Revisiting Coyne and Orr 1989

In a paper published in Evolution in 1989, Jerry Coyne and Allen Orr showed, through a meta-analysis of 119 pairs of closely-related Drosophila species at different stages of speciation, that mating discrimination, and sterility or inviability of hybrids, gradually increase with time since speciation. Coyne and Orr also demonstrated important differences in patterns between allopatric and sympatric pairs: in the former, mating discrimination and postzygotic isolation evolve at similar rates, while in the latter, mating discrimination is seen much before postzygotic isolation appears. Twenty-eight years after the paper was published, I spoke to Jerry Coyne about his motivation to carry out this study, the collaboration with Allen Orr and what we have learnt since about speciation in Drosophila.

Citation: Coyne, J. A., & Orr, H. A. (1989). Patterns of speciation in Drosophila. Evolution, 43(2), 362-381.

Date of interview: 25 February 2017 (via Skype)

HS: You were interested in Drosophila and the genetics of Drosophila right from the time of your PhD. What was the motivation for this particular piece of work?

Jerry Coyne: Well, the motivation is implicit in the paper. I was interested in the genetic basis of reproductive isolation in Drosophila. I realized that there were a lot of data out there on the genetic distances between different closely-related species of flies as measured by electrophoresis, and from reading a lot of the old literature – Patterson & Stone (1949, Univ. Texas Publ. 4920: 7-17), and The Genetics and Biology of Drosophila book series ‑that there is an immense amount of data on the crossability of flies, their sexual isolation, the sterility and viability of hybrids. And it came to me one day in Maryland – I can still remember this – that you could combine that different data using electrophoresis as the estimate of divergence time,and then the other parameters as estimates of the degree of reproductive isolation. By doing that, you could get some kind of estimate of the time course over which reproductive isolation evolves. After that, it was just a matter of compiling that data. It took a long time because it’s all in different places – papers, books and stuff. Nobody had thought to put them together before. It was just a matter of compiling the electrophoretic data with the crossability data and then seeing what came out of that. That was the motivation.

HS: How did you get interested in Drosophila genetics and evolution?

JC: That came in college. The interest in evolution came first, in fact, in my first very first biology class. My very first biology class – Bio101 – at eight o’clock on my first day at college in 1967, was a zoology course taught by an evolutionary biologist. He was very charismatic, and I just got turned on to evolution. And then, I realized that if you want to understand evolution, you have to know something about genetics. He talked to the genetics professor and let me take the genetics course in the beginning of my sophomore or second year, before one is normally allowed to. Evolution is just a very inspiring subject, and combining that with the clean-cut nature of genetics – you know, you get unambiguous results from making crosses – the combination of those two courses and the professors that taught them, who were both very charismatic, turned me into an evolutionary geneticist.

HS: What were the names of these two professors?

JC: The zoology professor was Jack Brooks. He’s still alive, but he is retired. The genetics professor, who became my advisor for my undergraduate thesis, was named Bruce Grant. He’s produced a number of other students, and is now retired as well. William & Mary, where I went to school, was a small liberal arts school. It was mainly a teaching school, with not a lot of emphasis on research, but Bruce, in particular, was such an inspiring presence and so excited about evolutionary genetics that he produced a lot of professional evolutionists. My first two students, including Allen Orr, with whom I wrote this paper, and Mohamed Noor, also went to William & Mary and were taught by Bruce Grant. There are a number of professional evolutionists who came out of that small school.

HS: How did you and Allen Orr decide to collaborate on this paper, and what did each of you bring to this piece of work?

JC: The original idea, of combining the electrophoretic data, as an index of divergence time, and the crossability data, was mine. I talked about it with Allen, he got enthusiastic about it and he suggested other ideas. So, it’s hard for me now, because it’s been so many years, to partition who had which ideas. Because, of course, there’s a number of sub-topics in the paper, like allopatry and sympatry. That may have been Allen’s idea; I can’t really remember. But I know that the work, which was the hardest work, of compiling all the data, was split between the two of us, and we just said, well, you do this group, I’ll do this group. Of course, a lot of the distances had to be calculated, because they weren’t presented in papers. We had to take raw tables of allele frequencies and convert them to a usable form. So, it was collaboration, in every sense of the word. The work was halved and, mostly, the intellectual input was split pretty evenly between the two of us.

