Experimentation – Comparing Chimpanzee Tools to Those of Our Potential Ancestors

Piecing together our evolutionary history can be particularly difficult because we are not able to study the behaviors of extinct hominin* species as they are occurring. That is why we look toward what these species left behind for clues and data. The earliest known primate archaeological evidence is known as the Oldowan. This consists of a tool-kit made of stone. The creation of these stone tools by hominins dates as far back as 3.3 million years ago with the Lomekwi, from West Turkana, Kenya (Harmand, 2015). With the Oldowan, we begin to see a systematic reduction of rock, rather than the creation of tools due to random bashing. In other words, these hominins would take a piece of rock and break pieces away from it, one by one, to create a tools. This process is known as knapping. While knapping, the main piece of rock that you are working with is referred to as the core, whereas the pieces that are broken away are known as flakes.

Knapping via Handheld Percussion

(Click Image to Enlarge – Image Found on Wikipedia article “Lithic reduction”)

Evidence for systematic knapping becomes especially clear at around 2.5 million years ago in areas such as Gona, Ethiopia (Semaw, et al. 1997). At this site, the researchers found both flakes and cores. By simply putting the pieces back together, they were able to display how systematic this process truly was. These carefully chosen rock pieces were broken down in a fashion that required both experience and at least some degree of planning. This planning can also be seen in the fact that the raw materials were clearly “chosen” and not selected randomly. Hominins were deliberately selecting rocks disproportionately to their distribution, based off of the material that they were made of (Wynn & McGrew, 1989). This implies active thought behind raw material selection.

While both ancient hominins and wild chimpanzees are known for tool-use (See the Bio Bay blog post titled “Chimpanzee the Toolmaker: A Study of the Complex Behaviors of Wild Chimpanzees”), there is a difference in the types of tools that we have evidence of them creating. Many of the tools used by chimpanzees are crafted using vegetation. Unfortunately, vegetation does not preserve well in the archaeological record. Therefore, if the Oldowan did contain wooden tools, we still have no evidence of it. On the other hand, chimpanzees in the wild are not known to create flaked stone tools. To see if chimpanzees are capable of making these sorts of tools, scientists turned to experimentation.

One of the most well-known cases of a chimpanzee creating flaked stone tools in an experimental setting comes from the study of Kanzi the bonobo (Schick, et al. 1999). This study involved the analysis of three years’ worth of artefacts created by him. During experimentation, Kanzi would be presented with the raw materials needed to knap sharp, flaked stone tools into existence. The researchers also presented Kanzi with a food reward that could be seen, but only accessed if Kanzi managed to cut through a thick, nylon cord that was used to keep the food container shut.

Kanzi the Bonobo Chimpanzee (Pan paniscus)

(Click Image to Enlarge – Image Found on Wikipedia article “Kanzi”)

Over the three-year period, Kanzi’s ability to flake stone tools under experimental conditions improved. Kanzi even began using flaking methods that were not previously demonstrated to him. Even though the researchers showed the bonobo how to knap using handheld percussions, he eventually began throwing stones at each other. This is perhaps due to the fact that the amount of force that can be generated from throwing is greater than that of handheld percussions. However, this does appear to decrease the accuracy of the strikes. It should also be noted that Kanzi preferentially used larger and heavier stone tools. The researchers believed that Kanzi had a good sense of the potential usefulness of flakes and fragments as cutting tools. Unfortunately, this experiment has not yet been replicated using other common chimpanzees/bonobos. Doing so would help increase the confidence of these results and would also help answer a few questions regarding the “range” of chimpanzee intellectual capabilities. In other words, it would help scientists discover if all chimpanzees are capable of performing these sorts of tasks once trained, or if Kanzi is a very special ape.

