Dating Mammalian Evolution

By Claire Asher, on 28 March 2014

When the age of the dinosaurs ended around 65 million years ago, mammals stepped in to fill the gap, and the age of the placentals began. However, whether early placental mammals were already present on Earth before the demise of the dinosaurs has been the subject of a long standing debate. Recent research in GEE used genomic data, in combination with fossil evidence, to show that the earliest placental mammals were indeed scurrying between the feet of dinosaurs.

Shrew-like mammals scurry between the feet of dinosaursThe huge diversity of placental mammals on Earth today first appeared shortly after the mass extinction event that killed the dinosaurs. It is thought that the loss of the dinosaurs, along with much of life on Earth, freed up niches which placental mammals to evolved to fill. But were early placental mammals present, waiting in the wings, during the age of the dinosaurs, or did they appear rapidly after their demise? One recent study suggested that, based on fossil evidence, the placental mammals must have appeared after the cretaceous-tertiary boundary (KT) when dinosaurs and most life on Earth was wiped out. However, a recent paper by GEE’s Mario dos Reis and Ziheng Yang, in collaboration with Philip Donoghue from the University of Bristol, highlights flaws in the methods used in this study, and utilitsed a more thorough approach to show that early placental mammals likely predated the KT boundary.

Using genetic sequence data from over 14,000 genes, combined with fossil evidence, GEE researchers applied 3 alternative statistical methods to estimate the age of the earliest placental mammal; ancestor to all modern placental mammals. Although different statistical methods yielded slightly different estimates, and differed in their accuracy, they all agreed that placental mammals must have already been around before the dinosaurs went extinct. The adaptive radiation of mammals that occurred after the extinction of the dinosaurs was dramatic, but it was initiated by a few shrew-like species which had already evolved. This study highlights the importance of using statistical methods to estimate the true age of ancestral species; the age of the oldest fossils is not the same as the age of the ancestral species that gave rise to them, and statistical techniques must be employed to estimate this. Using both molecular and fossil evidence to inform estimates also provides more robust evidence for the true age of the first placental mammals, and the theory that the earliest ancestors of placentals predated the disappearance of the dinosaurs.

Original Article:

This research was made possible by funding from the Biotechnology and Biological Sciences Research Council (BBSRC).

The Delicate Balance of Effect and Response

By Claire Asher, on 18 February 2014

We may not always be aware of it, but many wild plants, animals, fungi and even bacteria, provide crucial services to us which keep the ecosystems of Earth functioning. Environmental changes caused by human activities are now threatening many species, and those that cannot withstand these changes may be lost forever, potentially taking the services they provide away. New research from GEE and collaborators worldwide aims to improve our understanding of how the traits and evolutionary histories of species influence their ability to provide essential ecosystem services, and to persist in the face of ongoing environmental change.

The diverse array of species we share planet Earth with, and the complex ecosystems they form, are crucial to our continued survival and well being. Species and ecosystems provide a huge number of ‘ecosystem services’ – functions such as nutrient cycling, waste decomposition, pollination and food, to name just a few, which humans rely on. However, many species are now under threat from human activities like deforestation, hunting and pollution. Scientists are working to understand how species and ecosystems will respond to our continued activities in the future, and particularly how this may effect the vital ecosystem services upon which we rely. Recent research by GEE’s Prof. Georgina Mace, in collaboration with researchers from Cordoba National Univerity, Imperial College London, VU University, Yale University and CSIC, has attempted to develop a new framework for risk assessing the effect of human activities on ecosystem services.

The framework considers two key aspects of species: their effect on the generation of a specific ecosystem service (e.g. seed dispersal), and their response to specific environmental pressures (e.g. drought). Both the effect of a species and the response of a species are underpinned by its traits, and each is influenced not by a single trait but a combination of traits. The response of a species will determine it’s ability to survive and flourish through future environmental changes and to continue to provide it’s ecosystem effects. However, only a species’ response is the subject of natural selection, via changes to the underlying traits; the effect of a species is merely a biproduct of traits selected for their influence on survival. In this way, the aspects of a species’ biology upon which we rely are only indirectly influenced by natural selection, and will only be maintained if the traits that generate them are beneficial through the environmental changes we cause. The framework developed by GEE researchers and collaborators considers how the response of species to envinmental stressors interacts with the effect of that species on key ecosystem services, and whether species with a large effect are more or less vulnerable to environmental change.

A third key factor influencing the sensitivity of ecosystem system services is the evolutionary relationships between species providing them. Closely related species often share similar traits, which may or may not result in them having similar effects and responses. If this is the case, then ecosystems in which a particular service is provided by a group of closely related species may be more vulnerable to environmental change, since those species may well share similar responses, and be sensitive to similar environmental pressures. Although many species’ traits are known to be similar amongst related species, because effects and responses are each the result of a combination of traits, it is not known whether this relationship is also common for these variables.

