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Coral reef

New research published in Nature Ecology & Evolution from the Department of Zoology at Oxford University aims to show how big data can be used as an essential tool in the quest to monitor the planet’s biodiversity.

A research team from 30 institutions across the world, involving Oxford University’s Associate Professor in Ecology, Rob Salguero-Gómez, has developed a framework with practical guidelines for building global, integrated and reusable Essential Biodiversity Variables (EBV) data products.

They identified a ‘void of knowledge due to a historical lack of open-access data and a conceptual framework for their integration and utilisation'. In response the team of ecologists came together with the common goal of examining whether it is possible to quantify, compile, and provide data on temporal changes in species traits to inform national and international policy goals.

These goals, such as the Sustainable Developmental Goals (SDG) of the United Nations, have become fundamental in shaping global economic investments and human actions to preserve and protect nature and its ecoservices.

Essential Biodiversity Variables (EBVs) have been proposed as ideal measurable traits for detecting changes in biodiversity. Yet, the researchers say, little progress has been made to empirically estimate how EBVs in fact change through time at the regional and global scales.

To overcome this, Rob Salguero-Gómez and his international collaborators have developed a framework with practical guidelines for building global, integrated and reusable EBV data products of species traits. This framework will greatly aid in the monitoring of species trait changes in response to global change and human pressures, with the aim to use species trait information in national and international policy assessments.

Salguero-Gómez says: 'We have for the first time synthesised how species trait information can be collected (specimen collections, in-situ monitoring, and remote sensing), standardised (data and metadata standards), and integrated (machine-readable trait data, reproducible workflows, semantic tools and open access licenses).'

This latest review provides a perspective on how species traits can contribute to assessing progress towards biodiversity conservation and sustainable development goals. The researchers believe that big data is one of the keys to address the global and societal problems from security food, to preventing ecoservice loss, or effects of climate change. 

They say that the operationalization of this idea will require substantial financial and in-kind investments from universities, research infrastructures, governments, space agencies and other funding bodies. ‘Without the support of the Max Planck Institute for Demographic Research, NERC, Oxford, and the open-access mentality of hundreds of population ecologists, our work with COMPADRE & COMADRE would not have been possible,’ says Salguero-Gómez.

The integration of trait data to address global questions in ecology, evolution, and conservation biology is one of the main themes in Salguero-Gómez’ research group, the SalGo Lab.

This work was funded primarily by the Horizon 2020 project GLOBIS-B of the European Commission.

 Read the full paper in Nature Ecology & Evolution.

Artists reconstruction of fossil

Stephen Pates, a researcher from Oxford University’s Department of Zoology, has uncovered secrets from the ancient oceans.

With Dr Rudy Lerosey-Aubril from New England University (Australia), he meticulously re-examined fossil material collected over 25 years ago from the mountains of Utah, USA. The research, published in a new study in Nature Communications, reveals further evidence of the great complexity of the oldest animal ecosystems.

Twenty hours of work with a needle on the specimen while submerged underwater exposed numerous, delicate microscopic hair-like structures known as setae. This revelation of a frontal appendage with fine filtering setae has allowed researchers to confidently identify it as a radiodont – an extinct group of stem arthropods and distant relatives of modern crabs, insects and spiders.

Before and after view of Pahvantia Before and after view of Pahvantia

‘Our new study describes Pahvantia hastasta, a long-extinct relative of modern arthropods, which fed on microscopic organisms near the ocean’s surface’ says Stephen Pates. ’We discovered that it used a fine mesh to capture much smaller plankton than any other known swimming animal of comparable size from the Cambrian period. This shows that large free-swimming animals helped to kick-start the diversification of life on the sea floor over half a billion years ago.’

Causes of the Cambrian Explosion - the rapid appearance in the fossil record of a diverse animal fauna around 540-500 million years ago - remain hotly debated. Although it probably included a combination of environmental and ecological factors, the establishment of a system to transfer energy from the area of primary production (the surface ocean) to that of highest diversity (the sea floor) played a crucial role.