Due to the tremendous amounts of data collected regarding both the capabilities of chimpanzees and the Oldowan industries, scientists have been able to begin making assessments regarding the behaviors of the hominins that created these stone tools. The paper, An Ape’s View of the Oldowan (Wynn & McGrew, 1989) began to look at the records to determine the “minimum” capacity needed to replicate the behaviors that produced the Oldowan industries. This study was performed before the Kanzi experiments, and the researchers still determined through cognitive analyses of chimpanzees that the Oldowan does not massively exceed what chimpanzees are capable of. In other words, the Oldowan archaeological evidence alone does not prove that these ancient hominins had greater than an ape adaptive grade (they were not necessarily doing anything that a chimpanzee cannot). However, even Kanzi failed to replicate the full range of tools gathered at Gona, Ethiopia with regards to the variety of tools seen (Schick, et al. 1999) (Semaw, et al. 1997). With this in mind, it is interesting to begin to question just how advanced these ancient hominins must have been. To do so, we should consider the field of comparative psychology. This will be the topic that I focus on for my next blog post.

Until next time, carry on with curiosity.

 

* Definition of Hominin: any of a taxonomic tribe (Hominini) of hominids that includes recent humans together with extinct ancestral and related forms

Definition from https://www.merriam-webster.com/dictionary/hominin

See the Bio Bay post titled “The Men and Woman Who Walked Beside Our Ancestors” for more information.

 

Works Cited

Harmand, S., Lewis, J. E., Feibel, C. S., Lepre, C. J., Prat, S., Lenoble, A., … & Taylor, N. (2015). 3.3-million-year-old stone tools from Lomekwi 3, West Turkana, Kenya. Nature521(7552), 310-315.

Semaw, S., Renne, P., Harris, J. W., Feibel, C. S., Bernor, R. L., Fesseha, N., & Mowbray, K. (1997). 2.5-million-year-old stone tools from Gona, Ethiopia.

Wynn, T., & McGrew, W. C. (1989). An ape’s view of the Oldowan. Man, 383-398.

Schick, K. D., Toth, N., Garufi, G., Savage-Rumbaugh, E. S., Rumbaugh, D., & Sevcik, R. (1999). Continuing investigations into the stone tool-making and tool-using capabilities of a bonobo (Pan paniscus). Journal of Archaeological Science26(7), 821-832.

 

Chimpanzee the Toolmaker: A Study of the Complex Behaviors of Wild Chimpanzees

As humans, our closest living relatives are the chimpanzees. This term, chimpanzee, can be used in a general sense referring to the species within the genus Pan. This includes both Pan troglodytes, the “common” chimpanzee, and Pan paniscus, the “bonobo” chimpanzee. Studying these organisms, as well as the rest of the great apes, has been extremely helpful for scientists attempting to paint an evolutionary picture.

Common Chimpanzees (Pan troglodytes)

Bonobo Chimpanzee (Pan paniscus)

(Click Images to Enlarge – Images Found on Wikipedia article “Chimpanzee”)

It has also debunked the concept of “Man the Toolmaker”. While our species does have a particular reliance on technology, arguably greater so than any other species on the planet, we are not the only toolmakers. In fact, chimpanzees have a fairly impressive tool-kit that allows them to engage in complex activities. With this in mind, we can begin comparing “Man the Toolmaker” to “Chimpanzee the Toolmaker” by looking at three complex behaviors that wild chimpanzees partake in. These are nut-cracking, termite fishing, and the skewering of bush-babies using “spears”.

While nut-cracking may seem simple to some, it is actually a complex behavior that requires the use of two different stone tools. Nut-cracking requires both a “hammer” stone and an “anvil” stone. The nut is positioned onto the anvil and then struck with the hammer in order to crack open the tough outer shell of the nut to release the food reward in the center. A study by Boesch in 1991 discusses events in which mother chimpanzees would “provide” nuts or stones to their offspring to assist in nut-cracking. However, another study that also reviewed Boesch’s work (Lonsdorf, 2013) pointed out that the mothers seemed to be simply tolerant of their children taking the materials that they were working with. This brings about the question as to whether or not the mothers were actively making an effort to “teach” their offspring in these scenarios.

