Archive for the ‘Book review’ Category

Benchmark Papers in Quantitative Genetics (The Bill Hill’s List, part II)

December 19, 2014

As I promised, here’s the second part of the list, that corresponds to the papers commented in volume II. It was particularly difficult to find PDFs for all of them , and some links go to the publisher which sells the paper for a (in my opinion) substantial amount of money. I encourage you to go to the library, find alternative resources (JSTOR, archive.org…), or ask a colleague. I have most of them if anyone is interested.

The Hill-Robertson'66 paper, one of my all-time-favourites, is not in the list. Actually, Hill didn't include any of his own papers!

The Hill-Robertson’66 paper, one of my all-time-favourites, is not in the list. Actually, Hill didn’t include any of his own papers!

 

The Bill Hill’s List, part II

Nature of Selection Response

  • Castle WE (1905) The Mutation Theory of Organic Evolution, from the Standpoint of Animal Breeding. Science 21:521-525. [PDF]
  • Jennings HS (1916) Heredity, Variation and the Results of Selection in the Uniparental Reproduction of DIFFLUGIA CORONA. Genetics 1:407-534. [PDF]
  • Sturtevant AH (1918) An analysis of the effects of selection [PDF]
  • Castle WE (1919) Piebald rats and selection, a correction. Am Nat 53:370-376. [PDF]

Statistical Predictions of Selection Response

  • Lush JL (1935) Progeny Test and Individual Performance as Indicators of an Animal’s Breeding Value. J Dairy Science 18:1-19. [PDF]
  • Hazel LN (1943) The genetic basis for constructing selection indexes. Genetics 28:476-490. [PDF]
  • Falconer DS (1952) The problem of environment and selection. Am Nat 86:293-298. [PDF]
  • Dickerson GE and Hazel LN Effectiveness of selection on progeny performance as a supplement to earlier culling in livestock. J Agric Res 69:459-476. [PDF]
  • Henderson CR (1974) General Flexibility of Linear Model Techniques for Sire Evaluation. J Dairy Science 57:963-972. [PDF]

Genetical Prediction of Selection Response

  • Fisher RA (1930) The fundamental theorem of natural selection. In: The Genetical Theory of Natural Selection. Oxford Claredon Press. [PDF]
  • Haldane JBS (1931) Selection intensity as a function of mortality rate. Proceedings of the Cambridge Philosophical Society 27:131-136 [PDF]
  • Comstock RE et al (1949) A Breeding Procedure Designed To Make Maximum Use of Both General and Specific Combining Ability. Agronomy J 41:360-367. [PDF]
  • Robertson A (1960) A theory of limits in artificial selection. Roc Soc (Lon) Proc B153:234-249. [PDF]

Results from Selection Experiments

  • Dudley JW (1977) 76 Generations of selection for oil and protein percentage in maize. Proc Int Conf Quant Genetics Ames IA, ISU Press, 459-473. [PDF]
  • Mather, K (1941) Variation and selection of polygenic characters. J Genet 41: 159–193. [PDF]
  • Lerner IM and Dempster ER (1951) Attenuation of genetic progress under continued selection in poultry. Heredity 5:75–94. [PDF]
  • Robertson FW (1955) Selection response and the properties of genetic variation. Cold Spring Harbor Symp.Quant. Biol. 20:166–177. [PDF]
  • Falconer DS (1960) The genetics of litter size in mice. J Cell Comp Physiol 56(Suppl 1):153–167. [PubMed]
  • Clayton GA et al (1957) An experimental check on quantitative genetical theory. I. Short-term responses to selection. J Genet 55:131–151. [PDF]
  • Bell, AE et al (1955) The evolution of new methods for the improvement of quantitative characters. Cold Spring Harbor Symp Quant Biol 20:197-211. [PDF]

