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Male Promiscuity Boosts Role of Chance in Sex Chromosome Evolution

By Claire Asher, on 19 March 2015

Humans, like all mammals and birds, determine sex with chromosomes. Whether a fertilised egg develops into a male or female depends on what chromosomes it carries Scientists have long recognised that genes evolve a little differently on the sex chromosomes, and recent research in GEE suggests this may be due to differing patterns of inheritance that favour the influence of chance on gene sequence change. Furthermore, promiscuity in males has a large influence on the magnitude of this effect, with chance playing an even greater role in sex-chromosome evolution in highly promiscuous species. Using genetic sequence data in combination with physical and behavioural measurements of promiscuity in birds, Dr Alison Wright and Professor Judith Mank report strong evidence for the role of neutral forces in sex chromosome evolution.

In birds and mammals, along with some invertebrates and reptiles, sex is determined by the chromosomes you carry – the sex chromosomes, as they are aptly named. If you are a male mammal, you carry one X and one Y chromosome; a female mammal carries two X chromosomes. Similarly, if you are a male bird, you carry two Z chromosomes; a female carries one Z and one W. Whether it’s the XY system, the ZW system or even the UV system used by some species of algae, the result is more or less the same. Sex is determined by the presence or absence of particular chromosomes. This isn’t always the case – some species determine sex using temperature during development, other species determine sex based on social conditions, while others do away with fixed sexes altogether and are either hermaphrodite or possess the ability to switch sex. However, one of the most common, and certainly the best studied, systems among living organisms is to determine sex with chromosomes.

Unlike autosomal chromosomes (all our chromosomes that are not sex chromosomes), sex chromosomes are not inherited and expressed equally across the sexes. The Y and W chromosomes only ever appear in one sex, for example. This has some interesting consequences for evolution. For example, scientists have found that the ‘major sex chromosomes’ (X and Z chromosomes) tend to evolve faster than the autosomes. Known as the Faster-X (or Faster-Z) effect, this phenomenon is now well documented in a range of different species, and scientists have suggested a number of possible explanations for why this might be the case. Faster evolution on the major sex chromosomes might be caused by more effective natural selection favouring beneficial mutations (adaptive hypothesis) or due to less effective natural selection failing to remove harmful mutations (neutral hypothesis).

Why would natural selection act differently on sex chromosomes than autosomal ones? In a paper published in Molecular Ecology this month, Dr Alison Wright explains that the differences between chromosomes arise because of differences in the pattern of inheritance, which ultimately influences the number of chromosomes that are passed on to the next generation, called the effective population size. An individual who never reproduces is an evolutionary dead end, and as their genes are not passed on, and they are not counted in the effective population size. Individuals that do mate contribute sex chromosomes unevenly, and this can have a significant impact on the course of sex-chromosome evolution.

When two individuals mate, they each pass one of each pair of chromosomes to the offspring. Each chromosome has an equal likelihood of being carried by the offspring, and the effective population size (ie chance of being passed on) of all autosomal chromosomes is the same. But for the sex chromosomes, things are a bit more complicated. Each time a pair of individuals mate, between them they bring three major sex chromosomes and one minor chromosome to the table. This translates to major sex chromosomes having an effective population size three times larger than the minor sex chromosomes. And both sex chromosomes have a smaller effective population size than the autosomes.

But that’s only if everybody is monogamous. As soon as promiscuity is involved, things get even more complicated. If males are promiscuous (and they often are, in the animal kingdom), then this means some males in the population are likely to be very successful, while others fail to reproduce at all. In other words, the variance in male mating success is much higher. Promiscuity reduces the effective population size of the minor chromosomes even further.

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Why does effective population size matter? Well, the effective population size determines the relative influence of chance on gene sequence evolution. Although we generally think of evolution progressing as natural selection favours beneficial mutations and purges deleterious ones, chance also has a big role to play. Chance, known in this context as genetic drift, has a bigger impact on small populations, and rare mutations. This is because when a particular mutation is rare, it only takes a little bit of bad luck for it to be lost forever. Just think of the times you’ve walked home in the rain only to hear the characteristic crunch of the end of a snail’s life – here your foot is the agent of genetic drift. The death of that snail had little or nothing to do with the genes it carried, but your foot has altered the course of evolution, slightly. The effective population size of autosomal genes reflects the population size of the organisms they are found in, but for the sex chromosomes, their effective population size is even smaller, making them more prone to genetic drift.

