Saturday, September 16, 2017

Work-Life Balance or Work-Life Fusion?


We were in a remote area of British Columbia, having driven from our already remote cabin to the very end of an old logging road and then having hiked up a game trail for more than an hour. Cedar and Heather were out of sight a hundred meters or so away in the old growth timber, collecting information on obstacles that animals face while walking along the trail. Aspen and I were standing at a three-way split in the trait, setting up a camera trap to film animals as they selected one branch of the trail over the others. We had just turned on the GoPro for Aspen to walk the trail recording its obstacles, when just behind us we heard a loud WHOOOOSH , like a mix of a bark and a hiss (recorded [listen closely] in the video below). We spun around to see a big grizzly not 5 m behind us …

video

When I get back from a trip, which is exceedingly frequent these days, people I know outside of work – and sometimes even at work – often ask “Was it work or a holiday?” I always hesitate to answer because, for me the dichotomy is a false one. My personal interests (adventure, exploration, nature, diving, fishing, photography) are so closely relate to the things I do for work that every “work” trip involves some fun and every “holiday” involves some work. This might seem paradoxical to some who emphasize the need for work-life balance but, for me, it is instead a work-life fusion. I have chosen a job that I love – not just for the job itself but because I would do much the same even if I didn’t have the job.

Perhaps the most direct illustration of work-life fusion is research with your family, which I have found exceedingly rewarding – and I hope my family has too. In this post, I want to sketch little vignettes of the story behind research projects with my brother (Part 1), my kids (Part 2), my wife and kids (Part 3), and my wife and friends (Part 4). In doing so, I hope I can supplement the discussion of life-work balance with a recognition that life-work fusion is also rewarding. And, perhaps, along the way, I can inspire others to conduct research with their families.

Part 1. From fishing to fishery science

My brother (Mike) and I grew up with fishing being our primary passion. Much of this passion was concentrated at our cabin on the Kispiox River in northern BC, which my uncle Paul purchased in 1975 and my parents bought into in 1980. We, especially my brother and I, started fishing for coho salmon and then, in 1985 or so we transitioned to steelhead being our primary target. Soon this passion had spread beyond the Kispiox, with both of us choosing the University of Victoria so that we could fish for steelhead year-round.

Our first steelhead season, 1985.
In 1991, Mike started working at perhaps the most famous steelhead camp in the world – the Lower Dean River Lodge. (NOT coincidentally, my father had gone with Bob Stewart and Dick Blewett on their first scouting trip to Dean River 1961, a year before Bob started the lodge.) Soon after starting to work their, Mike was steeped in the lore and mythology of premier steelhead fly fishing.

Mike and I with a spectacular Dean River COHO salmon.
In 1995, I was a graduate student in the lab of Tom Quinn at the School of Fisheries at the University of Washington (UW), and Mike had just finished his undergraduate degree. I arranged for Mike to work for Tom on a variety of projects for which Tom’s students needed help. Being constantly surround by people conducing research on salmonids got Mike to thinking: “Hey, I should do this too” – so he hatched a plan to study the population structure of steelhead in the Dean River. 

Together, we planned a study in which Mike – and all the guides and clients on the Dean River – would collect life history information (size, scales for ageing) and genetic samples (small fin clips), and conduct mark-recapture sampling, of steelhead in the river. Mike wrote to all the Dean River fishermen telling them of his plans and asking for a small financial contribution to purchase equipment and do genetic analyses. To their credit, many of the fishermen chipped in and the study was a go.

Sampling over the summer of 1996 went very well, with 591 fish captured, measured, and tagged. In the fall, Mike brought the genetic samples back to UW and worked with John Wenburg in the lab of Paul Bentzen to analyze them genetically using DNA microsatellites – a cutting-edge technology at the time. The scales were analyzed for age by another researcher at UW, Kate Myers. Then – primarily over a Christmas at home with our parents – Mike and I analyzed the data and wrote the paper. Published in Transactions of the American Fisheries Society in 2002, the study provided the first evidence for population structure within this premier fishery.

While Mike hasn’t conducted additional formal studies, he has since helped me with my research in Alaska, Trinidad, Galapagos, British Columbia, Chile, and Uganda. He has also monitored fish in the creek that flows through the Hendry Vineyard, which he manages.

Part 2. Hendry Vineyard stickleback (excerpts from early post).

In 2009-2010, I completed my sabbatical at the University of California at Davis. In reality, however, much of my time was spent on my family’s vineyard in Napa, California, where I lived for that year. (The vineyard and winery are owned by my uncle, George, and the vineyard manager is my brother, Mike.)


Nearly every day, my kids (Aspen – 7 years old – and Cedar – 4 years old) and I would go for a stroll around the vineyard. A few weeks into our stay, we found ourselves walking along the creek that flows through the property. The kids got all excited about the small fish they could see rushing around in what little water remained in late summer. “Catch the fish Daddy, catch the fish.” Well, it is hard to resist the kids when they want to catch fish, and so we got some small nets and set to it. To my complete surprise, it turned out that the most numerous fish in these tiny pools were threespine stickleback, which I was studying in my own academic research.

