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Archive for August, 2014

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:

ERC

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

Extinction and Species Declines:
Defaunation in the Anthropocene

By Claire Asher, on 18 August 2014

We are in the grips of a mass extinction. There have been mass extinctions throughout evolutionary history, what makes this one different is that we’re the ones causing it. A recent review paper from GEE’s Dr Ben Collen discusses the current loss of biodiversity and suggests that our main concerns are species and population declines, which alter ecosystem dynamics and threaten our food, water and health. Understanding the drivers of local declines is more complex than understanding species extinction, but may be more pertinent to our ongoing health and survival.

The history of life on Earth has been punctuated by five mass-extinction events; from the Ordovician-Silurian extinction that killed 85% of sea life 443 million years ago, to the famous Cretaceous-Tertiary extinction that wiped out the dinosaurs 65 million years ago, mass extinctions have been a part of life. However, we are now in the middle of the sixth mass extinction event, and we’re the ones who are causing it. The last 500 years has seen humans cause a wave of extinctions of such speed and magnitude that it rivals the big five extinction events of the past.

Defaunation in the Anthropocene

Like other mass extinctions, the Anthropocene extinction event is affecting all taxonomic groups, although some are being hit harder than others. Since 1500, over 300 terrestrial vertebrates, 90 fish and nearly 400 are known to have been driven to extinction (although the real figures are likely much higher!). A conservative estimate suggests that we may be losing anywhere between 10,000 and 60,000 species each year. Many of these species go extinct before we ever even get a chance to identify them. Extinction is not evenly distributed, though – amphibians appear to be worse affected than birds, for example. Perhaps more worrying, many remaining species are suffering severe population declines. Globally, terrestrial vertebrate populations show declines of 25%, and 67% of monitored invertebrate populations are declining by 45%! The loss of species from ecosystems, either through local population declines or species extinction, will undoubtedly disrupt ecosystem function and the key ecosystem services humans rely on for survival and well being.

Scientists have coined the term ‘defaunation’ to include the extinction of species and populations as well as local declines in abundance. Defaunation can be thought of as deforestation for animals. It is an important point to make that although species extinctions are conspicuous and striking, the real damage to ecosystem function happens a long time before the final extinction event. Declines in populations will alter community composition far more than the final loss of the few remaining individuals of a population, and further, population declines have the potential to be reversed, if we act quickly enough!

Predicting Patterns of Defaunation

If we are to halt or even slow the current mass extinction, we need to identify both the causes of defaunation and the traits that make certain species so vulnerable to human disruption. The main drivers of defaunation are overexploitation of species, habitat destruction and introduced invasive species. These threats have all increased in severity over the past decade and look set to continue. In addition to these long-term threats, climate change is rapidly becoming the biggest threat to biodiversity. Most threatened species are under pressure from multiple human threats, but our understanding of the complex interactions and feedback loops between different threats is still in it’s infancy. It’s clear though that these threats do not act in isolation; a species trying to track suitable habitat as it moves with climate change will find that task much harder if habitat loss and fragmentation is also occurring.

Researchers have highlighted a number of life history and biological traits that tend to make species more vulnerable to human impacts. For example, species that have a small geographic range, large body size and produce just a few offspring after a long-development process, are more likely to be threatened with extinction due to human activities. However, our understanding of the traits that influence species’ extinction risk doesn’t help conservation as much as you might expect, because the relationship between these traits and extinction risk is often idiosyncratic and highly context-dependent. These relationships may also be more variable and weaker for individual populations than for whole species, making population declines more difficult to predict than whole-species extinctions. Defaunation, ultimately, is a synergistic function of the traits a species possess and the nature of the threat(s) it is exposed to.

Disrupting Ecosystems and Communities

The loss of biodiversity through defaunation is not just a concern because of the aesthetic appeal of an individual species, or of a world rich in diversity in general. It is also a major concern because defaunation will likely have a negative impact on the ecosystem goods and services upon which we rely upon for our wellbeing and survival. In fact, biodiversity loss is thought to be comparable to other threats such as pollution in terms of it’s impact on ecosystem function. Defaunation can be expected to have a negative impact on our food, water and health, as well as our psychological wellbeing.

Food

Insect pollination is required for the continued production of 75% of the World’s crops, and is responsible for 10% of the economic value of the entire World’s food supply. Declines in pollinators are now a major problem, particularly in Northern Europe and the USA, and have been linked to declines in insect-pollinated plants. Biodiversity, particularly of small vertebrates, is provides crucial pest control services, valued at around $4.5 billion a year in the USA alone. Declines in small vertebrate populations are linked to cascading changes in the whole ecosystem which allow increases in pest abundance and, consequently, a loss of plant biomass. If the plant in question is a crop or food source, the results can be catastrophic.

Nurtient Cycling and Decomposition

Invertebrates are also very important for their roles in decomposition and nutrient cycling. Defaunation can reduce these important services, and cause changes in the patterns of nutrient cycling that can have knock-on effects on a huge variety of ecosystems. Likewise, large vertebrates that roam large home ranges are important in connecting ecosystems and transferring energy between them, and yet these species are often the most severely impacted by human activities.

Water

Another key ecosystem service is the provision of clean, fresh water. Research has shown that declines in amphibian populations can result in increases in algae, reduced nitrogen uptake and changes to oxygen availability in the water. This too will likely have major knock-on effects for other species (including ourselves!).

Health and Medicine

Finally, we can expect defaunation to negatively affect our health. Species that are more robust to human disturbance are often also better at carrying and transmitting zoonotic diseases (diseases that are carried by animals and transferred to humans), and altering ecosystem dynamics can change behaviours that influence transmission rates. Defaunation is likely to also reduce the availability of pharmaceutical compounds and alter the dynamics of disease regulation. All of this may mean that defaunation leads to an increase disease and a reduction in the availability of therapeutic compounds.

The impact of defaunation is less about the absolute loss of biodiversity and more about the local shifts in species composition and functional groups, which alter ecosystem function and ultimately, our food, water and health. However, reductions in species exploitation and land-use change are two feasible actions that can be achieved rapidly and may buy us enough time to address other drivers of defaunation such as climate change. Globally, we need to reduce and more evenly distribute our consumption if we are to change current trends in defaunation, and open the possibility for refaunation.

Original Article:

() Science

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NSF

This research was made possible by funding from the Natural Environment Research Council (NERC), the National Council for Scientific and Technological Development (CNPQ), the Foundation for the Development of UNESP, the Sao Paolo Research Foundation, the Joint Nature Conservation Committee (JNCC), the National Science Foundation (NSF) and the National Autonomous University of Mexico/a>.

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).