In my recent paper published in Behavioral Ecology and Sociobiology, I described the results of some of the work I did while in Sweden (which I’ve written about previously 1,2,3). I discovered that individual quality (both male quality and female quality) and timing of reproduction impact reproductive success in the broad-nosed pipefish, Syngnathus typhle. This is an important finding because it highlights the complex dynamics of mating systems. The results are covered in a press release, and I wrote about my experiences for Biosphere Magazine, an online nature magazine. My story in Biosphere just came out (Issue 23) and you can read it here.
Selection is a process that acts on variation in traits to determine the fitness (i.e., evolutionary success) of individuals, and is a key mechanism of evolution as long as the selected traits have a heritable basis. Selection is often split into sexual selection, which arises due to variance in mating/reproductive success, and natural selection, which is due to variance in all other aspects of fitness. One reason that we often distinguish between these two types of selection is because they can often oppose each other – so an estimate of total selection over an individual’s life might come out looking really small if sexual selection and natural selection act equally strongly but in opposite directions. It would be like one person walking up 50 stairs (50) and another walking down 50 stairs (-50) and saying that on average they climbed 0 stairs.
But selection can have trade-offs at many different points during an individual’s lifetime, not just between natural and sexual selection. Males and females are often under different selection pressures, and natural selection can also be broken down into different episodes or components. When it comes to measuring selective pressure at different episodes, Arnold & Wade (1984a,b) developed a systematic approach to comparing phenotypes of individuals to their fitnesses at a given episode of selection to estimate selection strength. This has been a very popular approach to understanding how selection works in any given system (and I used it to quantify sexual selection strength in pipefish), but it doesn’t get at the heritability part of the story. To do that, we need genetics.
I’ve written about the idea of selection components analysis before, and it is basically the genetic equivalent of comparing phenotypes and fitnesses. Instead, the frequency of different gene variants (alleles) are compared between individuals at different stages in the life cycle. This method allows us to isolate the effects of different types of selection (like sexual selection vs natural selection).
In my most recent paper, Genome-wide selection components analysis in a fish with male pregnancy, which is published in the journal Evolution, I used the selection components analysis approach in a population of pipefish to identify SNPs that have different allele frequencies in adult males and adult females (to find SNPs associated with differential viability in the sexes) and between successfully-mated females and the females in the population (to find SNPs associated with sexual selection).
To compare successfully-mated females and the total population of females, I used one of the cool features of pipefish as a model system: male pregnancy. The males who have mated are collected with their offspring in their brood pouch, so at each gene we can rule out which of the alleles in the offspring was contributed by the father and therefore deduce which allele was contributed by the mother. For example, if the father has a genotype C/C and the offspring has a genotype C/T, then we know that the mother had at least one copy of the T allele. Doing this, I was able to estimate allele frequencies in the females that had mated and compare those frequencies to those in the population.
In the population of pipefish that I studied, I found that sexual selection and differential viability selection on males and females (in other words, selection that puts different pressures on males than females or vice versa) both affect regions throughout the genome. Interestingly, some of the genetic regions under selection were significant in both the sexual selection and the males-females comparison — these regions may be experiencing the type of tradeoffs between episodes of selection I discussed above. It’s also possible that those regions are involved in traits that are under selection acting in the same direction in both episodes. One limitation of selection components analysis is that we can’t say which traits are under selection without doing more experiments. But it is a useful tool at picking apart the types of selection affecting the genome, and could have widespread uses across biological disciplines.
Note: If you would like a copy of my paper and don’t have access to it through a university library, please email me! Due to copyright restrictions I can’t post the PDF but I’d be happy to send it to you.
Recently one of my dissertation chapters was published in the journal Molecular Ecology. It’s titled “Population genomics reveals multiple drivers of differentiation in a sex-role-reversed pipefish, Syngnathus scovelli“.
In the study, my labmate/coauthor Emily Rose and I collected pipefish from 12 populations in the Gulf of Mexico (I wrote about the collecting trip in a series of blog posts1,2,3,4,5,6,7,8). I took the DNA and cut it up into a bunch of little pieces using special proteins and sequenced those little pieces using ‘high-throughput sequencing’–basically, using the latest sequencing technology to get millions of short sequences reads. I then used the sequencing information to discover how similar the different populations were using a variety of statistical techniques. When we collected the fish, Emily and I had also photographed them, and from the photographs I was able to measure the size of the fish and to quantify the female bands (those silvery stripes on their bodies in the images above)–so I was able to compare traits in addition to genetics among the populations of pipefish.