A few weeks later, one of our walks took us past the two reservoirs on the property and I happened to look in and notice some small fish swimming around. I looked closer – stickleback again! Now fate just seemed too obvious to ignore – we were literally living between a reservoir and a creek, and my stickleback research focuses on lake and stream populations. Moreover, the two reservoirs had been created in the early 1970s by pumping water from the creek – and this would have been how the stickleback colonized the reservoirs. So not only was it a lake-stream stickleback pair in our backyard but it was also a potential “rapid” evolution scenario – one of my other major research interests. How could we not study it? 


The creek is shown in the white line and the reservoirs in the white circles.
Aspen and Cedar set and retrieved the minnow traps, Cedar “died” the stickleback, I photographed them, and Aspen labeled and preserved them. The next year back home in Montreal, we continued the project on rainy days and in the dead of winter. Aspen set the morphometric landmarks on the computer, Cedar took the fish out of the vials, I measured and dissected the fish (thanks to my Mom donating her dissecting microscope), and Aspen recorded the data in the computer and returned the stickleback to the vials. The next year it was back to the vineyard for a second round of sampling and then came another winter of fish processing.

Aspen checking traps.
Cedar searching (with Jake) for traps.
Our first major finding was the lack of noteworthy divergence between creek and reservoir stickleback. Although this was initially disappointing, it eventually became more exciting – because it represented a dramatic exception to many other lake-stream pairs and to the frequent evidence for rapid evolution in stickleback. Our second major finding was that morphological variation in Hendry Vineyard stickleback – in both reservoirs and in the creek – was extremely high. In fact, consultation with many stickleback biologists suggests that the variation at these sites was higher than that in any other known stickleback population.


 A really cool spin-off outcome from the paper we published in Evolutionary Ecology Research, and the blog post I wrote about it, was that several other researchers subsequently were inspired to conduct research and write papers with their kids. Here is one from Heather Gray and her son documenting some unexpected behavior in a tropical toad. Here is one from Steve Cooke and his kids studying the effects of “playing time” on the recovery of fish caught by hook and line.



Part 3. Walk this way.

In the remote area described at the start of this post, a very heavily used game trail meanders its way for several kilometers along a ridge between the river and a lake. As the trail winds along, it periodically splits into two (or even three) branches before reconnecting again just a few meters to a few hundred meters later. Why? Why should some animals go one way and others go another way? Do bears take one branch and moose the other? Do male moose with cumbersome antlers follow one route and female moose with calves another? Do animals take one branch going north and the other going south? Are some animals left-handed and others right-handed?

Aspen, Cedar, and Heather asking "which path would you take?"
I had often pondered these seemingly inconsequential questions when walking the trait and thought it would be a fun question to answer. So, this year, the whole family decided to find out. We set up 8 Reconyx game cameras to film animals at the various splits in the trail and, next year, we will pull the memory cards and analyze the resulting videos, which we can then relate to data on obstacles along the trails, which brings me back to that grizzly.

Working on a camera trap.
just behind us we heard a loud WHOOOOSH, like a mix of a bark and a sneeze. We spun around to see a big grizzly not 5 m behind us. For just a few seconds, we all just stood there looking at one other and then the bear wheeled around and ran 10 m or so back down the trail. At precisely the moment I realized “damn I forgot the bear spray,” the bear stopped and turned back toward us, sniffing the air and bobbing its head up and down. While I love watching bears unobtrusively, it struck me that this might be a good time to be more obtrusive, so I started to yell “Hey bear.” The bear continued to stare at us for another minute and then walked back the way it had come. “Whew”, I thought, “that was really cool” and then, just a second later, “Whoa, where are Heather and Cedar?” Off we went to find them and soon, all reunited we reminisced about the exciting adventure as we walked back toward the cabin.  

The video below records this entire sequence, with data collection starting seconds after the bear left. "Did it hiss at us?" Aspen asks. (Sadly, we never thought to point the camera at the bear - it happened too fast.)

video


Part 4. The Heir of Slytherin?

When our friends, Hans and Gemma, were renovating their house, we looked after their snake, which was great fun. When they took their snake back, they gave us another one as a way of saying thanks. The next year, we bought our first ball python. The year after that, we bought our second. These snakes became more and more a part of our menagerie and the first ball python, Nagini, has become a regular feature in the biology classes of both Heather (at Vanier College) and myself (at McGill).

Nagini helping me teach.
Now, a number of years later, we have more than 30 ball pythons and Heather has become obsessed with breeding them. The reason is that they show dramatic color variation and Mendelian predictions for the various morphs are well known, you can use the “genetic wizard” to plan your crosses to generate particularly rare or exciting morphs. Who wouldn’t want to breed an “emoji” ball python – as one breeder succeeded in doing.


Just a few of our snakes.
A couple of years ago, at the joint HenDRY-BARrett (DRY-BAR) Christmas party, we were all looking at the snakes and started talking about how great this system would be for studying the genetics of color. This, then, is our next big family (and friends) research project. Heather has been collecting shed skins from a number of cooperating breeders and we will use genomic methods in an effort discover the genes and causal mutations driving color variation.


