From a Kyoto garden to scientific discoveries. 

Since the 17^th century, medaka fish have been bred for their beautiful colors. Shortly after the 1900 re-discovery of Mendel’s laws of inheritance, medaka began to be used for genetic studies. Recessive inheritance of the orange-red (b) and white (r) variants, female-limited appearance of the white phenotype, and an additional allele on the b locus causing variegation (B′) were reported by three professors publishing in Japanese [1–3]. The first medaka article written in English was published in 1921 by Tatsuo Aida (1872-1957). One hundred years after publication of this landmark article in GENETICS, we reflect on Aida’s work and legacy.

When he was four years old, Aida’s samurai father cut off a thief’s arm, which remained a traumatic memory throughout his life. He liked playing in a neighboring farm in Kyoto, where he nursed his interests in zoology. He studied development and phylogeny of Chaetognaths at Tokyo Imperial University, but, due to a conflict with his supervisor, left there before getting his PhD and became a teacher in a high school in Kumamoto, where Soseki Natsume, a Japanese novelist, worked as a colleague. Besides his daily duties, he studied Larvaceans for five years and reported four new species [4]. 

When his father died, Aida returned to Kyoto in 1903. Teaching at Kyoto Higher Technical School, he started genetic studies in 1913 in his own home. He chose medaka because the fish could be bred en masse in small flowerpots, sex could be determined from appearance, and color variants were available from local fanciers. Studies of plants or mice would have required much larger spaces. Supported by Genzo Shimazu (a president of Shimadzu Corporation, where Aida was a counselor for zoological specimens), he constructed a breeding farm at his home consisting of 40 concrete tanks of 60 x 60 x 45 cm and 200 Yuzen dyeing pots of 30 cm diameter x 10 cm depth. Recording weather and air/water temperatures every day, he continued his research until 1954 at an age of 83. 

His results were published as three articles in GENETICS. In the first [5], Aida performed a total of 22 crosses of two generations, recorded body color of 17,281 fish (5,304 of which were also analyzed for sex) and demonstrated:

1. Mendelian-recessive and independent inheritance of the b and r phenotypes, 
2. dominant hierarchy of three alleles on the b locus, 
3. female-limited (i.e., sex-linked) inheritance of the r phenotype, and 
4. recombination between the X and Y chromosome. 

These findings, particularly the fourth, impressed the editor, William Castle, who expressly added a footnote and even paid color charges for Aida’s illustrations (Fig. 1). Richard Goldschmidt, also being impressed by this article, visited Aida’s breeding farm during his stay in Japan in 1924. 

Figure 1: Handpainted illustrations from Aida 1921, showing orange-red, white variegated with black, white, brown-black (wild form), orange-red variegated with black, and bIue-black medaka varieties.

In the second article [6], Aida analyzed nine fish (out of 13,065) with exceptional color and sex phenotypes and found that their descendants (16,385 in total) were variously unbalanced in sex ratios. He discussed this phenomenon from a viewpoint of non-disjunction of the sex chromosomes and suggested physiological differences between the X and Y chromosomes cause “one-sided crossing over”; i.e., dominant (functional) alleles tend to be lost from the Y chromosome rather than gained from the X chromosome. He also described new dwarf mutants, fused and wavy, analyzing their 8,930 inter- or back-crossed siblings.

In the third article, color and sex of 14,958 fish were analyzed [7], and Aida reconsidered the second article from a viewpoint of sex reversal, proposing a new hypothesis for sex determination, i.e., the total sum of “sexual exciters” on the X and Y chromosomes determines sex, and the potency of exciters fluctuates at various degrees (either positively or negatively) depending on inner (e.g., recombination or mutation) or outer (e.g., temperature) conditions. At that period, various opinions on sex determinants existed among researchers (e.g., Goldschmidt, Kosswig, Winge, and Bridges). It should be noted that Aida’s hypothesis was intrinsically correct and could explain sex-determining phenomena in other animals. 

These monumental achievements by Aida clearly showed the usefulness and effectiveness of medaka as a research model. Having a non-academic position, however, Aida had no students or colleagues to take over his studies or fish stocks. It was miraculous that in 1954 when Aida stopped his research due to illness, an undergraduate student at Okayama University, Tetsuro Takeuchi (1932-), visited him and became Aida’s first and last student. Aida proposed Takeuchi study a new body-color mutant, color interfere (ci), which was confusing him with its “interfering” phenotype. Aida died in 1957 and Takeuchi was awarded a PhD degree in 1968 for studying ci. Teaching at a college, Takeuchi constructed a breeding farm at his home and kept the ci and other Aida’s strains until now. Without his devoted efforts for decades, Aida’s fish, including the rare recombinants and new mutants, would not have survived to the present. 

After a long dormancy, the medaka color and sex genetics research that Aida initiated a century ago came into bloom. The color genes (b and ci, but still not r) and the male determinant (the Dmy gene) were unveiled [8–10]. An inbred strain derived from Aida’s collection (Hd-rR) enabled quick sequencing of the whole genome [11]. Knowledge of the molecular bases of color perception and mating preference is accumulating [12, 13]. Takeuchi, on reaching the age of 89, decided to close his farm in this memorial year and deposited all strains he had kept for 67 years to the Medaka bioresource project (NBRP Medaka). He also gifted the authors a pair of Aida’s Yuzen dyeing pots.（Figure 2). The NBRP Medaka was initiated in 2002 and has continued for 20 years. Now over 800 strains and 895000 BAC/Fosmid/cDNA clones and other information are available (https://shigen.nig.ac.jp/medaka/top/top.jsp) [14]. This blooming time may not last long in Japan [15], but the number of medaka researchers has markedly increased worldwide in the last 100 years. We imagine even more medaka researchers will appreciate Aida’s work next century, on the 200th anniversary, hopefully alongside important works from today’s era of medaka research. 

