These worms are as long as a pencil’s tip and only just visible without a microscope. They are among the smallest multicellular animals, but they still have complex organ systems. They are Caenorhabditis elegans, one of the most important organisms in modern biology and a key to understanding the most basic molecular processes of life. Work on these tiny roundworms is helping geneticists unravel how all animals morph from single-celled embryos into fully-grown adults.

This tiny worm’s journey to prominence was kickstarted by a landmark paper published by Sydney Brenner in the May 1974 issue of GENETICS. As part of the GENETICS’ Centennial celebrations, Bob Goldstein introduced this paper as a GENETICS Classic. He reflects on how Brenner chose C. elegans for the study of complex phenomena like behavior and development. Brenner was looking for a new model organism at an exciting time for molecular genetics; the structure of DNA, the existence of mRNA, and the genetic code had all just been uncovered. Building upon this backbone of fundamental discoveries, the field was just starting to tackle more complex biological processes. A new approach was needed.

Brenner wasn’t the first scientist to think of C. elegans. The cultures that he began working with in the 1960s were originally isolated from an English compost pile. C. elegans is a species of roundworm. Though they are so small the average person doesn’t notice them, roundworms are thought to be the most abundant animal group, making up 80% of all individual animals living on land and 90% living in water. Roundworms are found in nearly every habitat imaginable, including the depths of the ocean and the bottom of a kilometers-deep gold mine. Many cause human diseases like hookworm. But C. elegans is harmless; it lives in soil and rotting fruits and vegetables where it feeds on bacteria.

Part of the power of C. elegans as a model system is how easy it is to raise them in the lab. They are very small and can easily be grown on petri dishes in large numbers, and they have a generation time of only a couple of days. For experiments that require examining multiple generations, this speeds up the process immensely. Their hardiness is also a benefit—living cultures of C. elegans can be frozen and then thawed later for further study. The mating system of C. elegans also makes them particularly well suited for genetics. They exist primarily as self-fertilizing hermaphrodites, so maintaining homozygous lines is very easy. Males do occur rarely, and they can be used to perform crosses to generate new hermaphrodite lineages.

Tiny C. elegans is also transparent, so its anatomy is easy to observe with a relatively low power microscope. This simplicity is a large part of what drew Brenner to use C. elegans for his work on complex phenotypes. It is a multicellular eukaryote, but one that is small and simple enough to have its genetics and physiology thoroughly dissected and understood in the lab. In the introduction to his 1974 paper “The genetics of Caenorhabditis elegans,” Brenner outlines how his ultimate goal is to understand the complete genetics and structure of the nervous system. C. elegans is perfectly suited for this; it has fewer than a thousand cells, half of which are neurons. In fruit flies, which have billions of neurons, this undertaking would be impossible. Brenner then describes the first steps toward his goal—a massive mutational screen designed to identify as many genes as possible.

C. elegans eventually proved to be the powerful model Brenner had hoped for. By 1977, the developmental fate of every postembryonic cell was known. One groundbreaking consequence of this work was the identification of the genes involved in programmed cell death. The 2002 Nobel Prize in Medicine was given to Sydney Brenner, H. Robert Horvitz, and John E. Sulston for their use of C. elegans to illuminate the genetic regulation of development and programmed cell death. Many of the pathways that regulate these processes in C. elegans are found all across the tree of life.

In 1986, Brenner achieved his goal of describing the connectivity and structure of all 302 neurons in C. elegans. This remains the only fully described “connectome” of any species, though the scientists of the Human Connectome Project are working hard to achieve the same for the more complicated human brain. C. elegans has continued to lead the way in many other research areas. In 1998, C. elegans was the first multicellular species to have its genome sequenced. The use of RNA interference to silence gene expression was also pioneered in C. elegans. This allowed the creation of large-scale screens to decrease expression of each gene in the genome one by one and then observe the resulting phenotypic changes—exactly the kind of exhaustingly thorough genetic study that embodies Sydney Brenner’s pioneering vision.

CITATIONS

Goldstein, B. (2016). Sydney Brenner on the Genetics of Caenorhabditis elegans. GENETICS, 204(1), 1-2. DOI: 10.1534/genetics.116.194084

http://www.genetics.org/content/204/1/1

Brenner, S. (1974). The genetics of Caenorhabditis elegans. GENETICS, 77(1), 71-94.

http://www.genetics.org/content/77/1/71

In Kentucky 150 years ago today, a child was born who would—with the help of a hardy inhabitant of trash cans and fruit bowls— grow up to change the world.

That boy was Thomas Hunt Morgan. By the 1900s, the energetic young Morgan had become a well-respected expert investigating questions in experimental embryology and animal regeneration. But he is remembered today mainly for remarkable experiments in fruit flies that showed genes are carried on chromosomes, providing a tangible explanation for Mendel’s laws and establishing the first experimental system for mapping the units of heredity.

Drosophila melanogaster is a familiar pest found wherever there are piles of rotting fruit: orchards, vineyards, warehouses, kitchens, and dumps. But despite being easy to spot, it was not an obvious choice as the instrument of a genetics revolution. Drosophila are wild creatures; unlike the domesticated species favored by early geneticists—like Mendel’s round and wrinkled peas, or different colored “fancy” mice—fruit flies did not offer Morgan the luxury of visible trait variation. And there was no such thing as a pedigreed fruitfly. What drew Morgan to these humble insects?

Morgan was a wide-ranging thinker whose ideas came thick and fast, then had to be explored and tested quickly to make room for still more new ideas. “He wasn’t happy unless he had a lot of different irons in the fire at the same time,” remembered his student Alfred Sturtevant. Morgan worked with a huge variety of organisms and loved to try out new experimental systems and explore different species to find the most productive way to answer a particular question; sea spiders, brittle stars, frogs, chickens, pigeons, mice, fish, plants, and more.

In 1908 or so, Drosophila joined this endlessly rotating cast of experimental characters. Morgan had turned to fruit flies, (following the lead of W.E. Castle and C.M. Woodworth), in the hopes he could induce them to mutate. Some eight years earlier, Morgan had become interested in Hugo DeVries’ radical theory of evolution after a visit to the Dutch botanist’s garden to inspect some evening primroses. DeVries, who coined the term “mutation,”  had planted wild seeds of Oenothera lamarckiana gathered from an abandoned potato field, which spontaneously produced a large variety of new forms that he called “mutants.” This prompted him to develop a theory that new species originated not from the slow and gradual selection of slight variations, as the proponents of natural selection argued, but in great phenotypic leaps during times of enhanced mutation rates.

Morgan held a variant of DeVries’ view, believing that such “mutating periods” existed, but rather than creating new species in single bounds, they produced additional variation with the normal range of a particular species. Morgan hoped to test this idea by inducing such a creative phase of evolution in a wild species that could be studied in the controlled environment of the lab.

That was why, argues historian Robert E. Kohler, Morgan chose Drosophila over a domesticated species, and why he forced his student Fernandus Payne to initiate his experimental stocks by luring wild flies with ripe bananas, rather than simply asking colleagues for their existing fly stocks. Morgan likely believed that existing inbred lab stocks would have already begun their mutating period. But the data took him in a radically different direction.

He and Payne threw a variety of insults at their flies to see if they could produce mutations. Drosophila were heated, cooled, centrifuged, irradiated, fed acids and bases, and plied with alcohol. Though an occasional mutant appeared, few were heritable, and the number was never statistically significant. According to Kohler, Morgan then considered the possibility that a mutation period could be induced by strong selection and inbreeding. For months he created inbred lines by selecting flies with the most extreme varieties of a trident-shaped body marking — essentially mimicking the process of intense natural selection.

Among the first mutants to emerge in his evolving stocks was a male with white eyes, rather than the usual rich red. When crossed with a red-eyed female, almost* all the offspring were wild type. But when these red-eyed progeny were crossed, white eyes reappeared  exclusively in males.