Even though relatively small for a radiodont (FIG), Pahvantia was 10-1000 times larger than any mesoplanktonic primary consumers, and so would have made the transfer of energy from the surface oceans to the deep sea much more efficient. Primary producers such as unicellular algae are so small that once dead they are recycled locally and do not reach the deep ocean. In contrast large animals such as Pahvantia, which fed on them, produce large faecal pellets and carcasses, which sink rapidly and reached the seafloor, where they become food for bottom-dwelling animals.

Amateur enthusiasts provide research gold-dust

The presence of Pahvantia in the Cambrian of Utah has been known for decades thanks to the efforts of local amateur collectors Bob Harris and the legendary Gunther family.

‘This work also provides an opportunity to celebrate the exceptional contribution of local and amateur collectors to modern palaeontology’ explains Stephen. ‘Without their tireless efforts, knowledge, and generosity, thousands of specimens representing hundreds of new species, would not be known to science.’ 

Bob Harris is rumoured to have turned down a job offer from the CIA, instead opening up a fossil shop and a number of quarries in the spectacular House Range, Utah. He discovered the first specimens of Pahvantia in the 1970s, and donated them to Richard Robison, a leading expert on Cambrian life from the University of Kansas. The Gunther family are famous for their extensive fossil collecting in Utah and Nevada. Over a dozen species have been named in honour of their contributions to palaeontology, as they have shared thousands of specimens with museums and schools over the years. Among these were specimens of Pahvantia which they uncovered between 1987 and 1997. Donated to the Kansas University Museum of Invertebrate Paleontology (KUMIP), these specimens are described for the first time in our study.

‘I visited the KUMIP in the first year of my PhD,’ says Stephen. ‘It was awesome, exploring such a fantastic collection of fossils from the Cambrian of Utah and Nevada.’

The study has produced the most up-to-date analysis of evolutionary relationships between radiodonts. It shows that filter feeding evolved twice, possibly three times in this group, which otherwise essentially comprised fearsome predators such as Anomalocaris canadensis from the Burgess Shale in Canada.

Pahvantia adds to an ever-growing body of evidence that radiodonts were vital in the structure of Cambrian ecosystems, in this case linking the primary producers of the surface waters to the highly diverse fauna on the sea floor. It also shows the importance of museum collections like the KUMIP, and local collectors, such as Bob Harris and the Gunther family, in uncovering new and exciting findings about early animal life.

The article is available from Nature Communications via this link.

Coding

Amy Kao, PhD student at the Department of Psychiatry, Oxford University, reveals how she represented the UK at the international ActinSpace hackathon as part of an Oxford team which combined talents to take on a social problem.

Hackathons have a reputation as a software-heavy coding event welcoming only those with specific skill sets and domain knowledge in computer science. However, as diversity continues to emerge as a pivotal aspect of success for any project, the ActinSpace (AIS) hackathon invited anyone from any background to come and work up realistic ideas using space technology in innovative ways.

The experience was truly memorable. In the beginning stages at Harwell, Oxfordshire, within 24 hours my team and I proposed a satellite-based artificial intelligence application to address street harassment. We worked through the night, inspired by the knowledge that we could be building a technology that could truly make the world a better place.

Our proposed platform was a navigation app to guide you the safest way home. In order to find the safest route, the app estimates the danger on each road segment. Crime record databases in the UK and US are public and annotate with exact geo-location. These can be used to count the number of incidents on each road segment. Using convolutions neural networks and satellite data, the app could accurately estimate the number of pedestrians going along each road. This forms the technical basis of our platform. Additional features are AI-driven velocity tracking that can be used to identify whether the user suddenly stops moving, starts running or even deviating from the intended route, all of which are unexpected behaviours on a normal walk home. Using vibration or non-visual cues avoids the need to be constantly looking down at a phone making you appear less lost, and a much less of a viable target.

We pitched our product in seven minutes the following day, and won the hearts of the UK judges. This gave us the unique opportunity to represent the UK at the international semi- finals in Toulouse.

This was an enormous event gathering teams from over 30 countries, all with exciting and novel technologies.

The finals competition in Toulouse brought together people from across the world sharing a passion for technology and innovation. However, it also sadly highlighted the lack of diversity and representation that remains.

