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Joe Felsenstein’s Bible

August 3, 2018

Everybody in the evolution field knows who is Joe Felsenstein. Most people is familiar with his important contributions in phylogenetics. However, some of my young colleagues don’t know that he was a population genetics in his early years. Indeed, he has been a student/postdoc of Jim Crow, Dick Lewontin and Bill Hill, all renowned population and quantitative geneticists. (You can find more about Bill Hill in my old post.) Felsenstein’s paper on the advantage of recombination is among my all-time favourites, and his free textbook ‘Theoretical Evolutionary Genetics‘ is brilliant (in particular the historical notes included).

But Joe’s ability to gather and process information was not only invested in writing papers and books, but also in compiling publications in the field. He compiled near 8000 titles and published it in a hardback book in 1981 as ‘A Bibliography of Theoretical Population Genetics‘ (although there is an earlier 1973 version). In the pre-Internet times that was a very valuable resource. (Obviously not for me, I was just 1 years old when the volume was published.) A digital copy can be found at Felsenstein’s own webpage. Un-modestly (yet rightfully) the file is call ‘bible’. And for that reason I always refer to this work as Joe Felsenstein’s Bible.blankblank

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A few years ago I attempted to parse the file and convert it into BibTex, so it can be of some use in my LaTeX writings. However, I abandoned the project as I was always facing complex formatting errors and didn’t have the time to fix them all. Now, I decided to make public the BibTex version of the bible (as it is now), that you can find here. But before you make any use, I should warn you that there are many errors so, please check carefully the formatting of your final reference list. Below is my modest re-analysis of the papers, books and texts indexed in Holy Felsenstein’s Book.

 

Publications by year

Publications are dated from 1867 to 1981. The oldest work is the review by Fleeming Jenkin of Darwin’s ‘Origin of Species‘. Jenkin was an engineer (he invented the telpherage), so he had the necessary mathematical background that Darwin lacked to tackle the issue of inheritance and selection. In his paper he criticised Darwin’s theory of natural selection but arguing that, under blending inheritance, it is not possible. An excellent historical account by Michael Bulmer of this review and the reactions of Darwin and other can be found here. The most recent works listed are Elseth and Baumgardner’s ‘Population Biology’ and the very own Felsentein’s bible.

If we plot the number of papers/works published per year, one observed a decrease during the years of the Second World War (as expected in a total war, where everybody, specially scientists, are asked to contribute to the war efforts). This was more pronounced toward the last years of the war, being the year 1945 the one with less works published. This effect is more evident in the log plot below. However, among the 8 works listed, we find a classic: Sewall Wright‘s ‘The differential equation of the distribution of gene frequencies‘, in which he applies Kolmogorov diffusion equations explicitly to work out expected gene frequencies. This work was probably not the most popular among Wright’s contributions, but it heavily influenced Motoo Kimura. Only for that, this paper deserves a special place in the history of population genetics. (See my post on the use of diffusion equations in population genetics.)byyear

Publications per year in Felsenstein’s bible. The right plot shows the logarithm of the number of publications in its y-axis. The red lines indicate the years of the World War II.

 

Digging a bit more into the 1930’s and 1940’s literature, one can find papers on the efficiency of the German (Nazi) Racial law from the point of view of theoretical population genetics. For instance, Koller’s response to previous criticisms. However, this can be to long to be discussed here, and I may even consider write about it in a future post.

 

Authors and co-authors

Another interesting analysis that can be done using Felsenstein’s bible is to evaluate the productivity of different authors in the field. In this sense, Kimura is the clear winner. Way behind we find Wright and Masatsohi Nei who get the silver and bronze medals respectively.

Author Publications
M. Kimura 200
S. Wright 123
M. Nei 120
J. B. S. Haldane 119
T. Maruyama 98
N. E. Morton 97
R. A. Fisher 84
S. Karlin 84
A. Robertson 79
T. Ohta 75

 

Regarding joint authorships, again Kimura is the leader together with Tomoko Ohta (with 40 co-authored works). Second is the prolific geneticist and epidemiologist Newton Morton and his late collaborator D. C. Rao (I wonder if he was related with famous statistician C. R. Rao). And third, as it could not be other way, the Charlesworths, Brian and Deborah.

Author Author Publications
M. Kimura T. Ohta 40
N. E. Morton D. C. Rao 20
B. Charlesworth D. Charlesworth 19
T. Maruyama M. Kimura 18
N. E. Morton S. Yee 18
J. McGregor S. Karlin 16
L. L. Cavalli-Sforza M. W. Feldman 15
M. Kimura J. F. Crow 15
C. C. Cockerham B. S. Weir 13

 

Actually, it is interesting to see which authors publish mostly alone and which authors are more likely to work with someone else. For the top-10 authors we see a wide range of single authored /co-authored ratios. Wright was mostly a lonely writer whilst Samuel Karlin and Newman Morton (as it is well known) enjoyed more working in collaborative projects with other colleagues.

Author Publications Solo Joint Prop. solo
M. Kimura 200 120 81 0.597
S. Wright 123 112 12 0.903
M. Nei 120 65 67 0.492
J. B. S. Haldane 119 101 18 0.849
T. Maruyama 98 53 51 0.510
N. E. Morton 97 41 107 0.277
R. A. Fisher 84 77 9 0.895
S. Karlin 84 23 68 0.253
A. Robertson 79 50 32 0.610
T. Ohta 75 32 43 0.427

 

I tried to produce a graph of co-authorships but I had some technical problems and, as my grant applications and manuscripts deserve some attention, I decided to postpone the generation of the graph. However, I provide here the table of the most connected authors. Morton is the most connected scientist.

Author Co-authors
N. E. Morton 36
C. C. Cockerham 34
L. L. Cavalli-Sforza 32
R. E. Comstock 28
M. W. Feldman 27
S. Yee 27
R. C. Elston 26
J. L. Jinks 25
J. F. Crow 24
S. Karlin 24
W. F. Bodmer 24

 

A valuable resource

Felsenstein’s bible is a great resource to understand the history of population genetics. Indeed, it’ll be interesting to extract abstracts of even full texts, and parse the information to study trends in topics during these years. I bet ‘linkage’ will be one of this topics that exploded in the early 1970’s. But to do so, it will be necessary quite some work of programming and parsing and, unfortunately, I don’t have the time (and probably not the skills) to do it right away. But I hope this modest analysis and the BibTex file is of some use to some of you.

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