HS: Tell us a little more about how you actually put this data together and how long it took.

JC: It took about two years to do that. The data were just all over the place. The Genetics and Biology of Drosophila book series was one. The crossability data were frequently in papers. The usual situation was, we’d find the crossability data, which could have gone way back to the 20s and 30s by people like Patterson and Stone, but the electrophoresis data, of course, could not have been produced until after 1966 when Lewontin and Hubby introduced it. But that data was also very scattered. The University of Texas publications had some stuff; we frequently had to go there. I, fortunately, had an old collection of those. I spent a lot of hours in the library. And, of course, electrophoresis is now pretty much outmoded, as a way of calculating distance. People are using nucleotide sequence data and things like that. If you wanted to redo the paper, or update it, you’d have to start all over again. I haven’t followed the many studies that came after ours that used, sort of, the same methodology, but I suspect they’re using DNA sequence data, rather than electrophoresis.

HS: Do you know if such an analysis has been done subsequently, using Drosophila DNA sequences?

JC: I think Roman Yukilevich published one in Evolution a couple of years ago. I can’t remember if it has DNA sequence data. That’s the biggest update. He has lot more species and a lot more data. He came to, I think, the same conclusion we did.

HS: How long did it take you to write up the paper and when and where you did most of the writing?

JC: It was in the University of Maryland. I moved to Chicago in 1986, but I think we had already started writing it then. It took a long time to get accepted. It was rejected by Evolution the first time we sent it in, for not a very good reason. And so, We just wrote a letter back saying the reviewer is wrong because of this, this and this. And it was accepted! We didn’t have to change anything. But, you know, in those days, there was no online publishing, so it took like a year, from when we submitted it, until it actually appeared. We certainly started and largely completed the data analysis in Maryland. It was probably submitted in late 1987, here in Chicago, after Allen and I both came here.

HS: Was Evolution the first place you submitted it to?

JC: Yes, it was. It’s a long paper. It could not have gone to a place like Nature or Science. At that time, there were not that many journals in evolutionary biology. It’s an explicitly evolution paper so it couldn’t go to a journal like Genetics; it could, but it wouldn’t be appropriate. Current Biology didn’t exist then. I like Evolution. I was an editor for a long time, and later, president of the Society. I really like that journal. So there was no doubt that that’s where we were going to send it, from the beginning. You have to realize that, when we started, we didn’t know what the results would be. We just compiled the data. We had no idea if there be anything interesting at all. It was only after we did the analysis and found out that, yeah, there was some nice stuff in the results, that we decided to write it up.

HS: Can we go over the names of the people you acknowledge, to get a sense of who they were and how you knew them?

JC: Yeah, I’ll try and remember, because it’s been a long time.

HS: You thank “M. L. Cariou, D. Lachaise, and L. Throckmorton for permission to cite their unpublished data.”

JC: Marie-Louise Cariou and Daniel Lachaise worked at the BG in Gif sur Yvette in France. I suspect, although I can’t remember exactly, that they provided the crossability data for a number of species. Particularly, Daniel. He didn’t do any kind of electrophoretic work. They would provide crossability data for groups where we did not have that. Lynn Throckmorton is now dead. He was my predecessor here at Chicago and he worked on the Drosophila virilis group. He provided, both, crossability data and unpublished electrophoretic data for that group – Drosophila virilis – which contains about eight or nine species that we used.

HS: You thank B. Hedges “for calculating some genetic distances.”

JC: Blair Hedges. He was a graduate student at Maryland. He was very good at computers and stuff. He was in our program because he worked on reptiles and amphibians. He would enter the raw data into the computer to give genetic distances. Blair is a professor now, at Penn State University.

HS: S. Arnold

JC: Steve Arnold. He was here at the time. He works on crossability of amphibians and reptiles. He wouldn’t have given us Drosophila data, but I think he read the manuscript for us and gave us comments.

HS: B. Charlesworth

JC: Brian is a good friend of mine. He was my Chairman at the time. He would have also read the manuscript and given us comments on it.

HS: D. Futuyma

JC: Doug Futuyma. I think he would’ve given us comments. He wasn’t the editor of Evolution then, although he became that later. I suspect we also sent it to him for feedback.

HS: R. Lande

JC: Russ Lande. He was one of my Chicago colleagues at the time. He is another extremely good critical reviewer. I would have shown the manuscript to him for comments.