Amy Kao and Anna Jungbluth, DPhil students at Oxford Amy Kao and Anna Jungbluth, DPhil students at Oxford

The AIS 2018 had 23% female participation, but only one team among the six finalists had a female team member. There has been considerable movement in increasing this number; however, we see it as our social obligation to do our part and encourage our female peers to take part and pursue activities that they didn’t think they could achieve.

The best part of the team was our diversity, where we were five students from five different countries, coming to Oxford to study five extremely different disciplines (computer science, economics, medicine, physics, psychiatry) ranging from fresh undergraduates to seasoned DPhils. The hackathon really was a problem-solving event, not a software-heavy event at all. It provided the opportunity of working with other astute individuals to propose a holistic solution using space technology and creative business models. 

The burst of productivity over one 24-hour period can be extremely refreshing. I would really encourage others to take part, particularly if you’re not in any mainstream programming fields, and even more so if you’re part of an underrepresented demographic (e.g. women in STEM). My bachelor’s was in cell and molecular biology, and my postgraduate research degrees were in pharmaceutical science and neuroscience; perhaps as far removed from space technology as you can get, let alone participating in a hackathon! The mentality of industries are shifting from the limiting idea of entering a career based entirely on what you studied in school to a dynamic stage that embraces diversity and different approaches to solving a problem. Domain knowledge can be quickly accumulated, but the courage to pursue something outside your normal comfort zone and the confidence that you have meaningful contributions requires deliberate time and context to be developed. Just give it a try! 

MPLS runs an Enterprising Women lunch and learn in week 4 of each term, welcoming all researchers interested in developing of a supportive network of STEM women. Details are always advertised via eship.ox.ac.uk

Hunting the elusive Higgs boson

Professor Daniela Bortoletto of Oxford University’s Department of Physics explains how a new result from the Large Hadron Collider sheds vital light on the elusive Higgs boson.

Particle physicists have – at long last – observed the Higgs boson decaying into a pair of bottom (b) quarks at the Large Hadron Collider (LHC). This elusive interaction is predicted to make up almost 60% of the Higgs boson decays. Yet it took over seven years to accomplish this observation. This discovery was announced at CERN on August 28 both by ATLAS and CMS.

ATLAS is one of the four major experiments at the Large Hadron Collider (LHC) at CERN. It is a general-purpose particle physics experiment run by an international collaboration and, together with another experiment, CMS, is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

The result is a confirmation of the Standard Model. During the early preparations of the LHC, there were doubts on whether this observation could be achieved. Our success is thanks to the excellent performance of the LHC and the ATLAS detector, and the application of highly sophisticated analysis techniques to our large dataset.

UK groups including the Universities of Birmingham, Glasgow, Liverpool, Queen Mary, Oxford and UCL have made important contributions to this historic achievement.

Finding Higgs boson decaying into a pair of b quarks at the LHC is challenging. Since the LHC collisions produce b-quark pairs in great abundance it is essential to select events where the Higgs boson appears alongside a W or Z particle, which makes the events easier to tag. Our team in Oxford analysed elusive W and Z bosons decays where the decay products of these particles are not directly identified in the detector but are inferred from a large transverse energy imbalance in the event.

Our postdoc researcher, Elisabeth Schopf and my students, Cecilia Tosciri and Luca Ambroz, made significant contributions to the result. Elisabeth played a leading role in optimizing the sophisticated machine learning algorithms that allowed ATLAS to increase the sensitivity to these events. Luca established a new technique that used Monte Carlo events in a clever way and lead to a higher expected significance for the analysis. Cecilia upgraded a method to improve the resolution achieved in the measurements of the decay of the Higgs boson into b-quarks.

This is a very special moment for me personally, and the culmination of an even longer wait. I started looking for the decays of the Higgs boson to b-quarks at the US proton-proton TEVATRON collider with the CDF detector in 2005. Four of my former students completed their theses on searches for the Higgs in events with large transverse missing energy and b-quarks between 2007 and 2012.

