Friday, October 24, 2014
Phylogenetic Analysis Article
Daphne Gould
Phylogenetic Analysis Article
In this report, I will be examining the relationship between common house pets: canis lupus familiaris (dog), felis catus (cat), gerbillinae (gerbil), gekko gecko (gecko) and cavia porcellus (guinea pig). I decided to do this experiment on house pets because I have both a dog and cats and I formerly had a lizard, gerbil, and gecko. Though they share similarities, these animals clearly have important distinctions from one another. The phylogenetic question that I am interested in investigating through this experiment is how genetic differences in common house pets could potentially explain differences and similarities in phenotypic structure. To start off, I analyzed the cytochrome oxidase subunit I COI gene. I decided to utilize this specific gene because of the fact that it is common to all of the animals which I am testing, and it is fairly indicative of evolutionary history and phylogenetic distinctions.
In this experiment, I analyzed the DNA sequences of the various organisms. I was able to obtain these DNA sequences from the very same website that the packet suggests (www.ncbi.nlm.nih.gov), as I have found that this is a reliable source for genetic information. I also used Clustal X and NJ Plot to carry out my analysis in sorting through DNA sequences and making trees. Once I got over the initial complications with downloading the program, everything was relatively easy to work with. Prior to doing this experiment, I hypothesized that dogs, cats, gerbils, and guinea pigs would all be closely related with the gecko as the outgroup. I presumed that the gecko would be the outgroup because it is the only reptile of the bunch, while gerbils, guinea pigs, cats, and dogs are all mammals. My hypothesis was true, but I did not specifically anticipate the way that it would branch off. Upon further analysis with the phylogenetic tree, it seems as though guinea pigs are also more closely related to gerbils and cats are slightly more closely related to dogs. This makes much sense, as dogs and cats are both larger, and gerbils and guinea pigs are both smaller in comparison. Similarly, gerbils and guinea pigs are also both rodents, which would explain genetic alikeness. It appears as though the time of divergence for the rodent line from the dog and cat like was within approximately half the time since the divergence of the gecko’s lineage. Their structural, phenotypic similarities to one another were quite representative of their genotypic similarities in the end.
Phylogenetic Analysis Article
In this report, I will be examining the relationship between common house pets: canis lupus familiaris (dog), felis catus (cat), gerbillinae (gerbil), gekko gecko (gecko) and cavia porcellus (guinea pig). I decided to do this experiment on house pets because I have both a dog and cats and I formerly had a lizard, gerbil, and gecko. Though they share similarities, these animals clearly have important distinctions from one another. The phylogenetic question that I am interested in investigating through this experiment is how genetic differences in common house pets could potentially explain differences and similarities in phenotypic structure. To start off, I analyzed the cytochrome oxidase subunit I COI gene. I decided to utilize this specific gene because of the fact that it is common to all of the animals which I am testing, and it is fairly indicative of evolutionary history and phylogenetic distinctions.
In this experiment, I analyzed the DNA sequences of the various organisms. I was able to obtain these DNA sequences from the very same website that the packet suggests (www.ncbi.nlm.nih.gov), as I have found that this is a reliable source for genetic information. I also used Clustal X and NJ Plot to carry out my analysis in sorting through DNA sequences and making trees. Once I got over the initial complications with downloading the program, everything was relatively easy to work with. Prior to doing this experiment, I hypothesized that dogs, cats, gerbils, and guinea pigs would all be closely related with the gecko as the outgroup. I presumed that the gecko would be the outgroup because it is the only reptile of the bunch, while gerbils, guinea pigs, cats, and dogs are all mammals. My hypothesis was true, but I did not specifically anticipate the way that it would branch off. Upon further analysis with the phylogenetic tree, it seems as though guinea pigs are also more closely related to gerbils and cats are slightly more closely related to dogs. This makes much sense, as dogs and cats are both larger, and gerbils and guinea pigs are both smaller in comparison. Similarly, gerbils and guinea pigs are also both rodents, which would explain genetic alikeness. It appears as though the time of divergence for the rodent line from the dog and cat like was within approximately half the time since the divergence of the gecko’s lineage. Their structural, phenotypic similarities to one another were quite representative of their genotypic similarities in the end.