Recent studies have shown forms of teaching among chimpanzees regarding termite fishing (Musgrave, et al. 2016). Termite fishing is another complex behavior that requires the use of two different tools. In this scenario, a certain degree of future planning can be observed as the chimpanzee uses two sticks designed for different tasks. The first stick is generally stronger and more durable than the second as it is used simply to perforate the termite mound. Once this action has been performed, the second stick is then thrust into the mound and held there until termites begin to attack it. The stick can then be extracted, allowing the chimpanzee to eat the termites that are clinging on. Some groups of chimpanzees will also pull the end of the stick through their teeth before inserting it into the termite mound to craft a certain “brush-tip wand”. This has been shown to increase the efficiency of capturing termites and is an example of tool modification (Sanz, Call, & Morgan, 2009).

Bonobo Termite Fishing

(Click Image to Enlarge – Image Found on Wikipedia article “Tool use by animals”)

It is actually quite difficult to demonstrate teaching in the wild. However, researchers have now shown that some wild chimpanzees from the Goualougo Triangle actually donate termite fishing probes to naïve learners (Musgrave, et al. 2016). Regardless of the intentions of the “teacher” in this scenario, the researchers argue that teaching has occurred if three stipulations have been fulfilled. These stipulations are: “they occur in a learner’s presence, are costly to the teacher, and improve the learner’s performance.” Throughout this study, it is shown that these three criteria are met through this donation process. It is also suggested that teaching may be necessary for this particular activity because it is so complex. The chimpanzees here must make specialized, frayed tools from specific raw materials. Through studies like these, it is clear that teaching is not a uniquely human phenomenon.

Teaching is not the only activity recently thought to be unique to humans that we later observed in chimpanzees. Once scientists began noting that chimpanzees use and make their own tools, they then came up with the idea that humans were the only ones to use tools for advanced hunting. In other words, humans perform “tool-assisted predation” that goes well beyond using sticks to gather termites, but is this solely a human activity? As it turns out, some chimpanzees use tools to hunt monkeys known as bushbabies (Pruetz & Bertolani, 2007). Since these monkeys are nocturnal, they often can be found sleeping inside of hollow trees during the day. To get to these monkeys, chimpanzees will sometimes find holes in the tree and stab sharp sticks into them in an attempt to skewer the monkeys before they can get away. These chimpanzees have been observed personally modifying sticks for this purpose, stripping them of branches and sharpening the tip with their teeth. Clearly, they are adept hunters.

With these examples in mind, one may begin to question what activities are unique to humans. Where exactly do we draw the line that defines humanity? For my next blog post, I will further discuss this concept and chimpanzees through some of the data that have been gathered from controlled experiments. Until next time, carry on with curiosity.

Works Cited

Boesch, C. (1991). Teaching among wild chimpanzees. Animal Behaviour41(3), 530-532.

Lonsdorf, E. V. (2013). The role of mothers in the development of complex skills in chimpanzees. In Building Babies (pp. 303-318). Springer New York.

Musgrave, S., Morgan, D., Lonsdorf, E., Mundry, R., & Sanz, C. (2016). Tool transfers are a form of teaching among chimpanzees. Scientific Reports6.

Sanz, C., Call, J., & Morgan, D. (2009). Design complexity in termite-fishing tools of chimpanzees (Pan troglodytes). Biology Letters5(3), 293-296.

Pruetz, J. D., & Bertolani, P. (2007). Savanna chimpanzees, Pan troglodytes verus, hunt with tools. Current Biology17(5), 412-417.

 

ddPCR – Droplet Digital Polymerase Chain Reaction

In my previous blog post, I discussed a scientific process known as the Polymerase Chain Reaction. Using the simple steps in this procedure, one can take a small amount of DNA and reproduce it exponentially until they obtain an ample, usable sample. Using PCR, other more detailed techniques have been developed to give a more quantitative measure regarding the amount of DNA or RNA that is seen in a particular sample. One example of this is real-time PCR, which has been used in a number of important experiments throughout the years. However, today we will be discussing a newer procedure known as droplet digital PCR (ddPCR). Digital PCR is generally considered to have a higher precision rate than real-time PCR.