The results of this work were used in the final TEVATRON combination which reached about three standard deviations in 2012 - not enough for a discovery. I am delighted that the LHC finally unveiled this important decay mode of the Higgs boson. I did not have any doubt that at the end of this tour de force we will pass the significance of five standard deviations which is necessary to claim a discovery. The LHC is a more powerful accelerator than the TEVATRON and ATLAS is a superb detector.

I believe that this measurement will improve our understanding of the mechanism of mass generation and its possible connections with cosmology and astrophysics.

This is also a new confirmation of the so-called “Yukawa couplings”. Similar to the Higgs mechanism, these couplings to the Higgs field provide mass to charged fermions (quarks and leptons), which are the building blocks of matter. Combined analyses of the Run-1 and Run-2 datasets have resulted in the first measurements of these couplings, as seen in the recent ATLAS observation of Higgs boson production in association with a top-quark pair and the observation of the Higgs boson decaying into pairs of tau leptons.

This result also establishes, for the first time, the production of a Higgs boson in association with a vector boson above five standard deviations. ATLAS has now observed all four main production modes of the Higgs boson. These observations mark a new milestone in the study of the Higgs boson, as ATLAS transitions from observations to precise measurements of its properties.

We now have the opportunity to study the Higgs boson in unprecedented detail and will be able to further challenge the Standard Model.

Ethiopian wolf

Over the past month, a team from Oxford's Ethiopian Wolf Conservation Programme (EWCP) has implemented the first oral vaccination campaign to pre-empt outbreaks of rabies among Ethiopian wolves, the world’s most endangered canid, in their stronghold in the Bale Mountains of southern Ethiopia.

Described as a turning point in the plight to save Ethiopian wolves from extinction, the campaign follows a decade of intensive research, field trials and awareness work led by the University of Oxford’s Wildlife Conservation Research Unit (WildCRU) and supported by funding from the Born Free Foundation, among others. Working alongside the Ethiopian Wildlife Conservation Authority, regular oral vaccination campaigns will now expand to all six extant wolf populations to enhance their chances of survival. There are fewer than 500 Ethiopian wolves in the world, all in the wild and highly exposed to infectious diseases transmitted by domestic dogs.

WildCRU's Professor Claudio Sillero, EWCP director and founder, said: 'Thirty years ago I witnessed an outbreak of rabies which killed the majority of the wolves I had followed closely for my doctoral studies. We have learned much about these wolves and their Afroalpine homes since then. By the time we detect rabies in a wolf population, already many animals are fatally infected and doomed. We now know that pre-emptive vaccination is necessary to save many wolves from a horrible death and to keep small and isolated populations outside the vortex of extinction. I wholeheartedly celebrate the team’s achievement.'

Ethiopian wolfAn Ethiopian wolf takes bait containing rabies vaccine.

Long-term programmes and targeted research are the cornerstones of biological conservation, as success often relies on an intimate knowledge of the workings of populations, the behaviour of individuals, and the social, political and economic contexts. With a generous donation from pharmaceutical laboratory Virbac of 3,000 SAG2 oral vaccines, EWCP has launched a vaccination strategy, guided by strong empirical information and predictive modelling – and a key component of the National Action Plan for the conservation of the species.

Muktar Abute, EWCP's vet team leader, said: 'Vaccine contained within a meat bait was distributed at night time to three Ethiopian wolf packs. Our target is to immunise at least 40% of all wolves in each population, reaching as many family packs as possible, including the dominant pair – on which pack stability largely depends. We recorded good uptake, with 88% of 119 baits deployed consumed over two nights. Using camera traps we monitored bait consumption, and we will next measure rabies concentration levels in blood to confirm the effectiveness of the vaccine over a larger sample than that of the trials.'

Oral vaccination using SAG2 has been successful in controlling, and even eradicating, rabies in wild carnivore populations in Europe. This approach now raises hope for the survival of one of the rarest and most specialised carnivore species, the Ethiopian wolf. Preventive vaccination can improve the status of other threatened wildlife, and the Ethiopian wolf experience may lead other practitioners to embrace it as part of their conservation toolkit, in a world demanding closer control of pathogens shared by wildlife, domestic animals and humans.