The point of all this.

All of these projects are entirely curiosity driven. No funding body has made a “call” for proposals on them, no opinion papers in Science have pointed to a need for them, and none of them has (yet) become a citation classic. Nevertheless, each study has made (or will make) a small contribution to our understanding of the natural world that will aid and guide additional research. (Our steelhead paper has been cited 37 times and our stickleback paper 9 times.) Beyond that, the act of conducting these studies has helped to create a work-life fusion that makes the work more fun for everyone and the holidays more interesting at the same time. Perhaps it isn’t the right strategy for everyone – but it certainly is for us.

And, in closing, Cedar's moose trail obstacle simulation ...


video




Wednesday, September 6, 2017

Descent with Modification: The Evolution of a Conceptual Figure

Almost every student talk – and many by postdocs and profs – starts with a conceptual diagram linking ideas and concepts. The simplest possible version of such a diagram for eco-evolutionary dynamics is two boxes, one for ECOLOGY and one for EVOLUTION, with arrows linking the two. This figure still leads many talks as a way of emphasizing the fact that researchers have long focused on the arrow from ECOLOGY to EVOLUTION but not the reverse, which has recently become the primary new emphasis of research in Eco-Evolutionary Dynamics.


Starting from this simplest framework, I developed an expanded – but still simple – version that sought to make several key points explicit. First, phenotypes are the true nexus of eco-evolutionary dynamics because it is PHENOTYPES (not genotypes) that are under direct selection and it is PHENOTYPES (not genotypes) that have ecological effects. Thus, arrows from ecology to evolution and back must flow through phenotypes. Second, the direct effects of phenotypes on one ecological level (e.g., populations) can cascade to indirect influence other ecological levels (e.g., ecosystems).


I tried to unearth out when I first came up with this figure and was unable to be definitive. However, it was first published in Bailey et al. (2009), a New Phytologist “Forum” describing a symposium on eco-evolutionary dynamics at the ESA meeting in Albuquerque, New Mexico, in August of 2009. I had used the figure in my talk at that symposium. Another early appearance was an F1000 Biology Report that I did with Eric Palkovacs in 2010. Since those uses, the figure has become widely used in various publications and talks (and my book) as a simple intuitive way of conceptualizing eco-evolutionary dynamics.

In short, the basic figure has stood the test of time, largely without revision for almost 10 years. However, almost every time I show it, I end up having interesting discussions with someone about how it could perhaps be improved. In nearly all such cases, I have convinced myself that no change was necessary but, twice now, I have been compelled to admit that it could be better. The first time came during a “the genomic of eco-evolutionary change” symposium and workshop in Monte Verita, Switzerland, in 2016. Victoria Stork pointed out during her talk that my use of “genes” at the top of the figure ignored other, potentially important, genomic changes that influenced phenotypes and could therefore have ecological effects. Epigenetic changes, such as DNA methylation, are perhaps the most obvious example. At this point, my book was basically done and at the printer but I was able to add “genomes” to “genes” at the last minute. My intent in doing so was be inclusive of people studying epigenetics.


The second time I have felt compelled to make a change came just last week at a “significance of sexual selection for population fitness” workshop, again in Switzerland – but this time in scenic Fafleralp and organized by Claus Wedekind. I gave a talk on the first night of the meeting and, afterward, several people – most notably Jacek Radwan – argued for the addition of an arrow directly from population dynamics to genes (bypassing phenotypes). The most obvious reason for such a pathway would be that small population sizes can lead to genomic changes through inbreeding or drift, which could then have phenotypic effects with ecological consequences. I had heard this argument before and had not been convinced, because I felt that the effects still had to flow through phenotypes. This time, however, the argument was clearer to me because I had been specifically talking (and therefore thinking) about the genetic effects of population size.


Specifically, I now agree that small population sizes can directly influence genomes without having to pass through phenotypes, with my apologies to those who made this point previously and I dismissed it. However, I still think that effects of genomes BACK to ecology must flow through phenotypes. That is, inbreeding and drift will change genomes but they will have ecological effects only if those genomic changes modify organismal fitness (leading to a phenotypic effect on population dynamics that could cascade to indirectly influence communities or ecosystems) or traits (a potential direct effect on communities and ecosystems).

Here’s hoping no more major changes are needed. Or, wait, maybe not. Keep ‘em coming – just realize it might take me years to agree! 



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Fafleralp: our workshop was held in the building in the lower left.

Fafleralp: looking back where I had hiked on my first day.

Fafleralp: looking back where I had hiked on my second day.

More photos from Fafleralp.

Wednesday, August 23, 2017

I have the Imposter Syndrome.

At a recent meeting, I had a long discussion with a student about their struggles with the imposter syndrome - not just having it, but even admitting they had it. I was moved and inspired. I asked the student if they wanted to post their story on my blog, anonymously if they chose. So here it is. I hope you find it as helpful, honest, and - indeed - inspiring as I did. (Andrew).

