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Finding Shared Genes Between Species

By Claire Asher, on 7 May 2015

a guest blog by Natasha Glover, written for the 2015 Write About Research Competition.

Did you know we share approximately 98% of our protein-coding genes with chimpanzees? Chimps are commonly referred to as our evolutionary “cousins.” This makes sense to anyone who’s seen Planet of the Apes – chimps and humans share many of the same physical characteristics. But did you also know that we share approximately 90% of our genes with mice? About 70% of our genes with zebrafish? Even about 15% of human genes can be found in fruit flies!

These shared genes are evidence of evolution from a common ancestor and the relatedness of all life on Earth. The shared genes are called homologous genes, or genes which share a common ancestry either between or within species. They can be further classified into two main categories: orthologs, which are pairs of genes that started diverging through speciation, and paralogs, which are pairs of genes that started diverging through gene duplication. Finding and studying homologous genes is important, because the same gene in two different species (orthologs) are more likely to have the same cellular function than two duplicated genes (paralogs).

This brings us to the concept of model organisms, which are representative species studied by many scientists from which the knowledge learned from them can be transferred to other, closely related species. For example, this is why researchers experiment on mice instead of humans to test new drugs. Orthologs between mice and humans allow for observing basic human biological processes in mice, and then transferring the knowledge to humans. Orthologs are also applicable to agricultural research. Imagine if a scientist finds an interesting gene in the model plant Arabidopsis thaliana, perhaps a gene controlling an important agronomical trait like seed size, flowering time, or tolerance to drought. It would be useful to find the ortholog of this gene in another economically important crop such as rice, wheat or soybean in order to exploit the trait of interest.

Homologous genes correspond to shared attributes between species. We can identify the shared traits just by looking at them. But how can we identify orthologs and paralogs at the molecular level, that is, how do we identify these genes by analyzing their sequence? It’s important to keep in mind that the concepts of homology are purely from an evolutionary perspective. Thus, we can deduce orthologous and paralogous relationships between pairs of genes using a phylogenetic tree (See Box 1).

SharedGenes_fig1Box 1. This tree represents the relationship between 5 gene sequences. Each node of the tree either represents a speciation (S1 and S2) or duplication event (star). Thus to know the relation between pairs of genes, you just have to trace them back to their shared node (closest common ancestral copy). In this example, the blue genes between dog and human are orthologous to each other (because they trace back to a speciation event). The red dog and red human genes are also orthologous to each other. However, all the blue genes are paralogous to all the red genes because they trace back to a duplication node. All of these red and blue genes are orthologous to the black (frog) gene, an example of a many:1 relationship.

Evolutionary scenarios and relationships become complicated when dealing with many lineage-specific gene duplications and losses. In plants especially, homologous relationships are hard to infer because of their highly complex genomes compared to animals. Plant genomes tend to be much larger and much more duplicated than animal genomes, making ortholog inference in plants very challenging.

Several algorithms and tools are available to predict homologous relationships between genomes. OMA (Orthologous Matrix) is one of them. It’s a method and database for the inference of orthologs and paralogs among completely sequenced genomes. Launched by Dessimoz and colleagues in 2004, OMA has steadily increased the number of species in the database to 1706, including both prokaryotes and eukaryotes. With its many genomes and accurate orthology prediction, OMA is a great starting point for evolutionary biology and genomics analyses. Recently OMA has undergone its 17th browser release to include a website facelift, gene function prediction, and more support for plant genomes. For plants in particular, there is now over 450 million years of evolution represented with the orthology prediction between the species Selaginella moellendorffii (representing early vascular plants) and Physcomitrella patens (representing the non-vascular plants).

The burst of larger, more complex sequenced genomes in the past decade provides a unique challenge in terms of orthology prediction. OMA tackles this problem, and provides a valuable resource to the scientific community. So, want to find out how many genes humans have in common with yeast? Try OMA.

