Paleogenomics pulls back the curtain on evolution - School of Science, the University of Tokyo
Nov 23, 2015

Paleogenomics pulls back the curtain on evolution

Department of Earth and Planetary Science — Endo Laboratory

Kazuyoshi Endo
Department of Earth and Planetary Science
Graduate School of Science 


Professor Endo graduated from the University of Tokyo’s Department of Earth Sciences in 1985, and then obtained his Ph.D. in Geology from the School of Science at the University of Glasgow in Scotland in 1992. Following that, he became a research associate in the University of Tokyo’s Graduate School of Science, then an associate professor in the University of Tsukuba’s Graduate School of Life and Environmental Sciences. He took up his current post in 2010.

“When I was in high school I was obsessed with the question of where I came from, and where I was heading,” says Professor Kazuyoshi Endo. “So when I became a researcher, I chose evolution as the theme for my studies.”

All living things on Earth are part of an enormous tree. It continues to grow, creating new leaves and branches, but at its roots is just a single cell. The divisions are numerous; some organisms left the sea to occupy the land and some remained in the sea. But in each case, they adopted a form suited to their particular habitat. This genealogy is the incredible history represented by the tree of life. This is the phylogenetic tree of evolution.

Professor Endo is learning more about this phylogenetic tree using an approach called paleogenomics. This field examines ancient organisms at the molecular level, and pinpoints their location on the grand tree of evolution. Genetic analysis provides us with three kinds of information, starting with the genetic information passed on from parent to offspring. That allows us to see the “developmental program” that changes an ovum  into an organism, and comparing the genetic information and developmental programs of multiple organisms provides historical information. Combining this with the study of fossils gives us a deeper understanding of ancient organisms.

One of the areas that Professor Endo studies is marine life. This is an important phylogenetic branch in the search for the origins of life, and compared with dinosaurs, it also provides a richer, steadier source of samples. One question that Professor Endo is focusing on is why marine shells tend to form spirals.

Many varieties of shelled creatures, from bivalves to gastropods, have the same mathematical regularity in the structure of their shells—a logarithmic spiral. “This shared logarithmic spiral suggests that a wide variety of shelled species have a common growth mechanism,” says Professor Endo. “If we can provide an explanation for this from a molecular level, we will be able to extend our investigation to other shells. In fact, it already appears that when we apply our findings to nautilus shells, they exactly fit our predictions. Taking this further, we may someday be able to understand the small number of genetic mutations that provide the diversity among all mollusks. If so, we’ll start seeing the form of their common ancestor, and the origins of shells.”

Professor Endo’s group discovered that the BMP2/4 gene is related to shell spiraling. When the BMP2/4 gene is silenced in a living shelled organism, its shell becomes malformed and does not spiral. Focusing on the functions of this gene may help to understand how ancient organisms evolved to form shells. Professor Endo says, “Ultimately, we want to unravel the connections between this and the environment. We’re looking to find the intersection between the earth sciences and biology. If organisms are changing their form in response to environmental changes, we may be able to find a causal relationship between form and environment. However these changes occurred millions of years ago, so there are many obstacles in the road before us.”

The Endo Laboratory works hard not to shut down new ideas. “Coming up with new ideas is the very essence of science,” Professor Endo says. “Before taking on a new research project, it’s important to ask yourself what you want to know, and why knowing that is important. Every day I tell my students to think for themselves.”

“Part of what I love about evolutionary studies in his lab is that they don’t rely on only fossils, or only DNA,” says Dr. Davin H. E. Setiamarga, a postdoctoral researcher from Indonesia. “One needs a comprehensive approach that tackles the issue from multiple directions.” In the lab, students are also applying analysis methods developed for studying the evolutionary tree to Murasaki Shikibu’s classic work The Tale of Genji, in an attempt to discover the origins of the manuscript.

“Where did we come from, and where are we heading?” The motivating force behind the Endo Laboratory, which has been so successful in producing many talented new researchers, is this simple question.


rigakuru_52_2sBMP2/4 is a gene that plays an important role in shell formation. When this gene is silenced before the first shell is formed, normal shells (A) are not developed. Instead, the individual does not form a shell at all (B). When the gene is silenced later in the formation process, the shell is malformed and does not spiral (C).


Student Evaluations
“My research is related to the evolution of proteins. I’ve been studying with Professor Endo since my fourth year in college. He’s easy to talk to, and to go to with problems.” (Yoshinobu Isokazu, D3)
“I enjoy the lab because of its academic approach to examining evolution. When we have discussions he treats us like equals, which is a great feeling.” (Dr. Davin H. E. Setiamarga, Japan Society for the Promotion of Science Postdoctoral Fellow for Foreign Researchers)

― Office of Communication ―

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