Morgan knew that sex was specified by sex chromosomes; this had been established a few years earlier by his own student Nettie Stevens, and independently by his friend E.B. Wilson. Stevens had also shown that Drosophila females carried two X chromosomes, and males an X and a Y. Though he was skeptical of the Mendelians and the idea that chromosomes could carry specific genes, Morgan’s data eventually forced him to conclude that the white eyed mutation must be both recessive and located on the X chromosome. As the increased scale of his experiments turned up more and more mutants, and he immersed himself further in this new and overwhelmingly productive system, Morgan began to develop what remains our basic understanding of the mechanics of Mendelian heredity.

But this doesn’t answer the question of why Morgan picked Drosophila as his wild species of choice. Kohler has suggested fruit flies got their first foothold (pulvillus-hold?) in the laboratories of the early geneticists because they were well-suited to the classroom and for student projects:

“D. melanogaster’s natural history in orchards and cider mills, I have argued, matched the natural history of academic departments. Its seasonal demography matched the seasonal cycle of student projects and student labor; cheap and lowly, Drosophila was not shut out by the poverty of academic research funding.” —Kohler 1994

While Morgan was known to be personally generous, he was also legendarily miserly with grant money. And indeed, Morgan himself cited the lack of funds at Columbia University for “raising larger animals” as the reason he had turned to Drosophila. In those early years, the people Morgan encouraged to use the model tended to be either cash-strapped college teachers or others who could not contemplate more expensive and long-term projects: first-year grad students learning the ropes, technicians, women (who had limited career and funding prospects), a chronically-ill student, and undergraduates like Sturtevant and Calvin Bridges. The latter two would soon be transformed by their modest lab projects into rockstars of the field, and would quickly flesh out Morgan’s first insights into a detailed and incredibly productive theory of heredity.

“Just a few months after the white-eye discovery—Bridges and I got desks in his laboratory, the so-called “fly room” at Columbia, where the three of us worked together for the next 18 years. This was a room 16 × 23 feet in which there were eight desks. There was a place where we cooked fly food, and there were usually at least five people working in there. Bridges and I practically lived in this room; we slept and ate outside, but that was all. And we talked and talked and we argued, most of the time. I’ve often wondered since how any work at all got done with the amount of talking that went on, but things popped.” —Sturtevant 1967

From these cramped quarters, the first Drosophilists discovered mutants and mapped chromosomes and remade the fruit fly into a model organism that continues to provide answers to basic questions about how life works and evolves. By creating the experimental foundations of genetics, Morgan and his students and their flies created modern biology—and from that has come many of the advances that have dramatically changed how we live, eat, grow food, treat disease, and understand the natural world.

*See comment below by Paul K. Strode

This post was inspired by “Lords of the fly,” Kohler’s extremely readable history of the material culture and working customs of Morgan’s group.

Huettner, Alfred F. (Alfred Francis), b. 1884, “T.H. Morgan in the “Fly Room” Columbia University c. 1916″. History of the Marine Biological Laboratory. http://hpsrepository.asu.edu/handle/10776/2188

Citations:
Sturtevant, A. H. (2001). Reminiscences of TH Morgan. Genetics, 159(1), 1-5.
http://www.genetics.org/content/159/1/1
(Note for the confused: Sturtevant was speaking in 1967, but the account of his speech was published in 2001)

Kohler, R. E. (1994). Lords of the fly: Drosophila genetics and the experimental life. University of Chicago Press.
http://www.press.uchicago.edu/ucp/books/book/chicago/L/bo3617623.html

The beautiful cover of the August issue of GENETICS was created by artist Michele Banks to commemorate the fiftieth anniversary of a pivotal moment in the history of evolutionary biology: the 1966 publication of a pair of GENETICS papers using protein electrophoresis to reveal that natural genetic diversity is bountiful. Thanks to a conversation between two specialists from different fields, these papers delivered a jolt of data to a stagnating debate. As part of the GENETICS Centennial celebrations, Brian Charlesworth, Deborah Charlesworth, Jerry Coyne, and Charles Langley discuss this work and its impact in “Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics“

In 1966, two contrasting views of genetic variability held sway. The “classical” view posited that mutations were rare and harmful, and that most individuals in a population are homozygous for the wild type version of a gene. The “balance” view held that balancing selection often maintained multiple common versions of a gene in a population, with many individuals being heterozygous. But the debate was stuck. “Population genetics seemed doomed to a perpetual struggle between alternative interpretations of great masses of inevitably ambiguous data,” wrote Lewontin in 1991.

Part of the trouble was a lack of hard data. In the age before DNA sequencing, describing genetic variation in the wild was a piecemeal task, only possible in a few select cases. Geneticists could study the variability of specific traits with a clear genetic basis, such as snail shell patterns or human blood groups, or they could study major chromosomal variants, such as inversion polymorphisms in wild fruit flies. They could infer the extent of variation through statistical analysis of breeding experiments. But without the ability to isolate specific genes, there was no way to perform an unbiased survey of genome-wide variation.

As a student of pioneering evolutionary geneticist Theodosius Dobzhansky, Richard Lewontin was keenly aware of this problem, but could not find the right method to solve it. Then, a few years after graduating, he visited the University of Chicago and met a biochemist, John Hubby, who was analyzing proteins from fruit flies using electrophoresis. Hubby would grind up individual flies, run the protein extract on gels, and detect specific proteins through their enzymatic activity. Each protein migrated through an electric current applied to the gel at a characteristic speed. But if the same protein differed slightly between individuals —whether in charge, size, or shape—its migration pattern might be altered. Lewontin realized the biochemists already had the missing technique that population geneticists sorely needed:

“…not enough credit is given to the effect of talking to other people and dealing with other people. There’s too much emphasis on the great creative act of a great mind and it’s not like that. […] Here I was with a problem looking for a solution and here a guy was with a solution looking for a problem, and we got together. Many of the things we did in our lab in Chicago arose in the course of a conversation.”

—Richard Lewontin, 2004

So convinced was Lewontin of the importance of this insight that he moved his lab to the University of Chicago, where he collaborated with Hubby. The pair quickly began surveying protein variability in Drosophila pseudoobscura, a wild cousin of the famous laboratory fruit fly beloved by geneticists. As Lewontin had hoped, they found electrophoretic variation in D. pseudoobscura proteins showed simple Mendelian inheritance, meaning the protein differences they were measuring corresponded directly to genetic variants. But to their surprise, around a third of the surveyed genes varied between individuals. To quantify this variation across five different D. pseudoobscura populations, they developed a simple summary of genetic diversity, “H” or expected heterozygosity, that is still widely used today. H provides an estimate of the chance that any two alleles at one gene are different, and with this measure, Hubby and Lewontin demonstrated substantial natural variability in all the sampled populations.

But was the richness of protein variation just a fruit fly quirk? The beauty of the new approach was it could be applied immediately to any organism, not just those, like Drosophila, with long histories in the lab:

“Here was a technique that could be learned easily by any moderately competent person, that was relatively cheap as compared with most physiological and biochemical methods, that gave instant gratification by revealing before one’s eyes the heritable variation in unambiguously scoreable characters, and most important, could be applied to any organism whether or not the organism could be genetically manipulated, artificially crossed, or even cultivated in the laboratory or greenhouse.”

—Richard Lewontin, 1991

Charlesworth et al. write of the method’s immediate impact: “It triggered an explosion of “find ’em and grind ’em” studies of variability in natural populations of numerous different species, from bacteria to humans, which showed that the levels of variability originally found in Drosophila and humans were not unusual.”

It also turned out to be a boon for understanding the evolutionary histories of organisms without fossil records. In a parallel eruption of protein electrophoresis studies, geneticists combined the protein data with measures of “genetic distance” between species (such as Nei’s “D”) to estimate phylogenies and divergence times between populations and species.

Ironically, Lewontin was wrong in predicting the methods would break the deadlock of the classical/balance debate. Instead, the influx of data raised new questions and complications, and stimulated new avenues for debate. Hubby and Lewontin’s method is the direct ancestor of today’s studies of genetic variation using genome sequence data, but the field’s fundamental question remains active: What are the most important causes of genetic variation?

The solution to the problem of natural diversity may well emerge from another meeting between scientists from different fields, drawn into a new conversation.