HS: S. Orzack

JC: Steve Orzack. He was one of my fellow graduate students at Harvard, but he also was in Chicago, I believe, at the time of working on the paper. So we would have either discussed that with him, or shown him the manuscript.

HS: D. Schemske

JC: Doug Schemske. Another colleague of mine. He’s a botanist, but also a well-trained evolutionary biologist, and very critical. I would have shown him the manuscript as well.

HS: M. Turelli

JC: The same thing. He is one of my close friends. He was a colleague at UC Davis; he’s still there. I would have also sent him the manuscript to read.

HS: P. Verrell

JC: I have no idea who that is. It could have been a reviewer.

HS: M. Wade

JC: Mike Wade was another one of my chairmen here at Chicago. I would have discussed the results with him and probably shown him the manuscript as well.

HS: P. Ward

JC: Phil Ward. He was one of my colleagues at UC Davis, where I did my postdoc, and he’s still my friend, even though we’re in different places. I would have sent him the manuscript as well. He does electrophoresis to do phylogenies of ants.

So you can see that the manuscript was shown to a lot of people before we submitted it. We wanted to get as much, not only feedback, but as many possible ways in which we could look at the data. It was normal back then to show your manuscript to a lot of people for feedback; especially in Chicago.

HS: How was the paper received? Did it attract a lot of attention?

JC: Oh, yeah. I think it is still my most-cited paper. It’s not my most-cited work, which is my book Speciation. This paper and my review in Nature, which incorporated some of the data on speciation, are my most cited papers. But in terms of data papers, this is certainly most-cited by far. It got a lot of attention because it had a novel approach. It was a way of using static data to estimate what happened over time. And subsequently. it’s been used by other people in other groups, like, you know, fish, for example, or other kinds of insects. But no other group has the amount of data needed to do this kind of work. There’s a paper in 1997, I believe, where we updated that with more data. Even now, there’s no other group of organisms that comes close to that. And that’s not because of the electrophoretic data, but because we can cross Drosophila in the laboratory very easily and see what happens when you do that.You can measure sexual isolation quite easily in the lab. You can’t do that with, say, fish or mammals or anything like that. So the paper has been cited quite a bit and attracted a lot of attention; and pretty favorable attention. Other people, like Roman Yukilevich or my second student Mohamed Noor, went on to analyze the data in other ways that I hadn’t even thought of, and made the results even more interesting.

HS: Tell us a little more about the follow-up paper in 1997.

JC: The ’89 paper was gonna be just the paper – a standalone paper – but then data continued to accumulate, and we kept a file of the data. I can’t remember how many more species there were – like 60 or something. Then we realized that we wanted to, not only add this data, but to see if the results from the first paper still stood up in light of this new data; which they did. After that, electrophoresis was pretty much outmoded, and there was no point trying to continue that kind of approach.

HS: At the time when you did this work, did you anticipate, at all, the kind of impact it would have on the field? Do you have a sense of what it mostly gets cited for?

JC: Yeah, it gets cited for the reason that we wrote it, actually. Well, two things. First, It gives an idea of the time course of speciation. But also, the result showing that sympatric species get reproductively isolated much more quickly, in terms of pre-zygotic isolation, than allopatric species, was unanticipated. It supports the idea that there’s either reinforcement or reproductive character displacement. I just said, well, let’s look at these data. Then we went back to all the original papers and looked at the ranges to see whether the species lived in sympatry or not. That was a lot of work too because, a lot of the time, range data is not presented as ranges.You have to look at where the flies were captured and, sort of, get an idea of whether the ranges overlapped or not. Those two aspects of the paper were important. Remember, the paper is incomplete because it leaves out a number of forms of reproductive isolation that could be very important in nature, like post-mating pre-zygotic isolation, sperm competition, ecological isolation and temporal isolation. Those aren’t included, because there’s no data. But the support for reinforcement that we showed, the high degree of pre-mating isolation between sympatric species as opposed to allopatric pairs, stimulated, stimulated, I think, work on reinforcement. Even in my own laboratory, my student, Daniel Matute, worked on reinforcement, I think, partly because of the data from this original paper. So it had a number of influences on the field. I don’t know how important it is. It’s a novel approach. It’s one that you can’t really us with most species because of the lack of crossability data. There have been a few other studies. Leonie Moyle did a similar study in tomatoes, I think, and Tamra Mendelson did a study on darters collecting information on genetic distance. The problem with darters and all other groups is that you just don’t have the ability to do laboratory crosses that you have in Drosophila. So Tammie was limited to about 12-13 species.