References

  • Altenhoff AM, Dessimoz C. Inferring Orthology and Paralogy. In: Anisimova M, editor. Evolutionary Genomics. Totowa, NJ: Humana Press; 2012. pp. 259–279. Available: http://discovery.ucl.ac.uk/1395519/
  • Altenhoff AM, Škunca N, Glover N, Train C-M, Sueki A, Piližota I, et al. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res. 2014; gku1158. doi:10.1093/nar/gku1158

NatashaGloverNatasha Glover received her Bachelor of Science and PhD from the Department of Crop and Soil Environmental Science at Virginia Tech in the U.S. Her PhD was focused on plant genomics and biotechnology. She received a Marie Curie International Incoming Fellowship for her first postdoc and worked in Clermont-Ferrand, France at the Institut Nationale de la Recherche Agronomique for 3 years. There, she concentrated on computational biology, with a focus on synteny and duplication in the wheat genome. Natasha is a currently a postdoc based at Bayer CropScience in Ghent, Belgium as part of the Marie Curie PLANT FELLOWS program. Her co-advisor is Dr. Christophe Dessimoz in the department of Genetics, Evolution, and Environment at UCL.

Competitive Generosity Drives Charitable Donations

By Claire Asher, on 17 April 2015

Unconditional generosity is a characteristic of humans on which we pride ourselves, and billions of dollars is donated to hundreds of thousands of charitable organisations every year. But look at it from an evolutionary perspective, and this trait seems difficult to explain. In some situations, giving may have evolved to advertise positive characteristics of the giver in the aim of attracting a mate. Recent research from GEE suggests this may explain the charitable behaviour of men donating to female fundraisers online. Data from over 2500 fundraising campaigns showed that men donate £10 more on average if previous male donors have been particularly generous.

Helping others at random, with no promise of reciprocity in the future, should not be favoured by natural selection as it will tend to disadvantage the altruist. Yet we see people doing just that every day. One theory that may explain selfless, unconditional generosity in humans (and other animals) is the ‘competitive helping’ hypothesis, which suggests generosity may sometimes be used to advertise positive characteristics to potential mates. The hypothesis suggests that people will compete to be the most generous, particularly when they are in the presence of attractive potential mates. If generosity is costly, and competition for mates is tough, then competitive generosity could be favoured by natural selection as a mechanism to honestly communicate quality. Only the best quality males could afford to be so generous, making them more attractive to on looking females.

To test this hypothesis, GEE researcher Dr Nichola Raihani and Professor Sarah Smith from the University of Bristol reviewed 2561 online fundraising pages, and selected 668 that had public donations and an image of the fundraiser. They then calculated the average donation running up to a large donation of £50 or more. They compared these donations with those made after the large donation, according to the gender of the donors and the gender and attractiveness of the fundraiser. They found men tended to give larger amounts after other men had made large donations. Men were also more generous when the fundraiser was an attractive female, giving four times more to female fundraisers following a large donation from another male. Attractive female fundraisers received £28 more during these bidding wars than less attractive females and males!

Interestingly, while this pattern is clear in donations by men, the same is not true for women donating money online. This suggests that male charitable behaviour represents a competitive helping display, favoured by sexual selection as an honest signal of male quality.

It’s fascinating that evolutionary biology can offer insights into human behaviour even in the modern world. People are really generous and their reasons for giving to charity are generally not self-serving but it doesn’t preclude their motives from having evolved to benefit them in some way. Take eating for example, our primary drive is to dispel the feeling of hunger, which is pleasurable, but the evolutionary purpose is to make sure we don’t starve and die. Generous behaviours can be seen in a similar way – the motivation for performing them doesn’t have to be the same as the evolutionary function.” – Dr Nichola Raihani

Original Article:

() Current Biology

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This research was made possible by funding from the Economic and Social Research Council (ESRC) and the Royal Society.

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]

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.

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).

Handicaps, Honesty and Visibility
Why Are Ornaments Always Exaggerated?

By Claire Asher, on 23 October 2014

Sexual selection is a form of natural selection that favours traits that increase mating success, often at the expense of survival. It is responsible for a huge variety of characteristics and behaviours we observe in nature, and most conspicuously, sexual selection explains the elaborate ornaments such as the antlers of red deer and the tail of the male peacock. There are many theories to explain how and why these ornaments evolve; it may be a positive feedback loop of female preference and selection on males, or ornaments may signal something useful, such as the genetic quality of the male carrying them. One way or another, despite the energetic costs of growing these ornaments, and the increase risk of predation that comes with greater visibility, sexually selected ornaments must be increasing the overall fitness of individuals carrying them. They do so by ensuring the bearer gets more mates and produces more offspring.

