What would I do with more research support? Part One: Background.

One of the great joys of being a scientist is that we get to spend our lives exploring the aspects of the natural world that most intrigue and excite us. However, the equally great frustration of being a researcher is that our curiosity and passion invariably outstrip the resources available for our explorations. It often feels like we spend the bulk of our creative energy begging for money, and when this is declined — as it often is — it can be crushing. What keeps us going is the conviction that what we are doing, and what we have not yet found a way to do, is interesting and important and worth pursuing.

The primary focus of my research is the evolution of genome size in animals. Genome size is the amount of DNA in one copy of the chromosome set of a species, generally measured in terms of the number of base pairs (bp) or in mass (in picograms, or 10-12g). What makes this an intriguing topic of research is the enormous variability that exists across species: in animals, genome sizes range more than 7,000-fold. Think about that for a moment. Some animals have 7,000 times more DNA in their cells than others. Even within vertebrates, there is huge diversity at the genomic level: the largest (lungfish) is 350 times larger than the smallest (pufferfish). Or consider amphibians, which range about 120-fold from the smallest in some frogs to the largest in a few aquatic salamanders.

The human genome contains about 3.2 billion base pairs. In the simplest terms, one might expect this to be the largest genome of all — humans are the most complicated organisms (right?) and that should require the most genes (right?) which in turn means more DNA (right?). This was indeed the assumption when researchers began assessing genome sizes in the late 1940s — before the structure of DNA was elucidated, and even before it had been established that DNA is the hereditary molecule. At this time it was reported that the amount of DNA in a species’ cells is mostly constant (thus, genome size is also called “C-value”). This itself was suggested to indicate that DNA, and not protein, serves as the molecular basis of inheritance. However, it was also obvious by 1951 that the amount of DNA varies dramatically among species, and that the “complexity” of an animal and its genome size are decoupled. There are, it was discovered, salamanders with 40x more DNA per genome than in humans. This made no sense. DNA amount is constant within species because it is what genes are made of, and yet more complicated organisms (which presumably require more genes) may have substantially less DNA in their genomes than simpler organisms. This became known as the “C-value paradox” in the early 1970s.

It was not long before the apparent “paradox” was resolved: most DNA in animal and plant genomes is not genes (it is “non-coding DNA”). This means that genome size need not be related to the number of protein-coding genes, and that there is no reason to expect more complex animals to have more DNA in their genomes. However, this raised many new questions: What is this non-coding DNA? Where does it come from? How does it increase or decrease in amount in different genomes? Does it have any effect on the organism? Does it have any function? Why do some species have so much of it and others so little?

Despite several decades of research, most of these questions remain at best only partially answered. This is where my lab’s research comes in. We are interested in genome size diversity across all animals, in its effects on organism biology, and in the factors ranging in scale from individual DNA elements to ecological properties that accentuate or constrain amounts of DNA in the genomes of different species.

One thing that has become clear over the past several decades is that genome size is not randomly distributed across taxa. Some, like birds, all seem to have relatively small genomes. Others, like salamanders, all have large genomes. The quantity of DNA also relates to important features such as cell size and cell division rate, such that large genomes are found in cells that are big and divide slowly. Because all animals are made of cells, this means that any feature relating to cell size or cell division rate could be indirectly related to genome size. Body size is an obvious possibility, at least when cell numbers are held mostly constant. Metabolic rate is another possibility, because the larger a cell gets, the lower its relative surface area is, and this can influence gas exchange. Developmental rate is yet another, because slower individual cell divisions can add up to protracted development overall.

We have found that body size is correlated with genome size not only in some invertebrates like flatworms and copepod crustaceans, but also within specific groups of vertebrates like rodents, bats, and birds. Inverse relationships between genome size and metabolic rate have been reported in both mammals and birds, and in particular it has been argued that flight imposes a constraint on genome size due to its high metabolic demands. This latter idea has been around for several years, but it has recently become the subject of renewed interest and some intriguing new discoveries. For example, my colleague Chris Organ has used fossil cell size measurements to reveal that theropod dinosaurs (the lineage from which birds evolved) already had somewhat reduced genome sizes relative to other lineages before birds evolved, and that pterosaurs (the first vertebrates to evolve flight) also had small genomes. One of my students has been working on flight in birds, and showed that wing parameters associated with flight ability are related to genome size as well.