Dr Alison Wright, Professor Judith Mank and colleagues from GEE sequenced expressed genes in six species of birds, spanning 90 million years of evolution, to investigate the rate of evolutionary change in genes on different chromosomes. They compared sequence data from monogamous species like the Swan Goose (Anser cygnoides) and the Guinea Fowl (Numida meleagris) with promiscuous species like the Mallard duck (Anas platyrhynchos), wild Turkey (Meleagris gallopavo), and Peafowl (Pavo cristatus) to investigate how gene sequences and gene expression patterns vary both within and between species. They then matched data on the rate of evolution with characteristics of species that are associated with promiscuity, such as testes weight and sperm number. Their results indicate that natural selection is less effective on the Z chromosome in general, and this becomes even more pronounced in promiscuous species. The authors therefore conclude that Faster-Z evolution in birds is not adaptive, but is driven by neutral processes.

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Differences in gene sequences within and between species can tell us a lot about the rate of evolution for different lineages. This is because the genetic code has some redundancy in it – DNA is split up into three-letter words or codons, and there are many cases where different codons translate into the same amino acid. So, it is possible to have genetic sequence change that is essentially invisible to natural selection – it doesn’t alter the resulting protein sequence and so has no influence on the organism. Changes in gene sequence that swap between these ‘synonymous’ codons can therefore give us a rough baseline of neutral change. Non-synonymous differences (the ones that do have an effect on the organism), between individuals or between species, represent the rate of evolution. More non-synonymous changes suggests either positive selection, where evolution favours those changes because they are beneficial, or genetic drift, where selection is weaker and cannot remove slightly harmful mutations from the population. The authors found that genes on the Z chromosome show a faster rate of non-synonymous change than autosomal genes. Further, the ratio was significantly correlated with measures of promiscuity, with more promiscuous species having more non-synonymous changes.

Although this could be a mark of positive natural selection, the authors found no difference in the number of genes undergoing positive selection between sex- and autosomal-chromosomes, suggesting the Faster-Z effect is driven by genetic drift rather than positive selection. In fact, differences within species indicate that natural selection is less effective at removing mildly deleterious mutations from the Z chromosome than the autosomes. Combined with other analyses on gene expression, these results show strong support for the neutral explanation for Faster-Z evolution in birds.

Interesting, promiscuity increases the effective population size of X chromosomes, and that may explain why previous studies have found evidence that Faster-X chromosome may well be due to positive selection. These differences suggest that Z chromosomes may be less important in adaptation than X chromosomes.

Original Article:

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This research was made possible by funding from the Natural Environment Research Council (NERC) and the European Research Council (ERC).

Sloths Move Slow, Evolve Fast

By Claire Asher, on 11 March 2015

Sloth003Sloths might be notorious for their leisurely pace of life, but research published last year shows they are no slow coaches when it comes to evolution.

Sloths, as we know and love them, are small, slow-moving creatures found in the trees of tropical rainforests. But modern sloths are pretty odd compared to their extinct relatives. Sloths (Folivora) are represented today by just six species in two families; the Megalonychidae (two-toed sloths) and the Bradypodidae (three-toed sloths). But 20,000 years ago there were perhaps as many as 50 species of sloth spread across the globe, and most were relatively large, ground-dwelling animals quite unlike modern sloths. While most modern sloths weigh in at a modest 6kg, extinct species such as Megatherium americanum and Eremotherium eomigrans could weigh up to 5 tonnes!

[Read More at Curious Meerkat]

Write About Research – A GEE Research Blog Competition

By Claire Asher, on 3 March 2015

The GEE Research blog communicates UCL science with a wider, non-specialist audience, by providing short summaries of recent research in the department of UCL Genetics, Evolution and Environment. This provides an opportunity to engage with a broad audience, including other academics, students, members of the public, and even businesses and policy-makers. It is a great way to increase the reach and impact of your research. Now we’re offering the opportunity to contribute your own writing to the GEE blog – this is your chance to explain your research to the world, to improve your science communication skills, and maybe even win yourself some cash!

Public communication of science is a key skill for any scientist, and is increasingly being appreciated by academics and research councils as an important part of science education and training. It is a totally different medium from traditional academic papers; it offers the freedom to tell a story, but also presents challenges – you must communicate in a way that anybody can understand. Compared to academic journals, popular writing has the potential to reach a far broader range of readers and can have many benefits for your research – for example leading to new collaborations and inviting comment and feedback from readers who would never otherwise come into contact with your work.

If you are interested in writing a guest post for the GEE Research blog, now is your chance! Enter our “Write About Research” contest and not only will your blog post be published online, but you’ll also be in with a chance to win £50!