Theory predicts that sexually selected traits should be just as likely to become larger and more ostentatious as they are to be reduced, smaller and less conspicuous. However, almost all natural examples refer to exaggerated traits. So where are all the reduced sexual traits?

Runaway Ornaments

Previous work by GEE researchers Dr Sam Tazzyman, and Professor Andrew Pomiankowski has highlighted one possible explanation for this apparent imbalance in nature – if sexually selected traits are smaller, they are harder to see. Using mathematical models, last year they showed that differences in the ‘signalling efficacy’ of reduced and exaggerated ornaments was sufficient to explain the bias we see in nature. Since the purpose of sexually selected ornaments is to signal something to females, if reduced traits tend to be worse at signalling, then it makes sense that they would rarely emerge in nature. Their model covered the case of runaway selection, whereby sexually selected traits emerge somewhat spontaneously due to an inherent preference in females. It goes like this – if, for whatever reason, females have an innate preference for a certain trait in males, then any male who randomly acquires this trait will get more mates and produce more offspring. Those offspring will include males carrying the trait and females with a preference for the trait, and over time this creates a feedback loop that can produce extremely exaggerated traits. Under this model of sexual selection, differences in the signalling efficacy can be sufficient to explain why we so rarely see reduced traits.

Handicaps

However, this is just one model for how sexually selected ornaments can emerge, so this year GEE Researchers Dr Tazzyman and Prof Pomiankowski, along with Professor Yoh Iwasa from Kyushu University, Japan, have expanded their research to include another possible explanation – the handicap hypothesis. According to the handicap principle, far from being paradoxical, sexually selected ornaments may be favoured exactly because they are harmful to the individual who carries them. In this way, only the very best quality males can cope with the costs of carrying huge antlers or brightly coloured feathers, and so the ornament acts as a signal to females indicating which males carry the best genes. This is an example of honest signalling – the ornament and the condition or quality of the carrier are inextricably linked, and there is no room for poor quality males to cheat the system.

Using mathematical models, the authors investigated four possible causes for the absence of reduced sexual ornaments in the animal kingdom. Firstly, like the case of runaway selection, differences in signalling efficacy might explain the bias. Under the handicap hypothesis, ornaments act as signals of genetic quality, so it would be little surprise that their visibility or effectiveness at conveying the signal would be important. Smaller ornaments may simply be worse at attracting the attention of females, meaning that the benefits of the sexual ornament don’t outweigh the costs. Similarly, the costs for females of preferring males with reduced ornaments may be higher than for exaggerated ornaments, because it is easier to find males with exaggerated traits. Again, this could theoretically tip the balance of cost and effect away from selecting for reduced ornaments. An alternative explanation is that the costs of the ornament itself are different for reduced and exaggerated traits. This seems quite likely in many cases, since a large ornament would require more resources to grow. But in this case selection would be more likely to produce reduced ornaments with lower costs! In order to replicate the excess of exaggerated traits we see in nature, reduced traits would have to cost more – much less biologically plausible. However, if large ornaments tend to be more costly, then they may be more likely to be condition-dependent, a key tenant of the handicap principle. Exaggeration may be more effective at producing honest signalling and exaggerated traits may therefore be more useful to females as a signal of quality.

Honest Signals

The results of modelling highlighted two key ways in which exaggerated traits might be favoured by the handicap process. In the model, when exaggerated traits have a higher signalling efficacy or are more strongly condition-dependent, exaggerated traits tend to be more extreme than reduced traits. The model still predicts that reduced traits are equally likely to evolve, just that they will tend to be less extreme examples of ornamentation. The other two possible explanations – higher costs to females that prefer small ornaments or the males that carry them, failed to consistently produce the observed lack of reduced ornaments. Both explanations were able to produce this outcome under certain circumstances, but in other circumstances they produced the opposite effect. Exaggerated ornaments, therefore, may be more common because they are more effective signals that are more likely to be honest.