A few months back I was chatting with a friend and collaborator about my post-doc plans and options. He kept throwing what I felt were outrageous suggestions at me, funding that I wasn’t competitive for at all. I brushed the suggestions off. I told him that I would look into it, but needed to think more realistically, that I wasn’t in that league. He cut me off and said, “you need to get over this imposter syndrome thing.” To which I laughed and responded, “imposter syndrome? I think I have anti-imposter syndrome.”

I know anti-imposter syndrome is not a thing. But I really did not identify with the way that I heard imposter syndrome described. I had heard young PhD students talk about it as though it was an inevitable consequence of their genius. It was almost like humble bragging – “Oh of course I have imposter syndrome, I’m at _______“ (insert ivy-league institution of your choice here). I’ve never heard someone from a lesser esteemed school make such a claim. No, we know we are the academic scraps, having been rejected from far better schools for various reasons. Or at least that’s the mindset many of us have. I felt like people routinely under-estimated me. I don’t have imposter syndrome, I told myself. Quite the opposite, I was trying really hard to be accepted into a world I had longed to be a part of for so long. I knew that I would prove myself worthy if given the chance. I had so much confidence in myself and my abilities. I had an “I’ll show you who I am” kind of attitude, and it worked for me.



Actually, it worked really well for me. Doors opened. Connections were made. Suddenly I was receiving awards and praise from some well-known people. People not only accepted me once they saw what I was capable of, but for the first time in my academic career, people had expectations of me! Overnight it went from “who are you” and “you’ll probably fail but go ahead and try” (yes that was actually said to me), to “you always give such great talks” and “I can’t wait to see the results from your next project.”

And with that my friend’s words came storming back into my mind. Maybe I did have this imposter thing after all? For so long I believed in myself when few others did. I had felt like I belonged somewhere that I wasn’t being accepted into. I felt a need to prove myself. And now that things were finally falling into place and I was accepted, I couldn’t shake the thought that “maybe they were right all along, I don’t belong here.” I felt myself spiraling into an anxiety induced despair as I stressed over not having published enough. This was fueled by comments from mentors like “you know your reputation exceeds your publication record” and “you have so many publications on this topic, oh wait, you only have 2?” And the chasm between my metrics of success and people’s opinion of me seemed to grow at an ever-quickening pace.

But I was still not willing to accept that I had imposter syndrome. Things came to a head over a 72 hour period at a recent conference. Expectations were high, reinforced by nearly every conversation I had. “Please expect less of me” I found myself timidly asking people. This was not me. I am not timid. My self-confidence was shattered and I couldn’t put my finger on why. I ignored it. I tried to psych myself up. But my usual mantra of “I’ll show them” was no longer valid. Instead I was grappling with an internal monologue along the lines of “I have to show them again. And again. And again. And if I don’t, they’ll know they were right before, that I don’t belong here.” I was one talk away from people realizing I was a one-trick pony, one conversation away from people losing their confidence in my abilities, one failure away from the confirmation of “you don’t actually belong here.” I felt like I was caught in a storm of expectation and praise that was wholly unwarranted and that I couldn’t possibly live up to.  I wasn’t worried that I wouldn’t give a good talk. I know I give good talks, it’s one of my strengths. But I was paralyzed with fear that silently people would be thinking “oh this is crappy science” and “her previous work was so much better, what’s this nonsense?”. And maybe this is where the root of my imposter syndrome comes from. I perform well, but that doesn’t mean my ideas are good – maybe people are just blinded by the well-thought out presentation and pretty slides and not impressed by the science itself.

The night before my talk I sent a couple of text messages to trusted friends admitting that my confidence was gone and that I was struggling with expectations. The next morning I woke up to a flurry of messages reassuring me. Before my talk I spoke with a friend about what I was feeling in person and she reassured me that she often felt that way too, and that I had no reason to doubt myself. My confidence temporarily bolstered, I stood up and delivered a great talk that was well received. And I realized then that I could never let myself get that worked up about expectations again. More importantly, I realized I needed to talk to people about this. And so, the rest of the conference I talked to some of my conference buddies about this “imposter” feeling I’d been having. I was shocked at how many people responded by telling me that they were dealing with it too. People who I admire, consider successful and confident, and who I wouldn’t have guessed experience this. Sharing our experiences was cathartic for me. 



I’m sharing this story because I’ve been told it’s a unique perspective on imposter syndrome. Maybe it is, maybe it isn’t. My story isn’t meant to teach you about imposter syndrome, or to describe what everyone feels. It’s my story, that is all. I agreed to post this because I didn’t think my experience fit with what I understood imposter syndrome to be. But when I was able to give a name to it and talk about it with others, then I could start moving past it. Who knows, maybe someone out there is reading this thinking “Hey, that’s my experience too!” And maybe this will help them begin to deal with it. I hope that someday I’ll move past this entirely, and that self-doubt will be fleeting and merely a check of my humility. Until then, I’ve found a few strategies that keep me grounded when I begin to doubt myself:

1.     I re-assess my self-worth. I now keep a list of the compliments I get and screenshots if they are in digital form. I look at them to remind myself that I do belong and that the people I trust believe in me.