The new framework developed by GEE’s Professor Georgina Mace and collaborators attempts to address this by incorporating evolutionary relationships (phylogeny) into their response-effect model, and applying this model to 5 case studies. The case studies cover 5 species assemblages including a total of 480 species in Europe, Central America and Africa, for which response and effects could be estimated based on past studies of species’ traits and vulnerabilities. The case studies tended to show a strong relationship between phylogeny and both species’ effects on ecosystem services and their responses to environmental stressors. This indeed suggests that ecosystem services that rely upon closely related groups of species may be most at risk from environmental change. Cases where effects and responses are negatively correlated, so that the most influential species in terms of a given ecosystem service are also the most vulnerable to environmental stress, are most vulnerable to loss of that ecosystem service through human activities. Whether this type of relationship is common in nature remains to be investigated by future studies, and this framework provides a powerful basis with which to do so.

Our relentless demands on the natural world are inevitably leading to new pressures and stresses on natural populations, and it is of great concern that these pressures may negatively impact on the vital ecosystem services that we rely upon, often without even realising it. Ecosystem services provide us with food and fresh water, decompose our waste, recycle nutrients and remove harmful toxins. Without them our continued survival and well being would be seriously compromised. Scientists are still working to understand how species’ traits influence their ability to provide ecosystem services and their resilience to ongoing environmmental change. A new framework developed in collaboration between universities in the UK, Spain, Argentina, the USA and the Netherlands is beginning to shed light on the interaction between species’ traits, their effect on ecosystem services and their response to environmental change, and how these factors are influenced by evolutionary relationships between species. This framework offers a powerful new view of how the traits of species within an ecosystem translate into the ecosystem services upon which we are so reliant, and future research building upon this framework promises to improve our understanding of ecosystem services and environmental change.

Original Article:

() Ecology and Evolution

This research was made possible by funding from the Natural Environment Research Council (NERC), the Leverhulme Trust, and the US National Science Foundation

It’s All in the Wrist

By Claire Asher, on 20 December 2013

The evolution of the primate wrist has been dramatic, enabling primates to adapt to a wide variety of lifestyles and walking styles, including tree-swinging, climbing and terrestrial walking both on four legs and two. In hominids, the evolution of the bipedal gait freed up the forelimbs for tool use, and the wrist evolved independently from the feet enabling increasing dexterity that was crucial to human evolution. Recent research in GEE has provided a more thorough analysis of primate wrist evolution, and shed light on a long-standing debate in human evolution: did humans evolve from tree-swingers or knuckle-walkers?

Primates use their limbs to move in a wide variety of different ways, many of which are not seen in other animals alive today, such as vertical clinging, swinging and leaping, and upright walking. Furthermore, within primates, some species have moved towards a more upright stance, freeing the forelimbs for other tasks. This is thought to have been a key aspect of human evolution, increasing our ability to develop and use complex tools, and possibly even playing a role in the evolution of gesture and language. The morphological evolution of primate wrist bones has therefore been of great interest to evolutionary biologists.

Comparative studies looking at humans and other living and extinct apes and monkeys have previously attempted to deduce the early evolution of the human skeleton, in particular how our bipedal stance evolved. However, many of these studies have attempted to determine the rate of evolution (the speed of ticking of the evolutionary clock) using morphological characteristics, which may not provide an accurate view. Recent research by GEE academics, in collaboration with the University of Kent and the Max Planck Institute, has attempted a more rigorous analysis of primate wrist-bone evolution by mapping morphological features onto an independently-generated phylogenetic tree, using molecular methods to estimate the speed of evolution. This method allowed the authors to detect multiple independent appearances of the same feature, as well as more accurately measuring the speed of wrist evolution.

Gorilla Wrist Bones Dr Kivell (University of Kent) and UCL’s Anna Barros and Dr Smaers, compared wrist bone features across 24 living primate species and 16 extinct species. Primate wrists are composed of between 8 and 9 separate bones, and they discovered differing evolutionary patterns for different bones, indicating that each bone evolves at least partly independently from the others. Some of the evolutionary changes that occurred during primate evolution are shared between species which move in similar ways, whilst others are shared between closely related species, regardless of locomotion. Hominids tended to show more morphological variation than monkeys, suggesting stronger selection on the hominid wrist, possible relating to rapid and major changes in body size and locomotion in these species.

This study also sheds light on a long-standing debate over the early evolution of bipedalism in hominids; competing hypotheses have suggested that humans evolved to an upright position from a knuckle-walking stance (e.g. modern Gorillas), or that they evolved from an aboreal, tree-swinging ancestor. The results of this study show adaptations in the hominid wrist bone, which appeared in parallel with Gorillas and Chimpanzees, that are consistent with increased weight being placed on the wrist during knuckle-walking. Thus, it seems more likely that humans evolved from a knuckle-walking, terrestrial ancestor.

Our bipedal stance came with a huge number of skeletal adaptations, and enabled us to adapt to new environments. It may also have been crucial in freeing up our hands for other tasks, which in turn played a role in our intellectual development. Understanding how our skeleton, particularly our hands and feet, evolved through the primate lineage therefore sheds light on some of the deepest aspects of humanity. The bones in the primate wrist have evolved at least partly independently from each other, and this has generated a large variety of wrist morphologies, adapting different primate species to different modes of locomotion. Early hominids likely evolved their bipedal stance from a knuckle-walking ancestor, rather than an arboreal tree-swinger.

