Friday 16 December 2016

BioMaths Colloquium - 16/12/2016

BioMaths Colloquium Series - 2016/17

16 December 2016 - 3pm Maths Seminar Room

(room 224 Talbot Building 2nd floor)

Modelling evolution in structured populations involving multiplayer interactions

Professor Mark Broom

(Department of Mathematics,City University of London, UK

from: Broom et al. 2015

This week we welcome Prof Mark Broom from the Department of Mathematics at City University London. Mark is interested in Mathematical Biology, especially in Evolutionary Game Theory. His research comprises theoretical work on games, such as the development of multiplayer game theory, as well as developing methods to model specific animal behaviours, for example prey signalling behaviour or kleptoparasistsm. In addition to journal papers and book chapters, mark recently (2013) published a book game-theoretical models in Biology.

Within the last ten years, models of evolution have begun to incorporate structured populations, including spatial structure, through the modelling of evolutionary processes on graphs (evolutionary graph theory). One limitation of this otherwise quite general framework is that interactions are restricted to pairwise ones, through the edges connecting pairs of individuals. Yet many animal interactions can involve many individuals, and theoretical models also describe such multi-player interactions. 

We shall discuss a more general modelling framework of interactions of structured populations, including the example of competition between territorial animals. Depending upon the behaviour concerned, we can embed the results of different evolutionary games within our structure, as occurs for pairwise games such as the Prisoner's Dilemma or the Hawk-Dove game on graphs. Finally we consider some example population structures and evolutionary dynamics.

The discussions will continue over biscuits and tea/coffee after the seminar. 
Hope to see many of you!

Tuesday 6 December 2016

Biosciences Seminar Speaker 08 December 2016

Biosciences Seminar Series - Autumn 2016
08 December 2016 - 2pm - Wallace Lecture Theatre (room 113)

note change of time and venue!

Securing the global aquatic food supply - a shared responsibility between producer and consumer nations

Dr Grant D Stentiford

Our speaker of this week, Dr Grant Stentiford Director of the European Union Reference Laboratory for Crustacean Diseases and Principal Scientific Officer and Team Leader of the Pathology and Molecular Systematics Team at Cefas Weymouth LaboratoryAfter a PhD in invertebrate pathology from the University of Glasgow, Grant has extensively worked on devising new and improved methods for the classification and early detection of disease in experimental, farmed and wild aquatic animals, especially of novel and emerging pathogens. For his work on aquatic animal pathology Grant combines clinical and molecular, to provide relevant results to aid national and regional responses to disease outbreaks in wild and farmed aquatic animals. Given his work, in 2008 the EC requested Grant to establish the first European Union Reference Laboratory for Crustacean Diseases (EURL) - an organisation that now coordinates 27 Member State National Reference Laboratories across the EU and has become a leader in crustacean pathogen diagnostics and is a globally recognised expert centre able to respond to disease outbreaks in farmed and wild animals.


Hope to see many of you - everyone most welcome to attend!

For the list of forthcoming seminars, see here, and here.

Monday 28 November 2016

Biosciences Seminar Speaker 01 December 2016

Biosciences Seminar Series - Autumn 2016
01 December 2016 - 1pm - Zoology Museum (Wallace 129)

The devil is in the details: on a quest for causality in ecology and evolution

Dr Achaz von Hardenberg

Photo by Yves Adams

Our speaker of this week, Dr Achaz von Hardenberg from the Department of Biological Sciences at the University of Chester (UK) will present his research on the links between parasites, behaviour life history variation and genetics in mountain mammals, using causal inference methods for ecological research. Achaz is a conservation ecologist, interested in behavioural ecology, population dynamics and conservation, especially of mountain ungulates and marmots. Previous to Chester, Achaz worked at the National Centre for Statistical Ecology (University of Kent, UK) and before going back to Academia, Achaz was as a research biologist and head of the science section at the Gran Paradiso National Park (GPNP, Northwestern Italian Alps), responsible for the long term ecological research and conservation projects in the Park.