According to the Scientific Journal Genome Research, one study produced significant research on the genetic makeup of a cat, comparing to that of several other mammals, such rodents and dogs. This research concluded that one source of similarities within these animals is their susceptibility to similar viruses. This is the reason why animals, such as rodents, are often test subjects for pharmaceutical products.Virus receptors are similar throughout most mammals, including the ones studied in this experiment. If I were to redo this experiment, I would most likely attempt to use a gene used to combat viruses to see if that affects the flow of phylogenetic similarities.
It is true that there is a substantial variation within the level of similarities shown between genes. That being said, I feel as though the COI genes is a good indicator of these genetic similarities.
Phylogeny Analysis
Chigozie Amonu
Mr. Hammer
AP Biology
24 October 2014
Phylogeny Analysis: Humans, Chimpanzees, and Zebrafish
For this phylogeny analysis, I studied one question: How closely related are humans (Homo sapiens), chimpanzees (Pan troglodytes), and zebrafish (Danio rerio)? To answer this question, I searched for a gene that I could use to compare all of these organisms. The gene I chose to execute this comparison was the ALX homeobox 1 gene, or the ALX1 gene. The ALX1 gene provides instructions for making a protein that is a member of the homeobox protein family. The ALX1 protein is necessary for normal development of the head and face, and particularly the formation of the eyes, nose, and mouth. The ALX1 protein is a transcription factor, which means that it attaches to DNA and controls the activity of certain genes. This protein controls the activity of genes that regulate cell growth and division (proliferation) and movement (migration), ensuring that cells grow and stop growing at specific times and that they are positioned correctly during development (ALX1 Gene). After gathering this information, I hypothesized that humans and chimpanzees would be more closely related when I used the ALX1 gene for comparison because humans and chimpanzees share more similar facial structures than zebrafish and humans or chimpanzees.
I gathered the nucleotide sequences from the NCBI website by searching the genus species of humans, chimpanzees, and zebrafish. After I obtained the nucleotide sequences, I aligned them using the ClustalX program. I created a phylogenetic tree with the data that I gathered from the ClustalX program. From this phylogenetic tree I observed how closely related humans (Homo sapiens) and chimpanzees (Pan troglodytes) were compared to zebrafish (Danio rerio). The phylogenetic tree showed that all these organisms shared a common ancestor. This observation concurs with the fact that these three organisms all have the ALX1 gene. The phylogenetic tree also showed that the zebrafish diverged from the common ancestor earlier than humans and chimpanzees. This shows that humans and chimpanzees are more closely related to each other than to zebrafish. This conclusion falls in line with research done by biologists at Wayne State University School of Medicine in Detroit, Michigan. These biologists used computer methods to analyze the amount of similarity between 97 important human and chimp genes and as many of the same gene sequences as are currently available for less-studied gorillas, orangutans, and Old World monkeys. The results suggested that within important sequence stretches of these functionally significant genes, humans and chimps share 99.4 percent identity (Pickrell). Humans and chimpanzees are almost 100 percent identical when comparing major genes, and this finding coincides with the phylogenetic tree that I created.
The biologists at Wayne State University School of Medicine in Detroit, Michigan are also arguing with new genetic evidence that lineages of chimps (Pan troglodytes) and humans (Homo sapiens) diverged so recently that chimps should be reclassed as Homo troglodytes. If this suggestion was actually implemented, chimps would be full members of our genus Homo, along with Neandertals, and all other human-like fossil species. "We humans appear as only slightly remodeled chimpanzee-like apes," says the study (Pickrell). The recent divergence of humans and chimpanzees would also explain the similarity between the ALX1 gene sequence of these organisms. All in all, my hypothesis was correct. Humans (Homo sapiens) and chimpanzees (Pan troglodytes) are more closely related than zebrafish (Danio rerio) to humans or chimpanzees.
Tree
Works Cited
"ALX1 Gene." Genetics Home Reference. N.p., Apr. 2014. Web. 22 Oct. 2014.
Pickrell, John. "Chimps Belong on Human Branch of Family Tree, Study Says." National
Geographic. National Geographic Society, 20 May 2003. Web. 23 Oct. 2014.