Original Article:

() BMC Evolutionary Biology

This research was made possible by funding from the Natural Environment Research Council (NERC), the Natural Sciences and Engineering Research Council of Canada (NSERC), the Fundação para a Ciência e a Tecnologia , the Max Planck Society , and a General Motors Women in Science and Mathematics Award

The Transcriptional Profile of A ‘Wingman’

By Claire Asher, on 27 November 2013

In many species, males have special adaptations to attract females. From antlers to stalk-eyes, to bright plumage and beards, males across the animal kingdom work hard to look attractive to the opposite sex. In some species, looking good isn’t enough, though. Male wild turkeys need a less attractive ‘wingman’ to help him attract a woman. Wingman turkeys show less extreme sexual traits than the dominant males, and researchers from GEE have exploited this ‘intermediate phenotype’ to investigate how gene expression controls sexual traits. Subordinate male turkeys are physically demasculinised, and this is reflected in their gene expression. Whilst clearly male, these turkeys tend to express ‘male’ genes less and ‘female’ genes more, indicating that sexual phenotypes, at least in this species, exist upon a continuum. This has important implications for how we view sexual selection and sexual traits across the animal kingdom, as well as in our own species.

You might think this is a face only a mother could love, but to a female turkey, this guy is very attractive. Male wild turkeys have a number of physical traits that make them very, very sexy…. to female turkeys, at least. They are larger than females, their feathers are iridescent, their faces are bright red and adorned with caruncles, wattle and a snood. As they grow up, young male turkeys argue with their brothers for dominance. One brother wins, and the others become subordinate. These subordinate males rarely get the chance to mate themselves, but helping out their brother means passing on their genes indirectly. If, later in life, the dominant brother dies, the subordinate may get his chance in the limelight and develop a dominant phenotype. This shows just how plastic sex can be in the animal kingdom.

Differences in Gene Expression
Differences between the sexes form ‘sexual phenotypes’ that are largely the result of the differential expression of genes that are present in both sexes. Although sex chromosomes are also important in controlling the development of sexual traits, many genes on other chromosomes also contribute. Many genes show differences in expression between the sexes.

Theory suggests that genes expressed differently in different sexes are responsible for generating the sex-specific characteristics we observe. However, this hypothesis has been difficult to test in species where sex is binary. This is where wild turkeys come in handy – the existence of the subordinate male phenotype, with reduced sexual traits, provides a rare opportunity to decouple genetic sex and sex-biased gene expression. If sex-biased genes encode sex-specific phenotypes then the subordinate male phenotype should be expected to be the product of reduced expression of male-biased genes and increased expression of female-biased genes.

Researchers in GEE and the Department of Zoology, University of Oxford, investigated gene expression patterns in females, dominant and subordinate males. Around 2000 genes were male biased and nearly 3000 showed female bias.

Unravelling the ‘Wingman’ Phenotype
The gene expression patterns of subordinate males clearly clustered with dominant males. So subordinates are not intersex. However, there were subtle differences between the subordinate and dominant males. Subordinate males tended to express male-based genes at lower levels than dominant males, indicating transcriptional demasculinisation. They also expressed female-biased genes at a higher level than dominant males, suggesting transcriptional feminisation. Expressionally, subordinate males were less masculine and more feminine than dominant males. This is consistent with their visual appearance.

Furthermore, genes that were more strongly sex-based showed a greater level of demasculinisation in subordinates than those that were less strongly sex-biased. This suggests that the genes we find to be most strongly sex-biased may contribute the most to generating the male or female phenotype.

These patterns were also true for genes found on the z chromsome – the sex chromosome in birds (analogous to our ‘Y’ chromosome). However, the patterns were no stronger for these genes than for those on other chromosomes, suggesting that the sex chromosome does not contribute disproportionately to the male or female phenotype. This might come as a surprise – surely the sex chromosome should control sex? There is now a great deal of evidence that this isn’t the case, and many animals get on just fine without a sex chromosome at all!

Dominant and subordinate males reveal a continuum of sexual characteristics physically, and this is mirrored by gene expression patterns. Whilst clearly male, subordinate males showed up-regulated of ‘feminine’ genes and down-regulation of ‘masculine’ genes across the transcriptome. This demonstrates for the first time that sex-biased genes are indeed important in generating the sexual traits we observe in nature. Physical sex is determined by the combined action of many genes, some male-biased and some female-biased, and intermediate physical characteristics are possible simply through altering the expression of key sex-biased genes. This result has clear implications for how we view sex and gender in our own species, and greatly enhances our understanding of sexual selection and sexual dimorphism across the animal kingdom.

Original Article:

() PLOS Genetics

This research was made possible by funding from the European Research Council

Damage and Fidelity: The Role of the Female Germline in mtDNA Inheritance

By Claire Asher, on 11 November 2013

Billions of years ago, one single-celled organism engulfed another, beginning a symbiotic interaction that would change live on Earth forever. The mitochondria are what remains of this symbiotic event, and are responsible for producing energy in all eukaryotic cells. Derived from a free-living organism, they carry their own genes, but these genes are at risk of damage by a natural by-product of energy production – free radicals. Mitochondrial DNA in most cells are exposed to these reactive oxygen species and may be damaged over time, resulting in some diseases of age. However, if damage occurs to the mitochondrial genes in egg and sperm cells, this damage would be passed on to the next generation. Despite this, aging is not heritable, and very few mitochondrial mutations are passed from one generation to the next. Researchers in GEE have been investigating the mechanism responsible for this apparent paradox – mitochondrial inactivation – and have discovered that this mechanism is extremely widespread in the animal kingdom.

