Evo-Devo and Gene Regulation in Animals

Unfortunately, evolution is not a topic that is stressed enough in America’s educational system. Charles Darwin, the father of evolution, proposed that all organisms came to be via a gradual process known as descent with modification”. Simply put, this process allows for the accumulation of small changes that eventually cause far more dramatic ones. The natural human response to this concept is to think that such small changes cannot be responsible for the immense variety of life on this planet. This is nothing more than human bias. Without proper training, it is difficult for an individual to wrap their mind around the larger picture. Evolution has been shaping life on our planet throughout a timescale in which we are inconsequential, making the concept difficult to grasp.

The field of Evolution and Development (Evo-Devo) tries to answer questions in biology regarding how evolution shaped all organisms, allowing them to develop into a vast array of differing forms. What is interesting about this is that organisms tend to have a set body plan encoded within them at birth.

For the most part, animals have a general body plan that their DNA codes for. The environment can help play a role in this. For example, an individual who does not get proper nutrition may never reach their maximum height potential. However, unless an individual has some sort of serious birth defect, each one of us has the DNA sequences necessary for all of our major body parts. Within each of us is the genetic code to form two eyes, two arms, two legs, etc. Similarly, all non-human animals have the blueprints needed for their particular body plan.

It turns out that animals form in “segments.” Each of our limbs form as different segments that then specialize further and further until they take their particular shape. In these regards, even sections of our body that seem as different as our arms and our eyes can be looked at as similar. Each of these originally form as an individual “segment” of the body. These begin as clumps of stem cells. These stem cells have the ability to become any human cell type. A fair amount of this transformation from stem cells to mature cells is controlled by a set of genes known as the Homeobox genes.

The Homeobox genes, also known as Hox genes, code for the Homeodomain proteins. These Homeodomain proteins are transcription factors. Transcription factors bind to specific portions of the DNA. This binding affects which sections of the DNA get used to make messenger RNA (mRNA) and how much of the mRNA gets created. This is important because mRNA is the molecule that leaves the nucleus to code for proteins via the process known as translation. This allows for genes to be expressed at different amounts. These Hox genes play a similar role in all animals. They are part of a network of genes that help give an animal its form. There are multiple copies of the Hox gene in each animal. This is due to a number of tandem duplications, as well as a few whole genome duplications. Tandem duplications give rise to a copied segment of the DNA that is located beside the original copy. In contrast, whole genome duplications copy the entirety of an organism’s genetic sequence. Both of these phenomena can be seen by studying the evolutionary history of these developmental genes. In any case, the number of Hox genes may vary, but their coding sequences are fairly conserved. This is due to the importance of their function.

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Once again, Hox genes were crucial to the development of the vast array of organisms around us because they code for transcription factors. While they are not the only gene family to do so, they are one of the most important to animal development. A phenomenon known as gene expression is largely controlled by these transcription factors. To further explain gene expression, it is important to note that your DNA is essentially the same in all regions of the body, no matter how different two areas are. For example, the DNA sequence in your eye is the same as the sequence in your liver. However, how that DNA is expressed would be different. This is known as differential regulation. Depending on where you are in the body, some sections of the DNA will be more active than others. Differences in gene expression cause differences in protein levels. These differing protein levels cause the morphological (form) and physiological (function) differences that one can observe from one body part to the next. Similarly, gene regulation is responsible for a fair amount of the variation seen between organisms from distinct species. This is important to understand because most conventional evolutionary courses seem to imply that variation comes solely from changes in coding sequences. In other words, novel variation can come from mutations in the sections of the DNA that code for proteins, or it can come from mutations in the portions of the DNA that transcription factors bind to, changing gene expression.

The pioneers of the field of Evo-Devo have equipped us with what we need to move forward and continue expanding human scientific knowledge.

A Miniature, Aquatic World

Last year (2015), I had the pleasure of performing field work in Nome, Alaska with a professor named Dr. Derek Taylor. Dr. Taylor had devised a brilliant set of experiments to study animals local to the tundras of Alaska. We arrived at the end of July and stayed for approximately one week. While there, we witnessed environments unscathed by the touch of man. We beheld landscapes that seemed as though they were painted into existence, holding beasts of great magnificence and power. We heard muskoxen snort in discontent, warning that we were too close.