Disentangling cause-effect relationships is a primary, understated, goal in evolutionary biology and ecology. Controlled and randomised experiments, the golden standard in causal inference, can be used to study ecological and microevolutionary processes in the lab but are rarely applicable in ecological studies on wild populations, or when the interest lies in explaining the macroevolutionary processes behind the variability in traits among species. With few exceptions field ecologist and comparative evolutionary biologists thus renounce to make any inference about causality from their observational studies, resigning to the sobering precept - we all learnt during our undergraduate statistics courses - that correlation does not imply causation. 

However, recently new structural equation modelling (SEM) approaches have been developed, providing formal methods to specify and compare complex models of the relationships among ecological variables, in order to disentangle direct and indirect causal effects when only observational data is available. In this talk I will provide a short introduction to causal inference and show how we have applied these powerful methods to test causal models of the complex relationships between corticosteroid hormones, parasites, behaviour, genetic variability and life history traits in various wildlife species including Bighorn sheep (Ovis canadensis), Chamois (Rupicapra rupicapra), Alpine ibex (Capra ibex) and Alpine marmots (Marmota marmota). 

Recently we have also extended causal inference to phylogenetic comparative studies, developing a method for Phylogenetic Path Analysis which finally allows
evolutionary biologists to formulate causal models of hypothesised direct and indirect evolutionary relationships between life history, ecological and morphological traits in comparative studies taking into account the underlying phylogenetic signal. Finally I will discuss the potential of causal inference to provide better evidence to inform conservation.

Hope to see many of you - everyone most welcome to attend!

For the list of forthcoming seminars, see here, and here.

Tuesday 22 November 2016

Biosciences Seminar Speaker 24 November 2016

Biosciences Seminar Series - Autumn 2016
24 November 2016 - 1pm - Zoology Museum (Wallace 129)

Hot dogs: understanding climate change impacts in a tropical mammal

Prof Rosie Woodroffe

Our speaker of this week, Prof Rosie Woodroffe from the Institute of Zoology at the Zoological Society of London, will present her research on the ecological drivers of an African carnivore, the wild dog (Lycaon pictus). Rosie's research is wide ranging and interdisciplinary, at the interface of conservation biology, wildlife management, disease ecology, and animal behaviour/behavioural ecology, and with a strong commitment to using science to influence both policy and conservation action. Whilst hence most of her research applied, not rarely has it lead also to advancements of basic ecological interest. 

Rosie's main research focuses on three themes. Regarding the conservation of wildlife that conflicts with people, an increasingly important topic in human-dominated landscapes, her work has focused on identifying the ecological drivers of human-wildlife conflicts (especially in African carnivores) and finding technical measures to resolve the latter. Her work on infectious disease in ecology and conservation has lead her to become one of the most important UK researchers on the contentious issue of the role of badgers in bovine tuberculosis (TB; e.g. see here). Her work on species conservation planning has led her to become part of the IUCN/SSC Task Force on Species Conservation Planning, coordinate the African wild dog working group of the IUCN/SSC Canid Specialist Group, and in drafting recovery plans and national management plans for endangered species across America and Africa.

Last, but not least, Rosie won the Science Slam at the 2015 BES Annual Meeting (see here), so we might well expect an engaging talk!

Climate change imposes an urgent need to recognise and conserve the species likely to be worst affected. Physiologists predict direct impacts of rising ambient temperatures on tropical species, yet ecologists have mostly characterised indirect effects on temperate and polar species. In this talk I will describe direct impacts of high ambient temperatures on reproductive success in a tropical carnivore, the African wild dog (Lycaon pictus). 

High temperatures directly constrained wild dog packs’ foraging time, especially during the energetically-costly pup-rearing period. Packs which reared pups at high ambient temperatures produced fewer recruits, and took longer to produce their next litter, than did those rearing pups in cooler weather. Over time, rising temperatures coincided with falling wild dog recruitment, suggesting that climate change may already be impacting this endangered species. 

