A Budding Interest in Plants

As the first academic year of my PhD program draws to a close, with the qualifying exams in May the final remaining hurdle, we will soon be expected to decide on a lab where we will conduct our thesis research. It’s a big personal decision, and the title of this post somewhat gives away the decision I have made.

The purpose of this post is to describe the thinking behind making my decision. Maybe it will be useful to those who are in a similar position as me, or even those who are now thinking about applying to PhD programs or pursuing a career in research, but maybe it won’t.

First, what were my options? My core interest from the beginning has been in studying evolution using genomics and/or population genetics, and that was the guiding principle in picking the labs that I’ve rotated in. The four labs I’ve rotated in mainly study, respectively:

  1. The population and evolutionary genetics of plant domestication with emphases on cereal crop (rice) and fruit tree (date palm) evolution
  2. Copy number evolution and gene regulation in response to environmental conditions, using experimental evolution of yeast
  3. The evolution of transposable elements in natural populations, in a wide variety of taxa including frogs, lizards, and falcons
  4. Population dynamics and population genetics of bacteria, with recent work exploring recombination in bacterial populations

If you asked me at the beginning of the year to arrange the labs in order of my probability of joining them, the order, with descending probabilities, would be 4, 2, 3, 1. Population genetics of bacteria (4) combines my familiarity with microbes – I have a Master’s in Microbiology and Immunology – with my interest in population genetics. Experimental evolution of yeast (2) is a remarkable system to explore evolutionary dynamics in real time. As previous posts hint at, I am very interested in evolutionary conflicts (3), including those between hosts and pathogens and between selfish genetic elements like transposable elements and host genomes, and the prospect of working with natural populations appeals to my interest in basic science.

While these incentives still remain, I now have a whole set of new ones for studying evolution in the context of plant domestication (1). Lists are easier to follow, so here goes:

  1. Domestication of plants like rice has an inherent anthropological context in that it is intricately tied to the recent evolution of human populations. Agriculture is thought to have enabled much of what we consider to be unique to human culture, such as language, complex structures and tools, and cities. Domestication occurs through strong selective pressures imposed by selective breeding, and understanding how a crop was domesticated and how it dispersed can not only teach us about evolutionary processes in general, but perhaps also about human populations of the past.
  2. The PI is one of two true, traditional population or evolutionary geneticists in the department, which is why I rotated in a plant lab in the first place. This is important because I am now quite clear that I want to study population genetics, possibly in humans, in my own future research career. Being in such a lab would help me learn the right skills for what I want to do. For instance, this lab has demonstrated past hybridization and introgression events in plant genomes using essentially the same tools that were used to demonstrate introgression from Neanderthals into non-African human genomes, which endures as one of my favorite stories.
  3. The lab has recently set up a small space for working with ancient plant DNA. It seems like I will get to use it.
  4. Familiarity has bred a bit of boredom. I don’t want microbes to be my central focus anymore.
  5. Whatever organism(s) I end up studying in my own career, whether it is humans or something else, I am quite certain it is going to be a multicellular eukaryote. And even if I end up studying some aspect of host-pathogen coevolution in my future career, I really need to become more comfortable with the host side of things. The host will be a multicellular eukaryote. Plants are a great place to start.
  6. Plant genomes are crazy. Frequent polyploidy, the ability of many plants to undergo both selfing and sexual reproduction, and the high transposable element composition in many plant genomes make the study of plant population genetics, speciation, and genome structure a delightful prospect.
  7. It just has a sense of adventure for me. With the little that I know about plants, everything that I learn is new and exciting.

I have talked to the PI, and will be joining, but in the meantime, I am trying to familiarize myself with the lab’s previous work and the field of plant evolution in general. I’d like to briefly describe a book I’m reading as part of that.

G. Ledyard Stebbins is one of the few people in plant evolutionary biology that I had previously known about. Stebbins was a pioneering plant population geneticist who, alongside people like Ernst Mayr and Theodosius Dobzhansky, was a leading figure in defining the modern synthesis of evolution and genetics, building upon earlier work by Ronald Fisher, J.B. Haldane, and Sewall Wright. So, I bought one of his major works, Flowering Plants: Evolution Above the Species Level, originally published in 1974, for a bit of light reading.

Title page; I adapted the flowers for the featured image

Now, I know this is almost fifty years behind the current state of the field, but it’s a fun starting point to follow the progression of the field over the years. The central conceit of the book is that the same evolutionary processes (e.g. mutation, selection, drift etc.) that govern the relatively recent evolution of species and populations as understood from the study of natural populations also governed evolution at deeper evolutionary timescales further back in time, that has led to the formation of today’s genera, families, and orders. I suppose I have always taken that for granted.

I am enjoying Stebbins’ descriptions of variation in traits in natural plant populations. I do have to keep looking up more recent literature to see how some of his more speculative ideas have fared, but that seems like a great way to learn how the field has progressed. I may write about some of the themes covered in the book, and how they have changed or gathered more empirical support over time in future posts.

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