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-Photo taken by Mr. Bill Nichols of the University at Buffalo)

Despite all of the obvious wonders around us, we were there for something else entirely. Global climate change shifts aquatic ecosystems as the borders of bodies of water are altered rapidly. This is especially so for freshwater environments. These environments are the homes to a number of zooplankton* species.

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-Left – Daphnia, Top Right – Heterocope, Bottom Right – Chaoborus)

While in Alaska, we collected zooplankton samples from a variety of locations. The samples were gathered from numerous freshwater sources using D-nets or throw-nets depending on the depth of the water. D-nets are attached to a long wooden handle, whereas throw nets are thrown and then reeled back in, allowing the net to catch these tiny organisms as it passes. Samples were generally preserved using ethanol solutions or by drying them out. They would later be kept in freezers to maintain the integrity of their nucleotide sequences (see previous post – April 19th, 2016).

Dr. Taylor once told me that despite their small size, if one were to only consider the mass of zooplankton on our planet, the outlines of all of the major bodies of water would still be visible from space. This thought is truly astonishing and goes to show that there is an entire world of organisms that most people do not even consider.

These zooplankton are also a major component of the freshwater and saltwater ecosystems that they reside in. They can range from keystone predators to primary consumers that simply eat the algae in these waters. They are a major food source to countless organisms as they play their role in the food web.

Taking this a step further, there are viruses that are specifically adapted to infect individual species of zooplankton. These viruses can be extremely diverse and found in most (or all) types of zooplankton. Their tremendous numbers and quickly changing DNA makes them difficult, yet interesting to study. One method of doing so is known as metagenomics.

For a metagenomic analysis, a researcher sequences all of the genetic material in a given sample. In this case, it would be everything within a certain volume of water. This type of analysis then requires the researcher to take all of this data and compare it to known databases in order to find out which segments of DNA or RNA* are coming from which organisms (some viruses store their genetic information in the form of the molecule RNA, instead of DNA). This can be tricky since certain viruses are so new and underrepresented that they do not share high sequence similarity to anything in public databases. In our samples, I rarely saw viral segments of DNA/RNA that matched with known viruses to a degree of greater than 70%.

These zooplankton and their viruses have a massive impact on a number of organisms in their food webs. In this area of research, there are interesting stories around every corner. One just needs to ask the right questions.


Terminology Definitions*

Plankton – The aggregate of passively floating, drifting, or somewhat motile organisms occurring in a body of water, primarily comprising microscopic algae and protozoa

Zooplankton – The aggregate of animal or animal-like organisms in plankton, as protozoans

RNA – Acronym for Ribonucleic Acid – any of a class of single-stranded molecules transcribed from DNA in the cell nucleus or in the mitochondrion or chloroplast, containing along the strand a linear sequence of nucleotide bases that is complementary to the DNA strand from which it is transcribed: the composition of the RNA molecule is identical with that of DNA except for the substitution of the sugar ribose for deoxyribose and the substitution of the nucleotide base uracil for thymine.

Definitions from Dictionary.com


There are more pictures of our trip to Alaska in the Photography section of this blog.

What are Structural Variants and Why Do they Matter?

After spending some time in my Ph.D. program at the University at Buffalo, I ended up in the laboratory of a man by the name of Dr. Omer Gokcumen. In this lab, we study Evolutionary Biology. In particular, Dr. Gokcumen is a specialist with regards to what are known as structural variants. To understand what this means, we need to understand the basics.

All living organisms on this planet have a biological “blueprint.” This blueprint involves a particular coding system that utilizes four different nucleotides in a molecule known as deoxyribose nucleic acid, or DNA for short. These four nucleotides are Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). Each molecule of DNA consists of two strands that are connected by these nucleotides. A always pairs with T and C always pairs with G.

A mutation is a change in this code. The best studied mutations are ones that cause a single nucleotide to change from one to the other. For example, a Thymine could be placed where there should be an Adenine. These are called point mutations.