Before we delve into the actual methodology behind droplet digital PCR, we should first discuss why it is important to quantify DNA and/or RNA. One situation in which ddPCR comes in handy is when one is trying to look at CNVs, or copy number variants, in a particular sample. For example, the number of amylase genes in humans can vary depending on the individual. If you want to tell how many copies of the amylase gene a particular individual has, then you can use ddPCR to get the answer. Furthermore, active genes use RNA as their messenger molecule to create particular proteins, so measuring RNA levels using ddPCR can tell how active a particular gene is.

To begin the process, the samples will need to be mixed with specific primers and probes (with fluorescent tags) that recognize the sequence that you are attempting to get the copy number of, as well as a sequence of known copy number (or in the example of RNA – a region of questionable activity versus one with a stable activity level such as a housekeeping gene).

The first step of this procedure is partitioning. This simply means dividing up the sample into equal volume droplets. As the image shows, the target and background DNA will be randomly distributed throughout the droplets. This is done in an automated fashion.

The samples are then amplified through normal PCR in each droplet simultaneously, maintaining ratios of the targeted DNA segments.

(Click to Enlarge Images – Images Modified from http://www.laboratoryequipment.com/ sites/laboratoryequipment.com/files/legacyimages/Markets/Life_Science/Digital%20PCR %20Figure%201%20FINAL%20CMYK.jpg )

The ddPCR machine then detects the levels of fluorescence of both target regions. Using this, you will receive ratios that can then be used to determine quantities based off of your “known” segments.

In other words, we compare the amount of fluorescence given off by the segment of known value to those of the unknown value. We will use the example of salivary amylase to further illuminate how this process works. Let’s say that we are comparing a gene that we know has two copies in every healthy human against the salivary amylase gene. If the machine reads off a ratio of one to four respectively, then we know that the individual in question has eight copies of the salivary amylase gene. The simple math can be seen below.

1x = 2    Where x is the multiplier and the solution is the number of genes
x = 2

4 x = ?
4 (2) = 8

Droplet digital PCR is largely automated which cuts down on the amount of human error, making it very precise. This process is also more accurate than real-time PCR because of the way in which the machine reads the fluorescence. It does so through the previously mentioned partitioned droplets. Because the droplets are so small, the ideal situation would be for them to either have one fragment of target DNA, or none. This means that the droplets can, and will be measured as a “have” or a “have not.” This allows for easy and accurate measurements of the fluorescence.

And that’s all there is to it! Until next time, carry on with curiosity!

Works Cited

Laboratory Equipment. (n.d.). Retrieved August 05, 2016, from http://www.laboratoryequipment.com/

Polymerase Chain Reaction – Turning a Few Strands of DNA into Many

Prior to a process known as polymerase chain reaction, or PCR, studying DNA was a much more complicated process. With just a few drops of blood at a crime scene or dry brittle bones at an archaeological dig site, collecting a usable amount of DNA was nearly impossible. Then came a man named Kary Mullis who helped develop the innovative technique that is still used in laboratories worldwide today.

Kary Mullis is not your “stereotypical” scientist. As a local of California, he did a lot of his scientific thinking while surfing. He also often openly criticizes the way that scientists must apply for grants in this country and the system that this creates. Alongside this, he openly chronicled how he would develop and test his own psychedelic drugs, such as LSD. We could tell tales of his life behind the science.

Personal life aside, Kary Mullis will certainly go down in history for perfecting the polymerase chain reaction. PCR, while incredibly useful, is not a difficult procedure. To understand the process, we must go back to the basics of DNA. DNA is a double stranded molecule connected in the middle of the strands by bases known as adenine (A), thymine (T), cytosine(C), and guanine(G). In DNA, adenine always pairs with thymine (A-T), whereas cytosine always pairs with guanine (C-G). Attached to each of these bases is a sugar (deoxyribose) phosphate backbone. The molecule is weakest between the bases. This is because DNA is only held together between the bases by hydrogen bonds. There are two hydrogen bonds between adenine and thymine and three between cytosine and guanine. While these bonds are weak individually, together they hold the molecule into a stable, double-stranded form.

(Click Images to Enlarge – Images and Image Legends Found on Wikipedia articles “Base Pair” and “DNA”)

PCR works by manipulating temperature in a cyclic fashion. There are three steps to the procedure that occur over and over again.