Based on this and previous work by Dr Tazzyman and colleagues, asymmetries in the signalling efficacy of reduced and exaggerated traits is sufficient to explain the lack of reduced traits in nature. Whether ornaments evolve via runaway selection or the handicap process, asymmetrical signalling efficacy tends to favour exaggerated traits. However, in the case of the handicap process, asymmetries in condition-dependance of the trait may also be involved. These two explanations are not mutually exclusive, and it is likely that in reality many factors are involved.

Importantly, for both explanations and for both type of sexual selection, the models still predict that exaggeration and reduction will be equally likely. The differences emerge in terms of how extreme the ornament will become. Thus, this work predicts that there are many examples of reduced ornaments in nature, perhaps we just haven’t found them yet. This is especially likely if reduced traits that might be less noticeable anyway also tend to be less extreme. Alternatively, there may be other asymmetries not yet considered that make reduced ornaments less likely to emerge in the first place.

Where Next?

The authors suggest some very interesting avenues for future research. Firstly, they suggest that more complex models investigating how multiple different asymmetries may act together to produce sexually selected ornaments will get us closer to understanding the intricate dynamics of sexual ornamentation. Secondly, these models have only considered cases where evolution of the trait eventually settles down – at a certain ornament size, the costs and benefits of possessing it are equal, and the trait should remain at this size. However, in some cases the dynamics are more complex, and traits undergo cycles of exaggeration and reduction. Research into the impact of asymmetries in condition-dependence and signalling efficacy in these ‘nonequilibrium’ models would yield fascinating insights into the evolution of sexual ornaments.

Original Article:

() Evolution

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

The Importance of Size in the Evolution of Complexity in Ants

By Claire Asher, on 16 September 2014

Ants are amongst the most abundant and successful species on Earth. They live in complex, cooperative societies, construct elaborate homes and exhibit many of the hallmarks of our own society. Some ants farm crops, others tend livestock. Many species have a major impact on the ecosystems they live in, dispersing seeds, consuming huge quantities of plant matter and predating other insect species. One of the major reasons for their enormous success is thought to be the impressive division of labour they exhibit. Theory suggests that, during the evolution of ants, increases in colony size drove increases in the complexity of their division of labour. However, there have been few previous attempts to test the hypothesis. A recent paper by GEE’s Professor Kate Jones and Phd student Henry Ferguson-Gow tested this hypothesis across the Attine ants, a large neotropical group including the famous leaf-cutter ants.

Ants, along with other social insects such as some bees, wasps and termites, are eusocial. This means that reproduction in their societies is dominated by just one or a few queens, while most of the colony members never reproduce, but instead perform other important tasks such as foraging, nest construction and defence. This system initially puzzled evolutionary biologists, because it poses the question, “how do non-reproductive workers pass on their genes?”. More specifically, “how can genes evolve to generate different morphology and behaviour in workers if they never reproduce and pass those genes on?”. This question was resolved in the 1960s, when W.D. Hamilton proposed the concepts of inclusive fitness and kin selection. He pointed out that although members of the non-reproductive worker caste do not directly pass on their genes, they are helping to ensure the survival of their siblings. Closely related individuals, such as siblings, share a large percentage of their genetic information, so by helping relatives, you are indirectly passing on your genes. Inclusive fitness is a measure of the total reproductive success of an individual, including direct fitness (gained by producing your own offspring) and indirect fitness (gained by helping relatives to reproduce). Kin selection, a form of natural selection, can therefore favour genes that cause sterility in the worker caste through it’s positive effects on the reproductive success of relatives.

When eusociality first began to evolve, colonies were probably small and although the worker caste likely refrained from reproduction most of the time, they weren’t completely sterile. In small colonies, keeping your reproductive options open makes a lot of sense – if the queen dies you may have a good chance of taking over the colony and reproducing yourself. Through evolutionary time, however, colony size increased in some lineages, and it is thought this may have driven increasing specialisation and commitment of individuals to their queen and worker roles. As colony size increases, your chances for gaining any kind of direct fitness start to decrease very rapidly. As a worker it’s a much better bet to do what you can to maximise your indirect fitness benefits in large colonies, and this can be achieved by becoming increasingly specialised for your particular role. Increases in division of labour, for example, as individuals specialise more in particular tasks, may lead to increase colony efficiency and success. In turn, this may allow for the evolution of larger colonies, resulting in a positive feedback loop whereby increases in colony size lead to increases in division of labour which lead to increases in colony size, and so on. This force may have lead to the evolution of ant species with enormous colonies – over a million workers can be found in some leaf-cutter colonies!