HS: In the paper, you say, “Species status is therefore reached twice as quickly in sympatric as in allopatric taxa” and you suggest what the numbers might be. Do those numbers and that general conclusion still hold true?

JC: Well, certainly the difference between allopatry and sympatry still holds. I mean, that’s been rechecked by several people independently and found to stand up. So there’s no doubt that, at least in terms of sexual isolation, if you’re sympatric you become isolated much faster. I think it’s a lot faster, almost 10 times faster. I can’t really remember the figures right now. So, that all stood up, but there are two questions about that. First of all, sexual isolation is not the only component of speciation. We’re just looking at how fast one component evolves, but that would be interesting anyway, because sexual isolation is supposed to be reinforced during the process of reinforcement. So, at least that result, pretty strongly implies that there’s a form of reinforcement. Mohammed Noor did some other analyses of that data later and actually supported that hypothesis even more strongly. The other question is whether genetic distance is a good estimate of divergence time. We don’t know, really, in Drosophila, because we don’t have much fossil evidence. So, all I can say is, it’s probably correct within a factor of three or four. For allopatric taxa, at least for these components of reproductive isolation, it will probably take somewhere in the order of a half a million years to a million years to make species. But again, we’re neglecting many components of reproductive isolation. So this is an overestimate of how long it takes to make a species.That you become species faster in sympatry rather than allopatry, and that there is a geographical component, probably after secondary contact, is a pretty valid conclusion.

HS: In the 1987 paper, you say that there’s not much known about reinforcement, theoretically, and that there’s need for work. In the follow-up paper, you talk about how, although, reinforcement was earlier considered ubiquitous,this process is now questioned, but, also, that, again, there is more recent evidence that has begun to accumulate in its favor. What is your current view on reinforcement as a mechanism for reproductive isolation is?

JC: I’ll speak about Drosophila because that’s where the work has been done. And the work that’s relevant, has been done mostly by my student, Daniel Matute. He looked at reproductive isolation in sympatric and allopatric populations, not only in nature directly, like, Drosophila santomea and D. yakuba, which have overlapping regions, and didn’t find any, but he also did experiments in the laboratory and found strong evidence for reinforcement for sexual selection, as well as for something we didn’t measure, which is post-mating pre-zygotic isolation. Both forms evolve very quickly, within five generations. You can take two species of flies, or two strains of different species that have never seen each other, put them in a cage in the lab and just let them coexist. If they start driving each other extinct, you just replenish the population. Within five generations, you will see substantial sexual isolation and post-mating pre-zygotic isolation. That convinced me, and there are other papers as well. Dan Howard published a review paper, and there are other papers that all support the idea that reinforcement actually operates in nature. Mohamed Noor did a reanalysis of our data using a very clever method of using phylogenies, in which there was one outgroup and then two ingroups, one of which was sympatric, and the other was allopatric, to the outgroup, to see if there is a difference in the amount of sexual isolation. Sure enough, he found a highly significant difference. So there’s a lot of data accumulated after this paper supporting the idea that reinforcement is important in nature. Now, whether it’s ubiquitous during speciation, I don’t think so, because there’s a lot of allopatric species that have never seen each other, never had overlapping ranges, but nevertheless are explicitly reproductively isolated. We know that because their hybrids are either completely inviable or sterile. So, all we can show is that reinforcement is a fairly common process. We can’t say how common it is because we’re only using Drosophila as our model.

HS: How else did you follow-up on work in the 1989 paper, apart from the 1997 paper?

JC: That was the end of the endeavor. By that time, electrophoretic data was outmoded, and people were beginning to sequence DNA. I knew that if we were going to go on with this, we were going to have to use DNA- based methods of calculating relatedness and genetic distance. I was doing other things at the time, so I just wasn’t interested. And I knew that other people would take up the work, because it’s an interesting problem. Sure enough, people have. I’ll be leaving it to them to continue working. Roman’s paper in Evolution was a good example of much more comprehensive analysis using many more species.

HS: Do you think this paper has had a major impact shaping your career?