These impacts would have been missed by simplistic trait-based assessments of climate change vulnerability, highlighting a need for species-specific assessments where possible, especially among tropical wildlife.

Hope to see many of you - everyone most welcome to attend!

For the list of forthcoming seminars this term, see here, here, and here.

Tuesday 15 November 2016

Biosciences Seminar Speaker 17 November 2016

Biosciences Seminar Series - Autumn 2016
17 November 2016 - 1pm - Zoology Museum (Wallace 129)

The diversifiers of life history strategies in animals and plants

Dr Roberto Salguero-Gómez

Our speaker of this week, Dr Roberto Salguero-Gómez from the Department of Animal and Plant Sciences at the University of Sheffield, will present his research on the drivers of differences in life history traits across plants and animals. Rob's research is wide-ranging, comprising animal and plant demography, including novel research on senescence (see here), drivers of variation in life history traits, causes of animal and plant performance, or effects of climate change on native biota. 

In addition to his association with Sheffield, Rob is also associated with the Australian Research Council Centre of Excellence for Environmental Decisions at the University of Queensland, Australia, the Evolutionary Biodemography Laboratory at the Max Planck Institute for Demographic Research in Rostock, Germany, and the School of Natural Sciences at the Department of Zoology & Trinity Centre for Biodiversity Research at Trinity College Dublin, Ireland. Hence, this week's seminar at Swansea is a rare occasion to meet and chat to Rob in person somewhere else from an airport or a seat on a transcontinental flight :-)

Life history traits are the events in our lives that control our demographic performance, our well-being and the well-being of societies. Examples include the age at maturity, reproductive window, mean and maximum longevity, post-reproductive lifespan, number of babies produced, and mortality rate, to mention a few. These factors, which are rather well understood and known to influence human population dynamics, our economics, insurance plans, and retirement funds, to mention a few, are not unique to Homo sapiens. Life history traits can be calculated for any population from any species where the individual can be clearly defined and where demographic information is available. The great potential for application of the tools that allow for the calculation of life history traits from a rich repertoire of organisms, from orchids to ferns to redwoods, to mice, bats, bears and C. elegans would allow evolutionary ecologists to tap into questions of global scope such as what strategies are most successful in what environments, what are the factors enhancing the diversification of life history strategies, and which one restrain them. 

Up until recently comparative studies examining variation in life history traits had been limited mostly to mammals and birds, mostly due to the lack of comprehensive repositories for other taxonomic groups. Here, I introduce the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database (, which together contain high-resolution demographic data in the shape of matrix population models for over 2,500 animal and plant species around the globe. I use the demographic machinery developed in the last years to decompose biologically meaningful life history traits from these matrices to examine what are the phylogenetic and environmental factors driving the diversity in life history strategies across plants and animals.

Hope to see many of you - everyone most welcome to attend!

For the list of forthcoming seminars this term, see here.

Wednesday 26 October 2016

BioMaths Colloquium - 28/10/2016

BioMaths Colloquium Series - 2016/17

28 October 2016 - 3pm Maths Seminar Room

(room 224 Talbot Building 2nd floor)

Modelling collective motion in animal groups

Dr. Daniel Strömbom

(Uppsala University, Sweden & Swansea University, UK

pic by Daniel Strömbom

We are delighted to welcome our speaker for the second Biomath Colloquium seminar of this term, Dr Daniel Strömbom from the department of Mathematics at Uppsala University in Sweden. We are especially excited as Daniel has now also joined us at Swansea University, as an Independent Research Fellow, hosted by the SHOALgroup of Dr Andrew King at the Biosciences Department. Thus, Daniel has also become our newest member of our Biomathematics Centre, so please do come to meet him this Friday! Daniel is keen to present his work and establish new collaborations.

