Revisiting Ohta 1973

In a paper published in 1973 in Nature, Tomoko Ohta extended Motoo Kimura‘s neutral theory of molecular evolution to include slightly deleterious mutations, and examine the role of interaction of drift and weak selection in molecular evolution. Tomoko Ohta called this extension the “nearly neutral theory of molecular evolution“. Forty seven years after the paper was published, I asked Tomoko Ohta about how she got interested in this topic, her collaboration with Motoo Kimura and what we have learnt since about nearly neutral theory.

Citation: Ohta, T. (1973). Slightly deleterious mutant substitutions in evolution. Nature, 246(5428), 96-98.

Date of interview: Conducted over email between 19 January 2020 and 8 February 2020.

Hari Sridhar: Could you tell us what motivated you to develop the ideas presented in this paper?

Tomoko Ohta: The idea on slightly deleterious mutations is the continuation of my previous work (see refs. 3-5 of the paper). I had been thinking hard about the mutations around complete neutrality. Also, I had been very interested in the connection between evolution and molecular structure (see the Dickerson paper in the first issue of J Mol Evol). The secondary structure of RNA had been known, and the evolution of its primary structure had been helpful to have the idea.

HS: Could you flesh that out a little more for us, i.e. what was the previous work you were doing that led to this insight?

TO: I think that I was lucky that I studied the fixation probability of mutant genes as a function of 2Ns, the Kimura formula, while I had worked on the survival probability of new inversions as my PhD thesis under Kenichi Kojima in NC State. So I knew that the fixation probability was continuous around zero. I recognized that the negative correlation between population size and fixation probability would partially cancel the generation time effect of mutation rate on molecular evolution for mammalian species. This part is probably most original in my research, and may be a small eureka.

HS: Stepping back a bit, could you tell us how you got interested in population genetics and molecular evolution?

TO: When I came to Mishima, Kimura had just started to consider molecular evolution from the standpoint of population genetics. It was very natural that I was much interested in molecular evolution. I think that Kimura was a pure theoretician and he did not like complicated problems. He was better in handling the diffusion equations than I was. I was a biologist and more data-based in my thinking. So, we thought we may be good to complement to each other in research. I should thank Kimura because he allowed me to do whatever I like in research. In my country at that time, senior professors often had big power to control junior researchers.

HS: Could you tell us a little about your discussions with Professor Kimura during the development of these ideas, and what were his reactions to them?

TO: I had recognized that Kimura might criticize the Nature paper, so I did not show him the manuscript before sending. But I acknowledged him at the end of the paper because the discussion between us had been helpful. I remember that Kimura was not happy about the slightly deleterious problem, as we had lots of discussions when writing the Ohta-Kimura paper (J Mol Evolution, 1, 18-25). The final version was a result of compromise between us. Also our policy on Ohta-Kimura or Kimura-Ohta was based on our relative contributions.

HS: Could you also share with us the path that eventually led you to becoming a scientist working on population genetics and molecular evolution? Were you interested in biology and science as a child? Did you consider any other career options?