GEE Researchers Professor Kate Jones and Henry Ferguson-Gow, along with colleagues at the University of East Anglia and the University of Bristol, produced a phylogenetic tree for the Attine Ants (a group containing over 250 species), and mapped social and environmental data onto this tree in order to test for the effects of colony size and environment on the evolution of more sophisticated division of labour. The Attini are a good group of ants to test this hypothesis in, as they show large variation in colony size and the extent of morphological divergence between the queen and worker caste.

They collected published data on social traits (colony size, worker size, queen size) and environmental conditions (daytime temperature, seasonality in temperature and precipitation) for over 600 observations of populations for 57 species of Attine ant, including every single Attine genus. Using supertree methods, they constructed a phylogeny for the attine ants, which enabled them to control for evolutionary relationships and to estimate the speed at which evolutionary changes occurred.

Colony size ranged from 16 to 6 million individuals, with the largest colonies exhibited by the fungus growing leaf-cutter ants Atta and Acromyrmex. The authors found that increases in colony size through evolution are strongly associated with increases in both worker size variation (representing division of labour within the worker caste) and queen worker dimorphism (representing reproductive division of labour). Colony size showed a positve correlation with variation in size within the worker caste, and a weaker, but positive correlation with queen-worker dimorphism. Environmental factors such as temperature, rainfall and seasonality did not have any effect on colony size, indicating that climate and other environmental variables have not been an important factor in driving the evolution of increased colony size.

This study finds strong support for the size-complexity hypothesis, which suggests that during the evolution of eusociality, increases in colony size both drove and were driven by increases in division of labour and in specialisation of the queen and worker castes to their respective roles. This pattern may have also occurred during other major transitions in evolution, such as the evolution of multicellularity, which shares many similarities with the evolution of eusociality (e.g closely related group members, division of labour). The relationship between group size and complexity may therefore have been a crucial force in the evolution of complex life, and in the major evolutionary innovations that have generated the diversity of life we see today.

Original Article:

() Science

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

Understanding Catfish Colonisation and Diversification in The Great African Lakes

By Claire Asher, on 5 September 2014

Why some regions or habitats contain vast, diverse communities of species, whilst others contain only relatively few species, continues to be the subject of scientific research attempting to understand the processes and conditions that allow and adaptive radiation. The Great African Lakes exist as freshwater ‘islands’, with spectacularly high levels of biodiversity and endemism. They are particularly famous for the hyperdiverse Cichlid fish, but they are also home to diverse assemblages of many other fish, such as catfish. Recent research in GEE investigated the evolution of Clatoteine catfish in Lake Tanganyika, to investigate the forces driving evolutionary radiations in the Great African Lakes. Their results suggest that evolutionary time is of key importance to catfish radiations, with recently colonised groups showing less diversity than long-standing species.

Lake Tangayika is the World’s second largest freshwater lake, covering 4 countries in the African Rift Valley (Tanzania, the Democratic Republic of the Congo, Burundi and Zambia). It is home to the highest diversity of lake-dwelling catfish on Earth, however the evolutionary history of these catfish is not fully understood. GEE academic Dr Julia Day and PhD Student Claire Peart, in collaboration with colleagues at the Natural History Museum, London and the South African Institute for Aquatic Biodiversity, investigated the evolutionary history of nocturnal Claroteine catfishes in Lake Tangayika. This group of catfish offers an excellent opportunity to investigate the influence of different factors in evolutionary diversification, as it includes multiple genera with varying range sizes and habitat types.

The Drivers of Diversification

Previous research has suggested a number of factors that are important in enabling adaptive radiations that can produce extremely high levels of biodiversity – deep lakes that experience lots of sunlight tend to favour evolutionary diversification. Diversification is also more common for species that have had a lot of evolutionary time in which to diverge and that experience high levels of sexual selection. Interestingly, although lake depth is important, the total size of the lake does not appear to be so important for diversification. A large geographical area to diversify into may influence the duration of adaptive radiations, however, with river-dwelling species showing more consistent species-production through time. This data suggests that adaptive radiations may be, to some extent, predictable, however much previous work has focussed on key model groups such as the Cichlid fish, and these hypotheses need to be generalised to other species and locations.

