with the Somerset Otter Group provides considerable local expertise and the assistance of a well established volunteer network, as well as access to genetic data from spraint collected in 2000 (identifying 14 individual ranges), and annual surveys repeated every year since.
This is an attractive project addressing novel questions and providing diverse training opportunities within well-established teams, working on a charismatic European protected species.
This project will deliver interdisciplinary training in several areas, primarily, whole animal biology and ecology, molecular genetics and bioinformatics, analytical chemistry, statistical modelling and spatial analyses:
Molecular analysis & Bioinformatics: Training in PCR/bioinformatics etc – at Cardiff , in our world leading genetics laboratory. Training in individual identification from spraint will be provided in partnership with the Waterford Institute of Technology, with Dr Catherine O’Reilly.
Analytical chemistry: Training in sampling of VOCs on thermal desorption tubes and subsequent analysis on TD-GC-MS-TOF will be carried out at Cardiff University, under the guidance of Dr C Muller who has extensive expertise in the analysis of volatiles in an ecological context.
Dissection and anatomy: New samples (in addition to those already in store) will be collected by the student at Cardiff University as part of the activities of the Otter
Project, where the student will receive training in anatomy, pathology and dissection techniques as well as sample and data curation from Otter Project PI Dr E Chadwick.
Ecological survey: The student will work with our CASE Partner, Somerset Otter Group, and will receive training in field survey methods for otter populations.
Statistical and spatial analysis: At Exeter and Cardiff, the student will receive training in the statistical analysis of extensive wildlife survey data, spatial analysis, using ArcMap GIS and SatScan, and statistical modelling using ‘R’.
- This is a cross-institutional project, building on established and on-going interests in Cardiff and Exeter Universities.
- The project benefits from an established partnership with Somerset Otter Group, who have agreed to act as CASE partner. SOG are an extremely active volunteer group, and have previously provided support for two successful PhD studentships at Cardiff; one as CASE partner to a NERC funded project examining biliary parasites, and another providing volunteer support for spraint collection as part of a study of scent communication. The River Tone is one of the best studied otter populations in the UK, with 14 years of annual spraint survey data.
- The project offers the potential to deliver a major advancement to our knowledge of the processes that drive population structure in a mobile semi-aquatic predator. Given the otter’s status as an EU protected species, there is considerable interest from a conservation perspective.
- The otter is a charismatic European protected species with considerable appeal; the project is highly novel with training opportunities across a range of techniques. It is therefore expected to attract a large number of highly competitive applicants.