2.     I remind myself that I’m on track and re-assess my metrics of success. When I stress about my pace of productivity, I look up the CV of a young career scientist. Nine times out of ten, I’m right on track when I look at the pace and number of publications. Keeping my expectations and comparisons realistic is important. I’m right where I should be at this career stage, and I’m on pace to be where I should be at the next. More importantly though, I remind myself that everyone progresses at a different pace and there is no universal standard of success.

3.     I reinforce my accomplishments. I made a list of all of my awards, grants, invited talks, etc. When I need a little extra boost I look at the list to remind myself that so many people couldn’t possibly be wrong about my potential and my abilities.

4.     I talk about it. Not to everyone, but I have talked about this with a few trusted people and have been surprised to learn that they had similar feelings. This issue is far more common than we think it is. It is comforting to know that people I look at as confident and successful are dealing with this too. I can’t help but think if people were more open about this topic, then maybe I would have talked it through with my mentors instead of having a near meltdown over it. 

One final note, I have chosen to post this anonymously for several reasons. Feeling like this is a mental health issue that I do not want to be associated with is not one of them. On the contrary, I will gladly talk / commiserate with you in person. However, I did not want to open myself to judgement, assumptions, or personal attacks from people I do not know. I also did not want to invite personal compliments – this was not a humble brag and I don’t want you to tell me I’m awesome because you think I need to hear it. Actually, I think that would be counterproductive. To my friends, you probably know I wrote this, so thanks for being awesome. To those who don’t know who wrote this, I’m probably your student, post-doc, colleague, collaborator, or conference buddy – think about that.

Wednesday, August 16, 2017

Evolution in a common landscape: a tale of two stickleback species

All species cope to some extent with environmental heterogeneity. How do they achieve this? Do they tolerate or avoid extreme conditions? Or do they adjust to local selective environments through adaptive evolution? Many studies in evolutionary ecology look into these questions one species at the time. Yet, species do not live in isolation, but are assembled in communities. We might thus ask if members of the same community respond to environmental conditions similarly or in species-specific ways. Answering this question is important for understanding the eco-evolutionary dynamics of communities. Since anthropogenic impact on natural systems may simultaneously put multiple species at risk, a multi-species approach is also relevant for conservation and natural resource management. In a new article in Nature Communications, we investigate to what extent two stickleback species, the threespine stickleback and its relative the ninespine stickleback, evolve “collectively” across contrasting environments. That is, a tale of two stickleback species in a common landscape.

Evolutionary biologists have accumulated ample evidence for contemporary evolution in natural populations. Meanwhile, the question of why populations do (or do not) evolve and whether they evolve in a predictable manner will still keep us busy for quite some time. There are many species and many environmental contexts in which species can evolve. For as much as we know, the way populations evolve is species- and context-dependent – and thus highly variable. This is reflected in meta-analyses such as in last month’s issue of the American Naturalist, where Krista, Gregor, Caroline and Andrew illustrated that even when we expect populations to evolve in a predictable direction (i.e., parallel evolution), the extent to which they actually do so is highly variable (Oke et al 2017). Across species and environmental contexts, populations thus show anything from “very” parallel to “not-so-parallel” evolution. Aspects of evolution are thus not very predictable.

Things become clearer when focusing on one species at the time. One of the species that has been strongly fueling the debate of the importance of parallel and non-parallel evolution is threespine stickleback. Indeed, of the 92 studies included in Krista-and-friends’ meta-analysis, 26 studies featured this very species. One of the most convincing, wide-spread and best understood cases of evolution in nature is the rapid parallel evolution of reduced body armour (e.g. from high to low numbers of lateral plates and from long to short spines) when marine threespine stickleback populations colonize freshwater. Importantly, these populations often evolve in a predictable manner, but we also have a fairly good understanding for why they sometimes don’t. Gene flow, for instance, which homogenizes the gene pool and therefore slows down or halts adaptive divergence, explains some of the limits on the evolution towards low-plated populations in freshwater (Raeymaekers et al 2014). In another threespine stickleback ecotype pair, the lake-stream system, variation in phenotypic and genomic parallelism could not only be explained by gene flow, but also by the magnitude of the difference between the lake and stream environment, which has an amplifying effect on adaptive divergence (Stuart et al 2017). Studies like this generate a better mechanistic understanding of evolution, because they show how strong selection on ecologically relevant traits and their underlying genes has to be to contribute to local adaptation, and how often there is a common genetic basis for such traits.

Threespine stickleback populations can evolve rapidly from completely plated (top) to low-plated (bottom), while homogenising gene flow can slow down this process, even when selection on plate number is evident from one generation to the next (Raeymaekers et al 2014). Photo credit: Anna Mazzarella.