The mitochondria are the powerhouses of the cell, generating energy through oxidative phosphorylation down an electron transport chain. The electron transport chain occurs across the mitochondrial membrane, and was a key innovation during the evolution of multicellular life. Mitochondria originated as free-living single celled organisms that were engulfed inside another cell and subsequently formed a cooperative partnership that allowed cells to produce energy more efficiently. Because of their symbiotic origin, mitochondria brought an entire genome with them, and although this has been wittled down to only a small number of genes, some genes still reside inside the mitochondria. This is a big problem, however, because in the process of producing energy, mitochondria also produce harmful reactive oxygen species (ROS), also known as free radicals. These can cause mutations in DNA, and the mitochondrial genes are therefore at great risk because of their proximity to the site of ROS production. Mutations in mitochondrial DNA are thought to be a key cause of age-related diseases.

The Electron Transport Chain
Image by Rozzychan, creative commons.

Mutations in DNA (mitochondrial or nuclear) in most cells in the body can be harmful to the health of the individual, but will have no influence on the next generation. The genes which we pass onto the next generation are separated off during early development into special ‘germ line’ cells which form sperm and eggs. Great care is taken to minimise the risk of mutation to these genes – genes in germline cells act as a blue print for the next generation. This is essentially why aging is not heritable, and it is a system that works pretty well.

Sperm Cells
Image by be_sperm

However, sperm and egg cells need mitochondria to produce energy, and so mitochondrial genes in our germ cells may still be at risk of mutation. If the free radicals generated in germ-line mitochondria harm mitochondrial DNA, these damages would be passed on to the next generation! Research in GEE has uncovered a rather elegant solution to this problem – those mitochondria that will be passed to the next generation are maintained in an inactive state. It’s a bit like buying two toasters and keeping one in a cupboard, unused, to provide a template from which to build a new toaster when the old one breaks.

Mitochondria are only inherited through the maternal line – every mitochondria in your body came from your mother, and this is true for most animal species. The mitochondria in sperm are generally discarded at some point prior to fertilisation. So, in order to preserve the fidelity of mitochondrial DNA passed on to the next generation, we only need to ‘switch-off’ mitochondria in egg cells. This is great, since sperm really need their mitochondria to provide energy for all that swimming!

Egg Cell

Previous research by John Allen and colleagues in GEE indicated that mitochondria in egg cells of the moon jellyfish (Aurelia aurita) are inactive compared to mitochondria in sperm and somatic tissues. Recently, GEE’s Prof John Allen, along with Wilson de Paula (Queen Mary University of London) and colleagues have investigated this phenomenon further and discovered that this system of mitochondrial inactivation is widespread across the animal kingdom. Using qPCR, a technique for measuring and comparing expression patterns of specific genes, they found that in both fruit flies (Drosophila melanogaster) and zebrafish (Danio rerio) expression of three key respiratory genes (nad1, cob & cox1) is much lower in mitochondria in oocytes (egg cells) than in sperm and active muscle tissue. Expression levels were 15-fold lower in eggs, whereas sperm and muscle showed similar levels of expression. They also found that membrane electrical potential, a measure of the activity of the electron transport chain, was reduced in oocytes compared to both sperm and the surrounding tissue. Further, ROS production was 50- and 100-fold lower in the eggs of fruit flies and zebrafish respectively. Finally, they confirmed that oocyte mitochodria in both species exhibit a simpler structure, indicative of reduced activity. So, it seems that in both fish and flies, the mitochondria in egg cells represent little more than a blueprint, ready to be passed on to the next generation error-free. By deactivating ovarian mitochondria, the fidelity of information is ensured across generations, and aging is not heritable.

Wilson de Paula and Prof John Allen have now identified a similar pattern of mitochondrial inactivation in species across the animal kingdom, including jellyfish, fruitflies and zebrafish. Early in multicellular evolution, animals branched into two key groups distinguished by differing patterns of embryonic development; protostomes (including arthropods, molluscs and nematodes) develop their mouth first, whereas deuterostomes (including vertebrates, tunicates and starfish) develop their anus first. This seemingly small difference represents a fundamental divide in the animal kingdom. This study therefore demonstrates that mitochondrial inactivation occurs in both of these key branches. Previous work by de Paula and Allen has shown a similar pattern in jellyfish, members of the phylum Cnidaria which pre-date the great protostome-deuterstome divide. Together, this work suggests that mitochondrial inactivation, as a mechanism to ensure fidelity of mitochondrial DNA transmission across generations, is likely to have emerged early in the evolution of multicellular life on Earth.

Ensuring the faithful transmission of genes to the next generation is a key problem for all life on Earth. Although the mitochondrial symbiosis event which marked the emergence of eukaryotic life was a major breakthrough in efficient cellular energy production, it brought problems of its own. Mitochondria must carry a few genes in order to maximise responsivness to cellular demands, but these genes are at risk of damage from a natural by-product of energy production – free radicals. A system of mitochondrial inactivation in female germ cells (eggs) may serve to resolve this conundrum, and seems to be shared across all animal life.