Flocks of birds and schools of fish are a common sight. They come in all shapes and sizes and exhibit a variety of dynamical behaviours at the group level. For decades, researchers have worked on isolating sets of biologically plausible local interaction rules, such that if each member of a group follow these rules, the resulting structure and behaviour of the group as a whole will be similar to that observed in real flocks, schools, and other moving animal groups. 

from: PInterest
These local interaction rules are often of the type ‘stay close to your neighbours (attraction), but avoid getting close enough for collisions to occur (repulsion), and take the average heading of your neighbours (orientation)’. Mathematical, and/or computational, methods are typically employed to determine the group level properties that will emerge from a given set of local interaction rules.

In this talk I will provide an introduction to collective motion in animal groups, with an emphasis on mathematical/computational modelling approaches used in the field. In particular, the use of so called self-propelled particle models. Using work on the topic that I have been involved in from 2010 up to now as a backbone I aim to illustrate the utility of, and problematic issues with, the self-propelled particle model approach to collective motion in animal groups as it stands today. 

The discussions will continue over biscuits and tea/coffee after the seminar. 
Hope to see many of you!

Monday 24 October 2016

Biosciences Seminar Speaker 25 October 2016

Biosciences Seminar Series - Autumn 2016
25 October 2016 - 1pm - Zoology Museum (Wallace 129)

(note change of day!)

Plant Biomass Degradation by White Rot Fungi

Prof Kristiina Hilden

Our speaker of this week, Prof Kristiina Hilden from the Department of Food and Environmental Sciences at the University of Helsinki, will present her research on fungal molecular biology and enzymology, such as comparing the functional genomics of plant biomass degrading fungi across various biotopes. Her research is wide ranging, from work on intraspecies diversity in fungal wood decay (see here) to improving green energy solutions (biorefineries and business needs, improved catalysts for sustainable biomass conversion - see here and cost-effective industrial production - see here). Thus, be prepared to a wide-ranging, stimulating talk!


Hope to see many of you - everyone most welcome to attend!

For the list of forthcoming seminars this term, see here.

Wednesday 12 October 2016

Biosciences Seminar Speaker 13 October 2016

Biosciences Seminar Series - Autumn 2016
13 October 2016 - 1pm - Zoology Museum (Wallace 129)


the evolutionary ecology of animal colouration

Dr William Allen

Image from:

Our speaker of this week, Dr William Allen from Swansea University, is an ecologists and in his work he uses comparative approaches to understand patterns of diversity in animals’ traits, to understand their evolutionary history and ecological context. Given the title of his talk, come to listen and watch a colourful seminar! 

The colours and patterns of animals are perhaps their most apparent and charismatic features. This ease of observation along with the role colouration can have in a wide range of ecological and evolutionary processes (predation, competition, mate choice, thermoregulation etc.) also makes it an important phenotype for scientific investigation. In this talk I give an overview of my work on understanding broad scale patterns in colour pattern diversity between species. Studies span a wide range of vertebrate taxa including primates, ruminants, cats, geckos and snakes. Topics include the ecological and behavioural factors that underlie colour differences, what form can tell us about function and mechanism, and how investigating colouration can inform our understanding of basic evolutionary processes such as speciation. 

Hope to see many of you - everyone most welcome to attend!

For the list of forthcoming seminars this term, see here.

Friday 16 September 2016

BioMaths Colloquium - 19/09/2016

BioMaths Colloquium Series - 2016/17

19 September 2016 - 3pm Maths Seminar Room

(room 224 Talbot Building 2nd floor)

Large scale PDE constrained optimization of cardiac defibrillation

Dr. Chamakuri Nagaiah

(Johann Radon Institute for Computational and Applied Mathematics, Austria)

from: Chamakuri et al. (2015)
We have an early start this year! Our first BioMath talk of the 2016/17 series will be in September, by our guest Dr. Chamakuri Nagaiah, from the Johann Radon Institute for Computational and Applied Mathematics (RICAM), part of the Austrian Academy of Sciences (ÖAW).
In this talk we present a feasible study of optimal control techniques for cardiac defibrillation on the basis of the bidomain-bath equations posed on a realistic rabbit ventricle geometry. The bidomain model consists of a system of elliptic partial differential equations coupled with a non-linear parabolic equation of reaction-diffusion type, where the reaction term, modeling ionic transport is described by a set of ordinary differential equations. The bidomain model is coupled with the quasi-static Maxwell's equation to consider the effect of an external bathing medium.