Guidelines

Your blog should be written in a way such that an ‘educated non-specialist’ audience can understand and follow it. You can therefore assume a GCSE-level science background and jargon should be explained the first time you use it. Blogs should begin with a short opening paragraph that sets the scene – basically the abstract of the blog post – summarising the key points of the article and leading the reader into the post. The rest of the post should provide background, a summary of the focus paper(s) and should end with a broad conclusion, setting the research into the larger context, and highlighting it’s relevance and importance. Take a look at other GEE blog posts for an idea of what we’re looking for.

Choosing a Topic

  • Your blog post must cover your overall area of research
  • Entries should focus on one or two key papers
  • You could therefore write about one of your own publications or a recent publication in your area of research. Alternatively, you could write a general background to your research area, focussing on a few key (but not necessarily recent) papers in that field.
  • Just be sure not to scoop yourself – please don’t write about your own research that has not yet been published, or assessed work (e.g. MSc project) that has not yet been assessed.
  • If you are unsure whether your idea fits the criteria, feel free to contact c.asher@ucl.ac.uk with any queries

Eligibility

You must be an MSc, MRes or PhD Student, or a PostDoc undertaking a research project (or having completed a research project in the last 12 months) in the UCL Department of Genetics, Evolution and Environment.

How to Enter

  • One entry per person
  • Entries must be between 600 and 1200 words
  • All entries must include a reference list including any published papers that you refer to directly. In-text referencing is not necessary. The reference list does not count towards the word count.
  • Send your entry, along with a 150-word biography to c.asher@ucl.ac.uk
  • Please also recommend at least one photo to include with the post (either your own image or one from Wikimedia commons).
  • Entries must be received by 5pm 31st March 2015

Prizes and Publication

  • We will be posting all blog entries on the GEE Research blog over the next year (between April 10th 2015 and April 9th 2016).
  • Additionally, there will be a £50 gift voucher for each of the three best entries, as judged by Dr Claire Asher
  • Entries will be judged by Dr Claire Asher, and winners announced on 10th April 2015
  • Winners will be announced in a specific post on the GEE Research blog, and will bear no relation to the order in which each blog post is subsequently posted on the site.

If you have any questions or queries about the contest, please feel free to contact c.asher@ucl.ac.uk.

Good Luck!

Was Fermentation Key to Yeast Diversification?

By Claire Asher, on 17 February 2015

From bread to beer, yeast has shaped our diets and our recreation for centuries. Recent research in GEE shows how humans have shaped the evolution of this important microorganism. As well as revealing the evolutionary origins of modern fission yeast, the new study published in Nature Genetics this month shows how techniques developed for detecting genetic causes of disease in humans can be usefully applied to better understand the ecology, biochemistry and evolution of commercially and scientifically important microorganisms like yeast.

Fission yeast, Schizosaccharomyces pombe, is one of the principal ‘model’ species that cell biologists use to try and understand the inner workings of cells. Most famously, Paul Nurse used this yeast to discover the genes that control cell division. The laboratory strain was first isolated from French wine in 1924, and has been used ever since by an increasingly large community of fission yeast researchers. However, serendipitous collection of new strains has continued slowly since that time, and many of these are associated with human fermentation processes – different strains have been isolated from Sicilian vineyards, from the Brazilian sugarcane spirit Cachaça and from the fermented tea Kombucha. Despite it’s enormous scientific importance, little is known about the ecology and evolution of fission yeast.

Research published this month by Professor Jürg Bähler, Dr Daniel Jeffares and colleagues from UCL’s department of Genetics, Evolution and Environment, along with researchers from 10 other institutions across five countries, reveals an intimate link between historic dispersal and diversification in yeast and our love of fermented food and drinks. The project sequenced the genomes of 161 strains of fission yeast, isolated in 20 countries over the last 100 years, enabling the researchers to reconstruct the evolutionary history of S. pombe, as well as investigating genetic and phenotypic variation within and between strains.

Beer, Wine and Colonialism

Bähler and Jeffares were able to date the diversification and dispersal of S. pombe to around 2,300 years ago, coinciding with the early distribution of fermented drinks such as beer and wine. Strains from the Americas were most similar to each other, and dated to around 1600 years ago, most likely carried across the Atlantic in fermented products by European colonists. This is reminiscent of findings for the common bread and beer yeast species, Saccharomyces cerevisae, whose global dispersal is thought to date to around 10,000 years ago, coinciding with Neolithic population expansions. This research therefore reveals the intimate link between human use of yeast for fermentation and it’s evolutionary diversification, and highlights the power of humans to shape the lives of the organisms with which they interact.

