New paper alert from Dr Desire Dalton

New Publication: PAReTT: a Python package for the Automated Retrieval and management of divergence time data from the TimeTree resource for downstream analyses

Louis-Stéphane IV Le Clercq a PhD student of Dr Desiré Lee Dalton (Lecturer in Forensic Science, Teesside University) has developed PAReTT – a Python Automated Retrieval of TimeTree data. In order to study speciation (emergence of a new species, sub-species, or ecotypes) accurate fossil-calibrated, estimates of divergence times are needed. PAReTT is a biologist-friendly, easily accessible, and freely available algorithm that can be used to retrieve (1) divergence times, between an individual pair or between all species in a list, (2) evolutionary timelines, for individuals or a list species, and (3) time trees of the divergence times, either for all available species within a specified taxon or between individual species supplied as a list. Future updates will include the ability to switch between scientific names and common names for species as well as the ability to calculate diversification rates for a table of multiple lineages.

Access the publication through the publishers website with this link (DOI: 10.1007/s00239-023-10106-3)

https://link.springer.com/article/10.1007/s00239-023-10106-3

 

Digging up Memories – Making a Digital Exhibit

You may remember a previous blog post when we set out 3D scanning a whole range of different wooden artefacts for the Digging up Memories – Making Connections online exhibit with Vindolanda Museum. Well here we are, looking back at all the successes and improvements after the exhibit was released to the world! We’ve recently written about online exhibits in the book Hadrian’s Wall: Exploring Its Past to Protect Its Future, but here we’re going to review through our recently published paper on the Digging up Memories exhibit.

This exhibit focused on the precious objects that comprise the Wooden Underworld collection at Vindolanda. Objects were selected by museum workers, volunteers and contributors to ensure co-curation in the exhibit, branching the breadth of roles at Vindolanda Museum. The exhibit was held on the Vindolanda website to help ongoing public engagement during limited visitation times and beyond, still remaining accessible today.

The Digging up Memories landing page – a whole range of different themes and objects to explore!

Our early priority was multimedia excitement. Yes that sounds like a bit of a buzzy phrase but essentially, we want several types of media to engage the different preferences and interests of our audience. This meant not just 3D models but also photos, sound bites, video interviews, voice recordings of contributors, lectures, creative writing, published reports, all sorts! Clearly this had some attentive impact, achieving an average 1 minute 35 seconds spent viewing per page (compared to the “typical” museum exhibit times of half a minute).

Now you may be wondering, which objects were the most popular? First, why not take a look at the exhibit yourself and pick out which one is your favourite!

Had a look? Great! The Things We Share page was the most visited, with the Toy Sword achieving the most views overall. Personally, we love the toy sword – Rhys even gave an interview about it in the exhibit!

A key question was “so… was it worthwhile?”. Yes! We had so much valuable feedback but the most valuable measure for us was that 88% of respondents felt encouraged to look further into Vindolanda and Roman history. Now that is a clear success for museums hosting online exhibits! If you’re interested in setting up your own online exhibit, check out the publication which goes into more detail, and offers suggestions and recommendations for future projects.

Isn’t technology great?

External Speaker: Professor Mike Rogerson – When and Why does it rain in the Sahara?

On Monday, 24th April 2023, our TU Earth & Environment Group welcomed guest speaker, Professor Mike Rogerson of Northumbria University whose talk entitled ‘When and Why does it rain in the Sahara? (on orbital timescales)’ addressed his ongoing NERC-funded stalagmite palaeoclimate research in Tunisia and Libya.

According to Mike, the Greening of the Sahara which entails conversion of large, currently hyperarid areas into grassland during warm phases of the northern hemisphere, is one of the most spectacular examples of past climate change we have. Previous studies have revealed that the Sahara was not always the sun soaked hyperarid landscape with iconic rolling sand dunes that much of it is today. Instead, there is evidence that it was once much greener.