Selection and Maintenance of Genetic Variation

  • Wright S  (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proc VI Int Congress Genetics 1:356-366 [PDF]
  • Robertson A (1955) Selection in animals: synthesis. Cold Spring Harb Symp Quant Biol  20:225229. [PDF]
  • Bulmer MG (1971) The effect of selection on genetic variability. Am Nat, 105:201–211 [PDF]
  • Lande R (1976) The maintenance of genetic variation by mutation in a polygenic character with linked loci. Genet Res (Camb). 26:221-235. [PDF]

Nature of Quantitative Genetic Variation

  • Clayton GA and Robertson A (1955) Mutation and quantitative variation. Am Nat 89:151-158  [PDF]
  • Linney R et al (1971) Variation for metrical characters in Drosophila populations III. The nature of selection. Heredity 27:163–174 [PubMed]
  • “Student” (1934) A calculation of the minimum number of genes in winter’s selection experiment. Ann Eugenics 6:77–82  [PDF]
  • Thoday JM (1961) Location of polygenes. Nature 191:368-370 [PDF]
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Benchmark Papers in Quantitative Genetics (The Bill Hill’s List, part I)

July 21, 2014

Despite having a long time interest in evolutionary biology, I deliberately avoided papers on animal breeding and pure quantitative genetics, and I thought they were not relevant to modern evolutionary thought. As I gained more interest in mathematical models I started to read some of these classic papers, and realized that some of the issues I’m interested in (such as genetic linkage) were studied in depth by livestock breeders. Now I regret I didn’t pay more attention to them in the past. However, I have a chance to redeem myself and put some of these papers in my reading list. Which ones? Well, that’s a hard decision, but fortunately I found a list compiled by quantitative geneticist William Hill.

William G. Hill. Picture from the Genetics Society at http://www.genetics.org.uk

William (Bill) Hill was invited to contribute with a  volume to the famous “Benchmark Papers in Genetics” series by Springer. However, he came up with two volumes. I could not find any of them in the University of Essex library so I decided, for the first time, to visit the British Library. They had, indeed, both volumes. I forgot to bring some cash so I couldn’t afford to do copies. Hence, as in the old times, I grabbed a pencil and transcribed the lists of papers from both volumes. It was a hard yet rewarding task. Because most of these papers are quite old, I was confident that I should find them in JSTOR or another similar repository (and I did!).

The best bits of the books are the comments by Bill Hill himself on the papers which, obviously, I cannot reproduce here. However, just the list of papers is of great value, and I thought there may be someone else interested. So, I’ve compiled both lists and looked for PDFs and links to author’s biographies. Here’s the list of papers from volume I. The second bit will be posted soon. Hope you find it useful.

 

The Bill Hill’s List, part I

Foundations

  • Pearson K (1904) Mathematical Contributions to the Theory of Evolution – XII. Phil Trans R Soc Lond A 203:359-371. [PDF]
  • Yule GU (1906) On the Theory of Inheritance of Quantitative Compound Characters on the Basis of Mendel’s Laws – A Preliminary Note. In: Proceedings of the International Congress of Genetics. [PDF]
  • Weinberg W (1910) Further contributions to the theory of Inheritance. (English translation by K. Meyer in this compilation) [PDF NOT FOUND]
  • Fisher RA (1918) The Correlation Between Relatives on the Supposition of Mendelian Inheritance. Trans R Soc Edinburgh 52:399-433. [PDF]
  • Wright S (1921) Systems of Mating I. The Biometric Relations betweens Parent and Offspring. Genetics 6:111-123. [PDF]
  • Wright S (1921) Systems of Mating II. The Effects of Inbreeding on the Genetic Composition of a Population. Genetics 6:124-143. [PDF]
  • East EM (1910) A Mendelian Interpretation of Variation that is Apparently Continuous. Am Nat 44:65-82. [PDF]
  • Jones DF (1917) Dominance of Linked Factors as a Means of Accounting for Heterosis. Genetics 2:466-479. [PDF]

Synthesis

  • Mather K (1949) The Genetical Theory of of Continuous Variation. Hereditas 35:376-401. [PDF]
  • Wright S (1950) The Genetics of Quantitative Variability. In: Quantitative inheritance. [Google Books]