CITATIONS

Charlesworth, B., Charlesworth, D., Coyne, J. A., & Langley, C. H. (2016). Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics. Genetics,203(4), 1497-1503. DOI: 10.1534/genetics.115.185975
http://www.genetics.org/content/203/4/1497

Hubby, J. L., & Lewontin, R. C. (1966). A molecular approach to the study of genic heterozygosity in natural populations. I. The number of alleles at different loci in Drosophila pseudoobscura. Genetics, 54(2), 577.
http://www.genetics.org/content/54/2/577

Lewontin, R. C., & Hubby, J. L. (1966). A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura.Genetics, 54(2), 595.
http://www.genetics.org/content/54/2/595

Lewontin, R. C. (1991). Twenty-five years ago in Genetics: electrophoresis in the development of evolutionary genetics: milestone or millstone?. Genetics,128(4), 657.
http://www.genetics.org/content/128/4/657

Check out the August issue of GENETICS by looking at the highlights or the full table of contents!

ISSUE HIGHLIGHTS

This Month’s Centennial Articles

Horvitz and Sulston on Caenorhabditis elegans cell lineage mutants, pp. 1485-1487

Kenneth J. Kemphues

Kenneth Kemphues introduces Horvitz and Sulston’s 1980 GENETICS Classic, which demonstrated that systematic mutational analysis could dissect the regulation of the precise cell lineage of Caenorhabditis elegans. The paper heralded a new wave of developmental analysis that would eventually reveal much about the previously unknown relationship between genes and development.

Marcus Rhoades on preferential segregation in maize, pp. 1489-1490

James A. Birchler

GENETICS Associate Editor James A. Birchler introduces Marchus Rhoades’ 1942 Classic on the discovery of preferential segregation, a striking violation of Mendelian inheritance later known as meiotic drive.

Navigating the phenotype frontier: the Monarch Initiative, pp. 1491-1495

Julie A. McMurry, Sebastian Kohler, Nicole L. Washington, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine, Julius O. B. Jacobsen, Daniel Keith, Bryan Laraway, Jeremy Nguyen Xuan, Kent Shefchek, Nicole A. Vasilevsky, Zhou Yuan, Suzanna E. Lewis, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, and Melissa A. Haendel

Although numerous model organism resources exist, it is challenging to obtain a global mechanistic picture, since each resource focuses on a different species, disease, or data type. This Centennial commentary highlights challenges in integrating phenotypic data and introduces the Monarch Initiative, which aims to develop a computational infrastructure to bring together disparate data across sources, organisms, and scales.

The Hiroshima/Nagasaki survivor studies: discrepancies between results and general perception, pp. 1505-1512

Bertrand R. Jordan

Many people believe that survivors of the bombing of Hiroshima and Nagasaki in August 1945 suffered a very high cancer burden, dramatically shortened life span, and that their children also had higher mutation rates and frequent abnormalities. In fact, extensive and ongoing follow-up of 120,000 survivors and 77,000 of their children reveal more modest effects. This Perspectives article summarizes the results of these studies, which have been crucial for setting safe radiation exposure limits, and discusses possible reasons for the very striking discrepancy between the facts and general beliefs about this situation.

Hubby and Lewontin on protein variation in natural populations: when molecular genetics came to the rescue of population genetics, pp. 1497-1503

Brian Charlesworth, Deborah Charlesworth, Jerry A. Coyne, and Charles H. Langley

The 1966 GENETICS papers by John Hubby and Richard Lewontin were landmarks in the study of genome-wide levels of variability, revealing a surprisingly high level of protein sequence variability in natural populations. To mark the fiftieth anniversary of the papers and the hundredth anniversary of the journal, Charlesworth et al. discuss the methods used in these pioneering studies, and show how they led to subsequent developments in empirical and theoretical research on natural variation.

—————————————————–

Principles of microRNA regulation revealed through modeling microRNA expression quantitative trait loci, pp. 1629-1640

Stefan Budach, Matthias Heinig, and Annalisa Marsico

Transcriptional regulation of microRNAs is poorly understood, due to difficulties determining the start sites of transient primary transcripts. This challenge can be addressed using expression quantitative trait loci (eQTLs), whose effects represent a natural perturbation of cis-regulatory elements. Budach et al. describe a model to predict microRNA-eQTL SNPs in human lymphoblastoid cell lines based on their overlap with regulatory regions. Interestingly, the majority of overlapping microRNA- eQTLs and mRNA-eQTLs affect microRNA and host expression independently. MicroRNA-only eQTLs are enriched for intronic promoters, validating the existence of alternative microRNA promoters that can decouple microRNA and host transcription.

Crosstalk between mitochondrial fusion and the hippo pathway in controlling cell proliferation during Drosophila development, pp. 1777-1788

Qiannan Deng, Ting Guo, Xiu Zhou, Yongmei Xi, Xiaohang Yang, and Wanzhong Ge

Mitochondrial function and the highly conserved Hippo signaling pathway have been linked in growth control, but the molecular mechanisms are unclear. Deng et al. identify mitochondrial inner membrane protein ChChd3 as a regulator of tissue growth in Drosophila. The authors also show crosstalk between mitochondrial fusion and the Hippo pathway that is essential in controlling cell proliferation and tissue homeostasis in Drosophila.

Genomic prediction for quantitative traits is improved by mapping variants to gene ontology categories in Drosophila melanogaster, pp. 1871-1883

Stefan M. Edwards, Izel F. Sørensen, Pernille Sarup, Trudy F. C. Mackay, and Peter Sørensen

Predicting quantitative phenotypes from high resolution genomic polymorphism data is important for personalized medicine, plant and animal breeding and adaptive evolution. Edwards et al. hypothesized that mapping polymorphisms to genes and their gene ontology categories could increase the accuracy of genomic prediction models. They evaluate a Genomic Feature Best Linear Unbiased Prediction (GFBLUP) model using prior information on Gene Ontology categories and show it can increase the predictive ability of the genomic value for three quantitative traits in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP).

Refining the use of linkage disequilibrium as a robust signature of selective sweeps, pp. 1807-1825

Guy S. Jacobs, Tim J. Sluckin, and Toomas Kivisild

One signal used to infer positive selection at specific genome regions is a characteristic local distortion in linkage disequilibrium between loci. However, recombination rate can be highly variable along the genome, creating a rough linkage disequilibrium landscape that may confound this approach. The authors explore this effect, and suggest methods that use information on recombination rate variation to retrieve the true signal of selection.

The chromatin remodeling component Aridla is a suppressor of spontaneous mammary tumors in mice, pp. 1601-1611

Nithya Kartha, Lishuang Shen, Carolyn Maskin, Marsha Wallace, and John C. Schimenti

ARID1A is commonly mutated in many cancers. Using a mouse model of sporadic breast cancer, Kartha et al. show that most tumors lack one copy of Arid1a, and have decreased Arid1a mRNA. Re-expression/ overexpression of ARID1A in tumor cells slowed their growth and prevented re-formation of tumors upon transplantation, but only in p53-proficient cells. Overall, the results provide evidence for a tumor suppressive and/or maintenance role for ARID1a in breast cancer and suggest a potential strategy for therapeutic intervention.

Plasticity in the meiotic epigenetic landscape of sex chromosomes in Caenorhabditis Species, pp. 1641-1658

Braden J. Larson, Mike V. Van, Taylor Nakayama, and JoAnne Engebrecht

Successful meiosis relies on homology between chromosomes. But the sex chromosomes of the heterogametic sex are non homologous. To facilitate transmission despite lack of homology, such chromosomes are epigenetically modified by Meiotic Sex Chromosome Inactivation (MSCI). The role and conservation of MSCI has been controversial. Larson et al. examined MSCI in closely related Caenorhabditis species and found that, although conserved, the repressive chromatin marks which mediate MSCI and their underlying gene networks have diverged. The study provides evidence for epigenetic plasticity in regulation of transcription, checkpoint signaling, and DNA replication timing.

Contrasting levels of molecular evolution on the mouse X chromosome, pp. 1841-1857

Erica L. Larson, Dan Vanderpool, Sara Keeble, Meng Zhou, Brice A. J. Sarver, Andrew D. Smith, Matthew D. Dean, and Jeffrey M. Good

Evolutionary theory predicts that the X chromosome should evolve rapidly under some conditions, particularly for genes involved in male reproduction. Larson et al. tested these predictions in mouse spermatogenesis. They found faster protein evolution late in spermatogenesis and faster-X protein evolution at all stages, while expression divergence was slower late on the X chromosome. They also found slower-X DNA methylation divergence in sperm. The authors propose that slower-late regulatory evolution is a consequence of strong constraints during sperm development.