Original Article:

() Genome Biology and Evolution

This research was made possible by funding from the Natural Environment Research Council (NERC), and the The Leverhulme Trust

Size Matters: Why Reduced Sexual Ornaments are Rarely Seen

By Claire Asher, on 29 October 2013

Across the animal kingdom, males have evolved fancy physical ornaments, songs and courtship rituals, all in an attempt to attract the opposite sex. Most of the male ornaments and sexually-selected traits biologists tend to study are large, elaborate and flamboyant. But mathematical models predict that sexual selection is just as likely to make an ornament smaller or more modest as it is to make it more elaborate. Recent research by Dr Sam Tazzyman and Prof Andrew Pomiankowski from UCL’s Department of Genetics, Evolution and Environment, in collaboration with Prof Yoh Iwasa at Kyushu University, investigates why male ornaments tend to get bigger rather than smaller.

Male and Female Red Deer
Image by Deepsky, Creative Commons Licence

Sexual selection is the process whereby traits are favoured because they increase an individual’s success at obtaining mates, often at the expense of survival or condition. Sexual selection is a special case of natural selection, where natural selection is concerned with increasing the overall fitness of an organism. Sexual selection may act in opposition to natural selection, when traits that make you more attractive to the opposite sex also make you less fit in other ways. In these cases, the form a trait takes may be somewhere between the most attractive (sexual selection optimum) and the most fit (natural selection optimum). Sexual selection has been the focus of a great deal of evolutionary research, both experimental and theoretical, because it has the power to generate extreme physical and behavioural adaptations: huge antlers, complicated courtship displays, brightly coloured plumage, etc. Most research has focussed on bright, bold, exaggerated traits like these. But theory suggests that sexual selection should be just as likely to drive traits to be less extreme (than the natural selection optimum) as it is to make them more extreme. So why don’t we see sexually reduced traits much in nature?

First, Tazzyman and collegues searched the literature on mate choice and sexual selection for examples of reduced sexual traits – that is, cases in which females prefer males with a trait smaller, duller or less elaborate than the natural selection optimum. They found that for many types of trait, reduction simply isn’t possible, or is extremely difficult to define. For example, when a sexually-selected trait is a particular colour of a patch of plumage, how can we define exaggeration or reduction in this trait? Is the size of the patch most relevant, or the hue or saturation of colour? Similarly, for many traits, the natural selection optimum might be zero – no trait at all. For example, in many species the male is brightly coloured while the female is dull, here the dull colouration can be considered no trait and is assumed to be the natural selection optimum. Likewise, in many species the males carry physical adornments such as the red crests (or combs) of many gamefowl, which are totally absent in females.

Male and Female Junglefowl

Certainly, these issues with definition occur most frequently for colour, pheromone and behavioural traits. Morphological traits tend to lend themselves more readily to being classified on a simple scale, in which both exaggeration and reduction of that trait is possible. There are a few cases of females showing a preference for a smaller trait, but these examples are few and far between. Of 40 sexual traits for which both elaboration and reduction could be defined, 34 were found to be subject to sexual selection for exaggeration.

This imbalance may be partly explained by our own observation bias – smaller traits may be more difficult to detect and so tend not to become the subject of study. But, it is unlikely this is the full explanation. However, it seems that females may suffer a similar problem; if biologists aren’t noticing small ornaments, maybe the females aren’t either. This is one of three possible hypotheses that Tazzyman and colleagues tested to explain the apparent asymmetry in the direction of sexual selection. Male ornaments are signals, aimed at attracting a female – if that trait cannot easily be seen or detected by the female, then it cannot serve it’s purpose. Consistent with this, a mathematical model of sexual selection assuming asymmetrical signalling efficacy (where smaller traits are less effective at conveying their message) showed that exaggerated traits were more likely to undergo the ‘runaway’ selection characteristic of sexually-selected ornaments.

Peacock and Peahen
Image by ToastyKen, CC Licence

Their models also ruled out two other possible explanations – that it is more costly for a female to prefer a small trait than a large one, and that is it more costly for a male to carry a small trait than a large one. Neither of these models resulted in a bias towards exaggeration. Only models including an asymmetry in the efficacy of signalling produced results that mirror what we observe in nature.

Sexual selection acts upon traits that make one sex more attractive to the other, and can favour characteristics that are otherwise detrimental to survival or condition. Sexual selection has the power to generate the bright, flamboyant, exaggerated characteristics such as antlers that we see in many animals. Although many theoretical models predict both exaggeration and reduction in sexual traits, in wild populations, we rarely see this – almost all documented sexual traits are more extreme than their natural selection optimum. Sexual traits act as signals to the opposite sex, and this may explain why in the wild, sexual selection tends to exaggerate and elaborate traits which are more visible to females and so more effective at communicating their message.

Original Article:

() Evolution

This research was made possible by funding from the Natural Environment Research Council (NERC), and the Engineering and Physical Sciences Research Council (EPSRC)

GEE Science Uncovered

By Claire Asher, on 7 October 2013

On Friday 27th September, scientists in 300 cities across Europe got together with the public for a variety of activities and events to celebrate European Researcher’s Night 2013. In London, the Natural History Museum kept their doors open late for ‘Science Uncovered’ – an evening of special exhibitions, stalls and activities, engaging the public with researchers from universities and academic organisations across the capital.