  1. Denaturation
  2. Primer Annealing
  3. Elongation

Prior to the first step, you must add the DNA that you are attempting to amplify (AKA multiply), enzymes (proteins) to make the process work, free bases (nucleotides – the A’s, T’s, C’s, and G’s discussed above), and primers. Primers are simply sequences of nucleotides that bind to a segment of your target sequence in the DNA that you want to be amplified. One primer binds to the beginning and the other primer binds to the end of your particular sequence (forward and reverse primers). Once the primers attach, the proteins can go to work and add the rest of the bases.

The first step, denaturation, means that we simply raise the temperature to a point in which the DNA unwinds (since it is in a helix form) and all of the hydrogen bonds break between the bases in the DNA strands. This temperature must be hot enough to accomplish this, but not too hot as to denature the rest of the molecule. Generally, this is around 94 degrees Celsius.

Step two, primer annealing, simply involves the scientist lowering the temperature to a point in which the primers can bind to the DNA (generally around 56 degrees Celsius.) Once this has occurred, step three of the process can begin after the temperature is raised once more to approximately 72 degrees Celsius. One of the major enzymes needed for this process to run is known as DNA polymerase. Simply put, DNA polymerase actually goes through the newly single stranded molecules and adds the bases to make them double stranded once again. This process begins where the forward primer is attached.

One of the original problems with this process is that human DNA polymerase does not function at these high temperatures. The enzyme denatures, or breaks down. To remedy this situation, the polymerase of another organism is used. The Bacterium, Thermus aquaticus (Taq), lives and thrives in hot temperatures. Therefore, its DNA polymerase functions in these heated environments. This is why it can be used for this process. To reiterate, Taq Polymerase it does not denature in the heat the way that human polymerases do.

Once this process is complete, your DNA molecules should have duplicated. You then repeat this process approximately forty times. This causes an exponential increase. One molecule becomes two, two becomes four, four becomes eight, eight becomes sixteen, and so on and so forth until you are dealing with a usable amount of DNA.

With the correct ingredients and a cyclic change in temperature, we can prompt one of the most important molecules in the world to duplicate. Naturally, we do not change the temperatures manually. We have thermal cyclers to do this for us. Simply put the concoction together and add it to a PCR machine, apply the correct settings, close the lid and wait. We must thank the scientists who came before us for helping make our research a bit easier. Until next time, carry on with curiosity!

 

Works Cited

Base pair. (2016, May 28). In Wikipedia, The Free Encyclopedia. Retrieved 19:26, July 15, 2016, from https://en.wikipedia.org/w/index.php?title=Base_pair&oldid=722444608

DNA. (2016, July 24). In Wikipedia, The Free Encyclopedia. Retrieved 20:09, July 26, 2016, from https://en.wikipedia.org/w/index.php?title=DNA&oldid=731351649

Introgression from the Ancients

As stated in my previous blog, it appears that we were not the first “human-like” species to leave our mother-country of Africa. The Neanderthal and Denisovan people made this migration before our ancestors did. However, the Neanderthals and Denisovans may have played a role in our own ancestry. Unless your heritage comes solely from Africa, it is likely that you have a bit of Neanderthal DNA in you. This is partially because our ancestors mated with the Neanderthals in the Near and Middle East as they were leaving Africa. This caused major introgression events, meaning that the Neanderthals introduced non-human genetic material into the human population migrating out of Africa.

(Click Image to Enlarge – Image taken from Wikipedia article “History of human migration”
The numbers on this map represent how many years ago the human migrations occurred.
Homo erectus* – A hominin species whose DNA has not yet been sequenced)

Remnants of these introgression events (as well as others that took place at different points in time when the two groups came in contact with one another) can be spotted in our genomes. In fact, over half of the Neanderthal genome can be recreated using the DNA of today’s modern humans. This high percentage is due to an additive effect from the fact that each person with a heritage from outside of Africa gets approximately 1-3% of their DNA from Neanderthals. Keep in mind, your 1-3% might not be the same as my 1-3%. It simply depends on what part of one’s genome the Neanderthal bits survived in until today.