Basically, I found that most of the genetic differences between the populations are due to so-called ‘neutral’ evolutionary processes such as migration and random genetic drift (i.e., not selection). On the other hand, the traits values were not correlated with geographic distance, suggesting that something else (possibly selection) might explain variation in the traits. We did find some genetic regions correlated with the trait values, and some that were correlated with environmental variables like temperature. But overall, we found that the traits and genotypes followed different patterns. Because the gene regions I studied used were distributed throughout the genome, these findings suggest that selection acting on the traits we measured do not have genome-wide effects but may have effects concentrated in certain genomic regions.
My paper describes a population genomics study. Population genomics is the genome-wide extension of population genetics–both aim to understand microevolutionary processes (i.e., shifts in frequencies of different forms of genes), but population genomics does so on a genome-wide scale (Luikart et al. 2003). Population genomics studies are important because they help researchers understand how populations are related to each other, how populations differ, how species adapt to new environments and evolve into new species, and which genetic regions are associated with traits (including disease traits). Population genomics is in part what allows companies like 23andMe to tell you what proportion of your genome comes from your Neandertal ancestors, and population genomics has helped identify genes associated with diseases (e.g., BRCA1 and breast cancer). Population genomics has also started to become a common method within the fields of evolutionary genetics, molecular ecology, and conservation genetics.
So why should you care about my population genomics study? First, it shows us that multiple evolutionary processes (migration, genetic drift, and selection) are prominent in shaping the genome and traits of pipefish. Evolutionary biologists want to know the relative importance of these forces because we want to know whether evolution is adaptive (driven by selection to help the species better fit the environment) or whether it is stochastic (driven by changes in population demographics like being cut off from other populations). This helps us predict how species might react to various threats like climate change and fragmenting populations. As more population genomics studies of wild populations accumulate, we can start to compare between species and look for broad patterns that might provide insight into common patterns of evolution. Additionally, genomic studies such as this one can be used to identify possible genetic regions that are associated with environmental variables like temperature that could be useful for monitoring populations in the face of a changing climate.
Note: If you would like a copy of my paper and don’t have access to it through a university library, please email me! Due to copyright restrictions I can’t post the PDF but I’d be happy to send it to you.
Several months ago I completed a 35-hour yoga teacher training class. In the course of that training, and in the months following as I tried to maintain my yoga practice while finishing my doctoral dissertation, I found that several of the core yoga principles were translatable to my scientific process. By applying those translatable principles to my daily scientific life, I felt more productive and focused. So I want to outline the principles and my application of them to my life as a grad student here.
Follow your instincts. This is the number one lesson from my yoga teacher: a guided-from-within life. In a yoga class, this means that you should listen to your body and do what feels natural rather than force yourself into an uncomfortable or painful pose. If it’s a free-form class, being guided-from-within means that you flow through the poses in a natural way without thinking too hard about the sequence. In my life as a graduate student, I applied the guided-from-within approach to which project I wanted to work on in each moment. I always have a long list of things to do, so to apply this principle I choose to work on the one that I feel the most into at the moment. Sometimes I don’t feel like reading a paper but would rather work on an analysis and create a figure. When that no longer feels right, I’ll switch to reading the paper, or maybe working on writing up a manuscript. By following my instincts, I increased my productivity by not feeling as forced to do my work. And as long as I get started on a project well ahead of the deadline, this approach doesn’t compromise my ability to turn things in on time. Of course, there will always be some tasks that are always unappealing (I’m looking at you, animal care and use protocols) and some deadlines that must be rushed towards. But on the whole, the guided-from-within yoga mentality can be really useful for improving productivity as a scientist/grad student.
Be in the moment. In yoga class, we’re encouraged to set aside our to-do lists and focus on feeling the movements. This principle holds up for researchers as well. Once I’ve chosen a task to work on, if I apply this yoga principle to my work I set aside facebook, emails, and my to-do list to simply focus on the one task in front of me. It sounds easy, but it can be quite challenging, especially if the task is reading a rather dry paper. But focusing on a single task really improves my productivity.
Meditation. Yoga is really all about meditation. Meditation involves clearing the mind of all the mundane, day-to-day things and refocusing the brain. I like to think about meditation as listening to my subconscious, although each person has a different way to describe it. Meditation can be an incredibly powerful tool for a busy scientist, because we’ve always got so many projects at different stages (project ideas, experiments currently running, analyses we’re working on, and papers we’re writing) that it is easy to lose track of yourself in all the madness. Sitting and meditating for a few minutes reconnects me with why I got into all the crazy projects in the first place and leaves me feeling more centered, more grounded, and less likely to become a mad scientist.