Together with researchers from the Natural History Museum and UCL’s Department of Geography, academics from GEE displayed some of their work and chatted to the public about environmental change. GEE staff and students including Professor Georgina Mace, Dr Sarah Whitmee, Claire Asher and Stuart Nattrass, along with Sara Contu from the PREDICTS Project and Robin Freeman from ZSL, chatted to members of the public about their thoughts on environmental change and biodiversity loss.

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We are now becoming increasingly aware of the rapid climatic changes that are taking place globally, and with the release last week of the latest IPCC report, the climate has been a major talking point. Environmental change, including climate and land-use, will influence both us and the biodiversity with which we share our planet. Some animals may be able to adapt to climatic changes, but these will act in combination with human activities and land-use to influence which species persist and which perish.

PREDICTS Game NHMAs part of the GEE Environmental Change Stall, in collaboration with the PREDICTS Project, and ZSL, Claire Asher and Robin Freeman developed a game to test the public’s perceptions of present and future environmental change and biodiversity loss. Participants were asked to make a guess about future environmental change under two scenarios – a low-emissions scenario in which land-use decisions are based primarily on the agricultural value of the land, and a high-emissions scenario in which emissions pricing influenced land-use decisions. Predicted levels of global biodiversity were estimated up to 2100 using the PREDICTS model and well recognised scenarios of climatic warming and land-use change. The game proved very popular, with nearly 50 players during the night, competing to achieve the best score.

DSC06144 copyThe answer was not as simple as many of our players might have expected. Because climate does not act alone to influence species extinctions, land-use and other aspects of each scenario also played a major role. In the high-emissions scenario, emissions pricing (an attempt to minimise further warming) encouraged the preservation of primary forest, mitigating some of the negative effects of climate change on biodiversity. Meanwhile, in the low-emissions scenario, continued loss of primary forest in favour of agricultural land, particularly for the production of biofuels, meant that biodiversity suffered more than we might have thought from climate warming alone. Our decisions about emissions, land-use and conservation policies will have a far-reaching effect on global biodiversity.

The Future of Biodiversity game will be available to play online soon!

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Award-Winning Bat Conservation

By Claire Asher, on 16 September 2013

This year’s Vincent Weir Scientific award for bat conservation biology has been awarded to GEE’s Charlotte Walters for her PhD work on the iBatsID tool.

The Vincent Weir Scientific Award is an annual award given to a UK-based student for their outstanding contribution to the conservation biology of Bats. It is awarded by the Bat Conservation Trust (BCT), a national organisation devoted to the conservation of bats and their habitats within the UK. Charlotte Walters, who recently completed her PhD with the Zoological Society of London (ZSL), University College London (UCL), University of Kent and BCT, has been awarded the prize for her contribution to bat conservation and particularly her work for the Indicator Bats Program (iBats).

iBats is a partnership between ZSL and BCT, aiming to monitor global changes in bat biodiversity and provide valuable data for policy makers and conservation groups. They provide training and equipment to projects monitoring bat biodiversity to ensure standardised methodology which will enable global comparisons. They have also developed a number of free tools for iPhone and Android which enable fast, simple and efficient detection and identification of bats, and Charlotte’s iBatsID program is a key part of this.

Myotis bechsteini
Image Credit: Gilles San Martin, used under creative commons licence.

During her PhD, Charlotte developed the iBatsID tool, an automatic tool for acoustic identification of European bat ecolocation calls. The tool is able to identify 34 different species of bat based on their calls alone, and is enabling scientists to achieve consistent monitoring of bat populations across Europe. The tool uses ensembles of artificial neural networks to classify bat echolocation calls and identify which species or group the call belongs to. Dr Karen Haysom (Director of Science, BCT) says “New tools and techniques to assist monitoring help us find out more about these fascinating and vulnerable creatures, [and] Charlotte particularly impressed the judges with the innovation and technical quality of her research”.

Eptesicus nilssonii

Bats are ecologically important, playing a key role as predators and seed dispersers. They are also very sensitive to human activities, and are useful as ‘indicator species’ for monitoring biodiversity patterns in general. In Europe, all 52 species of Bat are protected by law as part of the “Agreement on the Conservation of Populations of European Bats“. However, being nocturnal and generally small, they are difficult to detect visually or by trapping. Recording bat calls can allow researchers to survey difficult habitats and gain a clearer picture of what bat species are present and in what numbers. But a standardised statistical method for identifying the species of bat based upon it’s call was needed. This has previously been difficult to achieve, but the recent publication of a global library of bat calls, EchoBank, enabled this type of large-scale identification project to be attempted.

Bat calls vary between species and have been shaped by natural selection relating to species’ ecology. However, calls also vary between individuals within a species according to sex, age, habitat and geographical location, and social environment. Bats also vary their calls depending on what they’re doing – calls are longer when a bat is searching for prey and become shorter as it narrows in on it’s target. So, identifying a species by it’s call is a little more complex than one might expect. Charlotte developed an artificial neural network which was trained on calls of known species and can then be used to identify new calls recorded in the field.