From Genotype to Phenotype

Fission Yeast, Schizosaccharomyces pombe

The researchers also used genome-wide association techniques to investigate the relationship between genotype and phenotype in the different strains. They began by carefully measuring 74 different traits in representatives of each strain. Some traits were simple, such as cell size and shape, but the researchers also measured environment-genotype interactions, for example by investigating growth rates and population sizes with different nutrient availabilities, drug treatments and other environment variables. In total, they identified 223 different phenotypes, most of which were heritable to some extent. Further, relatively few of the phenotypes were strongly linked to a particular population or region, making yeast ideal for genome-wide association studies (GWAS), unlike Saccharomyces cerevisae, for which it has not been possible to use GWAS successfully.

GWAS was developed to identify genes that are linked to specific diseases in humans, however this study highlights how the technique can usefully be applied to understanding evolution and genotype-phenotype relationships in other organisms. Tightly controlled experimental conditions that can be achieved with microorganisms in the laboratory make GWAS possible and informative for organisms such as yeast. The researchers found 89 traits that were significantly associated with at least one gene; the strongest association explained about a quarter of variation between individuals.

Hallmarks of Selection

Looking at variation in genomic sequence between strains also allowed the researchers to investigate which parts of the genome have undergone more evolutionary change than others, and which regions are likely to be particularly important for function. Genes and genomic regions that are crucial to survival (such as those involved in basic cellular function, for example), tend to change relatively little over evolutionary time, because most mutations in their sequence would be severely detrimental to survival. A process known as purifying selection tends to keep these genetic sequences the same over long stretches of evolutionary time. Less crucial genetic sequences have more freedom to change without having serious consequences; they are not subject to strong purifying selection and tend to show more variation between individuals and populations.

The authors found that genetic variation between strains was lowest for protein-coding gene sequences (those that produce protein products such as hormones and enzymes), which is to be expected. However, they found variation was also low in non-coding regions near genes. These regions are thought to be important in gene regulation, echoing an increasing appreciation that the evolution of the regulation of gene expression may be as important, if not more so, than the evolution of the gene sequences themselves.

This ground-breaking research from GEE reveals fascinating insights into the ecology and evolution of fission yeast, a microorganism that directly or indirectly influences our lives on a daily basis. It highlights how important humans have been in shaping the genomes of commercially and scientifically important organisms, whilst also expanding our knowledge of genes, genomes and phenotypes more generally. Applying techniques such as this to a wider range of organisms has the potential to vastly increase our understanding of the genomic dynamics of evolutionary change.

Original Article:

() Nature Genetics

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This research was made possible by funding from the Wellcome Trust, the European Research Council (ERC), the (BBSRC), the UK Medical Research Council (MRC), Cancer Research UK, the Czech Science Foundation and Charles University.

Planning for the Future – Resilience to Extreme Weather

By Claire Asher, on 15 January 2015

As climate change progresses, extreme weather events are set to increase in frequency, costing billions and causing immeasurable harm to lives and livelihoods. GEE’s Professor Georgina Mace contributed to the recent Royal Society report on “Resilience to Extreme Weather”, which predicts the future impacts of increasing extreme weather events, and evaluates potential strategies for improving our ability to survive, even thrive, despite them.

Extreme weather events, such as floods, droughts and hurricanes, are predicted to increase in frequency and severity as the climate warms, and there is some evidence this is happening already. These extreme events come at a considerable cost both to people’s lives, health and wellbeing, and the economy. Between 1980 and 2004, extreme weather is estimated to have cost around US$1.5 trillion, and costs are rising. A recent report by the Royal Society reviews the future risks of extreme weather and the measures we can take to improve our resilience.

The global insured and uninsured economic losses from the two biggest categories of weather-related extreme events. Royal Society (2014)

The global insured and uninsured economic losses from the two biggest categories of weather-related extreme events. Royal Society (2014)

Disaster risk is a combination of the likelihood of a particular disaster occurring and the impact on people and infrastructure. However, the impact will be influenced not only by the severity of the disaster, but by the vulnerability of the population and its infrastructure, a characteristic we have the potential to change. Thus, while it may be possible to reduce the frequency of disasters by reducing carbon emissions and slowing climate change, another key priority is to improve our own resilience against these events. Rather than just surviving extreme weather, we must adapt and transform.

The risks posed by climate change may be underestimated if exposure and vulnerability to extreme weather are not taken into account. Mapped climate and population projections for the next century show that the number of people exposed to floods, droughts and heatwaves will both increase and become more concentrated.