You can learn more about Aida’s life and work in an account from Dr. Takeuchi here. Note that the site can be translated into multiple languages using the Google Translate menu on the page.

Figure 3. Photos of Tatsuo Aida and his medaka nursery, courtesy of Tetsuro Takeuchi and Kiyoshi Naruse.

About the authors:

Shoji Fukamachi, Professor, Department of Chemical and Biological Sciences, Japan Women’s University.

Kiyoshi Naruse, Specially appointed Professor, National Institute for Basic Biology. Head of National BioResource Project Medaka, Japan.

REFERENCES

1. Ishikawa, C., 1913 Dobutsugaku Kogi [Zoological Lectures] Vol.1: pp 372. 
2. Toyama, K., 1916 Ichinino Mendel-Seishitsu ni tsuite. [On some Mendelian characters.] Nippon Ikushugakkai Hokoku [Report of Japanese Breeding Society] 1: 1-9.
3. Ishiwara, M., 1917 On the inheritance of body-color in Oryzias latipes. Mitteilungen aus der medizinischen Fakultät Kyushu 4: 43-51.
4. Aida, T., 1907 Appendicularia of Japanese waters. The journal of the College of Science, Imperial University of Tokyo, Japan 23: 1-25. 
5. Aida, T., 1921 On the inheritance of color in a fresh-water fish Aplocheilus latipes Temmick and Schlegel, with special reference to sex-linked inheritance. Genetics 6: 554-573.
6. Aida, T., 1930 Further genetical studies of Aplocheilus latipes. Genetics 15: 1-16.
7. Aida, T., 1936 Sex reversal in Aplocheilus latipes and a new explanation of sex differentiation. Genetics 21: 136-153.
8. Fukamachi, S., Shimada, A., & Shima, A., 2001 Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka. Nature Genetics 28: 381-385.
9. Matsuda, M., Nagahama, Y., Shinomiya, A., Sato, T., Matsuda, C., et al., 2002 DMY is a Y-specific DM-domain gene required for male development in the medaka fish. Nature 417: 559-563.
10. Fukamachi, S., Sugimoto, M., Mitani, H., & Shima, A., 2004 Somatolactin selectively regulates proliferation and morphogenesis of neural-crest derived pigment cells in medaka. Proceedings of the National Academy of Sciences of the United States of America 101: 10661-10666.
11. Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., et al., 2007 The medaka draft genome and insights into vertebrate genome evolution. Nature 447: 714-719.
12. Okuyama, T., Yokoi, S., Abe, H., Isoe, Y., Suehiro, Y., et al., 2014 A neural mechanism underlying mating preferences for familiar individuals in medaka fish. Science 343: 91-94.
13. Shimmura, T., Nakayama, T., Shinomiya, A., Fukamachi, S., Yasugi, M., et al., 2017 Dynamic plasticity in phototransduction regulates seasonal changes in color perception. Nature Communications 8: 412.
14. Sasado, T., Tanaka, M., Kobayashi, K., Sato, T., Sakaizumi, M. and Naruse, K. 2010  The National BioResource Project Medaka (NBRP Medaka), An integrated bioresource for biological and biomedical sciences. Experimental Animals 59, 13-23.
15. Fuyuno, I., 2017 What price will science pay for austerity? Nature 543: S10-S15.

New genetic data help explain the rapid adaptation of stickleback fish that invaded freshwater habitats in the 1960s.

In 1964, an earthquake shook the islands off the coast of Alaska, transforming the landscape as underwater terraces were thrust above the surface. From this cataclysmic event emerged a series of freshwater pools that became a natural laboratory in which to study evolution in action. A new report in GENETICS takes a closer look at how this sudden environmental shift influenced the adaptation of one particular inhabitant.

On the Alaskan islands, the newly-formed freshwater ponds were colonized by interlopers from the sea: marine stickleback fish. These ocean dwellers quickly adapted to the new environment, acquiring many traits not unlike those found in other, much older stickleback populations that are specialized for living in freshwater. Evolution at this dramatic scale is normally thought to take thousands of years rather than a half-dozen decades, which lead the authors to wonder how such rapid adaptation occurred. “It’s a great natural evolutionary experiment,” said Susan Bassham, one of the lead authors of the study.

Senior author William Cresko and his group have been studying sticklebacks (Gasterosteus aculeatus) for decades, and for good reason—the fish are an excellent model system for understanding adaptation and evolution.

“When our collaborator Frank von Hippel told us about his work surveying possible new stickleback habitats, including on these earthquake islands, we got excited. We immediately wanted to look at the phenotypic and genomic changes that might have happened after the island was uplifted and these new ponds were invaded by marine stickleback,” said Cresko. “This started a long and productive collaboration between our groups.”

Bassham explained that threespine stickleback have colonized a number of diverse environments over the millennia that the species has existed: as well as marine and freshwater stickleback varieties, there are sticklebacks that spend some time in both environments, much like salmon. Despite adapting to such varied habitats, all of these fish are still one species.

Marine (top) and freshwater (bottom) threespine stickleback fish. Photo by Emily Lescak.

To understand the genetics underlying the rapid adaptation of stickleback, the authors genotyped fish from three stickleback populations: those from the newly formed pools, those from other freshwater populations, and marine fish. They used restriction site-associated DNA sequencing, or RAD-seq, a technique that their lab has helped pioneer; this method allows for the rapid identification of genetic markers by sequencing regions of the genome adjacent to restriction sites. Cresko explained that RAD-seq’s focus on limited regions of the genome makes it more economical than other techniques, allowing for the acquisition of a complete genomic “snapshot” for thousands of individual fish. “This breadth of biological sampling was needed to answer some key population genomic questions about these fish,” said Cresko.