TO: I was born in a suburb near Nagoya. The Second World War ended when I was in 6th grade in elementary school. During war, we were educated to be a dedicated national citizen.  But after the war everything, i.e., social system, education and way of living, had changed. Our teachers had much difficulty how to face with us for the change. The education system had also changed. Before the war, boys and girls were in the different classes. But after the war co-education had started. The change was led by the US military people who came to Japan. The top was the general Douglas MacArthur. The 6-3-3-4 education system – elementary, junior high, senior high, and university – started. The most notable change was from “Nationalism plus Totalitarianism” to “Democracy, Freedom and Individualism”. I entered the junior high school in Toyota. There, I found mathematics and physics interesting and studied hard. At that time, there was plenty of free time for students. Nowadays, boys and girls are very busy in after-school studying and club activities. I was good in mathematics and physics, but not good in history and geography. I think that I was poor in memorizing. I was even worse in physical education. As for biology, I found Mendel’s laws very interesting, but the other subjects were not very attractive to me. I also remember that I found the biography of Madame Curie interesting. After senior high school, I entered Nagoya University, which was a prestigious university, the best one in Nagoya area. In the university, I tried to go to the medical school, because of better opportunity for getting a job, but failed the examination. So I moved to Tokyo Univ. Agriculture department, where transfer from the other university was accepted because of not enough students. I majored in horticulture but I found studying it was not attractive. After graduation, I had difficulty in finding a job, and I worked for 2 years in a publishing company. Then I found a position in the Kihara Institute for Biological Research, which moved from Kyoto to Yokohama because Kihara retired from Kyoto University and moved to Yokohama. Dr. Hitoshi Kihara was the most famous geneticist in Japan at that time. There, I studied the cytogenetics of wheat and sugar beet. After 4 years, I found a chance to study in Raleigh in the US. I studied population genetics there under Ken-ichi Kojima, who was the student of Kihara in Kyoto University before coming to the US. After 4 years, I got a PhD in Genetics and Statistics and came back to Japan. Kimura lab in the National Institute of Genetics was the only place where I could continue population genetics in Japan, and I asked him to hire me. At the beginning, he did not want to hire me, but he let me do a post-doc there. That was in 1966. After a year or so, Kimura decided to hire me as a member of his lab. As I mentioned before, this was the best time for me to start work on molecular evolution.

L -R Takeo Maruyama, Tomoko Ohta, Motoo Kimura, Yuriko Ishii and Norikazu Yasuda. Photo taken in the late 1960s soon after Tomoko Ohta joined Motoo Kimura’s lab (photo provided by Tomoko Ohta)

HS: Could you give us a sense of the time when you were doing this work – what was your daily routine, who were your peers, how challenging was the work etc.?

TO: When I was young and doing the original work, almost 100% of my time in the institute could be used for research, as there was no administration jobs for young people at that time. Also, the amount of money necessary for theory work was small; I did not need to apply for grant money. Kimura started the Population Genetics Lab in the National Institute of Genetics in the early 1960’s. Before I joined the lab, Drs. Takeo Maruyama and Norikazu Yasuda were already members. Maruyama obtained a PhD in Madison Wisconsin, under JF Crow, and Yasuda got his PhD under Newton Morton in Hawaii. Maruyama was excellent in mathematics, and he gave us several lectures on advanced mathematics that was difficult to me. Yasuda worked on human demography in the Mishima area by measuring the distance between the birth places of married couples. We sometimes had lab meetings on the topics of our interest. Kimura let us do whatever we like. This might not have been common in Japan at that time. Professors had big power and often controlled the activity of the young researchers. For this, I am thankful to Kimura.

HS: What are your recollections about the time when you were writing of this paper?

TO: I already had the original idea on generation time and population size when I wrote the 1971 paper, On the constancy of the evolutionary rate of cistrons. That was much criticized for the idea that the genes would deteriorate. In writing the 1973 paper, I had clearer vision, by considering the higher order structure of RNAs and proteins. The clover leaf structure of tRNA was known. Stem part evolution occurs in such a way as to keep the structure, and compensatory base substitution would follow if the deteriorating one occurs. I thought this is important. That’s how I wrote the 1973 paper. I think I wrote that within a few days in the lab. This paper was exceptional in that I did not show it to Kimura before submitting. Other manuscripts were read by him and sometimes by Crow before sent.

HS: Did you consider submitting it to other journals, or was Nature the obvious choice? Also, what do you remember about the peer-review and acceptance of this paper?

TO: I had chosen Nature because the Kimura 1968 paper was also in Nature, and had been read by many people. Also, I felt it would be good to publish the issue on the neutral theory in Nature. I think that I was lucky that the manuscript was reviewed by someone who understood the molecular biology. The evolution people might have had more criticisms at that time. In fact, there was almost no critical comment on the manuscript. I remember that my next paper on “Mutational pressure…” was also accepted just after correction of English. However, the third one was rejected. I think that was probably reviewed by population genetics or evolution people.