Generalizations

  • Kempthorne O (1954) The Correlation Between Relatives in a Random Mating Population. Proc R Soc London B 143:102-113. [PDF]
  • Cockerham CC (1956) Effects of Linkage on the Covariances between Relatives. Genetics 41:138-141. [PDF]
  • Willham RL (1963) The Covariance between Relatives for Characters Composed of Components Contributed by Related Individuals. Biometrics 19:18–27. [PDF NOT FOUND]
  • Robertson A (1952) The Effect of Inbreeding on the Variation Due to Recessive Genes. Genetics 37:189–207. [PDF]

Applications

  • Lush JL (1940) Intra-Sire Correlations or Regressions of Offspring on Dam as a Method of Estimating Heritability of Characteristics. Ann Proc Am Soc Anim Prod 33:293–301. [PDF]
  • Comstock RE, Robinson HF (1952) Estimation of average dominance of genes. In: Heterosis. [Google Book]
  • Griffing B (1956) A generalised treatment of the use of diallel crosses in quantitative inheritance. Heredity 10:31-50. [PDF]

 

The outgrowth of Muller’s eugenics program

February 14, 2014

Hermann Muller is one of my favourite scientists ever. Among other things he used the first balancer chromosomes to do genetic analysis, discovered X-rays induced mutations, and developed the concept of genetic load. Muller was also tireless and systematic, spending countless hours crossing flies with care and patience. No wonder he was the sole recipient of the Nobel prize in Physiology or Medicine in 1946 for his work in mutagenesis.

However, Muller’s name is strongly associated with ‘eugenics’, a word that is today a synonym of racism, or even Nazism. Because of that, I have been afraid of reading some of his writings that may jeopardize my idealization of Muller. A few months ago I changed my mind and decide to read more about his eugenics views. It took me a while, but I finally got a copy of his “Out of the Night: A Biologist’s view of the future”, his personal view on how science and eugenics will change the future. To my surprise, Muller was very critical with most eugenic programs, and fought against selective sterilization or similar practices. Muller, as a geneticist, was well aware that selective elimination of weak phenotypes had only a little impact to remove recessive deleterious alleles from the population. Noteworthy, Muller even sent his book to Joseph Stalin while living in the USSR, together with a lengthy letter, hoping that he would embrace Mendelism and his eugenic program. Muller soon heard that Stalin was “displeased by it, and has ordered an attack prepared against it“.

Cover of Hermann Muller's "Out of the night", 1936, Victor Gollancz Ltd, London.

Cover of Hermann Muller’s “Out of the night”, 1936, Victor Gollancz Ltd, London.

But “Out of the Nigh…”, more than a eugenics program, has become a description on how society have changed in the last century. Muller’s proposals have become a list of predictions, and most (if not all of them) have become a reality. Here’s the list of his ‘proposals’, and their current status.

1) Universal dissemination of knowledge about the means of birth control. Abortion must also be legalized and regulated.  Abortion is indeed legal in most European, Asian and North American countries. In these countries abortion is regulated and it is permitted under request or, in countries with a more restrictive law, when there is a risk for the mother or in cases of rape.

2) Better systems of pain relief during labour. In the UK (the case I know the best) there are various options for pain relieve during labour: Entonox, pethidine and epidural anaesthesia. In the US, more than 50% of women give birth with Epidura anaesthesia.

3) Better ways to deal with illnesses affecting children in their first six months. Nowadays many congenital disorders are routinely detected before birth thanks to ultrasound scans and maternal blood screens. In most North American and European countries, newborn babies have their blood test for several genetic and metabolic disorders (heel prick). In the near future, whole genome sequencing of a foetus would be possible by extracting only the mothers blood.

4) Develop public organization for food preparation, laundrering and other services for infants and young children. I think Muller was thinking on a huge collective nursery for all children in a community, or something like that. In any case, childcare is now an important part of our society and present day nurseries may somewhat fit Muller’s idealization.

