A New Approach to Sequencing Genetic Changes Through Time
The fruit fly Drosophila melanogaster. Photo Ralph Kränzlein
By Saulo Silvestre
Variation is the source material of evolution.
For a species to evolve, its population members must differ from each other, and now a pioneering new method has been developed to identify and study specific points of difference in an evolving species.
The sources of genetic variation within populations include:
- Mutations, which are changes in genetic material that can result from DNA copying errors made during cell division, exposure to ionizing radiation, exposure to chemicals called mutagens, or infection by viruses;
- Sexual reproduction, mixing gene pools in differing stages of adaptation to various and diverse environments;
- Genetic drift, which is unexplained or random changes in the gene pool of a population. According to Project Genome of the U.S.-funded National Human Genome Research Institute, “Genetic drift can cause traits to be dominant or disappear from a population. The effects of genetic drift are most pronounced in small populations;” and
- Gene flow, which is the rate of movement of genes between populations. Moreover, epigenetic mechanisms, which alter gene expression in response to external environmental stimuli, also contribute to variation among individuals.
A thought experiment leads to conclusion that differences within a species are rooted in its genetic history
Imagine, in a fictional universe where the features of an organism vary independently from those of its parents, the frequency of dysfunctional body shapes that emerge over time. This severely hinders the survival of the species, because all sources of its genetic variation have random elements. Thus, the probability of dysfunctional characteristics emerging is far greater than that of functional features. Additionally, after just one generation in this fictional universe, the organisms would probably be so distinct from one another that it would be impossible for them to reproduce.
This simple thought experiment illustrates the necessity of constraints on the variation that new individuals may exhibit within a population. The parameter that describes the degree to which individuals in a species can vary within specific boundaries is called “robustness”.
Variation is necessary for evolution to occur. Photographs of four closely related species of lizards of the genus Anolis for comparison. Image from Yánez-Muñoz et al. (2018). Source
Variation and robustness represent opposing sides in the evolutionary history of species.
Understanding the roles and limits of those qualities can help us better understand Evolution and the boundaries within which it operates. While we have made significant advances in our understanding of variation through genetic research and profiling genomes during the last few decades, studies on robustness experienced fewer innovations in that period.
A new approach to measuring genetic differences over time
A significant breakthrough, however, was achieved in 2021, when researchers at Northwestern University published an article in the Journal eLife on a groundbreaking new method to study the structure and form (or “morphology”) of organisms. This new method objectively gauges the robustness of populations, the specific constraints on the observed variations, and where these constraints operate.
The team compared the morphology of around 2,000 pairs of wings of fruit flies to map and quantify the variation between individuals.
Traditionally, studies like this one would rely on comparing just a few specific regions of the wings, called landmarks, of the individuals analyzed. However, the selection process of the landmarks not only adds arbitrariness to the assessments but also limits our ability to detect variation only where variation is expected to be, which is particularly problematic for structures with complex forms and patterns.
In their research, the team at Northwestern University selected flies from a population with a high degree of variation, including individuals that had developed under distinct conditions, like poor diets or varying temperatures. They set up this sample to guarantee the maximum variation in morphology that the robustness of the species should allow. Then they took high-resolution photographs of the wings under a microscope, standardized the images (see picture below) to fit into circles while preserving features such as the angles between the veins, and stacked and compared pixel by pixel, every one of the 30,000 pixels in each image.
Illustration of the landmark-free approach to compare the morphology of the fruit fly wings, showing how the images were standardized and stacked for comparison. Image extracted from Alba et al. (2021).
This meticulous approach revealed an unexpected uniformity between the individuals.
All the wings fit into a narrow range of variation, showing that the flies have a very limited array of possible structural configurations that they can develop to accommodate for different conditions and genetics. On top of that, the variation is heavily concentrated in specific regions of the wings, like in the area near their hinges and the shape of specific veins.
Mapping of the variation in the morphology of the wings of fruit flies comparing the wings of flies with different genetic mutations (egfr, mam, star, and tkv) to a reference wildtype group. Blue pixels show where test pixel intensity is smaller, and red pixels where it is larger than the reference. Image extracted from Alba et al. (2021).
The scientists also observed that the morphological variations in different regions of the wings seem to be linked.
They argue that this is evidence that strong global constraints regulate the development of the fruit flies. They hypothesize that this integrated model of variation arises from developmental processes in which the expansion or contraction of a specific region of the wing directly affects the size and position of the wing’s remaining parts. Dr. Richard Carthew, one of the authors in the study, said that this finding shows a “magical ability [of the flies] to correct for differences and create a very robust final form” as they grow into adults.
But the remarkable uniformity found in the wings of the fruit flies did not come as a surprise for everyone.
According to Dr. Luisa Pallares, an ecologist and evolutionary biologist at Princeton University, severe restrictions to variation are necessary for members of a species to look as similar as they do. Nevertheless, this study is the first one to be able to quantify this in such great depth, allowing us to see the theory around robustness in action much more clearly.
Future studies will be necessary to see if the restricted variation observed in the wings of fruit flies is an exception or a rule among different structures and species – and, ideally, they will include both living and extinct species. This quantitative method could be used to study how natural selection acts on the morphological variation of organisms and may even be useful to predict the appearance of new species, which would be a significant leap into a deeper level of understanding of Evolution and genetic bonds through time.
Original article: https://www.quantamagazine.org/mathematical-analysis-of-fruit-fly-wings-hints-at-evolutions-limits-20210920/