HS: In this paper, you pull together many pieces of evidence, including from your own work, to support your claim that “very slight genetic deterioration might play an important role in molecular evolution”. Today, 47 years later, I would like you to reflect on the current standing of the central claim of this paper.

TO: The applicability of the nearly neutral theory has expanded. For a long time, there have been arguments for the importance of gene regulation for morphological evolution than genes themselves. But only recently are the molecular mechanisms on gene regulation being clarified. It is now found that numerous complex molecular systems are involved. It is amazing that these systems are well organized and work to provide homeostasis as a whole. The proteins or RNAs of the systems are evolving under weak selection, and the nearly neutral theory is applicable. I have written about these subsequent developments in 2002 and again in 2011.

HS: Could you reflect on the impact this paper has had, both on your career and your research trajectory?

TO: I think that I got more energy for my research from the response and reprint request. However, I was already in a position of researcher in National Institute of Genetics. So, I just continued my work there. At that time, it was difficult for women to be employed in such a position in Japan.

HS: Could you say a little more about what were the kind of challenges that women faced in doing science in Japan during that time?

TO: Our institute has been exceptional about the gender problem. When I came to the Institute, there was already one lady researcher. That was exceptional in Japan at that time. Also, as I said before, Kimura’s concern was just science productivity. He did not care other things.

Outside the institute, the situation was very different. Male dominated society was everywhere. Another point is that my field (population genetics and molecular evolution) was very small at that time in Japan; only a small number of people, actually the Kimura group, were doing this kind of work. The response was mainly from the other countries. I remember being referred to as “he” by a British researcher.

HS: What kind of attention did your paper get from the larger academic community when it was published?

TO: I remember that at a meeting in France, biophysics people expressed favourable opinions on the slightly deleterious idea, but population genetics and evolution people were critical. They thought that the genes would deteriorate. Also, they said that such small selection coefficient could not operate. The symposium was organized by Zuckerkandl.

HS: In retrospect, would you consider this paper/study as your most important contribution?

TO: Yes, I think so. The reason is this paper has provided the basic mechanisms of molecular evolution, which are different from the Neo-Darwinism perspective on phenotype evolution. Remember that there was some discussion on the dichotomy between the phenotype and molecular evolution. Molecular evolution is clock-like, whereas phenotype evolution is irregular.

HS: This paper has been cited over 900 times today. Have you kept track of the life of this paper after it was published? Do you have a sense of what are the different ways in which it gets cited?

TO: I was concerned with the criticisms on the paper, and not on the number of citations. At that time, it was not so easy to see the number of citations. I thought that population genetics and evolution people who criticized me should study more about molecular biology and biophysics. I did not expect that this paper would get cited so many times.

HS: After the paper was published, did you ever go back and read the paper again? If yes, could you tell us in what context you reread it?

TO: Yes, I read this paper when I recognized that the nearly neutral theory had become more widely applicable than before, i.e., in this genome age. I also needed to read it when I wrote review articles on the theory.

HS: What would you say to a student who is about to read this paper today? Would you add any caveats they should keep in mind when they read it? Would you suggest that they read any other subsequent papers along with it?

TO: I would ask them to read the paper very carefully, and if they find difficulty in understanding the meaning, to examine some of the references of this paper. Understanding the background to this paper will be helpful. I would also recommend that they read the review papers that were published subsequently in Annual Review and PNAS

HS: Is there anything else you would like to share that wasn’t covered by my questions, but which you think is an important part of the history of this study?

TO: I’d only add that interdisciplinary thinking is very important in evolutionary biology. In our National Institute of Genetics, scientists study various areas of genetics, from molecular to classical. When I was young, we had a weekly seminar introducing the important papers of one’s own area. I learned a lot by attending these seminars. I was lucky to have had that opportunity.

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