Future changes in Earth’s hydroclimate under greenhouse gas forcing are notoriously difficult to predict yet people living in global drylands such as along the desert margins of the Sahara,  are incredibly vulnerable to changing water availability and at risk of acute humanitarian crises under human caused climate change.

Climate models used to predict future change over large parts of African and West Asian dryzones tend not to ‘converge’ which means that different climate models subject to the same climate forcings will give different answers as to whether the region will be wetter or drier in the future. Globally, models seem to predict that wet regions will get wetter and dry regions will get drier but how accurate is this? Also, according to Mike, this pattern does not match our understanding of the Sahara under previous warm periods such as the mid-Holocene around 5000 years ago when a greener Sahara prevailed.

Mike is leading a large team of researchers from the UK, Tunisia, Libya, Switzerland, Germany, and Austria, to achieve a step-change in the confidence of climate forecasts for the northern margin of the Sahara by examining the representation of rainfall in Tunisia and Libya general circulation models, and testing how consistent this representation is with new records of rainfall built from stalagmites from Tunisian and Libyan caves. Cave stalagmites preserve a record of past temperature and rainfall in their mineral chemistry as they grow. Depending on their size and growth rate, they have the potential to give us insight into seasonal scale climate variability many thousands of years into the past.

Mike gave an interesting and engaging talk that explained why this is such a difficult – and important – bit of climate science to solve, and provided us with an update on the team’s progress so far.

Mike directs research in Northumbria’s Geography and Environmental Sciences Department and has a wide range of research interests himself with a particular love for karst processes and landscapes. Mike and I have worked closely on several projects over recent years including my National Geographic Explorer project seeking to reconstruct West African Palaeoclimate and as founding members of ‘Karstaways’, a North England research collective of karst and cave researchers. You can learn more about Mike and his work here https://www.northumbria.ac.uk/about-us/our-staff/r/michael-rogerson/.

written by Dr Lisa Baldini

What came after the Woolly Mammoth

On the 26th April, Dr Ambroise Baker gave a fascinating talk about ‘What came after the Woolly mammoth’

The talk introduced some of the questions surrounding the late-Quaternary extinctions and their relevance when considering ecosystem management today. There was a focus on the consequence of this wave of megafauna extinction. Importantly, studying these consequences furthers our understanding of the ecosystem function that megafauna preformed before extinction. Understanding the loss of this function is increasingly relevant when managing ecosystems, especially when considering megafauna introduction as is the case with rewilding strategies. However, there remains many unknowns regarding the lost megafauna functions, how to re-introduce them and the benefits that can be achieved with re-introduction, pointing to the need for a thorough monitoring of current rewilding projects.

Call for Expressions of Interest in Leverhulme Trust Early Career Fellowships

Teesside University, the School of Health and Life Science, and the Earth, Ecology and Environment research collective are welcoming expressions of interest in Leverhulme Trust Early Career Fellowships.

The research areas of existing strength are as follows:

  • Climate change Impacts and palaeoclimate reconstruction
  • Archaeological advances in preservation and outreach
  • Sustainable agriculture and aquaculture
  • Rewilding for ecological recovery and sustainability
  • Sustainable food supply chain and environmental impact
  • Microbial biotechnology and bioremediation

Contact point for inquiries: Dr Ambroise Baker (A.Baker@tees.ac.uk)

Two PhD Opportunities

Our environmental group is delighted to announce 1 fully funded and 1 fees-only funded PhD opportunities. See below and follow the links provided for further information.

Investigation of moorland management practices and carbon dynamics for climate change mitigation (fully-funded)

Peatlands are increasingly being seen as part of nature’s solutions to deal with the environmental challenges of today, from tackling climate change through to flood protection and enhancing biodiversity. However, while all peatlands provide these services, research and conservation efforts have focused largely on deep peats (>40cm depth). Therefore this project will investigate the impact of different management practices on shallow peatland carbon balances. A field campaign will enable multiple sites across the North York Moors to be surveyed and monitored for peat and pore water chemistry, microbial communities and carbon dynamics.