Restriction of retrotransposon mobilization in Schizosaccharomyces pombe by transcriptional silencing and higher-order chromatin organization, pp. 1669-1678

Heather E. Murton, Patrick J. R. Grady, Tsun Ho Chan, Hugh P. Cam, and Simon K. Whitehall

Uncontrolled propagation of retrotransposons is potentially harmful to host genome integrity. Murton et al. reveal a novel host mechanism for controlling transposon mobilization through nuclear organization. The authors used a sensitive reporter assay to characterize the factors that suppress mobilization of an endogenous Tf2 LTR retrotransposon in the fission yeast Schizosaccharomyces pombe. Their analysis suggests S. pombe deploys the clustering of Tf2 elements in concert with transcriptional silencing to suppress retrotransposition.

For two weeks in the summer of 1953, Motoo Kimura enjoyed a welcome respite from loneliness and the austerity of post-war Japan. Crossing the Pacific from Yokohama to Seattle to commence PhD studies at Iowa State University, Kimura played deck golf, enjoyed full service meals, and napped to the soothing vibrations of the venerable passenger liner Hikawa maru. He also sought solace in equations, writing a paper on how populations evolve when the intensity of natural selection fluctuates at random. His chronic stomach troubles, which he attributed to stress, vanished.

A month later, Kimura took his fluctuating selection paper with him to a conference in Madison, Wisconsin.* Struggling with English, he managed to get lost in the corridors of the lakefront building where the meeting was held, until he was stopped by a tall American. The man, population geneticist Jim Crow, asked Kimura if he needed help finding his way.

Crow would later say this chance encounter changed both of their lives. Crow would become Kimura’s mentor, in the truest sense of the word. Crow guided and challenged him. Crow connected Kimura with scientific luminaries. He focused Kimura’s intensity and mathematical talent on important biological problems. Their lifelong intellectual partnership would link their names forever—Crow and Kimura—in an iconic textbook, but also—Kimura and Crow—in a 1964 GENETICS article that paved the way for the study of evolution at the molecular level. As part of the GENETICS Centennial Classic series published throughout 2016, Warren Ewens introduces Kimura and Crow 1964 as one of the journal’s most influential papers.

At their first meeting in Madison, Crow had been startled to hear Kimura’s name. Though Kimura was an obscure student, Crow had recently been forwarded some of his papers. Based on the originality and depth of the ideas, he had assumed Kimura was a distinguished professor, not an isolated student who had taught himself both population genetics and mathematics.

Kimura was originally trained as a plant cytologist; he had been fascinated by plants since boyhood, and cytogenetics had been the hot field in Japan at the time. But his interest in chromosomes waned as he began yearning to “do something in genetics like what the theoretical physicists were doing in physics.” This ambition was buoyed by Kimura’s regular, hunger-fueled excursions to the house of his cousin-in-law Matsuhei Tamura, a mathematical physicist. Kimura visited almost every Sunday, partly because he was intensely interested in the quantum physicist’s stories, and partly because he needed to fill his belly during the post-war food shortages.

Kimura joined the lab of Japan’s most famous cytogeneticist, Hitoshi Kihara, who recognized the quiet young man’s talent for theory and left him mostly to his own devices. So, while his friends picked apart the chromosomes of wheat and watermelon, Kimura indulged in the more abstract pleasures of population genetics. He would travel the full-day’s train journey to Tokyo to copy out by hand the papers of Sewall Wright, one of the founders of the field. Determined to understand Wright’s papers, Kimura haunted the math department, attending classes, asking questions, learning from books, until he gradually gained the sophistication to follow Wright’s arguments, and eventually, critique and extend them.

But this new intellectual world was isolating. Kimura’s lab mates took a dim view of his absorption in mathematics and the situation only worsened when he took a job at the newly founded National Institute of Genetics. The facility was housed in the makeshift and uncomfortable office of a wartime aircraft factory. There was no library, no access to foreign journals, and no colleague who could understand his work. The only geneticist there who saw its value was zoologist Taku Komai, who had studied in the fly lab of genetics superstar T. H. Morgan in the United States. Komai recommended Kimura extend his training overseas and introduced him to an American scientist working for the Atomic Bomb Casualty Commission. Before long Kimura had a scholarship, a Fulbright travel award, and a ticket to Seattle.

Once they met, Crow immediately took Kimura under his wing. He invited Kimura over for dinner to meet his idol Sewall Wright. Crow probed Kimura about the paper he had just written on the Pacific voyage and was impressed that it neatly reduced a formidably complex equation down to a simple relationship used by physicists to describe heat conduction. He encouraged Kimura to submit the paper to GENETICS, where Crow was an editor (the paper was later effusively and uncharacteristically praised by its reviewer, Wright).

James F. Crow, R. A. Fisher, and Motoo Kimura in the Crow lab in 1961. From Susman and Greenberg Temin 2012.

But after this giddy start, slogging through the reality of compulsory graduate courses in Iowa was a letdown. Kimura was bored by the quantitative genetics focus of his advisor Jay Lush and longed to return to the warm and intellectually bracing atmosphere he had enjoyed during his brief visit with Crow. Nine months later, Kimura transferred to Madison to study with Crow.

This turned out to be a career-making decision. Crow was famous not only for his keen insights, but also his ability to draw them out of others in his role as a generous teacher, mentor, and colleague. Daniel Hartl, Crow’s student from 1965-1968, described the atmosphere that Crow cultivated in his lab:

Professor Crow ran his laboratory on the principles of bringing smart people together to pursue their passions and encouraging interaction, mutual respect and support, constructive criticism, and the free sharing of ideas and resources. There were no formal group meetings or reports, as there was so much daily interaction that group meetings would have been superfluous. He would advise, suggest, and encourage, but never direct or cajole.

Kimura later judged the brief two years he spent earning his PhD under Crow as the most productive of his life. It was during this time that he developed his model of random drift and introduced an equation for modeling random dynamic processes (the Kolmogorov backward diffusion equation) to find the probability that a gene allele reaches fixation (i.e. is carried by every individual in the population). This equation would later become a standard tool in population genetics.

Kimura moved back to Japan after graduation, and a few years later, in 1958, Crow wrote to him about some interesting new data on the nature of bacterial mutations from his friend Joshua Lederberg. Most of the point mutations that arose in Lederburg’s experiments were independent. In other words, nearly every mutation yielded a new allele. This result fit with the emerging molecular view of the gene as a sequence of hundreds or thousands of nucleotides, in which every nucleotide substitution or rearrangement would count as a new allele. Crow wondered how this conception would affect population genetics models.

He posed a specific problem to Kimura: If you assume that every mutation generates a new allele and that a population has reached genetic equilibrium (i.e. allele frequencies are stable from generation to generation), what would be the proportion of loci in a population that are homozygous? A little over a year later, Kimura wrote back with the answer. Crow was once more impressed with the practical simplicity of Kimura’s solution, a straightforward equation based on mutation rate and the size of the population (technically speaking, the effective population size).

Working together in Madison in 1962 and 1963, this tidy equation became the core of their infinite alleles model (sometimes known as the “infinitely many alleles” model). The 1964 paper began by describing a basic model under the assumption that each mutation has no net effect on the bearer’s survival and reproduction, that is, each mutation is “neutral”. The rest of the paper built on this foundation by introducing the effects of natural selection and random drift, but it was the first, introductory section that was to become most influential. The infinite alleles model was ready and waiting for the arrival of molecular data to population genetics two years later when the field was electrified by Richard Lewontin and Jack Hubby’s analysis of protein variation by gel electrophoresis (another GENETICS paper).