Yet, single-species studies hold a major limitation for the study of contemporary evolution in nature: they do not provide insight in the generality of contemporary evolution. For instance, the evolutionary versatility of threespine stickleback may be exceptional, and thus levels of adaptation in this species may be not representative of the typical strength of adaptation in nature. And of course, species do not live in isolation but are assembled in communities. Members of the same community often face similar environmental gradients, but do not necessarily respond similarly to these gradients. From a community perspective, it is important to understand the variation in these responses, in particular because adaptation to local selective environments in one species may also influence adaptation in other species (e.g. through competition or dilution effects). So, in order to fully understand biodiversity patterns across ecologically diverse landscapes, we should consider multiple interacting species simultaneously, providing a more holistic view on the landscape processes shaping biodiversity. This also makes sense for conservation and natural resource management, since anthropogenic impact on natural systems may simultaneously put multiple species at risk.

In our new study, we performed a comparison between the threespine stickleback and its relative the ninespine stickleback (Raeymaekers et al 2017). We primarily wanted to find out to what extent both species differ in evolutionary potential to deal with challenges along the broad habitat gradient over which they coexist. In western Europe, both species co-occur frequently at the exact same spots, which includes both freshwater and brackish habitats. Yet, both species also have a wide-spread geographic distribution, are closely related (allowing us to compare homologous traits and genomic regions), show interesting differences in ecology, and are highly abundant, and thus represent an excellent pair of species for this type of study. We sampled both species at four freshwater sites and four brackish sites, and then compared them for various aspects of population divergence. We analysed 1) whether the two species show phenotypic and genomic signatures of adaptive divergence along environmental gradients, 2) to what extent both species show parallel patterns of population divergence, and 3) what are the most important spatial and environmental drivers of population divergence in each species.

“Von dem Stichling”. Description of threespine and ninespine stickleback in “Fischbuch: das ist ein kurtze, doch vollkommene Beschreybung aller Fischen so in dem Meer und süssen Wasseren…” by Gessner and Forer (Zürich, 1563).With two and six dorsal spines, the drawings of both species do not look very professional. Yet, even nowadays the number of spines is a source of confusion. Threespine stickleback sometimes have four spines, and in Dutch the ninespine stickleback is called “tiendoornige stekelbaars” – or "tenspine stickleback". Based on my own counts, this is a more appropriate name.

One or two species of stickleback? Each student has to pass the test.

Here are our most important findings and some reflections:

1) Phenotypic divergence was significant for 50 % of homologous traits in threespine stickleback vs only 7 % in ninespine stickleback, while the proportion of outlier loci (SNPs which are likely genomic targets of selection) was at least 2.5 times larger in threespine stickleback. This confirms a stronger tendency to adapt in threespine stickleback. Since this is the first time that both species have been compared in exactly the same environmental matrix, we now know the effect of species-level differences in evolutionary versatility on population divergence.
2) These results do not imply that ninespine stickleback cannot adapt, since populations might already be preadapted to the environmental gradients in the study area. However, we observed a numerical advantage of the threespine stickleback in freshwater. We proposed that this relative ecological success could possibly be attributed to their evolutionary versatility. Of course, two species only represents a very small community, but it shows the potential of merging landscape genomics with community ecology to understand whether or not species evolve “collectively” across landscapes.
3) We observed substantial phenotypic, but no genomic parallelism between both species. This result demonstrates that the evolution of similar phenotypes in the same selective environments might primarily involve different genes. Based on previous comparative genomic studies, this result is not unexpected, but it is exciting to observe this in exactly the same spatial matrix. 
4) Note that we wanted our study to allow for a “fair” comparison of evolutionary versatility between the two species. We therefore compared both species for homologous traits only. Indeed, even if one species would be extremely variable for a trait which is missing in the other species, it would be hard to decide which species is most versatile. Luckily, most measurable traits in both species are homologous anyway (lateral plates, first dorsal spine, pelvic spine, gill rakers, fins, …). Non-homologous traits include dorsal spine #4, #5, #6, … #10 (guess which stickleback species is lacking those spines).
5) A reference genome is often used to facilitate SNP-typing. Yet, at present a reference genome is available for threespine stickleback, but not for ninespine stickleback. While it is possible to use the threespine stickleback genome as a reference for ninespine stickleback, we didn’t do this since this would narrow down the comparison between the two species to homologous genomic regions. Homologous traits do not necessarily have the same genetic basis, and hence the entire genome should be considered to allow for a straightforward comparison of evolutionary versatility. In addition, homologous genomic regions may already have gone through a long history of selection - perhaps pre-dating the origin of both species, and hence may bias our analyses in unexpected ways. In this respect our choice for de novo SNP typing in ninespine stickleback seemed more "safe". It is waiting now for the assembly of the ninespine stickleback genome to look into homology effects in detail.

The results are further discussed with respect to how differences in genomic architecture, gene flow and life history may induce or reflect variability in evolutionary potential and ecological success among species sharing the same landscape. Read more here.

Joost

Cited literature

Oke KB, Rolshausen G, LeBlond C, Hendry AP. 2017. How parallel is parallel evolution? A comparative analysis in fishes. The American Naturalist 190:1-16.