A similar story can be told with the Denisovan people. Introgression events granting Denisovan DNA to our ancestors occurred as our people spread southeast throughout Asia. Nowadays, it is generally the Melanesians, Papuans, and Australians that have the largest segments of DNA that come from the Denisovan genome. Approximately 3-6% of their ancestry comes from the Denisovans.

You may now be wondering why our genomes still contain segments of Neanderthal/Denisovan DNA. Some scientists will attribute the majority of this to genetic drift, meaning that it is entirely due to chance (**see previous blog post – “Survival of the Fittest? Not Always…”***). However, certain fragments may still be in our genome due to a process known as adaptive introgression. According to Racimo et al., “As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments.” This states that some of these segments from Neanderthals/Denisovans may be in our genomes because they were beneficial enough to help our ancestors thrive and reproduce successfully.

For my next blog post, I will be changing gears to talk about a scientific procedure known as Polymerase Chain Reaction, or PCR for short. The discovery of this simple technique allowed for DNA studies to blossom and allow for an array of studies. These range from the study of ancient DNA, such as that of the Neanderthals and Denisovans, all the way to the forensic analyses used so frequently in America’s judicial system. Until next time, carry on with curiosity.

 

Works Cited

Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015). Evidence for archaic adaptive introgression in humans. Nature Reviews Genetics16(6), 359-371.

History of human migration. (2016, June 24). In Wikipedia, The Free Encyclopedia. Retrieved 20:47, July 13, 2016, from https://en.wikipedia.org/w/index.php?title=History_of_human_migration&oldid=726769187

The Men and Woman Who Walked Beside our Ancestors

As discussed briefly in my last blog post, there were populations of organisms from our own genus, Homo, that were so different from our ancestors that most scientists consider them their own species. These “people” lived long ago. However, the idea that they are their own species should be taken with a certain degree of criticism because of science’s loose interpretation as to what exactly constitutes a “species.” When discussing Neanderthals (Homo neanderthalensis), nobody can argue against the fact that they were fairly distinct from our ancestors (Homo sapiens). However, the extent of this distinction is worth discussing. For example, ancient Homo sapiens diverged from the Neanderthals at around the same approximate point in history in which western chimpanzees diverged from eastern chimpanzees (Prado-Martinez, et al. 2013). Despite this fact, we consider humans and Neanderthals different species, yet we consider eastern and western chimpanzees simply different subspecies.

(Click on image to expand. “Homo neanderthalensis, adult male. Reconstruction based on Shanidar 1 by John Gurche.” Image taken from:
http://humanorigins.si.edu/evidence/human-fossils/species/homo-neanderthalensis)

As we know, all human life began in Africa. All scientific evidence points to this fact. Our people eventually migrated out of Africa, but it appears as though the Neanderthals did this before our ancestors did. In fact, the majority of skeletal remains found from the Neanderthals were located in Europe. When they split off from the ancient group that contained both our ancestors and their ancestors, they likely migrated out of Africa through the North Eastern regions of the continent. They then traveled to Europe where they were able to continue evolving and developing the traits that made them unique from our own species. The discovery of Neanderthals was a grand one in scientific history, but it appears as though they were not the only group of “Homo” in the world other than our own species.

In 2010, a discovery was made in the Altai Mountains of Siberia. Specifically, it was made in a cave known as the Denisova Cave. The remains consisted mainly of a finger bone and a few molars (teeth). Despite the fragmented remains coming from different individuals, scientists were able to discover that they came from a new species that lived approximately 41,000 years ago! This species is now aptly named the Denisovans.

One might now be wondering how it is possible to tell that this was another species with nothing more than a few teeth and a finger bone from 41,000 years ago. The process is not a simple one, but it involves the isolation and amplification of ancient DNA from these sample. The isolation is necessary because there is so much “other” DNA that mixes with the ancient DNA. For example, countless bacteria exist, live, and thrive in the Denisova Cave, just as they do on the rest of our planet. Luckily, we are able to differentiate Hominin and bacterial DNA through bioinformatic analyses fairly simply because the two differ greatly. Then you run into the issue of “human contamination,” so you also need to separate the ancient DNA out from the highly similar human DNA that comes from the excavators and scientists working with the samples. Lastly, amplification is needed because only an extremely small amount of ancient DNA exists after 41,000 years. Amplification is done through a process known as polymerase chain reactions, AKA PCR, which takes a small amount of DNA and replicates it over and over again until you have enough to study. I will discuss this process further in a future blog post.