Molecular Phylogeny of Claroteine Catfish,
showing independent colonisation of
Chrysichthys brachynema

The authors sequenced nuclear and mitochondrial genes from 85 catfish covering 10 of the 15 species of Claroteine catfish, in order to construct an evolutionary tree for the sub-family. Estimates of the relationships between species and the evolutionary timescales of colonisation and divergence allowed the authors to distinguish between the possibilities of single or multiple colonisation events, and the processes driving diversification. The results indicated that most Claroteine catfish in Lake Tangayika originate from a single colonisation of the lake between 5 and 10 million years ago, followed by evolutionary radiations to produce the variety of species present today. One species, Chrysichthys brachynema was the exception to this rule, having independently colonised the lake around 1 – 2 million years ago. This species has not shown adaptive radiation since colonisation, probably because of the relatively short time it has been present in the lake. These results support previous work that has suggested that time is an important factor in producing highly diverse species assemblages.

Original Article:

() Molecular Phylogenetics and Evolution

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This research was made possible by funding from the Natural Environment Research Council (NERC), the National Council for Scientific and Technological Development (CNPQ), the National Geographic Society, and the Percy Sladen Memorial Trust Fund.

Sex Differentiation Begins During Early Development

By Claire Asher, on 27 August 2014

Males and females look different from each other, and these sexual dimorphisms are the result, largely, of sex differences in the expression of certain genes. Typically, scientists have studied sexual dimorphism in sexually mature adult animals, as this is the lifestage where differences are most apparent. However, many sex-specific phenotypes arise from sex-biased development, so sex-biased gene expression should be expected to begin during development. Recent research from GEE reveals complex patterns of sex- and stage-dependent gene expression, resulting from differing evolutionary pressures on difference sexes. In fact, sex-biased gene expression is actually most evident during early development.

Although there are some genetic differences between males and females, found on the sex chromosomes (Y in mammals, W in Birds), these contribute relatively little to the physical and behavioural differences between the sexes. Further, some animals (such as many reptiles) don’t possess a sex chromosome at all, instead determining sex based on environmental factors such as temperature. Scientists therefore believe that the majority of sexually dimorphic characteristics are generated from differences in the expression patterns of a shared set of genes, and there is now plenty of evidence for this in a variety of different species. In fact, sexual phenotypes appear to exist along a continuum, with some individuals in certain species exhibiting intermediate traits (e.g. subordinate male Turkeys).

The fruit fly,
Drosophila melanogaster

In most species, sex differences are less apparent during development and appear or become more pronounced at the onset of sexual maturity. This makes sense, since that’s generally when the sex-specific traits are useful. Nevertheless, the groundwork for producing these traits in adulthood must be laid during development, so we might expect to see sex-biased gene expression in juveniles as well. A recent paper by GEE academics Professor Judith Mank and Dr Peter Harrison, and Dr Jennifer Perry (University of Oxford) investigated gene expression patterns during larval development in the fruit fly, Drosophila melanogaster.

Juveniles Show Sex-Biased Gene Expression

The authors compared gene expression patterns in pre-gonad tissue in larvae and pre-pupae with gonad tissue in adult flies. Using transcriptome sequencing, which sequences all expressed genes, they were able to detect differences in gene expression between sexes at different developmental stages. By using a single tissue, the authors hoped to gain a clearer picture of gene expression in relation to sex and development, as tissue-specific gene expression can cloud the picture. Gonad and pre-gonad tissue was the obvious candidate, since this tissue forms sperm and eggs and is therefore likely to be under strong selection for sex-biased gene expression.

Despite the long-running assumption that sex-biased gene expression should not be prevalent in juveniles, the results of this study indicated that most genes show sex-bias in at least one pre-adult stage! Over 50% of genes showed at least 2-fold differences in gene expression between the sexes during larval or pre-pupae developmental stages. Sex was still the most important factor, however, with individuals within a sex showing greater similarity in gene expression patterns than individuals within a developmental stage.