Raeymaekers JAM, Chaturvedi A, Hablützel PI, Verdonck I, Hellemans B, Maes GE, De Meester L, Volckaert FAM. 2017. Adaptive and non-adaptive divergence in a common landscape. Nature Communications.

Raeymaekers JAM, Konijnendijk N, Larmuseau MHD, Hellemans B, De Meester L, Volckaert FAM. 2014. A gene with major phenotypic effects as a target for selection vs. homogenizing gene flow. Molecular Ecology 23:162-181.

Stuart YE, Veen T, Weber JN, Hanson D, Ravinet M, Lohman BK, Thompson CJ, Tasneem T, Doggett A, Izen R, et al. 2017. Contrasting effects of environment and genetics generate a continuum of parallel evolution. 1:0158.

Thursday, August 3, 2017

Journal Life List


Steve Heard just posted a blog on his journal life list – all of the journals in which he has published and how his papers are distributed across those journals. Kind of like a birder’s life list of species. Dividing the number of journals by the number of papers gives a very rough JOURNAL DIVERSITY INDEX (JDI**) for an author – Steve’s is 0.61, which he expects to be high. Although I hadn’t planned to write a blog on this topic, it reminded me that I am always excited when I expand my journal life list, favoring JDI increase. Yet at the same time, I tend to target particular journals that I think are in my core research area, favoring JDI decrease. So I quickly (on the train home) did an analysis similar to Steve’s, with some additions.



At first blush, it is clear that my JDI of 0.28 is way lower than Steve’s, presumably because I tend to target core journals: Evolution, The American Naturalist, and Journal of Evolutionary Biology. But then second blush made me realize that the above contrasting motivations (increase diversity vs. focus on core journals) is a function of the joint combination of submissions and acceptances given submissions. Hence, I next did the same analysis but based not on where papers were published but on where I first submitted them.

The general trend, and indeed the JDI (0.23), are similar – suggesting that I really do focus on core journals over journal diversity. But this number is probably biased by a single journal – Nature – to which I have often submitted first but in which I have only rarely published.* Deleting Nature gives a JDF of 0.26, so I still tend to favor core journals over diversity. In fact, it is interesting that my JDF for submissions is lower than that for publications, suggesting that my rejection rate at the core journals is slightly higher than at other journals. I therefore next compared numbers of submissions to journals with numbers of publications in journals.


The two are highly correlated, as one would expect, with my core journals (apart from Am Nat) seeming to have roughly similar or higher than expected acceptance rates. Of course, the difference between these numbers are not strictly acceptance rates because I sometimes publish in journals, including my core journals, papers that I previously submitted elsewhere. At the extreme, I have published in 11 journals to which I never done a first submission of a paper. At the other extreme, I have submitted first to 4 journals in which I have never published a paper.

So, what to make of this beyond my apparent emphasis on core journals. Perhaps it is that journals should give out frequent publisher miles that might, for example, lead to waived publication fees. For instance, I have published 19 papers in Evolution, 17 papers in Journal of Evolutionary Biology, and 11 papers in Molecular Ecology. However, I don’t think I have really had to pay publication fees for most of those. Maybe better would be discounted attendance at annual meetings – yeah, I like that.

Notes:

* I have included (for ease of generating this quickly), all publications in a journal even if they are introductions or notes or comments or news pieces. For example, my publications in Nature are News & Views and the like. 
** This is just a quick and simple metric - see Steve's blog for more comments on it.
*** Perhaps my favorite bird cartoon is below - simply a gratuitous plug for birdandmoon.com



Sunday, July 9, 2017

25 years later – Alaska on my mind

Several years ago, I wrote a blog post called “Trinidad on my mind”, for which I extracted a number of journal entries from my years of research in Trinidad. Today I am on a plane on my way to Haida Gwaii, British Columbia, for field work and I was debating what would be a post I would enjoy writing. I started digging through old journals on my computer – dating back to 1992, when I got my first computer. Among these were notes I had written from my pre-MSc work in Alaska – I ended up spending parts of 10 consecutive summers in Alaska. Much of the writing is a bit too flowery to put on this blog but reading it was fun enough to make me want to extract and compile some for a post “Alaska on my mind.” My edits are minimal – this is pretty much what I wrote at the time. I will presumably follow this post at some future date with other entries from field work.

Incidental catch

It was the summer of 1992 and I had a job as a deck hand on a tender converted to a gill-netter.  I was employed by the University of Washington to participate in a test fishery which was used to predict the size and timing of each year's Bristol Bay sockeye salmon run.*

It was 4:00 P.M. on June 27th.  It was miserable.  The sea was rough and the wind chill, blowing at 25 knots.  Flying spray stung cheeks, eyes smarted from the salt.  Waves broke over the back of the boat immersing us continually as we worked to strip salmon from the dripping gill net coming over the stern.  We were on our fourth set of the day.  Each of the earlier sets had broken records for numbers of salmon taken this year so far.  We were cold, wet, tired and hungry all at the same time.  I loved it.