It is important to note that since these findings, there has also been evidence of other “ghost” hominin species similar to these ones. However, most of these were likely in Africa, where the hot humid climate is not conducive to the fossilization process. For example, there is evidence that another hominin species known as Homo erectus existed, but scientists have not yet been able to sequence DNA from the fossilized remains that were found.

In my next blog post, I will discuss how our ancestors mated with the Neanderthal and Denisovan people and the imprints that this left on our genetic signatures. Until next week, carry on with curiosity!

 

Works Cited

Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., … & Cagan, A. (2013). Great ape genetic diversity and population history. Nature, 499(7459), 471-475.

Smithsonian’s National Museum of Natural History. (n.d.). Homo neanderthalensis | The Smithsonian Institution’s Human Origins Program. Retrieved July 05, 2016, from http://humanorigins.si.edu/evidence/human-fossils/species/homo-neanderthalensis

The Non-Linear March of Progress

Go to google.com and type in the word “evolution.” Then click on the “Images” tab and you will see the same image, or a variant of it, displayed over and over again. We have all seen the picture before. It was originally coined “The March of Progress” and is supposed to display human evolution throughout history.

(Click on the Image to Enlarge – The March of Progress by Rudolph Zallinger)

While this image is potentially the most famous and iconic scientific diagram ever constructed, it is extremely misleading. It has been the cause of a number of misinformed criticisms to the theory* of evolution. The king of all misinformed critiques asks why chimpanzees are seen on the left side of this diagram, modern humans are seen on the right, but none of the intermediate species still exist today. This is because the organism on the left of this diagram is NOT supposed to be a chimpanzee.

Humans did not evolve from chimpanzees, any other apes, or any monkeys that we see on the planet today. Instead, we all share common ancestry. This means that approximately 65 million years ago, a time period that represents less than 1.5% of the age of our planet, there existed a “base primate” species. This base primate species was not the same as any primate species that we know today. However, it would have had characteristics of each group of primates. As time passed, its genetic information would have been warped slowly and new groups would have formed as the progeny of this original population began separating from one another. These gradual changes would eventually form the branches to the tree of life that we see below:

(Click on the Image to Enlarge – Image of a Cladogram Taken as a Screenshot of Wikipedia)

This tree shows which groups formed first, from left to right (Primates, Haplorhini/Strepsirrhini, Simiiformes/Tarsiiformes, etc.) and some of the subdivisions that occurred within the primate lineage in order to form the Homo clade. This is where humans reside. We are known as Homo sapiens. We are also not the only group that has ever existed that falls within the genus Homo. However, we are the only group of Homo that is still alive today. That is why our closest living relative is the chimpanzee, a species that falls under the genus Pan (Pan troglodytes). As you can see, we do not directly come from chimpanzees. Instead, we simply share common ancestry with them.

Next week, I will discuss more about some of the other groups of Homo that walked alongside our ancestors, known as the Neanderthals and the Denisovans.

*It is important to note that a scientific theory is not the same as a theory in other fields. It is not simply a hunch. In order for a scientific explanation to become a theory, it has to have passed every test that it has ever been put through. Every bit of evidence that has ever been gathered by mankind supports the theory of evolution. In the scientific community, its existence is not something that is still debated. In laboratories around the planet, including the one that I am part of, we study specific aspects of evolution. However, we do not refer to the theory of evolution as a “fact” because we can still incorporate new data into the theory. It is malleable, but will not be disproven.

Works Cited

Primate. (n.d.). In Wikipedia. Retrieved May 11, 2016, from https://en.wikipedia.org/wiki/Primate

Rudolph Zallinger’s “The March of Progress” from Time-Life’s 1965 book Early Man

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