Genetics for Newbies
My research interests tend to revolve around understanding how genetics influence early development, and how the environment (usually temperature!) impacts those effects. My current projects study how genetic and epigenetic variation influence Oncorhynchus mykiss life history. It’s difficult for me to describe my research in depth to folks who have had little exposure to genetics, so I created this post to supplement my research page as a guide. This is by no means everything you need to know about genetics, mainly just a way for me to be able to talk more about what I’m working on. If you’re finding this is really catching your interest though, send me a message and I can send you more reading material your way, or you can explore Wikipedia’s Introduction to genetics page or the NIH’s Help Me Understand Genetics website.
What is dna anyway?
Figure 1: Depiction of deconstructed DNA double helix, forming a diploid chromosome.
To start off, DNA (deoxyribonucleic acid) functions as instructions for how to build, operate, and maintain an organism from scratch. DNA’s structure forms as a stable double helix and consists of a string of hydrogen, phosphates, and oxygens arranged into 2 backbones, that are connected by base pairs (Figure 1). Base pairs, or nucleotides, can be adenosine (A), cytosine (C), guanine (G), and thymine (T). When correctly aligned, a cytosine on a strand should be paired to the other half of the DNA strand by a guanine base pair, while adenosine binds to thymine. You may when notice looking at Figure 1, that adenine and guanine (double-ringed) and that thymine and cytosine (single-ringed) have similar structures to each other. Nucleotides are sometimes grouped by these structures, known as purines (double-ringed) and pyrimidines (single-ringed). The two complementary DNA strands store the same information, but run antiparallel to each other. DNA itself is stored in the nucleus, or control center, of every cell in the body. The DNA is coiled tightly into large blocks, called chromosomes. This means that every cell in your body holds the instructions to create every cell in your body!
The term “gene” generally describes DNA that codes for a protein. Not all DNA codes for proteins - in fact a very significant portion of it doesn’t! We’re still figuring out exactly why this is, but we do know that it is still extremely useful for studying molecular evolution. For cells to use the instructions in DNA, the strands of DNA are split apart so the base pairs can be transcribed into single-stranded RNA (ribonucleic acid), then translated into protein (Figure 2). RNA serves as an intermediate between DNA (instructions) and protein (the physical manifestation of those instructions). The RNA with the stored DNA sequence order is translated into protein that is then used by the cell or distributed to other cells. This can take form as body planning, behavior, physiological processes, etc. - basically anything you can think of that is related to body structure, function, and maintenance. This is how organisms use genetic instructions to build and maintain their bodies!
Now that you’ve run through this crash course in DNA structure and function (yikes! good job!), let’s start to consider how we can use genetic data to study organisms.
variation among individuals: genetic, environmental and genotype-by-environment
Figure 2: Depiction of the transcription, translation, and utilization of genetic instructions. Alleles, variants of genes (protein-coding DNA), are included by leading to the expression of different traits (feather color).
In terms of evolutionary biology, individuals vary from each other by both genetic and environmental factors.
The term “genotype” describes the structure of the DNA sequence of interest (aka the content and order of nucleotides) and the term “phenotype” describes the physical manifestation of the genotype through transcription and translation to protein (aka a trait of some sort). A lot of research is geared at trying to better understand the connection between genotype and phenotype. The process of expressing a genotype, as shown by my very brief description of genotype to phenotype, is extremely complicated! In addition to these major steps, each step has different methods to modify the forming product. These modifications influence phenotype formation. The environment influences the expression of genetic code as well, by affecting protein shape and quantity. These changes influence phenotype, or the physical expression of the genotype. These changes make understanding the process of converting a genotype into a phenotype really difficult!
If this isn’t complicated enough, genetic code can contain really complex structures. I explain these structures more in the upcoming genetic variation subsection, but just know they complicate things in studying how phenotypes come to exist in their form. Also, some phenotypes are very complicated to categorize. Quantitative traits vary continuously, like height, and are usually more difficult to study in comparison to discrete traits, like eye color. Quantitative traits follow similar laws in behavior as discrete traits, but on a massive scale. These phenotypes are produced as the result of the combined efforts of many alleles and environment influences. This is why it is often easier said than done when trying to determine how genetic code is translated to an organism. There are a lot of influencing factors that make it difficult to understand exactly what is going on! However, increasing power in computation and analysis is allowing us to get closer to untangling it all.