Using this approach and new computational tools developed in collaboration with second lead author Julian Catchen, the group identified several regions of the stickleback genome that vary significantly between the ancestral marine stickleback populations and those from the new freshwater pools.

Intriguingly, the changes that they found in the young freshwater populations on the Alaskan island were virtually identical to the changes seen in freshwater stickleback populations that have existed in other locations for thousands of years. They also found some of these same freshwater-adapted haplotypes scattered in the genomes of marine fish as far away as coastal Oregon—but at much lower frequencies.

These results suggest that the rapid adaptability of stickleback is largely attributable to standing genetic variation in the marine population. When environmental pressures change, the existing freshwater-adapted alleles face powerful selection and become prevalent. Although this idea was proposed a while ago, the current GENETICS study had the power to detect and accurately measure the frequency of these alleles in marine populations.

The similarities among different freshwater populations is also striking because those populations are otherwise genetically indistinguishable from marine stickleback. “When you look at the regions of the genome that are not divergent between ocean and freshwater and do a phylogeographic study, there’s no population structuring at all,” said Cresko. The genomes are so similar, he explains, that the only parts that differentiate them are the dramatic regions related to adaptation. “There’s very little  neutral divergence; it’s nearly all due to natural selection.”

Ironically, this fascinating finding has posed something of a technical stumbling block for learning more. Delving deeper into the precise genetic differences between freshwater and marine sticklebacks would usually be done with a genome-wide association study, but such studies require distinguishable variation between populations. In other words: these fish are evolving so quickly that it’s impossible to control for population structure.

That doesn’t mean these questions can’t be answered, though. Bassham, Cresko, and their colleagues are currently studying other wild stickleback populations to identify genes that might underpin their ability to rapidly adapt to freshwater conditions, and they are creating new models to experimentally validate those findings in the laboratory.

CITATION:

Repeated selection of alternatively adapted haplotypes creates sweeping genomic remodeling in stickleback

Susan Bassham, Julian Catchen, Emily Lescak, Frank A. von Hippel, William A. Cresko

Genetics July 2018 209: 921-939; https://doi.org/10.1534/genetics.117.300610
http://www.genetics.org/content/209/3/921

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Watch presentations from the conference, including talks from Katie Peichel and Jonathan Pritchard.

Now that the dust has settled from the whirlwind of the first ever standalone GSA Population, Evolutionary, and Quantitative Genetics Conference (PEQG18), we’re delighted to be able to share the audio and synched slides from the Keynote and Crow Award sessions.

We’re gratified too that attendees got so much of value from the conference. Many have approached GSA staff and the conference organizers with rave reviews of their experience, and, despite the usual growing pains of a new conference, the results from the attendee survey have also been overwhelmingly positive.

We’re excited to incorporate some of the lessons we’ve learned into planning the next PEQG. It will be held April 22–26, 2020 in the metro Washington, DC, area at The Allied Genetics Conference (TAGC20). PEQG will join the C. elegans, Drosophila, mouse, Xenopus, yeast, and zebrafish research communities for a mix of community-specific and cross-community sessions.

Stay tuned for more announcements on the upcoming conference and for several more PEQG18 blog reports in the coming weeks. Enjoy the talks below!

PEQG18 Keynotes

Jonathan Pritchard Stanford University/HHMI

Omnigenic Architecture of Human Complex Traits

Catherine Peichel University of Bern

Genetics of Adaptation in Sticklebacks

Trudy Mackay North Carolina State University

Context-Dependent Effects of Alleles Affecting Genetic Variation of Quantitative Traits COMING SOON

Finalists for the 2018 Crow Award for Early Career Researchers

Amy Goldberg UC Berkeley

A mechanistic model of assortative mating in a hybrid population

Emily Josephs UC Davis

Detecting polygenic adaptation in maize

Jeremy Berg Columbia University 

Population genetic models for highly polygenic disease

Katherine Xue University of Washington 

Evolutionary dynamics of influenza across spatiotemporal scales

Alison Feder Stanford University 

Intra-patient evolutionary dynamics of HIV drug resistance evolution in time and space

Emily Moore North Carolina State University 

Genetic variation at a conserved non-coding element contributes to microhabitat-associated behavioral differentiation in Malawi African cichlid fishes

Videos

Jonathan Pritchard 

[youtube https://youtu.be/H18k55ruCOY&w=500&rel=0]

Catherine Peichel

[youtube https://youtu.be/QRCcLixjUtc&w=500&rel=0]

Amy Goldberg 

[youtube https://youtu.be/kccUNkF7SgY&w=500&rel=0]

Emily Josephs 

[youtube https://youtu.be/CxQOrK9h6D4&w=500&rel=0]

Jeremy Berg

[youtube https://youtu.be/HqA1H24LPZc&w=500&rel=0]

Katherine Xue

[youtube https://youtu.be/fTdaAwqdt0k&w=500&rel=0]

Alison Feder

[youtube https://youtu.be/ntM0448h2lA&w=500&rel=0]

Emily Moore

[youtube https://youtu.be/aX4_HS0K1kA&w=500&rel=0]

David Kingsley

The Genetics Society of America Medal is awarded to an individual for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly-meaningful contributions to modern genetics, exemplifying the ingenuity of GSA membership.