Crow would later say that Kimura’s early work, including their collaboration on the infinite alleles model, was “preadapted” for this moment. It became a key tool in the debates that began to rage about the best interpretation of the abundant genetic diversity exposed by protein electrophoresis studies. This work was also the starting point for a series of elaborations modeling how neutral or nearly neutral alleles evolve. Crucially, it influenced Kimura’s later development of “neutral theory,” in which he argued that most variation at the molecular level is the result of random genetic drift of neutral mutations, as opposed to natural selection of beneficial ones. Although his idea was radical at the time, it is now the default starting point of molecular evolution studies. Crow described the critical importance of the theory as a kind of invisibility:

Haldane once said that the highest honor a scientist can have is for his theory to be so taken for granted that his name is no longer associated with it. We no longer mention Mendel when we conduct breeding experiments or Sturtevant when we map chromosomes. Likewise, neutral assumptions permeate modern studies of molecular evolution and population genetics. In most cases Kimura is not mentioned.

Crow and Kimura remained close friends and collaborators for the rest of their careers, and in 1970 they published a widely used textbook, An Introduction to Population Genetics Theory. With his share of the book earnings, Kimura built a greenhouse and bred a prize-winning orchid that he named “Paphiopedilum James Crow”. Though not an expert gardener like Kimura, Crow did know a great deal about cultivating students, providing just the right conditions to allow them to flourish and bloom.

Prize-winning orchid bred by Motoo Kimura and named in honor of James Crow. The photo shows a tile painted by Kimura and given to Crow as a gift. From Susman and Greenberg Temin 2012

CITATIONS
Warren J. Ewens (2016). Motoo Kimura and James Crow on the Infinitely Many Alleles Model.
GENETICS, 202 (4), 1243-1245.
DOI: 10.1534/genetics.116.188433
http://www.genetics.org/content/202/4/1243

Motoo Kimura and James F. Crow (1964). The Number of Alleles That Can Be Maintained in a Finite Population
GENETICS, 49 (4), 725–738
http://www.genetics.org/content/49/4/725

Motoo Kimura (1954). Process Leading to Quasi-Fixation of Genes in Natural Populations Due to Random Fluctuation of Selection Intensities.
GENETICS, 39 (3), 280-295
http://www.genetics.org/content/39/3/280

This Conversations in Genetics interview of Jim Crow by Dan Hartl includes several recollections of Kimura, including this account of his graduate student years:

[youtube https://www.youtube.com/watch?v=IN1xheqTwhk&start=2507&end=2615 ]

*Crow repeatedly described this as the Genetics Society of America meeting. But in 1953 the GSA annual meeting was held in conjunction with AAAS in Boston. The meeting held Sept 6-10 in the Union at Madison that year was the AIBS meeting, for which Crow was in charge of room assignments. Crow might have been confused because in the previous and following years the GSA meeting had been held at the AIBS meeting.

Sometimes, great advances in science come from combining the old with the new. Genomic selection is one such case; in 2001, Meuwissen, Hayes, and Goddard surveyed the changing landscape of genetics, had the foresight to work on a then-theoretical problem, and laid the foundation for a boom in biotechnology-assisted breeding that continues to this day. In the May issue of GENETICS, Associate Editor and G3 Deputy Editor Dirk-Jan de Koning introduces Meuwissen et al. as one of the journal’s 100th anniversary Classics.

Humans have been shaping plants and animals through selective breeding for thousands of years. In the 18th century, breeders started keeping detailed records, and a more systematic approach to selective breeding began after World War II. In this approach, the “breeding value” of a given animal was determined through detailed pedigree information, phenotyping of important traits, and test breeding. During the 20th century, the field of genetics grew by leaps and bounds, allowing breeders to add molecular genetic tools to their toolboxes and improving dairy cattle, sheep, and maize breeding – just to name a few.

To combine genetics and selective breeding, scientists had to identify genetic markers connected to traits of interest. When a marker is genetically linked to a gene or a quantitative trait locus (QTL) influencing the trait of interest, plant and animal scientists can indirectly test for the presence of the favorable alleles affecting the trait by genotyping for the marker. Many scientists thought this technique – called marked assisted selection (MAS) – would change the game for selective breeding, allowing faster progress in crops and livestock than phenotyping alone could achieve. But MAS relied on marker maps that were relatively sparse and QTL that had to be carefully – and labor-intensively – validated. It wasn’t quite the leap forward many had hoped it would be.

In 2001, on the cusp of the completion of the Human Genome Project, it seemed likely that marker maps with much higher density would soon be available for crops and livestock; maybe these dense marker maps would be the real game-changer. There was a problem, though: mapping QTL using the methods designed for sparse marker maps wasn’t greatly improved by a higher density of marker information. Without a better way to use such data, it wouldn’t markedly improve assessment of genetic value compared to traditional phenotyping and MAS.

In a move that showed great foresight, Meuwissen et al. took on this challenge, devising a way to accurately predict genetic value from dense marker maps.

Instead of finding the most significant markers or QTL, they focused on a way to estimate the effects of all markers together without testing for significance. Using a simulated data set of 1010 genetic markers and 1000 QTL, Meuwissen et al. tested four different modeling methods – least-squares linear regression, best linear unbiased prediction (BLUP), and two Bayesian analyses – for accuracy in predicting the breeding value of an individual genotyped for many alleles. According to their data, BLUP and the Bayesian methods were able to predict breeding values with accuracies upwards of 0.73.

This was a significant breakthrough, and it was met with enthusiasm by agricultural science communities, but at the time of publication, this work was still theoretical. The dense marker maps for crops and livestock necessary to build the marker haplotypes needed for this method – termed genomic selection – didn’t yet exist.

After spending five years in the realm of “potentially field-changing,” technology eventually caught up with theory for genomic selection: medium-density SNP arrays became available for many agricultural species, and the real-world applications took off almost immediately.

Dairy cattle breeders were the first to benefit. Traditional phenotyping of sires had been painfully slow and expensive – for example, testing important milk-related traits involved waiting years for the female offspring of a bull to reach maturity. An extensive data recording structure was already in place to facilitate progeny testing of candidate bulls, which made it easy to implement genomic selection without major changes in data recording. Genomic selection is now routine in the dairy cattle industry. It is also becoming an increasingly important tool for many other livestock and crop species, less than a decade since new genotyping technologies made genomic selection a reality. Fittingly, Meuwissen and Goddard were recognized this year by the National Academy of Sciences; they received the John J. Carty Award for contributions to the agricultural sciences.

Since Meuwissen et al. published their landmark work in GENETICS, the GSA journals have continued to serve as a crucial forum for advances and debate in genomic selection. GENETICS and G3 host an ongoing genomic selection series, which has >50 papers. This collection includes reviews, methods, tools, and applications, plus access to valuable data sets for comparing and benchmarking new approaches.

CITATIONS

Meuwissen, T.H.E., Hayes, B.J., Goddard, M.E. 2001. Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps. GENETICS, 157(4): 1819-1829. http://www.genetics.org/content/157/4/1819

De Koning, D.J. 2016. Meuwissen et al. on Genomic Selection. GENETICS, 203(1): 507. doi: 10.1534/genetics.116.189795 http://www.genetics.org/content/203/1/5

The Genetics Society of America (GSA) and the Editorial Board of the journal GENETICS are pleased to announce the winners of the first Centennial Award for outstanding articles published in GENETICS in 2015. The awards were inaugurated just this year in celebration of the 100th anniversary of GENETICS. Three exceptional articles are recognized from three categories: quantitative genetics, molecular genetics, and population and evolutionary genetics. Prizes for the lead authors of each article include subsidized attendance at The Allied Genetics Conference, an integrated GSA meeting that brings together researchers from the C. elegans, ciliate, Drosophila, mouse, yeast, zebrafish, and population, evolutionary, & quantitative genetics communities.

1ST CENTENNIAL AWARD FOR MOLECULAR GENETICS

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome

Stefan F. Pinter, David Colognori, Brian J. Beliveau, Ruslan I. Sadreyev, Bernhard Payer, Eda Yildirim, Chao-ting Wu, Jeannie T. Lee

GENETICS June, 2015 vol. 200:537-549; DOI: 10.1534/genetics.115.176263

Aside from genes affected by epigenetic phenomena, the two alleles of a gene are generally assumed to express at equal levels. Pinter et al. revealed the unexpected extent of allelic imbalance by measuring gene expression in hybrid offspring from genetically distinct mice. Genetic variation likely causes most of this imbalance, but surprisingly, some of the genes were expressed from only one allele in both hybrid and inbred strains.