Exposure risk to floods and droughts in 2090. Royal Society (2014)

Exposure risk to floods and droughts in 2090. Royal Society (2014)

In their recent report, the Royal Society compared different approaches to increasing resilience to coastal flooding, river flooding, heatwaves and droughts. Overall, they found that a portfolio of defence options, including both physical and social techniques and those that utilise both traditional engineering solutions and more ecosystem based approaches. Broadly, approaches can be categorised as engineering, ecosystem-based, or hybrids of the two. Resilience strategies that incorporate natural ecosystems and processes tend to be more affordable and deliver wider societal benefits as well as simply reducing the immediate impact of the disaster.

Ecosystem-based approaches can take a variety of different forms, but often involve maintaining or improving natural ecosystems. For example … Large, intact tropical forests are important in climate regulation, flood and erosion management and … Forests can also act as a physical defence, and help to sustain livelihoods and provide resources for post-disaster recovery. Ecosystem-based approaches often require a lot of land and can take a long time to become established and effective, however in the long-term they tend to be more affordable and offer a wider range of benefits than engineering approaches. For this reason, they are often called ‘no regret’ options. Evidence for the effectiveness of different resilience strategies is highly varied. Engineered approaches are often well-established, with decades of strong research to back them up. In contrast, ecosystem approaches have been developed more recently and there is less evidence available on their effects. The Royal Society report indicates that for coastal flooding and drought, some of the most affordable and effective solutions are ecosystem-based, such as mangrove maintenance as a coastal defence and agroforestry to mitigate the effects of drought and maintain soil quality. In many situations, hybrid solutions may offer the best mixture of affordability and effectiveness.

It is crucial for governments to develop and implement resilience strategies and start building resilience now. This will be most effective if resilience measures are coordinated internationally, resources shared and where possible, cooperative measures implemented. By directing funds towards resilience-building, governments can reduce the need for costly disaster responses later. Governments can reduce the economic and human costs of extreme weather by focussing on minimising the consequences of infrastructure failure, rather than trying to avoid failure entirely. Prioritising essential infrastructure and focussing on minimising the harmful effects of extreme weather are likely to be the most effective approaches in preparing for future increases in extreme weather events.

Original Article:

() Resilience to
extreme weather

Forecasting Extinction

By Claire Asher, on 5 January 2015

Classifying a species as either extinct or extant is important if we are to quantify and monitor current rates of biodiversity loss, but it is rare that a biologist is handy to actually observe an extinction event. Finding the last member of a species is difficult, if not impossible, so extinction classifications are usually estimates based on the last recorded sightings of a species. Estimates always come with some inaccuracy, however, and recent research by GEE academics Dr Ben Collen and Professor Tim Blackburn aimed to investigate how accurate our best estimates of extinction really are.

Using data from experimental populations of the single-celled protist Loxocephalus, as well as wild populations of seven species of mammal, bird and amphibian, the authors tested six alternative estimation techniques to calculation the actual date of extinction. In particular, they were interested in whether the accuracy of these estimates is influenced by the rate of population decline, the search effort put in to find remaining individuals and the total number of sightings of the species. The dataset included very rapid declines (40% a year in the Common Mist frog) and much slower ones (16% per year in the Corncrake), and different sampling regimes.

Their results showed that the speed of decline was a crucial factor affecting the accuracy of extinction estimates – for experimental laboratory populations, estimates were most accurate for rapid population declines, however slow population declines in wild populations tended to produce more accurate results. The sampling regime was also important, with larger inaccuracies occurring when sampling effort decreased over time. This is probably a common situation for many species – close monitoring is common for species of high conservation priority, but interest may decrease as the species becomes closer and closer to extinction. The total number of sightings was also an important factor – a larger number of sightings overall tended to produce more accurate estimates.

Finally, the estimation technique also influenced accuracy, but only in interaction with the other variables mentioned above. Some methods fared best for rapid population declines, others for slower ones. Many of the methods fare poorly when sampling effort changes over time, particularly if it decreases, although they were relatively robust to sporadic, opportunistic sampling regimes. Overall, optimal linear estimation, a statistical method which makes fewer assumptions about the exact pattern of sightings, produced the most accurate results in cases where more than 10 sightings were recorded in total.

This study highlights the challenges faced by ecologists trying to determine whether a species has gone extinct or not. Sightings of rare species are often opportunistic, and only rarely are they part of a systematic, long-term monitoring program. Thus, methods that produce accurate results in the face of changing or sporadic search efforts are of key importance to conservationists. If the history of a species’ population declines and of the sampling effort are known, then statistical estimates can be selected which provide the best estimates for the particular situation. However, this information is rarely available and so using techniques that can provide accurate estimates for a range of different historical scenarios are likely to be of most use in predicting extinction status. Ultimately, it is extremely useful for conservationists to know whether a species is extinct or not, but estimates will always be subject to error except in rare cases (such as the passenger pigeon, for example) where the extinction event is observed first hand. There will always be cases of species turning up years after they were declared extinct, and no estimate will ever be perfect, but understanding the sources of error and the best methods to use to minimise it can be of great benefit in reducing the frequency with which that happens.