Practice the mindset at a small scale. My yoga instructor talks about the actual yoga practice (all the poses we do on the mat) as a way to practice the yoga mindset (being in the meditative, guided-from-within, in-the-moment, connected-to-the-subconscious mindset) in an easy place. Does it feel good to have my arm that way? No? Then I’ll move it. It’s an easy way of listening to yourself and a safe and relatively easy place to practice that yoga mindset. I like to think about science in a similar way. For me, the best example is when I’m reading a scientific paper. I can just read the paper and take in all the words. That would be the equivalent of just going through the motions in yoga class. Alternatively, I can read the paper in a scientific way, and practice thinking critically, asking questions, and really evaluating the paper. Reading a paper is an easy place to practice the scientific approach, but it’s the approach I want to have for all of my scientific endeavors. I should approach my own experiments and writing with the same critical thinking and questioning approach as reading a paper. So just like yoga, there are ways to practice the appropriate mindset so that it becomes easier to slip into it and utilize the skills built in that easy space.
Sometimes we need the positive energy of a safe space. You can practice yoga alone or with other people. The two settings, alone or surrounded by people, result in very different energies. Sometimes what you really want and need from a yoga practice is the energy of other people doing yoga alongside you, even though it’s an independent practice and you don’t really interact much. The energy of having other people doing a similar thing in a safe space is incredibly therapeutic. Similarly, you can work alone at home/office or you can work in a crowded coffee shop/lab. Sometimes I want to work alone, holed up without any company to really focus on my work. Other times, I crave the company of others similarly slaving away on a grant proposal or paper—and that’s when it’s best to find a safe space like a coffee shop or a writing group or even just my shared lab/office space to work in.
Everything has multiple dimensions. Yoga comes in five types: Hatha yoga (movement of the body), Jnana yoga (knowledge and study), Bhakti yoga (love and creativity), Karma yoga (charity), and Raja yoga (meditation). A true yogi will be balanced in the practice of all five of these yogic schools. I believe that it’s important to balance these five aspects as a person, but especially as a scientist who is expected to be incredibly dedicated to the job. Being a scientist means that our lives are mostly guided by the Jnana yoga school of thought. However, I think it’s important that we don’t forget to be active (because activity leads to longer and healthier lives), to reconnect with ourselves (meditation), or to give back to the community (charity). Importantly, I think it’s incredibly important to remain connected to the creative and artistic aspects of ourselves. Coming up with our new ideas requires a lot of creativity, and I personally think it’s important to cultivate my creativity in my hobbies, which primarily involve reading fantasy novels and crafting. Finding a balance between these five aspects helps enrich my life and also helps enhance my scientific practice.
I try to apply these lessons from my yoga training to my life as a graduate student (soon-to-be-postdoc!). They help me stay grounded and happy while improving my productivity. What do you think? Do you have other ways of staying productive?
Women are consistently under-represented at the upper levels of the scientific enterprise, such as at the level of professors1, administrators1, or as members of scientific academies2 (Fig. 1). The lack of diversity in science is something that most people in the scientific community wish to address, but there seems to be a lack of consensus about the best way to do so.
Many people point to motherhood as being one of the major leaks in the so-called ‘leaky pipeline’ of science, but the repeated sexist ‘twitterstorms’3 and cases of sexual harassment in academia4 point to a hostile or inherently sexist work environment as the real culprit. However, there have been some major strides recently, including the election of the first female president of the Howard Hughes Medical Institute (one of the richest biomedical research institutions in the world)5.
One of the problems with the discussion of the inequality of women in science is that it often conflates many different issues: (1) the often grueling hours and/or expectations of an academic career6,7; (2) finding a work-life balance; (3) a lack of sufficient parental leave programs/family support programs7; (4) a long history of casual sexism in science and society7; (5) a lack of diverse role models in science7; and (6) women being unprepared for things like negotiating.
One solution is to generate and create support networks and host educational conferences aimed at educating and connecting women in science. About a week ago my university’s Women In Science and Engineering (WISE) group had a day-long conference, in which six distinguished women in science were invited to come and give a talk. The theme of this year’s conference was finding a work-life balance–which most agreed is best described as an equilibrium (Fig. 2). The reason it’s not a balance is because an equilibrium will maintain the same overall energy but the proportion of work and life can shift based on the various things we need to do. Each person’s equilibrium or balance will be different. Tied into this idea of equilibrium was using mindfulness and positive thinking to help make your work, which takes up a huge amount of your time, into feeling more like an enjoyable, or at least rewarding, part of your life.