Co-lead author Stefan Pinter is an Assistant Professor in Genetics and Genome Sciences at UConn Health and member of the Institute for Systems Genomics at the University of Connecticut. His primary interest is to learn how chromosome folding, non-coding RNAs, and chromatin modifiers orchestrate gene expression, particularly in the context of allele-specific regulation. The vast majority of disease-associated variation does not change the content of genes but rather their dosage. Classic models of dosage compensation, such as X chromosome inactivation (XCI), provide a uniquely tractable perspective on these questions, because they use a variety of gene regulatory mechanisms. Building on his XCI, stem cell, and epigenomics work with GSA member Jeannie Lee at MGH/Harvard Medical School, the Pinter lab at UConn Health aims to develop scalable systems approaches to these questions, with a focus on genes that escape XCI and are implicated in Turner’s syndrome (XO karyotype). Pinter’s enduring interest in chromosome biology originated in his PhD training on DNA replication with Virginia Zakian at Princeton University, supported by a Komen Breast Cancer Research Foundation dissertation fellowship. His postdoctoral training was funded by the German Research Foundation and the Fund for Medical Discovery at MGH. Current work in the Pinter lab is supported by UConn Health. http://facultydirectory.uchc.edu/profile?profileId=Pinter-Stefan

Co-lead author David Colognori is a graduate student in Jeannie Lee’s lab in the Department of Genetics at Harvard University. His work focuses on the genetic and epigenetic mechanisms responsible for monoallelic expression of genes, for example during imprinting, random monoallelic expression, and sex chromosome dosage compensation. The latter involves an entire chromosome being silenced in female mammals in order to balance gene expression levels between males, which have one X chromosome, and females, which have two. This process is orchestrated by a long noncoding RNA, Xist, expressed from the inactive X. He is currently studying the interactions between Xist RNA and its associated proteins, which are necessary for the ensuing cascade of epigenetic modifications that lead to X chromosome inactivation in mice.

1ST CENTENNIAL AWARD FOR POPULATION AND EVOLUTIONARY GENETICS

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

Rohan Maddamsetti, Richard E. Lenski, Jeffrey E. Barrick

GENETICS June, 2015 200:619-631; DOI: 10.1534/genetics.115.176677

Maddamsetti et al. reconstructed the dynamics of 42 mutations over 20,000 generations of bacterial evolution. They show that cohorts of multiple beneficial mutations typically accumulated before a lineage was able to complete a selective sweep. In one striking case, two bacterial types with different sets of mutations coexisted for thousands of generations.

Lead author Rohan Maddamsetti recently completed his PhD in evolutionary biology at Michigan State University and will start a postdoc in the Department of Systems Biology at Harvard Medical School in the fall. In his dissertation, Rohan studied how populations of Escherichia coli adapt in evolution experiments, and compared patterns of molecular evolution in those experiments to patterns found in natural E. coli populations. Rohan is broadly interested in the molecular evolution, and is inspired by an analogy between the complex molecular machinery encoded by the products of ‘selfish genes,’ and the complex societies built by humans motivated by self-interest.

1ST CENTENNIAL AWARD FOR QUANTITATIVE GENETICS

The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses

Armando Caballero, Albert Tenesa, Peter D. Keightley

GENETICS December, 2015 201:1601-1613; DOI:10.1534/genetics.115.177220

The mystery of the “missing heritability” of many complex traits is the mismatch between their heritability and the total variance explained by SNPs identified in genome-wide association studies (GWAS). Caballero et al. used simulations to show that, contrary to previous results, common variants of large effect are responsible for most variation and switching to GWAS of full sequence data is unlikely to substantially reduce the missing heritability.

Lead author Armando Caballero is Professor of Genetics at the University of Vigo, Spain. He completed his PhD at Universidad Complutense, Madrid (1990) and a postdoctoral research fellowship at Edinburgh University (1990-1996). His main scientific interests are conservation genetics, quantitative genetics, and evolution. He has been an Associate Editor of the journals Evolution (1999-2001), The American Naturalist (2005-2009), Journal of Evolutionary Biology (2007-2011), and Genetics, Selection, Evolution (2009-2016). He has served as Head of Department (2005-2011), Secretary of the Spanish Society of Genetics (2007-2010), and coordinator of MSc (2009-2012) and PhD (1997-2016) programmes.

At the time of her death in 1912, Nettie Maria Stevens was a biologist of enough repute to be eulogized in the journal Science by future Nobelist Thomas Hunt Morgan and for her passing to be noted in The New York Times. In 1910 she had been listed among 1,000 leading American “men of science.”

Yet in 1916, when Calvin Bridges published his proof that genes lie on chromosomes (the first paper in the first issue of GENETICS), Bridges cited the pioneering observations of a “Miss Stevens.” He also offered sincere thanks to “Dr. T.H. Morgan” and to his lab mates “Dr. A.H. Sturtevant and Dr. H.J. Muller.”

But “Miss Stevens” had in fact earned her PhD under Morgan’s supervision, just like Alfred Sturtevant, Hermann Muller, and Bridges himself. Why then did Bridges address the men as “Dr”, but granted Stevens only a “Miss”? The reason was likely convention. It seems to have been common in  academic journals, including GENETICS, to refer to a woman with a PhD as “Miss” or “Mrs.”  Indeed, Morgan’s obituary in Science is titled “The Scientific Work of Miss N.M. Stevens.”

In honor of Women’s History Month and the Centennial celebrations of GENETICS, Genes to Genomes takes a closer look at the “Miss Stevens” cited in the journal’s very first article.

Becoming a biologist

Before becoming a biologist, Stevens had been a teacher and occasional librarian for more than a decade. Her first career allowed her to save up for college; at the age of 35, she resigned from a high school teaching job in Massachusetts and traveled across the country to enroll at Stanford University in California.

At the time, Stanford was a five-year-old institution that was attracting many women interested in science majors. Stevens earned a baccalaureate degree, followed by a Master’s degree with research on the life cycle and microanatomy of ciliates. In 1900, the same year Mendel’s “laws of inheritance” were rediscovered, Stevens traveled back East to commence her PhD research at Bryn Mawr, a women’s college in Pennsylvania.

Stevens continued her ciliate work under embryologist and biology department head Morgan, who was impressed by her talent and independence (he was five years her junior). In 1901 Stevens was awarded a fellowship to study in Europe, where she worked with German zoologist Theodor Boveri.  Around the time of Stevens’ visit, Boveri was conducting exciting experiments linking heredity to mysterious dark-staining entities in the cell nucleus known as chromosomes. Boveri’s work revealed that a complete set of chromosomes was needed for development to proceed normally, revealing that each chromosome maintained its own distinct identity.

Sex determination

After her European adventure, Stevens was eager to apply her impeccable histology skills to the hot topic of chromosomes and Mendelian inheritance. Once she graduated with her PhD in 1903, she and Morgan planned a collaboration on the controversial and unresolved question of how sex is determined in the developing egg. Did external factors, like food and temperature, set the sex of an egg? Or was it something inherent to the egg itself? Or was sex inherited as a Mendelian trait?

But by this time, Stevens was running out of savings. Without other means of support, she worried that her dreams of devoting herself to research would be buried in teaching duties. Morgan encouraged her to apply for a Carnegie Institution research fellowship and gave her an enthusiastic reference. Stevens was eventually awarded the fellowship and “freedom from anxiety over the money question.”

Part of the money was used for Stevens’ and Morgan’s collaborative work, in which they investigated the relation between sex determination and food source in aphids. But Stevens also pursued a side project on some alluring hints that sex was determined by inheritance of specific sets of chromosomes. In 1901, Clarence Erwin McClung had proposed that a peculiar chromosome in the insect Pyrrhocoris was responsible for determining its sex. At meiosis, this “accessory chromosome” was sorted into only one of the two sperm precursor cells.