Above and below ground carbon stocks and biotic changes during rewilding

This project will quantify changes in biodiversity, ecosystem function, carbon stocks and their interactions during the initial phases of rewilding. At the primary field site, some 66 experimental fixed plots are set up within formerly agricultural land comprising a variety of arable, improved, and natural grasslands. Rewilding was initiated in 2022, with the cessation of agricultural activities which will be followed by large herbivore re-introduction (eg hardy free-ranging cattle and pigs). The analysis will quantify ecosystem changes in time, against baseline data collected in 2021-2022, and enable an assessment of rewilding contribution notably to net-zero and nature recovery policies.

We anticipate the project to be a unique opportunity to work with a range of collaborators inside and outside academia. We are looking for candidates with a strong interest in combining biodiversity, microbiological and environmental science, to develop novel evidence contributing to the UN decade of ecosystem restoration.

1 kilometre under the surface: Researching organisms from extreme environment

MSc Microbiology students Orakan Jones and Nathalia Thompson with Drs Paul Dean and Jens Holtvoeth collected brines for extremophile research 1,000m below the surface in the Boulby salt mine.

In October, a team from Teesside University took part in the 10th annual field event on astrobiology, robotics, and planetary exploration (MINAR X), organised by the UKRI Underground Laboratory at the ICL salt mine at Boulby. Dr Jens Holtvoeth was joined by Dr Paul Dean and two microbiology MSc students, Orakan Jones and Nathalia Thompson to travel 1.000 meters down the shaft and underneath the North Sea, together with scientists from the Universities of Edinburgh, York, Manchester, and Newcastle, the California Institute of Technology, and NASA’s Jet Propulsion Laboratory (Pasadena).

The aim of our team was to collect samples of salt and brine for biomarker and DNA analyses to produce a geochemical fingerprint of fossil and living microbial communities and to gain information on cellular adaptation mechanisms of halophile microorganisms to the extreme conditions. This will help to interpret fossil biomarker distributions found in the salt with regard to environmental conditions at the fringes of the evaporating Zechstein Sea about 250 million years ago.

While the team were able to collect brines from a disused part of the mine, aptly named Billingham Bath, the collection of salt samples by coring the salt with sterilised drill bits had to be postponed due to a technical fault of the corer. Thus, the team is looking forward to going down the shaft later this semester, again.

Partnering with Durham Wildlife Trust to address microplastics pollution in the River Wear

An update on a previous blog post about our microplastic project in Co Durham, UK.

Environment Group researchers Drs Baldini, Baker, He, Rollason and Scott, along with recent Environmental Science graduate, Zhuhaa Siddiq, recently partnered with Durham Wildlife Trust to investigate microplastics in the River Wear. Fieldwork happened over several weeks in late summer 2021 and involved standing in the river with a microplankton net and flow meter for 20 minutes to collect a known volume of river water for microplastics detection. We sampled water and sediments at five locations along the river Wear from the source (near Wearhead) to the tidal limit (Chester-le-Street). Laboratory analysis revealed a pattern of increasing microplastics in river water downstream from the source until river flow was altered by Durham city weirs. A sharp decrease in microplastics was observed at the furthest downstream site, Chester-le-Street. In sediments, there was a clear pattern of microplastics accumulation downstream of wastewater treatment plants. In summer 2022, Environmental Management research project student, Patrick van Loo Jenner, investigated our hypothesis of microplastics accumulation upstream of weirs in Durham as a precursor to scheduled dredging by the Environment Agency. In March 2022, Dr Baldini presented preliminary findings to a Source to Sea workshop addressing plastics pollution at Durham County Council and in July 2022, submitted a final report to Durham Wildlife Trust. A manuscript of our findings is currently in prep. For more on this successful Teesside University collaboration with local partners see https://www.durhamwt.com/source-sea.