Example of an Artificial Neural Network
Image by Chrislb, used under creative commons licence.

Artificial neural networks are computer models inspired by the central nervous system of animals. They are represented as an interconnected set of ‘neurons’, each of which makes simple calculations which together generate complex behaviour. Artificial neural networks are ‘trained’ first and this training determines the simple algorithms performed by each neuron. The trained network can then be used on real data. In the case of iBats, this involves training the network using calls for which the bat species is known, and the finished neural network can then be used to estimate which species an unknown recorded call belongs to. ANNs are a form of computer learning, and will improve in their accuracy with training – the network of neurons is able to ‘learn’ from it’s mistakes and refine the algorithm to improve classification. This method proved to be highly accurate; 98% of calls from 34 species can be accurately classified into a ‘call-type’ group, and 84% can be classified to species-level.

The iBatsID tool is freely available online, enabling researchers to utilise a standardised methodology for identifying bat species across Europe. This will facilitate large-scale comparative studies and will be particularly useful for studying European bats that have a large geographical range or are migratory. This data will be important for making conservation decisions for the future, and is therefore crucial for bat conservation but also for biodiversity monitoring in general, as bats can provide an accurate assessment of the health of entire biological communities.

Original Article:

() Journal of Applied Ecology


This research was made possible by funding from the Natural Environment Research Council (NERC) and the Bat Conservation Trust

Maintaining the Status Quo:
Constraints on the Evolution of Gene Regulation

By Claire Asher, on 10 September 2013

Every living cell, whether solitary or part of a larger multicellular organism, is an extremely complex system, involving a multitude of simultaneous chemical reactions regulated by proteins and RNA. Keeping this machine running relies upon a careful balance of gene expression and protein degradation, and cells must be prepared to modulate these processes in response to environmental variation (both internal and external). Homeostatic mechanisms can be an efficient way to regulate gene expression, however one key mechanism – negative autoregulation – is rarely used in organisms like flies and humans. Mathematical modelling by GEE’s Max Reuter and Andrew Pomiankowski shows that evolutionary constraints in the evolution of negative feedback may exist for species who carry multiple copies of each chromosome in their cells.

A Eukaryotic (Animal) Cell and a Prokaryotic (Bacterial) Cell

Homeostasis: From Radiators to Cells
One of the simplest ways to regulate any system is through negative feedback, whereby a particular process is inhibited by the products of that process. This is the system employed by central-heating systems, which use the temperature to regulate the action of a radiator. The radiator pumps out heat, and when the thermometer detects too much heat in the room, it signals the radiator to stop. Negative feedback systems can be highly efficient, stable and responsive.

Negative feedback, or homeostasis, would also be a sensible way to regulate the expression of genes within a cell – a particular gene would continue to be expressed and produce its protein product until there is enough of that product in the cell, at which point expression would stop. This system would be sensitive to the demands of the cell – if the product was being used up quickly, then expression would continue as long as demand was high. In fact, many simple, single-celled organisms, such as E. coli, use this system to respond quickly to changes in their environment.

Around half of all genes in Escherichia coli are regulated by this kind of negative feedback loop, known as negative autoregulation. However, when we look at other organisms such as yeast (Saccharoymyces cerevisiae), fruit flies (Drosophila melanogaster), and humans, we find a very different picture – almost no genes show signs of negative autoregulation (around 2%). If negative autoregulation is such a neat solution to apparently common problem, why aren’t humans and flies using it?

By Ehamberg (Own work)
[CC-BY-SA-3.0 or GFDL],
via Wikimedia Commons

A Matter of Ploidy
One of the key differences between humans and E. coli (although probably not the one that springs to mind!), is that E. coli carry only a single copy of each gene in each cell. They are haploid, with a single circular chromosome in each cell that carries a single copy of each gene in the E. coli genome. By contrast, humans, yeast and fruit flies are all diploid, meaning that they carry two copies of each gene in every cell. Our genes are split up into many, straight chromosomes, and we have two copies of each chromosome. Recent research in the department of GEE has used a mathematical modelling approach to investigate how diploidy (having two sets of chromosomes) might constrain the evolution of negative autoregulation.

In a paper in PLoS Computational Biology in March this year, Dr Alexander Stewart, Professor Rob Seymour, Professor Andrew Pomiankowski and Dr Max Reuter from UCL’s GEE produced a mathematical model of how gene regulation might evolve differently in species with one or two sets of chromosomes. Their model focuses on mutations in the promoters of genes, which alter how other protein molecules interact with and repress the expression of those genes.

In haploids, with a single copy of each gene, negative autoregulation produces very tight regulation of gene expression, giving a very rapid response to changing demand. Likewise, in a diploid species with two identical copies of a particular gene, negative autoregulation tends to be beneficial and achieves very efficient gene regulation.

