New Metric Helps Identify Natural Selection in Protein Evolution

New Metric Helps Identify Natural Selection in Protein Evolution

The European mole and the Australian marsupial mole are both able to dig through the ground with ease, thanks to their well-adapted digging appendages. Despite living in different parts of the world, these two species have evolved similar features that are perfectly suited for their subterranean lifestyles.

In the scientific community, this phenomenon is known as “convergent evolution,” which occurs when different species of animals or plants independently develop similar features that have comparable shapes and functions.

There are numerous examples of convergent evolution in nature. For instance, both fish and whales possess fins, even though whales are mammals. Similarly, birds and bats have wings that allow them to fly, and many creatures, ranging from jellyfish to scorpions to insects, have evolved venomous stingers to protect themselves from attackers.

Scientists worldwide are interested in understanding the genetic changes responsible for identical characteristics evolving in species with no apparent relationship.

Plant physiologist Dr. Kenji Fukushima from the Julius-Maximilians-Universität (JMU) Würzburg explains that these traits, known as phenotypes, are always encoded in genome sequences.

Mutations or changes in genetic material can trigger the development of new traits. However, genetic changes usually do not lead to phenotypic evolution because underlying mutations are mostly random and neutral.

As a result, over the vast time scale at which evolutionary processes occur, an enormous amount of mutations accumulate, making it extremely challenging to detect phenotypically important changes.

Fukushima and David D. Pollock of the University of Colorado have created a new method that provides more accurate results than previous methods in identifying the genetic basis of phenotypic traits. Their approach is presented in the journal Nature Ecology & Evolution.

Their new method is a novel metric of molecular evolution, which accurately represents the rate of convergent evolution in protein-coding DNA sequences. This can reveal genetic changes that are associated with the phenotypes of organisms over an evolutionary time scale of hundreds of millions of years. It has the potential to enhance our understanding of how changes in DNA result in phenotypic innovations that give rise to the great diversity of species.

Fukushima and Pollock’s research is based on recent advancements in decoding genome sequences of various organisms, allowing for the study of the correlation between genotypes and phenotypes at a macroevolutionary level. This approach is promising, but there is a risk of “false-positive convergence” due to molecular changes that are nearly neutral and do not impact traits, as well as methodological biases. To address this issue, the researchers have developed a new metric of molecular evolution that can more accurately represent the rate of convergent evolution in protein-coding DNA sequences. This method offers the possibility of expanding our understanding of how genetic changes lead to phenotypic innovations, contributing to the diversity of species over hundreds of millions of years of evolution.

Fukushima explains that they expanded the framework and created a new metric to address a problem in studying protein evolution. The metric measures the error-adjusted convergence rate of protein evolution, which helps to distinguish natural selection from genetic noise and phylogenetic errors in both simulations and real-world examples.

The approach they developed is enhanced with a heuristic algorithm, which enables bidirectional searches for genotype-phenotype associations. This method can be used even in lineages that have diverged over hundreds of millions of years.

The scientists analyzed more than 20 million branch combinations in vertebrate genes to test the effectiveness of the new metric.

In their next step, the researchers plan to apply this method to carnivorous plants. The aim is to decode the genetic basis that plays a role in the plants’ ability to attract, capture, and digest prey.

Deep Dive

1. Schmitz, J. F., & Moritz, R. F. (2018). What’s the buzz about? The ecology and evolutionary biology of insect pollination. Annual review of ecology, evolution, and systematics, 49, 19-42.
2. Pennisi, E. (2018). The CRISPR craze. Science, 359(6374), 928-931.
3. Londoño, I. B., & Voelker, G. (2018). Genomic perspectives on the evolution of bird song. Biological Reviews, 93(4), 1776-1796.
4. Togninalli, M., Seren, Ü., Meng, D., Fitz, J., Nordborg, M., & Weigel, D. (2018). The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. Nucleic acids research, 46(D1), D1150-D1156.
5. Lenz, T. L., Wells, K., Pfeiffer, M., & Sommer, S. (2018). Diverse MHC IIB allele repertoire increases parasite resistance and body condition in the long‐tailed giant rat (Leopoldamys sabanus). Molecular ecology, 27(8), 1860-1873.