Sadly, our Captain, Blake (shown here), perished at sea a year later.
There was something aesthetically pleasing about wading ankle deep in salmon while racing the other crew members to see who could remove the most fish from the net without breaking the mesh.  Every so often an unexpected bonus would come along in the form of a 30 pound king salmon.


On seeing the big grey form in the net a hundred feet away, my first thought was that we had an even bigger king.  A second look however, and I realized that this was much larger than any king I had ever seen. "Dolphin!"  It was an exclamation of pure horror from the entire crew when we realized what was in the net.  We had all heard stories of the horrors of drift nets but this was striking much too close to home.  Almost instantly, everyone was galvanized into frenzied action.

Mike quickly reeled the net and the surprisingly placid harbor porpoise to the back of the boat.  Chris and I leaned out and began to frantically break the mesh around the porpoise.  Blake manned the boat controls giving us as much stability as possible to work.  Initially, the porpoise was so calm, I feared it was already dead but when we had it beside the boat we could see it was moving slightly.  It didn't appear to be badly injured. and the only sign of damage was blood from a cut on the dorsal fin.  Was it drowning?

From our position at the extreme stern of the boat, we were still 4 or 5 feet from the porpoise but the holes we were ripping in the net were getting us closer.  I was leaning out so far and pulling so hard on the mesh that my legs lifted 2 feet off the deck before Mike grabbed them and held me from going overboard.  The following sea continued to wash waves through the stern opening threatening to wash everything away.  I continued to pull on the mesh until it felt like my fingers were going to be amputated.  A last convulsive heave on the net and the porpoise's body fell free.  Realizing now it was close to freedom, it began to try and swim with only its tail still caught in the mesh.  Then in a frenzy it ripped free.  As it swam slowly off, we all watched in physical and emotional exhaustion.

Bristol Bay, Alaska

The Russians Have Landed

Scholarship is a great way to cross national and international boundaries.  Scholarship brings people together where national policy and human kindness fail.  The  Bering Sea has a western coast line as well as its better known eastern shore in Alaska.  Not surprisingly, the rivers of the Kamchatka and Siberia also welcome the return of the salmon each summer.

Four Russian fisheries biologists visited us at our camp on Porcupine Island, Illiamna.  They had a translator with them and during their visit discussed common problems, ongoing studies, and issues in fisheries management with the professors from the University of Washington.  Apparently, this trip was also the first for the translator and we could usually communicate as well without her help as with it.  She did spend a long time teaching me some survival words in Russian.  Basically, "I am hungry, feed me now."  This brought my command of that phrase to a total of five languages. 

What I remember most though was that these two particular Russians were musical and, in the evening, provided rare entertainment.  One played the accordion and the other the guitar.  Picture this.  Two Russians who spoke virtually no English entertaining a bunch of American graduate students and professors in Alaska with classic American cowboy songs, sung in English.  It was great.  Their favorite, and mine, was "Ghost Riders in the Sky."    Someday, I may want to study fisheries in Kamchatka, go fishing on the other side of the Bering sea or simply to listen to a Russian concert of cowboy songs or a Beatles medley.

Alaska underwater

Research at Iliamna was really fun because most of it was in the water.  Although I had not brought my dry suit and had no initial research project, I managed to weasel my way into an average of an hour in the water each day.  It was quite cold (8-10 degrees C) considering the old wet suit I had, which was too large.  After a 1/2 hour or so I would be chilly, cold at 45 minutes and shivering by an hour.  I took to wearing socks, long underwear and two T-shirts to reduce water flow through my suit.

I had several jobs.  One was to collect sculpins.  To do this, I would simply kick my feet on the rocks in a salmon spawning area.  When the sculpins swam out I would dive down and catch them in an aquarium net.  After I had a few in the net, I would swim to shore and put them in a floating cage.  While I quite enjoyed it, several times I had to collect 100 of the little devils after I had already been in the water for over an hour at one stretch.  During these episodes, I was always amazed at how many sculpin sized crevices could for refuges for my diminutive prey. A second job was to count sculpins in a series of quadrants.  This was rather mundane and consisted of digging through all the rocks in 14, 1m2 quadrants and tallying the sculpins in four size classes.


I also had my own study, designed to determine how separate two adjacent spawning populations actually were.  Every day I would swim a 100m transect which ran across both populations and record the condition of each female and the number of attendant males in each 2.5m section.  The second part was more fun.  I used a 'Hawaiian sling', with a sharpened tube loaded with a barbed tag, to tag the right side of 22 males at one site and the left side of 22 males at the other site.  I did this twice, the second time using 1/2 sized tags.  Then, each day I would record the numbers of males of each tag type at each site along the transect.  It was a blast but occasionally I would make three or four dives in a row where every male had its wrong side toward me.  Twice, I was able to tag two fish on a single dive.**



That's all for now. I will revisit some field notes again at some future date. 

--------------------------------

* I also worked on this test fishery in 1993. Later that summer, our boat – the 69’ Nettie H – sank with all hands lost, including our captain for my two years on the test fishery, Blake Grinstein.

** I later published this as my first first-authored paper. 


Yep - that's right - the first study I ever led was at a site called "Fuel Dump Island"