One of the most useful parts of the WISE conference was the workshop on negotiating. A major reason that women have lower pay than men is because they fail to negotiate. This workshop walked us through how to determine a reasonable negotiating range and helped us prepare for the negotiation conversation itself. It was an incredibly informative and useful workshop and I highly recommend everyone look into attending a similar workshop if possible.
An interesting theme I noticed throughout the workshop was that some of the advice was to take on characteristically ‘male’ traits to be successful in the workplace, especially if dealing with the more ‘traditional’ (aka sexist) men. One of the panelists even suggested that women start manspreading and taking up physical space to exert dominance and maintain power in a conversation or relationship. Several of the women recommended setting strong boundaries with male colleagues, such as not going out for drinks after work, or not staying past 9pm. Discussions of appropriate behaviors in the workplace (e.g. not getting too ‘flirty’) also included being the ‘being one of the guys’ approach.
These suggestions are all good approaches to dealing with sexism and gender bias in the workplace, but it also made me wonder if that will just perpetuate the problems. A component of modern feminism includes embracing feminine traits and not just having women break the glass ceiling by adopting masculine traits and behaviors. So just like the problem of helping keep women in science, the solutions are nuanced and layered and not at all straightforward. How can we change the culture in science while simultaneously succeeding?
What are your thoughts? Let me know what you think in the comments!
1Urry, 2015. Science and gender: Scientists must work harder on equality. Nature 528, 471–473. http://www.nature.com/news/science-and-gender-scientists-must-work-harder-on-equality-1.19064
2Gibney, 2016. Women under-represented in world’s science academies. Nature. http://www.nature.com/news/women-under-represented-in-world-s-science-academies-1.19465
3Morello, 2015. Science and sexism: In the eye of the Twitterstorm. Nature 527, 148–151. http://www.nature.com/news/science-and-sexism-in-the-eye-of-the-twitterstorm-1.18767
4Harmon, 2016. Chicago Professor Resigns Amid Sexual Misconduct Investigation. New York Times. http://www.nytimes.com/2016/02/03/us/chicago-professor-resigns-amid-sexual-misconduct-investigation.html?_r=0
5Willyard, 2016. Howard Hughes’s next president: ‘Promote under-represented groups in science’. Nature. http://www.nature.com/news/howard-hughes-s-next-president-promote-under-represented-groups-in-science-1.19347
6Duffy, 2015. You do not Need to Work 80 Hours a Week to Succeed in Academia. http://sasconfidential.com/2015/11/25/80-hours/
7Shen, 2013. Inequality quantified: Mind the gender gap. Nature 495, 22–24. http://www.nature.com/news/inequality-quantified-mind-the-gender-gap-1.12550
I will be defending my PhD thesis in May to graduate with a doctoral degree in Biology in August, which means this is my final semester/6 months as a PhD student. This last stretch has a lot of significance to me, but most people (even those in academia) don’t have a good idea of what I’m actually doing during these last few months. So I thought I would write a post to make it clear.
**DISCLAIMER: This post is about my own experiences and is not necessarily true of all PhD students**
First, let me tell you what a dissertation can look like. In some disciplines (e.g. psychology or philosophy), it is one long research document where the chapters truly are chapters, just like in a textbook or a novel. Alternatively, in many science fields, including biology, the thesis is often a collection of several research studies that are all generally on the same theme but are not necessarily directly related to each other. In my thesis, I’ll be including three ‘chapters’, each of which will be in the format of a scientific paper (one of them will be my simulation study paper), plus an introduction and a conclusion. The three chapters are all somewhat related, but they don’t *necessarily* tell a single cohesive story. Each is a publishable unit.
So based on that description of a PhD thesis, you might think my final stretch will just be me sitting in front of a computer writing all day long. You’d be half correct. I’m definitely sitting in front of a computer all day long, but I’m generally not doing a whole lot of writing–I’m analyzing data.
I already have two of my chapters written (one is already published and the other is under review at a scientific journal), so I have one chapter plus the introduction and conclusion remaining. Before I can get around to actually writing the final chapter (and the introduction and conclusion to tie everything together) I have to have results from the experiment for my third chapter. And this is no easy task–my project involves a new type of analysis of next-generation sequencing data, so I’m dealing with data for ~300,000 genetic loci in over 400 individuals. So not only am I trying to implement a brand-new analytical technique, I’m also dealing with huge amounts of data. Therefore, progress in analyzing my data is slow and painstaking. However, I am making progress and I should be on-track to finish the analysis and write it all up with plenty of time to get my thesis to my committee.