. Venn diagrams of the number and percentage of genes showing sex-biased gene expression in larvae, pre-pupae, and adults. Image from open access article.

Venn diagrams of the number and percentage of genes showing sex-biased gene expression in larvae, pre-pupae, and adults. Image from open access article.

Continuity and Sex Differences

The majority of sex-biased genes showed expression patterns that remained consistent throughout development, however a significant minority (~25%) of genes showed varying sex-bias according to developmental stage. For example, a gene that showed lower expression in females during the larval stage might then show higher expression in females during adulthood.

In the majority of previous studies have found that more genes show male-bias in adults. By contrast, this study showed that in larval and pre-pupal stages of development in Drosophila melanogaster, more genes show female-biased gene expression. Females were also more likely to show stage-dependent sex-biases in gene expression. The exception to this was genes showing very extreme sex-bias, which tended to be male-biased. This is consistent with the finding that the overall magnitude of gene expression differences tended to be higher in male-biased genes.

The Rate and Form of Evolution

The authors then investigated the evolutionary dynamics that lead to these patterns of gene expression. Genes showing the most rapid recent evolution were those that showed male-biased expression continously throughout life, and those that showed female-biased expression in the larval stages. The evolutionary pressures in male- and female-biased genes were different for each sex. For female-biased genes expressed in larvae, rapid evolution was the result of a relaxation of purifying selection for stage-dependent genes (natural selection that removes harmful mutations), whereas rapid evolution in consistently male-biased genes was a result of stronger purifying selection on stage-dependent genes.

This study reveals complex and intricate relationships between sex, age, development and gene expression in the fruit fly, Drosophila melanogaster. Despite minimal visible differences between the sexes during larval and pre-pupal development, there were vast differences in terms of gene expression. Although this is contrary to previous assumptions about the nature of sex-biased gene expression, it is consistent with the fact that many sexually dimorphic traits exhibited by adults must by necessity begin to develop before adulthood. It is therefore not surprising that sex-biased gene expression is evident in juveniles, however the extent of this bias is quite a surprise. More research is needed to understand the evolutionary dynamics shaping development- and sex-specific gene expression, and how these patterns vary across different tissue types.

Original Article:

() The Ontogeny and Evolution of Sex-Biased Gene Expression in Drosophila melanogaster Molecular Biology and Evolution

Further Reading:

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This research was made possible by funding from the European Research Council (ERC), the Elizabeth Hannah Jenkinson Fund and the John Fell Oxford University Press Research Fund

Evolving Endemism in East Africa’s Sky Islands

By Claire Asher, on 8 August 2014

The World’s biodiversity is not evenly distributed. Some regions are hot spots for species richness, and biologists have been trying better to understand why these regions are special and what drives evolution and diversification. A recent paper by GEE’s Dr Julia Day and recent PhD graduate Dr Siobhan Cox, investigated the diversification of White-Eye Birds in East Africa’s Afromontane Biodiversity hotspot. Their results indicate that speciation in these birds has likely been driven by adaptation to a gradient of environmental conditions.

The East Afromontane Biodiversity Hotspot (EABH) is one of the most biodiverse regions on Earth, but it is under constant threat from increasing urbanisation in the area, which is predicted to continue over coming decades. It is therefore crucial to quantify what biodiversity is found in this hotspot, and understand the evolutionary processes that have made it a hotspot. The geography in this region is quite special, and is thought to have been a key factor driving high levels of species richness here. The Afromontane region is formed of a chain of ancient massifs (mountains created by faults and flexures in the Earth’s crust) and relatively young volcanoes. The low-lying regions between these peaks are covered in arid savannah, but montane forests appear on the peaks above about 800m. These forests exists as “ecological islands”, isolated from each other since the early Oligocene around 33 million years ago. Before this, conditions in the region were less arid and continuous forests covered the mountains and the valleys. As the forests retracted and fragmented, their inhabitants became isolated from one another, and this may have led to the emergence of new species, unique to each isolated montane fragment.