The 2017 recipient is David M. Kingsley, whose work in mouse, sticklebacks, and humans has shifted paradigms about how vertebrates evolve. Kingsley first fell in love with genetics in graduate school, where he worked on receptor-mediated endocytosis with Monty Krieger. In his postdoctoral training, he was able to unite genetics with his first scientific love — vertebrate morphology. He joined the group of Neal Copeland and Nancy Jenkins, where he led efforts to map the classical mouse skeletal mutation short ear. Convinced that experimental genetics had a unique power to reveal the inner workings of evolution, Kingsley then established the stickleback fish as an extraordinarily productive model of quantitative trait evolution in wild species. He and his colleagues revealed many important insights, including the discoveries that, major morphological differences can map to key loci with large effects, that regulatory changes in essential developmental control genes have produced advantageous new traits, and that nature has selected the same genes over and over again to drive the stickleback’s skeletal evolution. Recently, Kingsley’s group has been using these lessons to reveal more about how our own species evolved.

An abridged version of this interview was published in the December 2017 issue of GENETICS.

What inspired you to become a scientist?

My dad died of cancer when he was 34. As a little kid I was aware that you don’t know how long you have left, and I grew up wanting to make sure I spent the time I have doing something interesting and important. I thought that tackling age-old mysteries about life’s origin and mechanisms was a good way to spend my life.

What did you learn from your first mentors?

I was a kid who loved dinosaurs and skeletons. That interest was nurtured by a great high school teacher, Jack Koch at Roosevelt High School in Des Moines, Iowa. I dedicated my PhD thesis to him.  In his advanced biology class we memorized the names of every bone and muscle in the cat and human skeleton. A lot of people hated it, but I loved it because you could see so much about the function and lifestyle of the organisms from the size and shapes and patterns of bones. I’m lucky because I still work on skeletal anatomy and evolution!

In graduate school, I fell in love with the power of genetics. I had a set of teachers at MIT, including David Botstein and Monty Krieger who helped me learn that with genetics you didn’t have to assume anything about the answer. You didn’t have guess you were looking for a particular type of molecule or anything like that.  Genetics was an algorithm that would take you to the key components controlling a biological system no matter what they were. I saw how genetics had the power to dissect old, hard problems like cell cycle and development, which had been mysteries when I first came across them in biology class.

Why did you choose to work on the short ear gene?

As a postdoc, I got to bring together my love of genetics with my love of vertebrate morphology — I went to a mouse genetics lab where they were among the first to walk down chromosomes and identify the molecular basis of classic mouse mutations. In graduate school, I had heard a great seminar from David Hogness from Stanford, who was carrying out some of the first chromosome walks to the homeotic genes in Drosophila. Here was someone studying one of the most interesting morphological problems you could imagine: how to turn one body part into another. He was turning morphology into genes and DNA and sequence and development, and I thought that was electrifying. I could see that mouse would go through the same revolution that had come to fly.

Vertebrate genetics takes a long time, so you should pick your problem carefully. I didn’t want to pick something that was better studied in bacteria, yeast, or powerful invertebrate systems. The skeleton was perfect; it’s the defining feature of vertebrates. It also plays such an important role in animals’ external appearance that many classic mutants had already been picked up in simple morphological screens.

Near the end of grad school, I took out from the library “Genetic variants and strains of the laboratory mouse” and read the whole book—one mutant after another. We decided to go for the short ear gene, which had been worked on for decades by the person who put that wonderful book together—Margaret Green from the Jackson Labs. She was both a very perceptive scientist and a great editor and collator. So, I felt like I was dipping into one of her favorite mutations, but there were also practical reasons to choose short ear. After World War II there had been a lot of interest in the effects of radiation on the mammalian germline, and there were two big mouse forward mutation experiments in the UK and US. They both used a test strain carrying seven homozygous recessive mutations with visible phenotypes. These were six pigment mutations and short-ear.

Millions of wild-type mice were mutagenized and crossed with the test strain to measure the rate of recovering new alleles at any of the seven loci.  As a result, there were lots of newly induced mutations, including a whole set of deficiency chromosomes that took out both short ear and one of the closely linked pigmentation loci.  We essentially had the equivalent of a Drosophila genetics playground for this particular region of the mouse genome! We would be able to orient ourselves using the same kind of deletion breakpoints that Hogness had been using in flies. And my postdoc advisors Nancy Jenkins and Neal Copeland had already found a retroviral insertion that caused the closely-linked dilute coat phenotype, so we even had a good entry point that was within a millimorgan of the short ear gene. That was one of the reasons why I chose short ear out of the 150 or so classic skeletal mutations.

What did you learn from the short ear project?

It took about five years to do the chromosome walk in the region, and I was already an assistant professor by the time we eventually isolated the gene for this classic skeletal trait. But it was incredibly gratifying. The gene controlling skeletal morphology encoded a secreted signal already named a “bone morphogenetic protein” (BMP).

It had been named by biochemists who found that if you took an adult bone and ground it into powder and injected it under the skin of an animal, there was some magic ingredient that could generate a brand new bone at the site of implantation. And if you put the implant in the shape of a circle, for example, it would come out as a circular bone, so you could even see that the pattern in which the signal was expressed controlled something about the rough shape and morphology of the bone that resulted.