JC: That’s a difficult question.There are two questions there. One is whether it shaped the direction of my research and the other is how famous it made me. As I said, after the second paper, I pretty much gave up this line of work. My students, like Daniel, picked up the questions of how fast does reinforcement occur, is it ubiquitous in nature, and is it common in nature. So, in terms of affecting the field: yes, that has happened. In terms of my own personal career trajectory: well, I had tenure already before that was published. It didn’t help with that. But it was a well-enough known paper, and it certainly burnished my scientific credentials somewhat. I think the book Speciation probably did a lot more in terms of shaping my career, than this paper. But this paper was, of course, one of the ideas that that we talk about in Speciation.

HS: Would you count this piece of work as one of your favorites?

JC: Oh, yeah, absolutely. It’ll be in the top five papers. My view is that I’ve had only a couple of good ideas in my life. What success I’ve had, I attribute not to having a lot of good ideas, but working hard. But this paper was a good idea, and it’s an idea that nobody else had. So I particularly like that one. I’ve only had a couple of other good ideas in my life; not very many. And those big idea papers are among my favorites. But remember, this paper does not represent original research on my part. It’s a meta-analysis of a lot of work done by a lot of people. But it’s a good example of how a lot of obscure papers – the University of Texas publications, and, if you look at the literature cited, a lot of those papers aren’t in big journals – how a lot of useful data can be lying around in small, underappreciated journals, and you can put it together in a large meta-analysis to provide some useful information.

HS: In the very last sentence of the paper, you say,“we hope that further synthesis of genetic analysis with estimates of divergence time will reveal patterns clarifying Darwin’s mystery of mysteries, the origin of species.” I’d like you to reflect on to what extent this has happened in the 27 years since this paper was published.

JC: You are making me feel old! That is a long time. Well, as I said, several people have done similar kinds of work. The problem is that people that do genetic analysis of specific groups are, very often, interested more in phylogenies than they are in patterns of speciation. And so, in order to get them to do this kind of work, you not only need the genetic data, you also need the crossability data. Or, even better, crossability data and some measure of how different, ecologically, species are. As I said, we only looked at three components of reproductive isolation.There are many other components! But the sort of methods used in this paper, combining different indices of reproductive isolation into an overall index, that’s another thing that has influenced the field. For example, John Willis, who works on speciation in Mimulus, uses combinations of reproductive isolation to get an overall index. That’s, by the way, why our paper was rejected in the first place by Alan Templeton; he signed his review, so it’s no secret. He said you could not combine pre- and post-zygotic isolation by a multiplicative method, which I thought was mistaken. The paper was rejected because of that! I had to throw it back to the editor and say, look, here’s a simple analogy: if you have a jar full of cookies, and the first person takes half the cookies, and then the second person takes half of the remaining cookies, well, then you’re only going to have a quarter of the cookies left. That’s exactly what we’re doing with reproductive isolation. And, sure enough, the editor said, okay, we’ll accept the paper.

HS: Have you ever read the paper after it was published?

JC: You know, when you told me you’re gonna interview me, I was gonna read it, but I decided I’ll just go on what I remember. I read it again, very carefully, for the Speciation book. Allen and I read every paper that is cited in that book – there are thousands of them – in order to refresh ourselves about what they said. We also reproduced some figures from the paper in the book. But I’m not sure I’ve actually read it since. Oh, yeah, I taught Speciation here in Chicago, every other year until about three years ago, and, I think, we read this work – maybe the 1997 paper more often – as part of the readings for the course.

HS: What would you say to a student who’s about to read this paper today? Would you guide his or her reading in any way? Would you point them to other papers they should read along with this? Would you add any caveats to their reading?

JC: I’m retired now, but, as I said, we did read it and discuss it for the Speciation class. I would say, although it’s called Patterns of Speciation, we’re only dealing with three components of reproductive isolation. That’s one caveat. Another caveat, of course, is that this is Drosophila. We didn’t know how well these patterns would hold up in other groups, and we still don’t really know, because there haven’t been a lot of groups analyzed. I would suggest that they read this paper in conjunction with the paper on darters and other related papers on this question, and also Mohamed’s analysis, which, I think was published in American Naturalist. I’d tell them to read Roman’s paper as well.

One thought on “Revisiting Coyne and Orr 1989

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s