Of course, finishing my thesis is not the end of the work towards my PhD. I have four additional side-projects that will not be part of my thesis but which I would like to have at least mostly done before I leave for my post-doc. So I’m busy analyzing data for those projects as well and will be writing those papers as the data analysis gets wrapped up.
What this means is that even though I’m done taking classes and all I’m doing is “working on my thesis”, I’m mostly analyzing data, reading papers to be able to place my work in a broader context, and writing up the results of several projects. It’s going to be a busy 6 months, but I embrace the challenge and am glad to see the light at the end of the tunnel!
About a month ago my labmate and I published a paper with our advisor titled “The effects of synthetic estrogen exposure on the sexually dimorphic liver transcriptome of the sex-role-reversed Gulf pipefish”. It’s published in an open-access journal, PLoS One, so everyone with internet can access it! However, I wanted to write a more-accessible summary of the paper here on my blog to help non-specialists understand what the paper was about.
To describe the paper, I’ll de-construct the title, starting with the end. We did this study in a species of marine fish, called the Gulf pipefish (scientific name Syngnathus scovelli). Pipefish have male pregnancy, so the males provide all of the parental care, and in this species the males can only brood a clutch of eggs from a single female, but females can impregnate multiple males (for more information on pipefish, check out my citizen science project, Pipefish World!). Because males then become the limiting factor in reproduction, females end up competing for males and males become the choosy sex, so we talk about the species as being sex-role-reversed. In this study, we extracted RNA from the liver of pregnant males, non-pregnant males, and females. RNA is a molecule similar to DNA that acts as a messenger between the DNA sequence and the rest of the cell, and tells the cell what proteins to make based on the code in the DNA. When a gene has RNA in the cell we describe that gene as being expressed. So we extracted the RNA and sequenced it to generate a transcriptome, which is all of the RNA that is expressed at the time of RNA extraction in a particular tissue, in this case the liver. We then looked at how RNA was in the liver for each gene in both sexes and discovered that males and females have different levels of expression for different genes, meaning that the liver is a sexually dimorphic tissue. This is actually not as surprising as it may seem at first, since many other species (including mammals like humans) have sexually dimorphic livers when it comes to DNA expression. One interesting feature of the Gulf pipefish liver transcriptome is that, unlike behavioral roles in this species, the gene expression roles seem to follow conventional patterns of sex roles. In other words, although the species is behaviorally sex-role-reversed, their sexually dimorphic organ, the liver, does not show a reversal compared to other species (genes expressed in females are still expressed in female pipefish). That’s pretty cool, but it leaves a lot of questions still unanswered–namely, what genetic mechanisms actually underlie sex-role-reversal?
The final component of the paper was investigating how exposure to synthetic estrogen, a hormone analagous to the estrogen produced by our bodies, affects the patterns of gene expression in the pipefish liver. We know from previous studies (e.g. this one by a former labmate or this one by my labmate who is the first author of this paper) that synthetic estrogen can alter and disrupt the mating system of the Gulf pipefish, and in high enough doses it feminizes male pipefish so that they no longer have a brood pouch and start developing the female ornamentation patterns. So we were interested to see whether the sexually dimorphic liver responds to this feminizing hormone in expected ways. By comparing the expression levels in pregnant males, non-pregnant males, and females that were both exposed and not exposed, we were able to show that exposure to estrogen makes the male transcriptome more female-like, in that female-biased genes (like some that are involved in the production of eggs) are up-regulated in exposed males.
So why does this matter? Well, understanding how sex-role-reversal occurs at the mechanistic/genetic level is a major goal of evolutionary biology, because it is a major shift in the targets of sexual selection. And sexual selection and sexual dimorphism are often related, since sexual selection can drive the proliferation of exaggerated traits in one sex. So understanding gene expression in a sexually dimorphic liver in a sex-role-reversed species is a good first step: we can say that the liver is likely not directly involved in the sex-role-reversed behaviors of the Gulf pipefish. However, it may play a role in sexual selection, especially because it produces egg-related proteins, which could be experiencing rapid evolution because of female-female competition or to keep up with rapidly evolving sperm proteins. Additionally, we now know that synthetic estrogen at low levels feminizes the male liver. This is important because synthetic estrogen is one of many endocrine disruptors that are polluting water systems worldwide and affecting reproductive and endocrine systems in many species, including Gulf pipefish. It is possible that pipefish could be used as an indicator species by screening gene expression in the livers to identify whether a particular population has been exposed to endocrine disruptors.