The short ear mice provided the first genetic evidence that BMPs were the endogenous signals that vertebrates were using to set the form and pattern of skeletal structures. If you had a mutation in one of the BMPs you very selectively removed the aspect of skeletal morphology controlled by that particular member of the BMP family. The short ear deficiency strains turned out to be important because they included 29 alleles at the short ear locus, of which half a dozen were regulatory mutations disrupting the flanking DNA. These later helped us to identify a whole series of modular, remarkably specific enhancers controlling different aspects of skeletal morphology.  We think of them as anatomy elements because they might control expression for example in just the ribs, and maybe only in a 90-degree sector on the outside of the ribs. There would be a different controller for the inside of the ribs, allowing you to tune the overall shape. For someone originally interested in those beautiful piles of bones, to be able to break down their shapes into the expression patterns of secreted signaling molecules was an incredibly satisfying answer.

Why did you choose sticklebacks?

If you can find a way to turn old biological problems into genetics problems, then you can often find the answers to even intractable questions. A brave postdoc Katie Peichel and I spent a really fun summer in 1998 figuring out how to turn classic evolutionary questions into a genetics problem. We wanted to identify the number and type of genes and mutations that control species differences in nature. The trick was to figure out some way to cross different species, which sounds paradoxical because one definition of species is that they are reproductively isolated. The loophole is that reproductive isolation can occur through either postzygotic or prezygotic mechanisms. Postzygotic mechanisms include inviability and sterility, which are obviously hard to overcome.  However prezygotic isolating mechanisms are things like behavioral or mechanical incompatibilities in mating, which can be overcome using artificial fertilization in the laboratory.

We went around talking to biologists, reading all kinds of books, looking for very young species with recently evolved dramatic skeletal differences that could still be crossed in the laboratory. We looked at wild mice and birds, but the thing that was attractive about fish was the clutch sizes tended to be very large. With a bird system, nests might have a couple of eggs, while a fish nest would have hundreds of thousands. For using a genetic approach, especially for mapping complex traits in the wild, the bigger the family size the better.

Somewhere in the middle of that summer, I found a great book chapter by Mike Bell of Stonybrook University talking about all the cool skeletal traits that had evolved in sticklebacks after the end of the last Ice Age. There was a remarkable previous literature on stickleback morphology, ecology, and behavior in new freshwater streams and lakes. And new forms had evolved not just once but thousands of times. That was because their main ancestors were migratory like Salmon and would come from the ocean into coastal areas to breed every spring. So, when the glaciers melted and lots of new lakes and streams formed, it generated all these brand new, empty environments that were colonized by sticklebacks. It was like nature had set off a replicate series of evolution experiments 10,000 years ago, producing new forms over and over again. That was beautiful to us because not only could we figure out how evolution worked in a particular lake or stream, but the system as a whole would make it possible to tell whether the mechanisms used in evolution have any repeatability to them. Is it going to be different every time? Or are there rules and principles that underlie the way organisms adapt to new conditions.

What did you learn about repeatability of evolution?

I had a debate with a fellow faculty member when I started the project because he thought the project was not worth doing. Firstly, because evolution is complicated, and if it’s controlled by lots of genes with tiny effects you’ll never find anything. But his killer argument was: even if you could do it, he wouldn’t care. And his reason was related to repeatability. He figured we would knock ourselves out trying to figure out what happened in one lake and all we would find would be historical minutiae that accumulated in that particular location, and that if you then studied a second place you’d get a different answer and then a third would give you a different answer again. It would just turn out to be postage stamp collecting, and there wouldn’t be any generality.

At the time, we didn’t have evidence one way or another. But my best reply was: how do you know? That was the great thing about genetics – it would tell you the answer no matter what the answer is. We could have learned that all the traits are controlled by tiny effects that are almost unmappable. And we could have gotten the answer that all those little tiny effects are distributed across the genome in a way that is just due to history. But that’s not what the genetics showed.

We started crossing these fish with huge skeletal differences. And by huge, I mean thirty-fold differences in the number of plates along the anterior-posterior body axis, or complete presence or absence of an entire fin, or doubling the number of teeth, or black fish vs. white fish, the kind of dramatic changes you would normally see between different genera of wild species. And we found that while none of these evolutionary differences were simple Mendelian traits, they typically had genetic architectures with one or two chromosome regions showing very large effects, perhaps explaining up to three-quarters of the variation, along with a handful of other modifier regions controlling five to ten percent of the variance. So, the genetics was manageable.

And if you compared the results from crosses done in different lakes, it tuned out the very same chromosome regions were being used over and over again in different populations. So even before we identified the genes, we knew this was going to be both interesting and doable.

We’ve subsequently taken lots of traits down to genes and molecules. We’ve found that key signals and transcription factors that developmental biologists have been studying for years turn out to be the same molecules that nature is using to redesign anatomical features.  And we’re finding the reuse isn’t just from lake to lake, it’s from organism to organism. For example, although we didn’t set out to test any particular candidate genes, the genetic data showed us that some of those stickleback skeletal traits are controlled by the same kinds of bone morphogenetic proteins that we found in mouse.

How does the stickleback work all connect with your studies of human evolution?

We’re interested in why particular genes are reused throughout evolution, and we’re also interested in applying the patterns we’ve found in sticklebacks to the evolution of ourselves. We’ve found that classic traits in people, like blond hair color, or height, are evolving in humans using the same types of key control genes and regulatory mutations we have found in fish. And unlike rare genetic diseases, there are derived alleles at these human loci where a large fraction of the population carry the selected version. So rather than studying diseases that affect 1 in 100,000 people, it’s been really interesting to study variants that, because they have been subject to selection, are now present in billions of people. In some cases, the selected alleles may actually increase susceptibility to late-onset diseases like cancer or arthritis. It’s not a huge effect, maybe 1.3 to 1.8-fold. But when an allele slightly increases risk of a disease and is carried by a few billion people through selection, then suddenly you find an awful lot of the burden of a common human disease is controlled by our own evolutionary history.