It should be noted that a single set of DNA “blueprints,” referred to as a genome collectively, is approximately 3 billion bases (nucleotides) in length in humans. This means that there are 3 billion A’s, T’s, C’s, and G’s in a single set. Each human has two sets. One of these sets comes from your mother, while the other set comes from your father. Despite this vast number of bases, if a single change is made in the wrong place, the effects can be tremendous. For example, sickle cell anemia, a life threatening blood disorder, is caused by a single point mutation. Conversely, a mutation could have no effect whatsoever.

Not all changes to the genetic code are caused by point mutations. This is where structural variants come into play. Structural variants involve taking an entire segment of this code and altering it in some way. The segment can be deleted out, duplicated, moved elsewhere (translocation), or flipped backwards (transversion). When these alterations cause a change in the number of times you see a particular DNA segment in the genome, the result is referred to as a copy number variant (CNV).

(Click the Picture to Enlarge – Figure from tutorhelpdesk.com (4))

When compared to single nucleotide variants (SNVs), which are caused by point mutations, these structural variants often seem to have a much greater effect on the human genome. In fact, according to one study (2), structural variants affect a minimum of seven times more human nucleotides than SNVs do! Despite this astonishing figure, the majority of research has been focused on SNVs. Why might this be?

The answer is simple; it’s easier. The current method of sequencing and mapping DNA involves cutting the DNA into small portions and then comparing it to the reference sequence. This means that if you have segments of DNA that have been moved, duplicated, or deleted, these small portions might not align to where they are supposed to be (i.e. where they originally came from in the genome prior to being cut up). One new study stated that 40 to 50 percent of CNVs have not been recognized yet (3)! This leaves much of the genome a mystery. Luckily, new technologies that utilize longer DNA sequence reads may solve this problem.

Structural variants are involved in a number of disorders including spinal muscular dystrophy, which is the result of a deletion. We must understand the cause of these diseases if we hope to one day fully remedy them. A number of these alterations could have also been involved in what made our lineage unique throughout our evolutionary history. For example, certain duplication and deletion events have been linked to body morphology (shape) and brain development in humans.

This is why the work done in laboratories that focus on structural variation is so important. We cannot hope to understand human genetics without a proper understanding of this type of variation. That is why I spend my time in the Gokcumen lab working on the discovery and understanding of SVs.


Works Cited

  1. Alkan, C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363–376
  2. Conrad, D. F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., … & Fitzgerald, T. (2010). Origins and functional impact of copy number variation in the human genome.Nature464(7289), 704-712
  3. Huddleston, J., & Eichler, E. E. (2016). An Incomplete Understanding of Human Genetic Variation.Genetics202(4), 1251-1254
  4. Modification of Chromosome Structure. (n.d.). Retrieved May 27, 2016, from http://www.tutorhelpdesk.com/homeworkhelp/Biology-/Modification-Chromosome-Structure-Assignment-Help.html


Survival of the Fittest? Not Always…

Imagine, if you will, this hypothetical scenario. It is not too long after the origin of life, and a population of organisms emerges. These organisms are the best adapted, compared to other species of organisms, to their particular environment. They have the potential to expand throughout the world. If left to their own devices, in this hypothetical situation, this population would continue adapting to their environments. By April 5th, 2016, this population of organisms would have evolved to the point that each individual would be that of tremendous intellect. In this scenario, they would have understood the world enough to create renewable energy sources to prevent themselves from altering their environment in detrimental fashions. They would have been a species of nonviolence, living in peace and harmony without concern or hatred over trivial matters. While progression toward complexity is not always the case in evolution, these magnificent beings could have become a reality with their roots residing in this population of primitive organisms. This is the potential power of selection. Now consider that this population of well adapted organisms found themselves in a small body of water that dried up, killing all of them. This then allowed for a species of violent, semi-intelligent primates to rule the world. This is the power of genetic drift.

The process of Natural Selection is commonly referred to as “survival of the fittest.” This states that the organisms best adapted to their particular environment are the ones that are more likely to produce viable offspring, affecting the allelic frequencies in their population. This concept generally increases the frequency of beneficial alleles and decreases the frequency of detrimental alleles. This is selection.