"Supplemental Content." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 22 Oct. 2014. <http://www.ncbi.nlm.nih.gov/nuccore/154813200?report=fasta>. (Homo sapiens ALX1)
"Supplemental Content." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 22 Oct. 2014. <http://www.ncbi.nlm.nih.gov/nuccore/113682306?report=fasta>. (Danio rerio ALX1)
"Using Nucleotide." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 22 Oct. 2014. <http://www.ncbi.nlm.nih.gov/nuccore>. (Pan troglodytes ALX1)
Nida's Phylogenetic Analysis
Nida Ali
Mr. Hammer
AP Biology
October 24, 2014
Phylogenetic Analysis
Are humans more closely related to mice, chickens or black spotted frogs in terms of their genetic makeup? Within this analysis, the TYR gene is analyzed among the protein sequences. This gene provides specific instructions on how to construct the enzyme tyrosinase, which is located in specialized cells called melanocytes that are responsible for producing the pigment melanin. This pigment is the substance that provides the color for skin, hair and eyes. In order to distinguish a similarity among the several different species of homo sapiens (humans), mus (mice), Gallus gallus domesticus (chickens) and black spotted frogs, The TYR gene was selected as the basis of analysis to determine the degree of relatedness among the organisms homo sapiens (humans), mus (mice), gallus glasus domesticus (chickens), and the pelophylax nigromaculatus (black spotted frogs).
Because humans, mice, chickens, and black spotted frogs all had DNA containing the TYR gene, I chose to compare the sequences from these particular species. I decided to compare humans to mice because 95% of mice’s genome is similar to humans, displaying an abundant amount of similarities. In addition, mice have a similar order in chromosomes as humans. Considering the fact that mice have similar digestive systems, metabolism, circulation and immune defenses, determining whether or not mice would display similar production of melanin pigment due to the TYR gene was a relevant consideration (Office of Science Education- Mice and Humans Are Biologically Similar). Furthermore, humans and chickens contain a number of similarities in their genes as well. More than half of chicken genes are similar to those of humans. On average, 75% of corresponding pairs are present among humans and chickens (Researchers Compare Chicken, Human Genomes). Based on this fact, I wanted to determine whether or not the TYR gene was within that 75% similarity.
Considering the fact that humans and frogs share a similar body plan, such as their skeletons, organ systems and their location, size and purpose, concluding whether or not these two species contain a similar gene is worth analyzing (The Frog Skeletons vs. Human Skeletons).
To start, I began my research by determining the animals that I wanted to compare and find similarities among. Then I found the TYR gene to base my results off of. I decided to go with this gene mainly because it is an essential to producing pigment in our hair, eyes and skin. After I figured out what gene I wanted to base my analysis on, I began to research whether or not this gene was present in the animals I originally chose for this analysis. At first, I decided to switch which animals I wanted to compare, but finally I decided to determine which species are most similar to each other among the ones I chose including homo sapiens (humans), mus (mice), Gallus gallus domesticus (chickens) or the pelophylax nigromaculatus (black spotted frogs). Next, after choosing and analyzing for protein sequences, I began to use the software, ClustalX, in order to align and compare DNA sequences. This program was downloaded onto my computer in order to compare the sequences of humans, mice, chickens and black spotted frogs. After finishing the complete alignment, I chose the “draw tree” feature in order to construct a cladogram.
One common ancestor among these species is presented in the cladogram above. The cladogram above reads, in order from top to bottom, as mouse, human, chicken, and black spotted frog. In comparison to the TYR gene, humans and mice are equally related. Since mice and humans have over 95% of genetic similarities, they are listed closely together, which suggests that they are closely related through the TYR gene. Chicken, mice and humans are much more closely related to each other than to the black spotted frog. There are more similarities than differences among the mice, human and chicken. The black spotted frog is represented as an outgroup due lack of many similarities it has with the other three monophyletic groups of organisms. This cladogram matches evidence showing the relationship and similarity among humans, mice, chickens and black spotted frogs. 
The results of my findings corroborated Winstead’s conclusions from his research. More similarities rather than differences are seen among humans and mice. Over 700 mouse genes are grouped in the same order as in humans. Researchers at Celera Genomics in Rockville, Maryland recognized the vast implications of using the mouse as a model organism for researching human health and disease, commenting that “even researchers who are not mouse geneticists will find tremendous value from examining the sequence” (Winstead).