The optimal control approach is based on minimizing a properly chosen cost functional depending on the extracellular current as input at the boundary of torso domain, which must be determined in such a way that wave fronts of transmembrane voltage in
cardiac tissue are smoothed in an optimal manner. The existence and uniqueness of a weak solution for the primal and dual problems, the derivation of the optimality system and the description of its discretisation is given. In parallel computations, the domain decomposition of such realistic geometry consists of heart surrounded by torso is not a trivial task.  

I will present domain decomposition techniques and their efficient implementation of such PDE constrained optimization of bidomain model. The parallel algorithm efficiency is demonstrated not only for the direct problem but also for the optimal control problem.

The discussions will continue over biscuits and tea/coffee after the seminar. 
Hope to see many of you!

Monday 8 August 2016

Postgraduate Seminar Speakers 11th August 2016

Postgraduate Seminar Speakers 11th August 2016
1pm - Zoology Museum (Wallace 129)

S P E A K E R   1
O ye of little plague? Linking genetic diversity of North American Signal Crayfish populations (Pacifastacus leniusculus) with prevalence of crayfish plague (Aphanomyces astaci)

Chloe Robinson

Signal crayfish (Pacifastacus leniusculus) were first introduced to the UK in the 1970s through aquaculture and currently occupy a widespread distribution. Signal crayfish cause detrimental effects on native biodiversity, namely on their conspecific the white-clawed crayfish (Austropotamobius pallipes). The invasive crayfish are larger, more aggressive and more fecund than A. pallipes and subsequently outcompete them for food and shelter. The spread of crayfish plague (Aphanomyces astaci) from P. leniusculus causes 100% mortality in A. pallipes populations without having any adverse effects on the invasive crayfish. Despite their current status, very little is known about the dispersal and population genetics of P. leniusculus, especially in relation to plague infection levels. Catchments which are free of crayfish plague despite the presence of signal crayfish, could potentially see the coexistence of natives and invasive crayfish and identifying rivers early which are at risk of infection could minimise loss of native populations and aid in conservation of the species.

S P E A K E R   2
From Community to Individual: DNA Metabarcoding Reveals Pollen Transport by Hoverflies

Andrew Lucas

Pollination by insects is a key ecosystem service, and important to wider ecosystem function.  Using DNA metabarcoding to identify pollen, I have constructed pollen transport networks for hoverflies (Syrphidae) in the genus Eristalis and investigated pollen transport networks in grasslands in west Wales. The results are giving new insights into how pollen transport networks are structured.

S P E A K E R   3
The importance of body orientation in collective herding behaviour

Dan Sankey

For social animals, coordinating their motion to remain cohesive can provide selective advantages. An early study by Herbert Prins suggested that during stationary periods, ungulates can use body orientation to ‘vote’ on their preferred travel direction. Modern empirical and theoretical studies have since emphasised the importance of inter-individual alignment (a product of orientation) in collective decision making, although generally this has not been explored in the ‘pre-departure period’, or in free ranging animal groups. I will present high-resolution GPS (1 Hz) and inertial sensor (40Hz) data for a herd of n=16 goats over a 10-day period in the Namib Desert, Namibia. I will show how integrating compass heading from magnetometer/ accelerometer data with other measures from GPS data (e.g. linear distance; speed) provide information on individuals’ orientation even when sedentary or slow moving, allowing for a fuller understanding of the specific movement cues and social interactions that drive group movement dynamics.