New software to untangle genetic factors linked to shared characteristics among different species

Aston University has worked with international partners to develop a software package to help scientists answer key questions about genetic factors associated with shared characteristics among different species.

Called CALANGO (comparative analysis with annotation-based genomic components), it has the potential to help geneticists investigate vital issues such as antibacterial resistance and improvement of agricultural crops.

This work ‘CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species’ has been published in the journal Patterns. It is the result of a four year collaboration between Aston University, the Federal University of Minas Gerais in Brazil and other partners in Brazil, Norway and the US.

Similarities between species may arise either from shared ancestry (homology) or from shared evolutionary pressures (convergent evolution). For example, ravens, pigeons and bats can all fly, but the first two are birds whereas bats are mammals.

This means that the biology of flight in ravens and pigeons is likely to share genetic aspects due to their common ancestry. Both species are able to fly nowadays because their last common ancestor—an ancestor bird—was also a flying organism.

In contrast, bats have the ability to fly via potentially different genes than the ones in birds, since the last common ancestor of birds and mammals was not a flying animal.

Untangling the genetic components shared due to common ancestry from the ones shared due to common evolutionary pressures requires sophisticated statistical models that take common ancestry into account.

So far, this has been an obstacle for scientists who want to understand the emergence of complex traits across different species, mainly due to the lack of proper frameworks to investigate these associations.

The new software has been designed to effectively incorporate vast amounts of genomic, evolutionary and functional annotation data to explore the genetic mechanisms which underlie similar characteristics between different species sharing common ancestors.

Although the statistical models used in the tool are not new, it is the first time they have been combined to extract novel biological insights from genomic data.

The technique has the potential to be applied to many different areas of research, allowing scientists to analyze massive amounts of open-source genetic data belonging to thousands of organisms in more depth.

Dr. Felipe Campelo from the Department of Computer Science in the College of Engineering and Physical Sciences at Aston University, said, “There are many exciting examples of how this tool can be applied to solve major problems facing us today. These include exploring the co-evolution of bacteria and bacteriophages and unveiling factors associated with plant size, with direct implications for both agriculture and ecology.”

“Further potential applications include supporting the investigation of bacterial resistance to antibiotics, and of the yield of plant and animal species of economic importance.”

The corresponding author of the study, Dr. Francisco Pereira Lobo from the Department of Genetics, Ecology and Evolution at the Federal University of Minas Gerais in Brazil, said, “Most genetic and phenotypic variations occur between different species, rather than within them. Our newly developed tool allows the generation of testable hypotheses about genotype-phenotype associations across multiple species that enable the prioritisation of targets for later experimental characterization.”