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However, genetic drift involves changes in allelic frequency due to chance events. Not every event throughout evolutionary history was a direct result of selective pressures. In other words, new alleles that would have been beneficial could very well have been wiped from existence before ever being propagated if the organism carrying said allele is killed prior to reproduction.

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The interplay between these two mechanisms seems simple enough, but it is still discussed at great lengths today. Population geneticists often seem to feel that certain evolutionary biologists overplay the power of selection, stating that chance events have had a much larger role in shaping the organisms around us today. This would mean that there isn’t an adaptive reason for every trait that ends up reaching high frequencies in populations.

It is important to note that these chance events have greater effects on a particular population if the number of individuals in that population is lower. Consider a group of three puppies being sold. In this group of dogs, each one is a different breed. For this example, we will say that there is one Chihuahua, one Maltese, and one Pomeranian. Now imagine that one of these dogs is randomly adopted. This would affect the diversity of puppies there in a much greater fashion than if there were twenty of each type of dog. This is a simple way of considering the effect of genetic drift on groups with different population sizes.

So when asking yourself how a particular trait is adaptive for the population that it resides in, one must consider the fact that it might not be adaptive at all.


Terminology Definitions

Allele – one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.

Definition from Google.com


The Bio Bay

Hello scholars! This message is going out to inform anyone who might be reading this that I am revitalizing this page. My goal here is to help spread some of the more interesting scientific topics and discussion points that I learn throughout my career. I plan to do this using the least amount of jargon possible, so that I might be able to help spread my love of Biology to anybody who is interested, regardless of training.

With these new intentions and the revitalization of the page, I am renaming it the “Bio Bay.” I wish you all the best and hope that you enjoy the posts!

Feel free to comment!

The Thorny, Gender-Switching, Giant Water Lily

There is a species of water lily that is known as Victoria amazonica. While lily-pads may not seem interesting to some, this particular plant has a certain grandeur about it based on its size alone. They can grow to be up to seven feet in diameter.


Being as large as they are can be both beneficial and harmful at the same time. While having an immense upper surface is good for attracting potential pollinators and performing photosynthesis, this could mean that the lower surface ends up being a hefty, sought-out meal for hungry fish. To prevent this from happening, these water-lilies have developed a system of thorns on their underside.


Their flowers are unique as well. When it is time for them to be fertilized, they give off a fruity aroma to draw in potential pollinators. Once the pollinators get there, they are welcomed by particular warmth. The flowers themselves generate heat through a process known as thermogenesis. Therefore, any pollinators that enter the flower are offered a warm place to stay for the night.

It is in the plant’s best interest for the pollinator to stay until morning. This is because these “floral lounges” have the ability to change gender overnight. They are female when the pollinators get there, allowing them to be pollinated. By the time the pollinators are preparing the leave, the gender-swapping has already occurred. Therefore, the pollinators are pollinated once more upon leaving the structure.

Read more at: http://www.kew.org/plants-fungi/Victoria-amazonica.htm


Stranger than Fiction: Spider-Goats


Genetically modifying organisms to suit our needs may seem like science-fiction to some, but it has already happened. One such example stemmed from Nexia Biotechnologies’ idea to splice the genes for spider silk protein into goats. When the splicing was successful, a female goat would then produce the protein in her milk. Once filtered out of the milk, the protein could be used to create an incredibly strong, natural silk. The material made from this silk was termed Biosteel™. Biosteel™ can be used to make thin, flexible, bullet-proof armor and can also be used in aerospace technology. Thus, much of it was bought by the U.S. government upon its creation. Each female goat that was capable of producing the protein in her milk sold for approximately half a million dollars. This just goes to show that being a creative scientist can really pay off.


One other interesting bit of information regarding this study is that the goats were, at one point, housed at the old Air force Base in my hometown of Plattsburgh, New York.

Read more at: http://beastsofhongkong.blogspot.com/2012/09/giant-spiders-and-quest-for-bio-steel_10.html