Constraints in the Evolution of Regulation
The problem arises when the diploid carries two different variants of the same gene. This would be the situation whenever a new mutation arises – new mutations appear in a single copy of a particular gene. For a new mutation to be favoured and spread through the population, it must be able to do well, at least initially, as a single copy. The mutated gene must be able to work well alongside the original version. And this is where the problem arises. Stewart, Seymour, Pomiankowski and Reuter (2013) found that mutations that altered the negative autoregulation of a gene didn’t tend to play well with others. Their model considered mutations that alter the strength of the binding site – essentially how strongly regulated that gene is. An individual carrying one strongly regulated gene and one weakly regulated gene actually did worse than an individual with two weakly regulated genes. These heterozygote individuals responded more slowly to changes in demand, and there was more noise in the system. This situation, known as underdominance, where a genetic variant has a lower fitness in the heterozygote form, could be a major constraint to evolution.


Underdominance in negatively autoregulated systems arises because of the disparity in binding site strength between the two different copies of a gene. As each gene pumps out gene product, the stronger binding site is quickly suppressed by the product produced by both genes. It takes much longer for the weaker binding site to be suppressed, as it requires more product to be activated, and most of this is being used up by the stronger binding site. Compared to a haploid, the strong site shows faster response times but the weak site shows a much slower response time, and this averages out to an overall slower response.

Stewart et al (2013)’s model showed that the extent of underdominance depended on how different the two genetic variants were. Large differences in the strength of their binding sites reduced response time and created more noise than smaller differences. Slower response times and increased noise in heterozygotes mean that the maximum strength of regulation achievable in a diploid may be as much as ten-fold lower than in haploids.

Because very small differences between genetic variants in their binding site strength did not experience such a strong effect of underdominance, they were more likely to lead to the evolution of autoregulation. Evolution in diploids could proceed through many very small changes, however there is also likely to be lower limit on the size of mutations – very small changes cannot be ‘seen’ by natural selection and are unlikely to spread. Likewise, multiple binding sites, each relatively weak but which act together cooperatively, were also more likely to overcome the issue of underdominance in the model. However, in general, diploids had a much harder time evolving negative feedback as a mechanism for gene regulation. This evolutionary constraint might have forced diploids such as fruit flies and humans to develop alternative mechanisms to achieve rapid responses, such as increased rates of protein degradation or alternative regulatory mechanisms.

Original Article:

() PLOS Biology

This research was made possible by funding from the Natural Environment Research Council (NERC), the Engineering and Physical Sciences Research Council (EPSRC), and the McDonnell Foundation

The Global Future of Consumption

By Claire Asher, on 30 August 2013

The ever-growing human population, our increasing consumption of natural resources and our environmental impact, are a major concern. However, population growth and consumption varies dramatically from country to country and therefore our predictions of what the future may hold are also likely to differ between nations. Recent research in GEE used mathematical models of different population scenarios over the next 100 years to investigate the relative importance of curbing consumption and population growth.

In 1800, the global human population reached 1 billion, and by 2011 it had soured to seven times that. Although population growth is now slowing, current UN projections suggest that we will have reached 10 billion by 2080. Meanwhile, lifespan has tripled in the last thousand years while reproductive output (number of children) has halved worldwide, meaning many regions now have aging populations. However, there is considerable variation in this between countries and regions. In particular, developing nations tend to have higher mortality and higher birth rate. As countries develop and mortality decreases, they undergo what is known as the ‘demographic transition’, moving towards a lower birth rate as is observed in developed nations now.

As population size increases, so do our demands on the environment. We are now undergoing global climate change, environmental pollution and loss of species, although these magnitude of these changes is heterogeneous across the globe. In general, while birth rate tends to decrease with population size, consumption per capita increases. This pattern is not sustainable, and resources are becoming an increasingly limiting factor for development, especially to the world’s poorest nations. Reduced pressure on the environment can only be achieved through either reducing the number of people, or reducing the consumption of resources per person. Reductions in population growth rate or consumption may therefore be able to mitigate these effects over coming decades, however the effects of changes in birth rate, demography, consumption and efficiency are unlikely to be uniform across the developed and developing world. To investigate this, Professor Georgina Mace and Dr Emma Terama from UCL and Professor Tim Coulson from the University of Oxford modelled consumption in the USA and India over the next 100 years under different scenarios. Reductions in both birth rate and emissions are needed to stabilise global consumption over the next century. A 1% reduction in both birth rate and C02 emissions over the next 50 years would be sufficient to achieve stability, however the impact of different scenarios varied between developed (USA) and developing (India) countries. In particular, short-term benefits are associated with reducing consumption in high income countries such as the USA, but long-term gains can be achieved through early reductions in population growth in developing countries.

The effect of changes in population growth are slow to become apparent, especially in young populations where there can be a considerable lag. However, early reductions in population growth yield substantial benefits in the long-term. By contrast, reductions in individual consumption in high-income countries can have a very rapid impact on national consumption, and may be easier to achieve in countries fitting this profile. Steps to reduce consumption now in countries such as the USA and the UK may be important in securing long-term global sustainability.

The world’s resources are rapidly becoming a limiting factor for our growing population. Reductions in per capita consumption, achieved through lower consumption or improved efficiency from technological innovations, can yield immediate benefits in reducing environmental pressures in developed countries. By contrast, long-term benefits can be gained through early reductions in population growth in developing countries. Understanding the dynamics of growth and consumption in relation to current and future development and demography is crucial if we are to plan for the future and act to minimise our impact on the global environment.

Original Article:

() Environmental and Resource Economics