Stevens examined a range of insect species in a hunt for other accessory chromosomes. When Stevens examined the meal worm Tenebrio melitor, she made a striking observation. This species produced two classes of sperm: a type that carried ten large chromosomes, and a type that carried nine large and one small chromosome. Body cells in the females contained 20 large chromosomes while males carried 19 large and one small chromosome. She reasoned that when an egg is fertilized by a sperm that carries the small chromosome, the result is a male offspring. The presence of the small chromosome might be what decided the individual’s “maleness.”

As is so often the case in science, one of Stevens’ colleagues discovered something similar at almost the same time. Prominent cell biologist Edmund Beecher Wilson made related observations of the behavior of an extra, unpaired chromosome in two hemipteran (bug) species.

But even combined with Wilson’s observations, it was not clear whether the pattern Stevens saw was just a quirk of an obscure species. The next important step, she concluded, was to examine a wider range of insects.

Stevens embarked on a painstaking survey that eventually covered 50 species of beetle and nine species of fly (including Drosophila melanogaster). Every species she examined had accessory chromosomes that either resembled Tenebrio (now known as an XY system) or they had an unpaired chromosome like Wilson’s bugs (now known as an X0 system). Clearly Tenebrio was no anomaly.

Sadly, Stevens never got to see final confirmation of her hypothesis. Though she continued pursuing evidence for several years, she died from breast cancer in 1912, at the age of 50.

Plate IV from Stevens (1905) showing hand-drawn micrographs from Tenebrio molitor samples.

American women of science

Morgan’s obituary for Stevens was ambivalent. He praised her “single-mindedness and devotion, combined with keen powers of observation; her thoughtfulness and patience, united to a well-balanced judgment.” Scientists had been slow to recognize the significance of her discovery, he said, because of their scientific conservatism. In almost the same breath, however, Morgan diminished Stevens by characterizing her as over-cautious and “at times wanting in that sort of inspiration that utilizes the plain fact of discovery for wider vision”. He portrayed her as a great technician but not a great theoretician.

Ironically, Morgan had been considerably more cautious than Stevens on the question of sex chromosomes. Indeed, his reference to “conservatism” in Stevens’ obituary may have been a subtle joke at his own expense, since he had only started to accept the evidence for sex chromosomes two years earlier. Some have also argued that Wilson was less willing than Stevens to embrace the Mendelian implications of the evidence. Either way, it would not be fair to characterize Stevens as over-cautious in her interpretations of sex chromosomes. The truth was, even though her observations were suggestive, she was right in concluding they fell short of proving that chromosomes determine sex. In 1908, she suggested the only hope of testing whether sex is indeed a Mendelian character must come from breeding experiments. Though she did not live to see it, she was correct. The matter was settled with Morgan’s own results mapping a Mendelian factor (the white eye mutation) to a sex chromosome in Drosophila.

In 1910, Stevens earned a coveted “star” next to her entry in “American Men of Science”, which meant she had been ranked among the top 1,000 scientists in the country. In a statistical analysis of this science elite, the directory’s publisher (who was also the editor of Science), noted that only 18 women ranked in the list, down from 19 women seven years earlier. He saw this as evidence that women were not as fit for the job as men:

“There are now nearly as many women as men who receive a college degree; they have on the average more leisure; there are four times as many women as men engaged in teaching. There does not appear to be any social prejudice against women engaging in scientific work, and it is difficult to avoid the conclusion that there is an innate sexual disqualification. Women seem not to have done appreciably better in this country than in other countries and periods in which their failure might be attributed to lack of opportunity. But it is possible that the lack of encouragement and sympathy is greater than appears on the surface, and that in the future women may be able to do their share for the advancement of science”

–James McKeen Cattell, 1910

Today, the idea that women scientists in 1910 faced no social prejudice seems absurd. Nettie Stevens succeeded within a system that devalued her work. For example, the year she graduated from Stanford, the university’s co-founder Jane Stanford capped enrollment of women at 500 students, fearing her university was turning into a girls’ college. As a woman, Stevens could not have enrolled in graduate school at some of the most respected institutions in the country. Women were severely restricted in the types of academic jobs open to them. Women who did gain jobs in academia were expected (in some places legally compelled) to give up paid employment upon marriage.

Stevens lived in a world that assumed her inferiority and repeatedly emphasized that she was different from her male colleagues. Even in the dry pages of academic journals, her gender was appended, like an asterisk, to her name and accomplishments until long after her death.

Thanks to Casey Bergman for a Twitter conversation that prompted me to wonder about the use of “Miss Stevens” in Bridges’ 1916 paper.

Nettie Stevens’ microscope at Bryn Mawr College. This instrument was reserved for the use of advanced graduate students after Stevens’ death and was “much valued and treasured and affectionately known as the ‘Nettie Maria’.” (Ogilvie and Choquette 1981) Photo: Bryn Mawr College [CC BY-SA 3.0], via Wikimedia Commons

In the early 1940s, many biologists doubted bacteria had genes. After all, they seemed to play by their own genetic rules: they appeared to lack chromosomes, meiosis, mitosis, sex, and all the other trappings of Mendelian inheritance. They even seemed to show a kind of Lamarckian inheritance, in which an individual could pass on traits acquired during its lifetime.

Then, in 1943, Salvador Luria and Max Delbrück published an article in GENETICS that marked the birth of bacterial genetics, revealing that this apparently Lamarckian inheritance was in fact a case of random mutation. Luria and Delbrück’s work wasn’t just a boon for bacterial genetics. Brought together by biophysics and war, the duo’s brief decade of collaboration also fostered the emergence of molecular biology by developing the viruses that infect bacteria into a streamlined genetic model.

In the February issue of GENETICS, Andrew Murray introduces the 1943 paper as one of the journal’s 100th anniversary Classics.

The roots of Luria and Delbrück’s partnership traced back to a paper published just as war was brewing in Europe in 1935. Luria was in Italy, a newly qualified doctor who was bored with medicine; Delbrück was in Germany, a young physicist who had grown bored with physics. Delbrück had collaborated with some biologists from a discussion group—his “little club”— contributing a quantum mechanical model of the gene to a paper on mutations and gene structure. Luria read the paper a few years later when he was in Rome completing a specialty in radiology and dabbling in physics under soon-to-be-Nobel-Prize-winner Enrico Fermi’s wing. Luria’s imagination was sparked by the paper’s proposal that the abstract concept of a gene, which was then still hazy with mystery, could be investigated as a concrete “collection of atoms.” It seemed, he would later say, “to open the way to the Holy Grail of biophysics.”

Luria wondered how to test the new ideas and stumbled on a possibility. He met a microbiologist on a stalled trolley car who turned out to be measuring bacteria in the Tiber River using bacteriophages—viruses that infect bacteria. Luria became intrigued by the possibilities of probing gene structure using the phage as a stripped-back biological system.

Bacteriophages (white polygonal shapes) attached to a bacterial cell, ready to transfer their genome into the bacterium. By Dr Graham Beards [CC BY-SA 3.0] via Wikimedia Commons.

“I didn’t make much progress in reading these forbidding-looking papers; every genotype was about a mile long, terrible, and I just didn’t get any grasp of it.”

–Max Delbrück, 1978

Then he began talking to Emory Ellis, a postdoc in the department at Caltech who had isolated some bacteriophage from Los Angeles sewage; Delbrück realized that he had found the system he had been searching for:

“I was absolutely overwhelmed that there were such very simple procedures with which you could visualize individual virus particles; […] This seemed to me just beyond my wildest dreams of doing simple experiments on something like atoms in biology.”

–Max Delbrück, 1978

Back in Italy, Luria was encouraged to hear of Delbrück’s phage epiphany and, in 1938, hoped to use a government fellowship to travel to the US to work with the displaced physicist. But just as soon as he was awarded the money, Italian dictator Benito Mussolini announced a series of Nazi-influenced race laws. Luria’s fellowship was unceremoniously withdrawn because he was Jewish. With no funding to work with Delbrück, he sought shelter and grant money at Marie Curie’s Radium Institute in Paris, where he bombarded bacteriophage with radiation to study their molecular make up.

Then, on June 13, 1940, as the German Army advanced on Paris, Luria and his friends were forced to flee the city on bicycles. After making his way nearly 500 miles to Marseilles and the US embassy (via a combination of bike and freight train), Luria took a ship to New York. Once the US, he quickly obtained funding to restart his investigations and at a conference in December, he finally met the one other person in the world who thought phage was the key to understanding the gene: Delbrück. They immediately agreed to join forces.