Original Article:

() Conservation Biology

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This research was made possible by funding from the Natural Environment Research Council (NERC).

Changing Perspectives in Conservation

By Claire Asher, on 18 December 2014

Our views of the importance of nature and our place within have changed dramatically over the the last century, and the prevailing paradigm has profound influences on conservation from the science that is conducted to the policies that are enacted. In a recent perspectives piece for Science, GEE’s Professor Georgina Mace considered the impacts that these perspectives have on conservation practise.

Before the late 1960s, conservation thinking was largely focussed on the idea that nature is best left to its own devices. This ‘nature for itself‘ framework centred around the value of wilderness and unaltered natural reserves. This viewpoint stemmed from ecological theory and research, however by the 1970s it became apparent that human activities were having severe and worsening impacts on species, and that this framework simply wasn’t enough. This led to a shift in focus towards the threats posed to species by human activities and how to reduce these impacts, a ‘nature despite people‘ approach to conservation. This is the paradigm of protected areas and quotas, designed to reduce threats posed and ensure long-term sustainability.

Changing views of nature and conservation, Mace (2014)

Changing views of nature and conservation, Mace (2014)

By the 1990s, people had begun to appreciate the many and varied roles that healthy ecosystems play in human-wellbeing; ecosystem services are crucial to providing clean water, air, food, minerals and raw materials that sustain human activities. Shifting towards a more holistic, whole-ecosystem viewpoint which attempted to place economic valuations on the services nature provides, conservation thinking entered a ‘nature for people‘ perspective. Within this framework, conservationists began to consider new metrics, such as the minimum viable population size of species and ecosystems, and became concerned with ensuring sustainable harvesting and exploitation. In the last few years, this view has again shifted slightly, this time to a ‘people and nature‘ perspective that values long-term harmonious and sustainable relationships between humans and nature, and which includes more abstract benefits to humans.

Changing conservation paradigms can have a major impact on how we design conservation interventions and what metrics we monitor to assess their success. Standard metrics of conservation, such as the IUCN classification systems, can be easily applied to both a ‘nature for itself’ and a ‘nature despite people’ framework. In contrast, a more economic approach to conservation requires valuations of ecosystems and the services they provide, which is far more complex to measure and calculate. Even more difficult is measuring the non-economic benefits to human well-being that are provided for by nature. The recent focus on these abstract benefits may make the success of conservation interventions more difficult to assess under this framework.

The scientific tools, theory and techniques available to conservation scientists have not always kept up with changing conservation ideologies, and differing perspectives can lead to friction between scientists and policy-makers alike. In the long-term a viewpoint that recognises all of these viewpoints may be the most effective in directing and appraising conservation management. Certainly, greater stability in the way in which we view our place in nature would afford science the opportunity to catch-up and develop effective and empirical metrics that can be meaningfully applied to conservation.

Original Article:

() Science

Function Over Form:
Phenotypic Integration and the Evolution of the Mammalian Skull

By Claire Asher, on 8 December 2014

Our bodies are more than just a collection of independent parts – they are complex, integrated systems that rely upon precise coordination in order to function properly. In order for a leg to function as a leg, the bones, muscles, ligaments, nerves and blood vessels must all work together as an integrated whole. This concept, known as phenotypic integration, is a pervasive characteristic of living organisms, and recent research in GEE suggests that it may have a profound influence on the direction and magnitude of evolutionary change.

Phenotypic integration explains how multiple traits, encoded by hundreds of different genes, can evolve and develop together such that the functional unit (a leg, an eye, the circulatory system) fulfils its desired role. Phenotypic integration could be complete – every trait is interrelated and could show correlated evolution. However, theoretical and empirical data suggest that it is more commonly modular, with strong phenotypic integration within functional modules. This modularity represents a compromise between a total lack of trait coordination (which would allow evolution to breakdown functional phenotypic units) and the evolutionary inflexibility of complete integration. Understanding phenotypic integration and its consequences is therefore important if we are to understand how complex phenotypes respond to natural selection.

Functional modules in mammals, Goswami et al (2014)

Functional modules in mammals, Goswami et al (2014)

It is thought that phenotypic integration is likely to constrain evolution and render certain phenotypes impossible if their evolution would require even temporary disintegration of a functional module. However, integration may also facilitate evolution by coordinating the responses of traits within a functional unit. Recent research by GEE academic Dr Anjali Goswami and colleagues sought to understand the evolutionary implications of phenotypic integration in mammals.

