“Over the last decade, there have been enormous efforts to sequence hundreds of genes from lineages across the tree of life,” said Professor Stephen A. Smith, Department of Ecology and Evolutionary Biology, University of Michigan. “What we have discovered after analyzing this genetic data is that the individual genes often disagree about the relationships in the tree of life.”

The paper, “Phylogenomic conflict coincides with rapid morphological innovation,” was published in the Proceedings for the National Academy of Sciences, May 11, 2021. Coauthors with Smith, who is also affiliated with the U-M Department of Computational Medicine and Bioinformatics, are alumnus Caroline Parins-Fukuchi (U-M EEB Ph.D. 2019), currently a postdoctoral fellow with the Department of Geophysical Sciences, University of Chicago; and Gregory W. Stull, who was a National Science Foundation collections postdoctoral fellow at U-M, hosted by EEB and the U-M Herbarium. He is currently a postdoc with the Kunming Institute of Botany, Chinese Academy of Sciences, and a research associate in the Department of Botany, Smithsonian Institution.

“We analyzed the "hotspots" of those disagreements (i.e., where many genes disagree about how things are related) and we found that these areas are where there is a lot of morphological change,” Smith explained. “Specifically, we looked at mammals, birds and several groups of plants. In each case, where there was a lot of conflict among the genes, there was a lot of morphological change. This suggests that the processes that cause the conflict among the genes, such as changes in population size or structure, are probably important and/or correlated with large scale morphological changes. All of this suggests that gene tree conflict, something previously considered a nuisance, holds important clues for understanding the evolution of lineages across the tree of life.”

To explain gene conflict, Smith explained that different genes can reflect different evolutionary relationships. “For example, even though we understand humans to be most closely related to chimps, some of our genes actually show humans to be more closely related to gorillas, or chimps more closely related to gorillas. While there is more evidence for chimps being more closely related to humans, this conflict in the genetic data remains. It is not an anomaly, but expected, due to different population processes.”

Parins-Fukuchi said that she “found this project really exciting because our findings demonstrate that we can identify the link in evolutionary patterns generated by processes that occurred many millions of years ago at both the genetic and phenotypic levels. As someone who is particularly interested in studying the origin of new phenotypes, this suggests that we can combine genomic with phenotypic data to better understand how really interesting traits evolved at the population level. This opens many new possibilities for future work, for example, linking these genomic patterns to those in the fossil record to generate a more detailed picture of how organisms have changed over evolutionary time. Although we are quite a ways off from the type of ‘grand-unified’ perspective that is a goal in evolutionary biology, our findings bring us one step closer in a very concrete way.”

Parins-Fukuchi’s advisors were EEB Professor Christopher Dick and Professor Dan Fisher, with affiliations with the Museum of Paleontology, the Department of Earth and Environmental Sciences and EEB. She will begin a faculty position at the University of Toronto in the Department of Ecology and Evolutionary Biology in January 2022.

Compiled by Gail Kuhnlein

Co-occurring patterns in gene-tree conflict and morphological rates of evolution across the mammal (A and B) and bird (C and D) datasets. Conflict is measured as the proportion of gene trees that disagree with the species tree. Morphological rate is measured as the number of changes per million years for qualitative datasets and Brownian variance per million years for quantitative datasets. Vertical lines correspond to the onset of the Paleogene (66 Ma) and the Miocene (23.03 Ma). Image: Stephen Smith and Caroline Parins-Fukuchi