We’re now going back and forth between humans and the patterns we see in fish. We thought it might take us 50 years to get enough examples to pull out general principles, but it turned out to be much faster than that. We now have a whole bunch of genomic regions—maybe 200—that have been repeatedly selected in stickleback. We’ve been able to answer how often evolution uses coding versus regulatory genes. That question was debated a long time. However, we can now say empirically the answer is both, but 85% of the time it’s regulatory and 15% coding. When I say there’s things we learned from fish that we apply to other organisms, we’re already applying things like that 85 percent rule in our human studies. If regulatory changes are by far the most common way to preserve viability and fitness when sticklebacks are evolving under a whole range of fitness constraints. then I think the things that make us human are likely to also be regulatory. So, we can prioritize our human work using the rules we learned from repeated evolution in stickleback.

What’s the best advice you ever received?

Genetics can be used to study anything.

What advice would you give to younger scientists?

Genetics can be used to study anything! I fell in love with genetics watching it be used by people who loved it. It’s such an honor to receive this award because I feel like I’m continuing that tradition— especially since it has previously been given to many of my own teachers and heroes in the field. I hope my students will also be convinced of the power of genetics and will use it to study their own favorite problems as well.

David Kingsley

We are pleased to announce that David Kingsley, PhD is the 2017 recipient of the GSA Medal for outstanding contributions to the field of genetics in the past 15 years. His experimental work has shifted paradigms about how the physical traits of vertebrate organisms evolve. Kingsley is a Professor and Howard Hughes Medical Institute Investigator in the Department of Developmental Biology at the Stanford University School of Medicine.

“David Kingsley has helped transform evolutionary theory into experimental genetics, and is identifying the genetic foundation of vertebrate structure,” says Jasper Rine, PhD (University of California, Berkeley).

The three-spined stickleback is a small fish species divided into many naturally isolated groups that vary in appearance and skeletal structure. Because individuals from these separately evolving populations are still able to produce fertile offspring, geneticists can use powerful breeding experiments to trace the molecular details of this species’ evolution. When Kingsley began his work on sticklebacks in 2001, prevailing ideas about how morphological traits like skeletal structure evolve emphasized the accumulation of small changes in a large number of genes controlling a particular trait. Kingsley and his team used the three-spined stickleback to test this theory using quantitative trait mapping. They constructed a genetic map and then analyzed the number, type, and magnitude of genetic effects on features such as body armor and pelvic and dental structure.

The remarkable result of this work was that much of the trait variation between different natural populations could be mapped to a few major genes, with other loci modifying the contribution of the major loci. Strikingly, reintroduction of single major genes found by genetic mapping could reverse evolutionary differences found in nature. And even more stunningly, the same genes were implicated as major contributors to similar traits that arose independently in many different populations. “Given the chance to rewind time and play the selection again, evolution largely used the same genes to shape these traits, illustrating the limited trajectories of evolutionary change,” Rine explains.

Three-spined stickleback. Photo: Flickr user Jack Wolf. Shared under a CC BY-ND 2.0 license.

Kingsley has continued his investigation into the underpinnings of vertebrate evolution by expanding this work into human traits. He and collaborators have searched the human genome for the same types of regulatory mutations that predominate when sticklebacks diversify in nature. Their comparative genomic studies have identified hundreds of regulatory changes that distinguish humans from our closest relative, chimpanzees. By recreating individual mutations in animal models, Kingsley is again testing the importance of particular genetic changes. His work has already shown that classic blond hair color in humans has evolved through a regulatory mutation in the same key developmental signaling gene that also controls repeated pigment evolution in sticklebacks. Regulatory changes near other key developmental genes may contribute to many other human traits, including distinctive skin, skeletal, and brain changes that have evolved in the human lineage.

The Genetics Society of America Medal is awarded to an individual member of the Society for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics within the recent history of the field; awardees exemplify the ingenuity of the GSA membership.

To learn more about the GSA awards, and to view a list of previous recipients, please see http://www.genetics-gsa.org/awards.

#TAGC16 Shorts are brief summaries of presentations at The Allied Genetics Conference, a combined meeting of seven genetics research communities held July 13-17, 2016 in Orlando, Florida.

Elbows, knuckles, and the other synovial joints in your body are mobile marvels of evolution. These joints allow a huge range of possible movements thanks to the presence of a cavity between the articulating bones that is lined by smooth cartilage and filled with a lubricating fluid. This elaborate structure, however, is highly susceptible to wear-and-tear, and inflammation of synovial joints leads to painful arthritis. Results presented at The Allied Genetics Conference last week reveal that, contrary to a widely held view, fish have synovial joints. The results reveal that these joints evolved before the last common ancestor of all bony vertebrates, opening up a promising new avenue for arthritis research.

Synovial joints were widely thought to have evolved as fish left the water and became tetrapods (amphibians, reptiles, birds, and mammals), and to be absent in ray-finned fish, the largest taxonomic group of vertebrates. Joanna Smeeton (University of Southern California) presented evidence for the hallmarks of synovial joints in the jaw hinge and pectoral fin joints of zebrafish, three-spine stickleback, and spotted gar, which are three ray-finned fish species separated by hundreds of millions of years of evolution.

These fish joints are freely movable and surrounded by a joint capsule, with articulating bones separated by a cavity. The cells lining the cavity express a proteoglycan known to lubricate synovial joints. Mutating the gene encoding this lubricant caused zebrafish to develop progressive deterioration of the jaw and fin joints, similar to the effect on mouse and human synovial joints of mutations in the homologous genes. Smeeton hopes a zebrafish model of synovial joint development and degeneration could provide important insights into arthritis and how this widespread chronic disease might be treated.