Figure 3: Mutations can consist of point-mutations, indels, gene duplications, chromosome mutations, and genome duplications. Mutations result from errors and directly create new genetic variants.
Genetic variation
“Genetics” generally describes the study of genetic variation among individuals, as well as the study of the transfer of that genetic variation from parents to offspring through inheritance. Genetic variation just means that the DNA sequences slightly differ from each other in a population of a species. Variations of a gene are called alleles. Genetic variation occurs from mutations that are transmitted from parents to offspring. Mutations to DNA sequences result from errors in handling genetic material. There are different levels of mutations, and I’m going to go through them quickly because I am studying a specific mutation in Oncorhynchus mykiss.
The types of mutations are: point-mutations, insertions/deletions, gene duplications, chromosomal mutations, and genome duplications. Point-mutations occur when there is an error in a single DNA position (Figure 3). Sometimes nucleotides are inserted into sequences, or nucleotides are deleted entirely. These insertions and deletions are sometimes called “indels” (Figure 3). Gene duplications describe the copying of a gene multiple times (Figure 3). This often results in gene copies that are closely located. These gene families can often lead to the creation of genes with new functions. Chromosomal mutations describe big changes to chromosome structure, such as deletions, pieces of chromosomes breaking off and inserting elsewhere (translocation), and chromosomal inversions (Figure 3). Chromosomal inversions occur when a piece of chromosome breaks off, inverts, and reinserts back into its original position. This effectively locks these genes together by preventing breakup of the inversion, allowing genes to co-adapt and give rise to complicated traits. I study an inversion on chromosome Omy05 in O.mykiss and how it influences juvenile development and life history (if a fish becomes a rainbow trout or steelhead). Genome duplications describe the duplication of an entire genome (Figure 3). This happens most commonly in plants, but has been recorded in animals, including salmonids! This is also called polyploidization and contributes big time to plant speciation by preventing plants with different chromosome numbers in be able to cross-pollinate.
Studying genetics allows for studying heritable variation among individuals. This means variation that is inherited by offspring from their parents. We inherit our DNA from our parents from them each donating a gamete (egg / sperm) to form a zygote (fertilized egg) that eventually develops into a reproducing adult, if all goes well of course. Heritable variation is significant to evolution because one of the required postulates for natural selection to work is at least some of the variation among individuals must be heritable. I’ll explain natural selection and other evolutionary forces in another post someday (?!), but essentially it is the mathematical outcome of a nonrandom subset of individuals in a population putting more offspring into the next generation. If these offspring have inherited the variation that gave their parents higher reproductive success, then they will likely reproduce successfully as well. Natural selection produces populations with individuals more adapted to their local environments and can even lead to speciation, the formation of new species. Evolutionary biology concerns itself with studying adaptations of species, how those adaptations were formed, and the process of speciation. This is why understanding genetics (and genotype-by-environment interactions) is important!
Environmental variation
Environmental variation occurs when individuals experience unique environments and those external factors influence how a protein is made from genes or how the proteins work. This alters gene expression, therefore altering phenotype. These changes are generally not transmitted from one generation to the next. A really exciting field of research has been studying a very specific form of environmental variation that can be transmitted from parents to offspring. This field is called epigenetics. Epigenetic changes occur to an individual’s genetic code and alter the code’s expression (the proteins it creates), not the code itself (the order or content of nucleotide bases). These changes result in response to the environment and can be transmitted from parents to offspring. The rapid advancement of molecular technology has led to the development of epigenetic markers that allow researchers to track and quantify epigenetic changes.
The most studied epigenetic marker takes advantage of a process called DNA methylation. During an organism’s lifetime, methyl carbon groups are added to certain cytosine nucleotides to change how those genes are eventually expressed. Rapidly improving molecular technology is now allowing us to compare epigenetic differences among individuals, but costs are still pretty expensive. The other aspect of my project with Mokelumne River Hatchery considers epigenetic differences between hatchery fish with different life histories (fish heldover in freshwater vs. fish allowed to migrate to sea and back).
I will be posting more information about this project as time comes, as well as more about the exciting research that is the foundation of this project.
Again, this is by NO MEANS everything you need to know about genetics, but I hope at the very least, it helps you!