French refugees, 19 June 1940. After the Nazi invasion, millions of people fled South. Photo: Bundesarchiv, Bild 146-1971-083-01 / Tritschler / CC-BY-SA 3.0 via Wikimedia Commons

Among the first problems the pair tackled was the emergence of resistance in bacteria. When a culture is grown from a single cell and then exposed to phage, the infected cells die. But if left for a few hours or days, virus-resistant cells start growing and the culture revives itself. Many biologists held the view that these survivors were the descendants of cells that had developed resistance to the phage as a result of some direct interaction between the virus and bacteria.

But others saw no reason to believe that bacteria operated under entirely new rules of heredity. Just as for plants and animals, they argued that resistance mutations arise at random, and the virus acts as selective force that enriches the population for pre-existing cells that happen to be resistant.

At first, Luria and Delbrück struggled to come up with experiments to put this disagreement to rest. Luria tried measuring the proportion of virus resistant cells in growing bacterial cultures, but he seemed to get different results every day. Then, he had a chance encounter with a colleague at a slot machine:

“Not a gambler myself, I was teasing him about his inevitable losses, when he suddenly hit a jackpot, about three dollars in dimes, gave me a dirty look, and walked away. Right then I began giving some thought to the actual numerology of slot machines; in so doing it dawned on me that slot machines and bacterial mutations have something to teach each other.”

-Salvador Luria 1984

Luria realized he could distinguish between the acquired resistance and the random mutation hypothesis using statistics. If resistance were caused by exposure to the virus, it should arise only after the virus was added, at a relatively consistent proportion. But if resistance emerged by mutation at random times, then the proportion of resistant cells would be much more variable, depending on how early the mutation arose. Delbrück calculated the statistical distribution they would expect from random mutations and, to their joy, Luria’s experimental data matched it. They had shown that bacteria had genes that mutate at random, providing fodder for natural selection. Their approach also provided a quantitative approach for studying bacterial mutation rates.

The Luria–Delbrück experiment. (A) If resistance is induced by the presence of the phage in the final, assay plate, independent cultures should yield roughly similar numbers of resistant colonies. (B) If resistance mutations arise spontaneously during the cell divisions prior to plating, the number of resistant colonies will depend on how early in the culture the mutation arose. Image: Madprime via Wikimedia commons

The fruit of this community-building was a transformative molecular understanding of heredity within a remarkably short period. Luria and Delbrück’s phage epiphanies turned out to be science jackpots.

CITATIONS

Bertani, G. (1992). Salvador Edward Luria (1912-1991). Genetics, 131(1), 1. http://www.genetics.org/content/131/1/1

Fischer, E. P. (2007). Max Delbrück. Genetics, 177(2), 673-676. http://www.genetics.org/content/177/2/673

Luria, S. E., & Delbrück, M. (1943). Mutations of bacteria from virus sensitivity to virus resistance. Genetics, 28(6), 491. http://www.genetics.org/content/28/6/491

Murray, A. (2016). Salvador Luria and Max Delbrück on Random Mutation and Fluctuation Tests Genetics 202(2) 367-368; DOI:10.1534/genetics.115.186163  http://www.genetics.org/content/202/2/367

In 1917, amidst the turmoil of the Russian Revolution, a bug-obsessed teenager in Kiev discovered a new species of ladybird beetle in the debris washed up on the banks of the flooding Dnieper River. The following year, he described the species in his first scientific publication. That 18-year old ladybug spotter —Theodosius Dobzhansky— would go on to publish nearly 600 more papers, not just describing species, but exploring what a species is, and how they evolve. In the process, he would establish the paradigm for modern evolutionary biology. In the latest issue of GENETICS, Jerry Coyne introduces Dobzhansky’s 1936 article on the genetics of hybrid sterility in Drosophila as one of the journal’s 100th anniversary Classics.

Dobzhansky’s beetle-collecting hobby morphed into a promising career in entomology, which provided plenty of opportunities for expeditions to remote regions. He was eventually inspired to branch out into genetics after reading reports from Thomas Hunt Morgan and the pioneering geneticists crammed into Morgan’s famous “Fly Room” at Columbia University. In 1927, Dobzhansky traveled to the United States to join Morgan’s hive of fruit fly wranglers.

Staying on with the group through their move to Caltech in 1928, Dobzhansky soon fulfilled his mission of becoming a “splendid Morganoid” by isolating mutants, mapping genes, and studying the mechanics of heredity. But Dobzhansky’s bent towards natural history soon resurfaced. He had been immersed in evolution and population variation since his pre-Drosophila field biology days, which had centered around understanding how a species becomes divided into geographic “races”. Dobzhansky became interested in genetics, he would later say, primarily as a means to understand evolution.

At that time, the field of population genetics had just come into existence. The work of Ronald Fisher, Sewall Wright, and J. B. S. Haldane had shown how Mendelian genetics could be formally united with Darwinian evolution by natural selection. But the first population geneticists described a theoretical framework, not an experimental one; they presented arguments supported mainly by equations. No matter how well reasoned these arguments, this new field lacked tangible evidence from real world populations; the wider community of biologists needed results they could sink their teeth into.

Dobzhansky used his training in cutting-edge genetic analysis to fill this gap and to approach a problem barely addressed by Fisher, Wright, and Haldane: how does one species become two or more? Dobzhansky recognized a unique opportunity for studying speciation using “Race A” and “Race B” of Drosophila pseudoobscura (later reclassified as D. pseudoobscura and D. persimilis). Other Drosophila species were dead-ends for such studies because they produced only sterile hybrids when crossed. In contrast, while male hybrids of Race A and B were sterile, the females were fertile.

Dobzhansky’s 1936 paper used these fertile hybrid females to establish that the causes of hybrid sterility were located on chromosomes (still a matter of debate at the time) and were found at multiple locations across the genome. Eighty years later, his hypothesis on how hybrid sterility can arise in the face of natural selection is still current.

Male Drosophila pseudoobscura. Image by Sarah L. Martin, from J.T. Patterson, Studies in the genetics of Drosophila. III. The Drosophilidae of the Southwest. University of Texas Publications. https://commons.wikimedia.org/w/index.php?curid=28579593

The year this work was published, Dobzhansky also delivered a lecture series that marked the birth of the “Modern Synthesis” of evolutionary biology. Published in 1937 as Genetics and the Origin of Species,” the manifesto wove together disparate threads of twentieth century biology into a unified vision of evolution that was profoundly influential, catapulting population thinking to the forefront of biology. Leading evolutionary biologist Ernst Mayr called its arrival “clearly the most decisive event in the history of evolutionary biology since the publication of the Origin of Species in 1859.” Dobzhansky’s book also helped establish the field of empirical population genetics, with his D. pseudoobscura work demonstrating how questions of evolution could be fruitfully addressed in the field and the lab.

Dobzhansky would also eventually expand his “Genetics of natural populations” series (of which the 1936 paper was the second installment) to a mammoth 43 papers, cementing his experimental program and setting the agenda for generations of empirical population geneticists. He spent many years with his students and collaborators in the field collecting flies to explore their evolutionary and genetic dynamics. He also retained a lifelong affection for ladybugs.

The Ladybugs’ Picnic by The Real Estraya. CC BY-NC 2.0

Read more on Dobzhansky 1936 in Coyne’s introduction and Allen Orr’s 1996 Perspectives article.

Read more on Genetics and the Origin of Species in Jeffrey Powell’s 1987 Perspectives article.

Read more on the influence of Dobzhansky’s early years in The Evolution of Theodosius Dobzhansky.

Read more on 100 years of GENETICS here at Genes to Genomes.

Browse the GENETICS Centennial collection at the journal website, with new content each month.

CITATIONS

Coyne, J. A. (2016). Theodosius Dobzhansky on Hybrid Sterility and Speciation. Genetics, 202(1), 5-7. Doi: 10.1534/genetics.115.184770
http://genetics.org/content/202/1/5

Dobzhansky, T. H. (1936). Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics, 21(2), 113.
http://www.genetics.org/content/21/2/113