Darwinian genomics and diversity in the tree of life

Authors: STEPHAN, TAYLORLYN - National Human Genome Research Institute; BURGESS, SHAWN - National Human Genome Research Institute; Cheng, Hans; DANKO, CHARLES - Cornell University; GILL, CLARE - Texas A&M University; JARVIS, ERICH - Rockefeller University; KOEPFLI, KLAUS-PETER - George Mason University; KOLTES, JAMES - Iowa State University; LYONS, ERIC - University Of Arizona; RONALD, PAMELA - University Of California, Davis; RYDER, OLIVER - University Of California, San Diego; SCHRIML, LYNN - University Of Maryland; SOLTIS, PAMELA - University Of Florida; VANDEWOUDE, SUSAN - University Of Colorado; ZHOU, HUAIJUN - University Of California, Davis; OSTRANDER, ELAINE - National Human Genome Research Institute; KARLSSON, EINOR - Broad Institute Of Mit/harvard

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2021
Publication Date: 1/18/2022
Citation: Stephan, T., Burgess, S.M., Cheng, H.H., Danko, C., Gill, C.A., Jarvis, E.D., Koepfli, K., Koltes, J.E., Lyons, E., Ronald, P., Ryder, O.A., Schriml, L.M., Soltis, P., Vandewoude, S., Zhou, H., Ostrander, E.A., Karlsson, E.K. 2022. Darwinian genomics and diversity in the tree of life. Proceedings of the National Academy of Sciences(PNAS). 119:4. https://doi.org/10.1073/pnas.2115644119.
DOI: https://doi.org/10.1073/pnas.2115644119

Interpretive Summary: Genomics is defined as the study of genes and their functions, and related techniques. The most well-known examples include the generation of the human genome assembly and next generation sequencing. The field of genomics has fundamentally changed human medical research and to a lesser extent, farm animals and common experimental species. However to get a complete understanding how genomes of any organism work, this paper argues that a broader view needs to be taken that include the entire tree of life and scientific contributions from those outside of biology. Strategies are proposed to accelerate this new field of Darwinian genomics.

Technical Abstract: Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ~2,000,000 eukaryotic species (<1%) have a representative genome sequence in GenBank, and only a fraction of these have ancillary information on genome structure, genetic variation, gene expression, epigenetic modifications, and population diversity. This imbalance reflects a perception that human studies are paramount in disease research. Yet understanding how genomes work, and how genetic variation shapes phenotypes, requires a broad view that embraces the vast diversity of life. We have the technology to collect massive and exquisitely detailed datasets about the world, but expertise is siloed into distinct fields. A new approach, integrating comparative genomics with cell and evolutionary biology, ecology, archaeology, anthropology, and conservation biology, is essential for understanding and protecting ourselves and our world. Here, we describe potential for scientific discovery when comparative genomics works in close collaboration with a broad range of fields as well as the technical, scientific, and social constraints that must be addressed.