Expanding on existing mathematical models, and applying these to data from 1635 skulls from nearly 100 different mammal species including placental mammals, marsupials and monotremes, Dr Goswami investigated the effect of phenotypic integration on evolvability and respondability to natural selection. Comparing between a model with two functional modules in the mammalian skull and a model with six, the authors found greater support for a larger number of functional modules. Monotremes, whose skulls may be subject to different selection pressures due to their unusual life history, did not fit this pattern and may have undergone changes in cranial modularity during the early evolution of mammals. Compared with random simulations, real mammal skulls tend to be either more or less disparate from each other, suggesting that phenotypic integration may both constrain and facilitate evolution under different circumstances. The authors report a strong influence of phenotypic integration on both the magnitude and trajectory of evolutionary responses to selection, although they found no evidence that it influences the speed of evolution.

Thus, phenotypic integration between functional modules appears to have a profound impact on the direction and extent of evolutionary change, and may tend to favour convergent evolution of modules that perform the same function (e.g bird and bat wings for powered flight), by forcing individuals down certain evolutionary trajectories. The influence of phenotypic integration on the speed, direction and magnitude of evolution has important implications for the study of evolution, particularly when analysing fossil remains, since it can make estimates of the timing of evolutionary events more difficult. Failing to incorporate functional modules into models of evolution will likely reduce their accuracy and could produce erroneous results.

Phenotypic integration is what holds together functional units within an organism as a whole, in the face of natural selection. Modularity enables traits to evolve independently when their functions are not strongly interdependent, and prevents evolution from disintegrating functional units. Through these actions, phenotypic integration can constrain or direct evolution in ways that might not be predicted based on analyses of traits individually. This can have important impacts upon the speed, magnitude and direction of evolution, and may tend to favour convergence.

Original Article:

() Global Environmental Change

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This research was made possible by support from the Natural Environment Research Council (NERC), and the National Science Foundation (NSF).

The Best of Both Worlds:
Planning for Ecosystem Win-Wins

By Claire Asher, on 16 November 2014

The normal and healthy function of ecosystems is not only of importance in conserving biodiversity, it is of utmost importance for human wellbeing as well. Ecosystems provide us with a wealth of valuable ecosystem services from food to clean water and fuel, without which our societies would crumble. However it is rare that only a single person, group or organisation places demands on any given ecosystem service, and in many cases multiple stakeholders compete over the use of the natural world. In these cases, although trade-offs are common, win-win scenarios are also possible, and recent research by GEE academics investigates how we can achieve these win-wins in our use of ecosystem services.

Ecosystem services depend upon the ecological communities that produce them and are rarely the product of a single species in isolation. Instead, ecosystem services are provided by the complex interaction of multiple species within a particular ecological community. A great deal of research interest in recent years has focussed on ensuring we maintain ecosystem services into the long term, however pressure on ecosystem services worldwide lis likely to increase as human demands on natural resources soars. Ecosystem services are influenced by complex ecosystem feedback relationships and food-web dynamics that are still relatively poorly understood, and increased pressures on ecosystems may lead to unexpected consequences. Although economical signals respond rapidly to global and national changes, ecosystem services are thought to lag behind, often by decades, making it difficult to predict and fully understand how our actions are influences the availability of crucial services in the future.

Trade-offs in the use of ecosystem services occur when the provision of one ecosystem service is reduced by increased use of another, or when one stakeholder takes more of an ES at the expense of other stakeholders. However, this needn’t be the case – in some scenarios it is possible to achieve win-win outcomes, preserving ecosystem services and providing stakeholders the resources they need. Although attractive, win-win scenarios may be difficult to achieve without carefully planned interventions, and recent research from GEE indicates they are not as common as we might like.

In a comprehensive meta-analaysis of ecosystem services case studies from 2000 to 2013, GEE academics Prof Georgina Mace and Dr Caroline Howe show that trade-offs are far more common than win-win scenarios. Across 92 studies covering over 200 recorded trade-offs or synergies in the use of ecosystem services, trade-offs were three times more common than win-wins. The authors identified a number of factors that tended to lead to trade-offs rather than synergies. In particular, if one or more of the stakeholders has a private interest in the natural resources available, trade-offs are much more likely – 81% of cases like this resulted in tradeoffs. Furthermore, trade-offs were far more common when the ecosystem services in question were ‘provisioning’ in nature – products we directly harvest from nature such as food, timber, water, minerals and energy. Win-wins are more common when regulating (e.g. nutrient cycling and water purification) or cultural (e.g. spiritual or historical value) ecosystem services are in question. In the case of trade-offs, there were also factors that predicted who the ‘winners’ would be – winners were three times more likely to hold private interest in the natural resource in question, and tended to be wealthier than loosing stakeholders. Overall, there was no generalisable context that predicted win-win scenarios, suggesting that although trade-off indicators may be useful in strategic planning, the outcome of our use of ecosystem services is not inevitable, and win-wins are possible.

