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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.

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.

It’s All in the Wrist

By Claire Asher, on 20 December 2013

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

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

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

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

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

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

Original Article:

() BMC Evolutionary Biology



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

Continental Catfish Show No Sign of Stopping

By Claire Asher, on 14 June 2013

The tree of life is a vast tangle of branches and twigs representing around 9 million species. Understanding the patterns and processes by which these species originated is a fundamental topic in evolutionary biology. Previous studies have suggested that the generation of new species may not be uniform over time, often with an initial burst of speciation, slowing as the lineage expands to fill the available niches. However, recent research in the department of GEE suggests this may not always be the case, and a previous focus on island species may have skewed our perspective of species accumulation.

When a new lineage begins to diverge, adapting to exploit new habitats or lifestyles, this often leads to an adaptive radiation, with many new species appearing over a short space of time. This initial rush of new species eventually begins to slow, as all the available niches become saturated, and slowly speciation grinds to a halt. This is the traditional view of how lineages have diversified to produce the vast array of species we see today (as well as many who have long since gone extinct). However, much of the research in this area has focussed on species confined to islands and lakes, where different processes may influence the appearance of new species. Continental species have a larger area to expand into, and a wider array of climatic conditions to cope with, providing a different set of parameters which may influence speciation. Recent research in the department of Genetics, Evolution and Environment suggests the pattern of species generation in continental lineages may differ from that of islands.

Tree of Life image © 2007 Tree of Life Web Project. Image of rose © 1999 Nick Kurzenko. Image of annelid worm © 2001 Greg W. Rouse

In their recent paper in Systematic Biology, Day and colleagues determined species relationships for 81 species of squeaker catfish from Africa in order to investigate the patterns of species generation and diversification during their 35 million year evolution. Using genetic data along with fossil evidence, they constructed a squeaker catfish tree and estimated divergence dates and historical geographic distributions. This tree revealed an almost constant rate of species generation over time. Across 35 million years of evolution, through major climatic and environmental changes, the squeaker catfish have been churning out new species at approximately 1 every 8 million years, and look set to keep going for another 90 million years, or so.

Syndontis 'squeaker' catfish. Photograph by Roger Bills

Syndontis ‘squeaker’ catfish . Photograph by

So why don’t the continental, river-dwelling catfish follow the same rules developed through years of studying island and lake-dwelling species? Continents are, of course, generally much larger than islands, and rivers provide more opportunity for movement than lakes. Continents allow for more constant species generation, as there is more space and habitat diversity available for species to move into and exploit. The climatic changes in Africa over the last 30 million years may have also helped the catfish maintain constant production of new species – creating a variable environment which is much less likely to become saturated with species. The squeaker catfish have survived through major tectonic activity in the East African Rift valley, including volcanoes and earthquakes, as well as huge climatic changes that influenced sea level and temperature. By combining phylogenetic and biogeographical data, Day et al suggest these environmental variations may have played an important role in African catfish diversification.

The processes shaping species diversification are varied and complex, and differ markedly between geographically isolated lineages (island / lake ecosystems) and wider ranging ones (e.g. continental rivers). Continental groups may take longer to reach species saturation, with environmental fluctuations facilitating continued species generation at a relatively constant rate. Moving beyond ‘model organisms’ and well-studied systems has the potential to reveal new processes and patterns, and illuminate old ones.

Original Article:

() Systematic Biology

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