Adult zebrafish jaw joint stained with alcian blue (cartilage) and alizarin red (bone). Courtesy Joanna Smeeton.

TAGC Program Number Z589:

Fish synovial joints as new models for joint development and disease.

Joanna Smeeton¹ Amjad Askary ¹ Sandeep Paul ¹ Simone Schindler¹; Ingo Braasch^2,3; Nicholas A. Ellis⁴; John Postlethwait²; Craig T. Miller⁴; Gage Crump¹

¹University of Southern California, Los Angeles, CA; ²University of Oregon, Eugene, OR; ³Michigan State University, East Lansing, MI; ⁴University of California, Berkeley, CA.

Further reading: https://elifesciences.org/content/5/e16415

The relative contributions of nature and nurture to behavior are a perennial source of dispute. That there is a genetic component is clear, but frustratingly, only a handful of specific genes are known to directly influence behavior in vertebrates. In the June issue of GENETICS, Greenwood et al. describe how they pinned down one of these elusive genes.

From their prior work, the researchers knew that in threespine stickleback fish, the ability and motivation to school—a complex behavior—is associated with variation in a few regions of the genome. One of those regions includes the gene Eda, which affects the development of sensory organs that the fish use to detect movement in the water near them. Sensing these vibrations is crucial for fishes’ ability to perceive other fishes’ swimming patterns, so the researchers wondered whether the Eda gene might also affect schooling behavior.

A stickleback with sensory cells of the lateral line (neuromasts) stained. Courtesy of Abby Wark.

To test this, the researchers took advantage of the fact that sticklebacks that live in the open water school more frequently and in a more coordinated fashion than do benthic sticklebacks, which live in highly vegetated habitats. Since the open-water sticklebacks express higher levels of Eda than do their benthic brethren, the researchers modified the genome of benthic sticklebacks so that they carried a continuously active Eda gene.

The researchers needed an objective measure of schooling behaviors, so they used a unique assay previously developed in their lab. In the assay, a stickleback is placed in a tank with several robotic fish, and when the robots begin to move, the stickleback attempts to school with them. This allows the researchers to quantify both the fish’s willingness to school and its ability to maintain a body position parallel to the robots, which is a proxy for its schooling skill.

A stickleback joins a school of robotic fish. Courtesy of Anna Greenwood.

Using this assay, the researchers found that the transgenic sticklebacks’ schooling ability was more like that of the open-water sticklebacks, blowing the wild type benthic sticklebacks out of the water. The transgenic fishes’ willingness to join the model school was not affected, as measured by how long they took before beginning to swim in tandem with the robots. This suggests natural variants of Eda directly affect sticklebacks’ schooling behavior, making it one of the few genes of its kind known in vertebrates. Future research targeting the mechanisms of Eda and genes like it could uncover more clues about the genetic underpinnings of behavior.

CITATION:

Greenwood, A.; Mills, M.; Wark, A.; Archambeault, S.; Peichel, C. Evolution of Schooling Behavior in Threespine Sticklebacks Is Shaped by the Eda Gene.
GENETICS, 203(2), 677-681.
DOI: 10.1534/genetics.116.188342
http://www.genetics.org/content/203/2/677.long

A fisherman trying to catch rainbow trout (Oncorhynchus mykiss) needs the right tools: proper flies, a strong rod, and a little bit of know-how. A scientist trying to understand the genetic population structure of rainbow trout in the Fall River watershed of northern California also relies on a trusty toolkit – albeit a very different one.

This scientist might turn to massively parallel sequencing, but for most researchers, sequencing the full genome of a large group of individuals is prohibitively expensive. More economical techniques use only a subset of the genome for sequencing, performing sequence capture or reducing genomic complexity through restriction-site based techniques. However, each of these techniques still has drawbacks. Sequence capture library preparation is expensive and has low multiplexing capacity. Restriction-site associated DNA (RAD) sequencing is relatively fixed to the number and location of loci that can be sequenced.

In this month’s issue of GENETICS, Ali et al. describe a new method for analyzing large groups of individuals with a quick, cost-effective, and flexible technique; they demonstrate its effectiveness by exploring genetic diversity in rainbow trout. They introduce an improved protocol for generating RAD markers as well as a new genotyping method called Rapture (RAD capture). Their updated RAD protocol outperforms the older version by reducing the number of clonal sequencing reads produced, which leads to higher coverage per locus.

The authors designed RAD tags specific to rainbow trout and used them to capture DNA for sequencing, eventually producing a single library containing samples from 288 individuals. This Rapture method allowed for high coverage with minimal sequencing at RAD loci and allowed the researchers to separate the fish into two distinct populations based on where they originated. This result was unexpected for such a small watershed and suggests that natal homing – the return of an animal to its birthplace to reproduce – plays an important role in resident populations of O. mykiss.

Innovative updates to existing sequencing methodologies continue to move the field forward, giving scientists the ability to dive deep into genomes and to avoid shallow coverage.

CITATION
Ali, O.A., O’Rourke, S.M., Amish, S.J., Meek, M.H., Luikart, G., Jeffres, C., Miller, M.R. 2016. RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping. GENETICS, 202(2): 389-400. doi: 10.1534/genetics.115.183665 http://www.genetics.org/content/202/2/389

For Lake Whitefish, history has repeated itself. Across the St. John River region that spans Québec and Maine, these freshwater fish have continually evolved in the same way. Within the many individual lakes in this area, Lake Whitefish have diverged into two groups differentiated by size and body shape. These two groups, known as “dwarf” and “normal,” give geneticists a powerful model to study parallel evolution.