They also identified major gaps in the literature that need to be addressed if we are to gain a better understanding of how win-win scenarios may be possible in human use of ecosystems. In particular, case studies are currently only available for a relatively limited geographic distribution, and tend to focus of provisioning services. Thus, the lower occurrence of trade-offs for regulating and cultural ecosystem services may be in part a reflection of a paucity of data on these type of services. Finally, relatively few studies have attempted to explore the link between trade-offs and synergies in ecosystem services and the ultimate effect on human well-being.

Understanding how and why trade-offs and synergies occurs in our use of ecosystem services will be valuable in planning for win-win scenarios from the outset. Planning of this kind may be necessary if we are to achieve and maintain balance in our use of the natural world in the future.

Original Article:

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This research was made possible by support from the Ecosystem Services for Poverty Alleviation (ESPA) programme, which is funded by the Natural Environment Research Council (NERC), the Economic and Social Research Council (ESRC), and the UK Department for International Development (ERC)

Life Aquatic:
Diversity and Endemism in Freshwater Ecosystems

By Claire Asher, on 6 November 2014

Freshwater ecosystems are ecologically important, providing a home to hundreds of thousands of species and offering us vital ecosystem servies. However, many freshwater species are currently threatened by habitat loss, pollution, disease and invasive species. Recent research from GEE indicates that freshwater species are at greater risk of extinction than terrestrial species. Using data on over 7000 freshwater species across the world, GEE researchers also show a lack of correlation between patterns of species richness across different freshwater groups, suggesting that biodiversity metrics must be carefully selected to inform conservation priorities.

Freshwater ecosystems are of great conservation importance, estimated to provide habitat for over 125,000 species of plant and animal, as well as crucial ecosystem services such as flood protection, food, water filtration and carbon sequestration. However, many freshwater species are threatened and in decline. Freshwater ecosystems are highly connected, meaning that habitat fragmentation can have serious implications for species, while pressures such as pollution, invasive species and disease can be easily transmitted between different freshwater habitats. Recent work by GEE academics Dr Ben Collen, in collaboration with academics from the Institute of Zoology, investigated the global patterns of freshwater diversity and endemism using a new global-level dataset including over 7000 freshwater mammals, amphibians, reptiles, fishes, crabs and crayfish. Many freshwater species occupy quite small ranges and the authors were also interested in the extent to which species richness and the distribution threatened species correlated between taxonomic groups and geographical areas.


The study showed that almost a third of all freshwater species considered are threatened with extinction, with remarkably little large-scale geographical variation in threats. Freshwater diversity is highest in the Amazon basin, largely driven by extremely high diversity of amphibians in this region. Other important regions for freshwater biodiversity include the south-eastern USA, West Africa, the Ganges and Mekong basins, and areas of Malaysia and Indonesia. However, there was no consistent geographical pattern of species richness in freshwater ecosystems.

Freshwater species in certain habitats are more at risk than others – 34% of species living in rivers and streams are under threat, compared to just 20% of marsh and lake species. It appears that flowing freshwater habitats may be more severely affected by human activities than more stationary ones. Freshwater species are also consistently more threatened than their terrestrial counterparts. Reptiles, according to this study, are particularly at risk from extinction, with nearly half of all species threatened or near threatened. This makes reptiles the most threatened freshwater taxa considered in this analysis. The authors identified key process that were threatening freshwater species in this dataset – habitat degradation, water pollution and over-exploitation are the biggest risks. Habitat loss and degradation is the most common threat, affecting over 80% of threatened freshwater species.

That there was relatively little congruence between different taxa in the distribution of species richness and threatened species in freshwater ecosystems suggests that conservation planning that considers only one or a few taxa may miss crucial areas of conservation priority. For example, conservation planning rarely considers patterns of invertebrate richness, but if these groups are affected differently and in different regions than reptiles and amphibians, say, then they may be overlooked in initiatives that aim to protect them. Further, different ways to measure the health of populations and ecosystems yield different patterns. The metrics we use to identify threatened species, upon which conservation decisions are based, must be carefully considered if we are to suceeed in protecting valuable ecosystems and the services the provide.

Original Article:

() Global Ecology and Biogeography

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This research was made possible by funding from the Rufford Foundation and the European Commission