A Brief Introduction to Speciation
The processes by which new species arise depend upon the circumstances. Traditionally, speciation was thought to occur as a result of geographic separation of populations of a single ‘parent’ species. Once isolated and unable to interbreed, the two populations would slowly diverge from each other both due to random genetic change and adaptation to differing conditions. If enough time passed before the two populations came into contact with each other again, then they would eventually be so distinct that they were unable to interbreed even if they were reunited, and therefore should be classified as separate species. This is the standard model of speciation, known as allopatric speciation. It is now appreciated that new species can arise even without geographical isolation in a process known as sympatric speciation, often this can be caused by isolation of other kinds, such as behavioural isolation or through selective mate choice. It is generally accepted, however, that speciation requires, at least, a massive reduction in the rates of interbreeding between two populations or subspecies. Interbreeding will tend to restrain divergence as it mixes genes between the populations.

Evolving Endemism
There are two main hypotheses for how the extraordinarily high levels of endemism arose on the montane forest ‘islands’:

  1. The Montane Speciation Model suggests that montane ‘islands’ became refugia for species as they tracked suitable conditions up the mountain. This idea is based on a general theory for speciation and divergence known as ‘niche conservatism’, which suggests that geographical isolation of populations is driven by an inability to adapt to changing conditions. Once isolated, populations begin to diverge from one-another and over time this generates very high species richness.
  2. The Gradient Speciation Model by contrast, hypotheses that new species emerge as a result of adaptation to different conditions along a gradient. In this model, adaptation and niche divergence drive speciation, and we expect to find related species living in adjacent habitats.

The EABH is home to over 1300 described species of bird, of which 110 are known to exist nowhere else on Earth. In a recent paper in Molecular Ecology, Dr Day, along with colleagues at the Natural History Museum (Tring, Hertfordshire), the Technical University of Munich and the National Museums of Kenya, investigated the pattern of divergence in African montane white-eyes (Zosterops), a group of small, gregarious birds. Each montane forest fragment houses a single, endemic species, while other species live on real islands, and others live in other habitats on the mainland. This makes them an ideal group to test the competing hypotheses of niche conservatism and niche divergence.

The authors collected mitochondrial and genomic DNA samples for 148 birds from 15 species found across the EABH and elsewhere. They estimated the evolutionary timing of each species’ divergence based on both geological and molecular data, to investigate whether the montane taxa speciated in their current habitat or elsewhere, and whether they speciated before or after the climatic changes that isolated forest fragments.

A Late Pleistocene Colonisation
Based on molecular data, the authors estimate that White-eyes colonised Africa in the late Pleistocene, around 1.55 million years ago, and then exhibited brief pulses of diversification from 0.9 million years ago until around 0.3 million years ago. The genus Zosterops therefore colonised the region long after the montane forest habitat had fragmented into ecological islands, discounting the montane speciation hypothesis. Montane species diverged from their lowland sisters around 1 million years ago, during the last major wet phase. In some cases, montane species were found to be older than species found in neighbouring lowland areas, indicating colonisation in the other direction. They found no evidence that diversification of the White-eyes corresponded with volcanic activity in the region, which has previously been suggested.

They found that many of the so-called ‘species’ of Zosterops in fact include multiple sub-species, and they found strong support for already identified subspecies. This suggests that different species and subspecies independently colonised the montane habitat, and have remained more or less the same since. That the lowland savannahs that exist between the montane islands is a strong barrier that isolates montane populations is strongly supported by their results – species on neighbouring sky islands are very different from each other genetically, indicating they have not interbred for a great deal of evolutionary time. This is similar to the pattern of colonisation and diversification seen in White-eye species that live on real islands, which likely present similar evolutionary pressures to the ecological islands found in fragmented habitats.

Overall, their results support a niche divergence explanation of speciation in Montane White-Eyes, consistent with the gradient hypothesis, and ruling out niche conservatism models, such as the montane speciation hypothesis. However, the authors point out that their results do not distinguish between the gradient hypothesis and similar alternative, the vanishing refugia model, which suggests that speciation occurs through adaptation to less favourable habitats as suitable habitat contracts and refugia become unable to maintain viable populations. Further research is needed to conclusively distinguish between these models. The relative climatic stability of the highland montane habitats, couples with frequent climatic fluctuations in low-land areas may have played a key role in diversification in White-eyes, and may be a key driver of endemism in this region.

Original Article:

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