In the July issue of G3, Laporte et al. clarify the genetic mechanisms that underlie parallel phenotypic changes in these Lake Whitefish populations. Do parallel phenotypes indicate genetic parallelism, in which body shape in each population evolved via the same genetic mechanism? Or could such changes in morphology occur through multiple genetic routes?

In five different lakes, the authors found dwarf individuals had larger eyes, more slender bodies, and longer tails than their normal counterparts. Normal and dwarf Lake Whitefish use different ecological niches in each lake: normal species feed on benthos while dwarf species feed on zooplankton. The differences between the two morphological types of whitefish match the traits expected to be selected for by their given niches.

With phenotypic differences confirmed, the investigators next explored how many genes are involved in determining body shape. The authors identified 138 quantitative trait loci (QTL) underlying this variation, with each shape trait associated with an average of five QTL. This finding suggests many genes influence body shape, in line with the theory that rapid adaptation of complex traits involves simultaneous selection at many loci.

Then, the authors tested for genetic parallelism using a method that accounted for multiple genes involved in the trait. This method tested for selection on the identified QTL and revealed genetic parallelism in three of the five lakes. The remaining two lake populations each showed no evidence of genetic parallelism with the other lakes. This supports the conclusion that those three lake populations followed the same genetic routes as they diverged, while the other two each underwent unique mechanisms to reach the same phenotypic differentiation. Laporte et al. therefore conclude that both genetic parallelism and multiple genetic routes underlie the parallel evolution of body shape in the Lake Whitefish.

CITATION:

Laporte M, Rogers SM, Dion-Côté A-M, Normandeau E, Gagnaire P, Dalziel AC, Chebib J, Bernatchez L. (2015) RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs. G3, 5(7): 1481-1491 doi:10.1534/g3.115.019067 http://www.g3journal.org/content/5/7/1481.full

Since the 17th century, the tiny medaka fish that dart through rice paddies in Japan have been bred as living ornaments. Though in the wild they are a nondescript mud color, medaka occasionally turn up in flashier mutant varieties — orange-red, pearlescent white, black splotched — that were much prized by generations of fish fanciers. Around 1913, medaka color varieties caught the attention of zoologist Tatuo Aida.

Aida was interested in a hot new field that was beginning to be called “genetics.” On the heels of emerging reports that medaka color traits followed Mendelian laws of inheritance, Aida started breeding the fish at his Kyoto home. He filled the garden with a network of canals to supply freshwater to his medaka nursery, and while World War I raged, he meticulously mated fish and recorded the colors of their offspring.

The results, published in 1921 in GENETICS, revealed that medaka had an XY sex determination system and that a gene linked to orange coloration was carried on the Y chromosome (one of the first examples of Y-linked inheritance). Most significantly, Aida demonstrated that the X and Y chromosomes could exchange genetic material via crossover, contrary to results from the best known XY system at the time, Drosophila.

Fast-forward nearly a century, and a Genetic Toolbox Review in the April issue of GENETICS reveals how far medaka research has come since Aida published the fruits of his home-grown experiments.

Left: Mutant strain lacking pigmentation, allowing visualization of internal organs in adults; Center: In vivo analysis of medaka embryo somites differentially labeled with the Gaudí brainbow toolkit; Right: In vivo imaging of neuronal GFP expression from a brain-specific enhancer. Autofluorescent pigment cells are red. All images from Kirchmaier et al.

Aida laid the groundwork for generations of Japanese medaka geneticists, along with physiologists, embryologists, and ecotoxicologists. During the last few decades, biologists outside Japan have taken increasing advantage of the model’s experimental benefits, including its small genome, ready access to wild stocks, and a high tolerance of inbreeding. The ease of generating inbred lines makes medaka an important complement to the widely used zebrafish model, which can be maintained only as polymorphic lab stocks. An international collaboration of researchers is now constructing a panel of more than 200 inbred lines sourced from a single wild population, which will serve as a powerful resource for high resolution genetic mapping of complex traits.

Much of the genetic technology developed for zebrafish has also been adapted for medaka. Today’s researchers can look up a gene in the medaka reference genome, manipulate it with the new genome editing tools TALENs, zinc finger nucleases, or CRISPR, light up individual cells with brainbow labeling technology, and perform live-imaging of adult fish in transparent mutants. Such tools are helping an international research community explore important questions in genomics, evolution, and human disease, just over a century since Aida began investigating the mysteries of heredity from his Kyoto garden.

Tatuo Aida in his garden, photographed by the late Toki-o Yamamoto, another pioneering medaka researcher. Photo courtesy of Kiyoshi Naruse, who received it as a gift from Tokihiko Yamamoto.

CITATIONS:

Aida, T. (1921). On the inheritance of color in a fresh-water fish, Aplocheilus latipes Temmick and Schlegel, with special reference to sex-linked inheritance.
Genetics, 6(6), 554 http://www.genetics.org/content/6/6/554

Kirchmaier, S., Naruse, K., Wittbrodt, J., & Loosli, F. (2015). The Genomic and Genetic Toolbox of the Teleost Medaka (Oryzias latipes).
Genetics, 199(4), 905-918
doi:10.1534/genetics.114.173849 http://www.genetics.org/content/199/4/905.full

Spivakov, M., Auer, T. O., Peravali, R., Dunham, I., Dolle, D., Fujiyama, A., Toyoda, A., Aizu, T., Minakuchi, Y., Loosli, F., Naruse, K., Birney, E., & Wittbrodt, J. (2014). Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
G3: Genes| Genomes| Genetics, 4(3), 433-445
doi:10.1534/g3.113.008722 http://www.g3journal.org/content/4/3/433.full