5) Inspire “women of the highest type of intelligence” to be mothers. Maternity leaves permit working women to have a career break to have children without losing their jobs. I don’t agree at all with this obsession for “intelligent parents to have intelligent children”, but benefits and leaves do help successful woman to become mothers.

I do not aim to state whether Muller was right or not, or whether abortion or benefits are right or wrong. What I want to point out is that, the eugenics program described by Muller, as such, has become a reality. One should take into account that what we call now eugenics, it was a different thing decades ago. Actually, some journals with the ‘eugenics’ word in their title were actually journals of genetics such as “Eugenics Review” (which published papers on human genetics) or “Annals of Eugenics” (which changed its name to “Annals of Human Genetics” in 1954). William Provine has stated that ‘Eugenics has merely been renamed genetic counselling‘. In this sense, Muller’s “Out of the night” may have become the first eugenics/genetic-counselling manifesto that has been fully fulfilled.

Is evolution driven by mutation?

June 18, 2013

This post is a review of Masatoshi Nei‘s book Mutation-Driven Evolution (Oxford University Press, 2013); 256 pages, price £55/$89.95/€66.88.

As an undergrad student I spent countless hours at the University’s library. The “evolution” section was small, yet it contained the most important volumes, so I used to pick a random book every now and then and read it. That’s how I stumbled upon Nei’s book ‘Molecular Evolutionary Genetics’, and as I read its last chapter my life changed for good: I wanted to be an evolutionary geneticist! I have devoured ever since any book or paper by Nei. In 2008 I was doing a post-doc with Sudhir Kumar (a former Nei’s student). I remember once that Sudhir and I were talking about hypermutability and selection, and then Sudhir told me: “Nei is preparing a new book on mutation”. Since that day I’ve been patiently waiting until the book was ready. Now, five years after that conversation, the book is published. It was worth the wait.

neisbook

Masatoshi Nei’s book have a special place in my library

Nei’s ideas on mutationism were already sketched in his population genetics book published in 1975, and they were fully presented in a book chapter in 1983 and in his 1987 book I mentioned at the beginning of this post. He builds on the neutral theory, arguing that mutation and drift are more important than selection in molecular evolution. In this sense he continues Motoo Kimura‘s tradition. But Nei emphasizes the role of mutation over all, following the lead of Thomas Morgan and Hermann Muller. Indeed, the contribution of Morgan to evolutionary biology has only been recently acknowledge (as far as I know) by Nei, whilst other evolutionists (probably influenced by the biased account by Ernst Mayr) have completely ignored it.

‘Mutation-Driven Evolution’ is written as an historical account on how our knowledge about evolution has changed in the last 100 years. The first three chapters review the development of early evolutionary theories, with a strong focus on population genetic models (one of Nei’s fields of expertise). Chapters 4 and 5 account for the advent of molecular data and how it demonstrated that evolution is mutation-dependent. In chapters 6 and 7, Nei links the evolution of genomes with the evolution of phenotypic characters and speciation, a frequently missed aspect in many molecular evolution texts. Chapters 8 and 9 cover the role of mutation in adaptation and evolution. A last chapter summarizes the whole book and can be read as a stand-alone piece of text.

The book touches every aspect of evolutionary biology, and Nei gives his view on the cis/trans gene regulation debate, evolution of sex, the emergence of eusociality, Ohno‘s duplication model and Ohta’s nearly neutral theory, among other topics. He clearly states that mutation often produces adaptation, and much of the adaptation we believed to be the product of natural selection is not adaptation at all. In his words: “(adaptation) represents a human perception of the living status of the organism”.

If I have to say something negative about the book, I could only mention that Nei’s style is… well, Nei’s style. Somewhat opinionated and very critic with his opponents. Sometimes one gets the feeling that he is using modern arguments/evidences to attack postulates made by others some decades ago. Some may think this is unfair. Others (as I do) will understand that a point has to be made clear, sound and bold, and Nei has no problem in doing so.

The best way to describe what you’ll find in this book is to reproduce here the last couple of sentences:

“[…] mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.”

Quod erat demonstrandum.