Researchers compared chickens genomes to those of humans and came to the same conclusion as I discovered: that these two species share more than half of their genes. Humans and chickens roughly the same number of genes, but the chicken genome is slightly smaller than those of humans. A slight discrepancy was seen within this source. The source stated that humans and chickens contain 60% similarity in terms of genes, whereas 75% of similarity was stated from another article, from which I based my research. The alignment of chicken and human genes were off of 2,000 chicken genes, adding onto the slight 25-40% difference seen between these two species (Spencer).
To add, Rochester's ‘Jumping Frog Lab’ results were comparable to the results I concluded within my analysis. Emphasized Rochester's results, he stated how humans and frogs share several features in the earliest stages of their development, such as the development of the nervous, skeletal, and immune systems, which is similar in both humans and frogs. What I found out within his research was that similarities between these two species also derive among genes related to proteins, such as the MHC (major histocompatibility complex) protein. This protein allows for organisms to detect and control cancerous cells (The Frog Skeletons vs. Human Skeletons) .
To conclude, homo sapiens and mus were the most closely related species. The level of similarity among these two species were seen mainly through their DNA sequences. The TYR gene added onto the 95% similarity. Within my results, the tyrosinase enzyme in humans and mice provides similar construction and production of providing pigment in hair, eyes and skin. More similarities than differences were seen among chickens and humans. Roughly 70% of similarities were mainly seen within the DNA sequences. The slight differences were in result to the added 2,000 human genes in the sequence. Lastly, humans and black spotted frogs contain minimum similarities among their genetic makeup while comparing the TYR gene. Only specific organs and its location, size and purpose, among these two species addressed the similarity. In essence, my research concluded that homo sapiens and mus were most similar to each other than among the other animals in this study.
Works Cited
"The Frog Skeletons vs. Human Skeletons" HowStuffWorks. N.p., n.d. Web. 24 Oct. 2014.
"Office of Science Education- Mice and Humans Are Biologically Similar." Office of Science Education - Animals In Research - Amazing Facts - Mice and Humans Are Biologically Similar. N.p., n.d. Web. 24 Oct. 2014.
"Researchers Compare Chicken, Human Genomes: Analysis Of First Avian Genome Uncovers Differences Between Birds And Mammals." ScienceDaily. ScienceDaily, n.d. Web. 24 Oct. 2014.
Rochester. "Genome Sequence Marks Big Leap Forward for Frog Researchers." - News Room. N.p., n.d. Web. 23 Oct. 2014.
Spencer. "2004 Release: Researchers Compare Chicken, Human Genomes." 2004 Release: Researchers Compare Chicken, Human Genomes. N.p., n.d. Web. 23 Oct. 2014.
Winstead. "Humans and Mice Together at Last." Humans and Mice Together at Last. N.p., 31 May 2002. Web. 23 Oct. 2014.
Rameia's Phylogeny Article
Phylogenetic Article
My question for my investigation is how are leopards(Panthera pardus) and tigers (panthera tigris) related to wild deer mice(Mus musculus)? My hypothesis is that the leopard and tiger are more closely related to each other than to the wild deer mouse, and that the wild deer mouse would be the outgroup organism. This question was interesting to me at first because I was curious about how the leopard and tiger obtained their color patterns. Further down in my research it also interested me that the same gene that determines color patterns in the leopard and tiger is the same gene that colors a wild deer mouse, which is the Agouti gene. Overall I was curious as to what genes and mutations in the genes were responsible for the colors and patterns of these organisms.
To figure out which genes are responsible for the color pattern of each organism, I initially used google to search for the names of the genes. After discovering the gene name, I procceded to use www.ghr.nlm.gov to understand the specifics of the gene and how it works in organisms. By doing this I also discovered that I would be using only protein sequences in order to compare the organisms I had chosen. Knowing this I used www.ncbi.nlm.gov to find the protein sequences I would need in order to compare and create a phylogentic tree for all of the organisms. By using the program Clusterx, I copy and pasted the sequences into a plain text file in order to align them. After aligning the sequences, I was able to use Njplot to create a phylogenetic tree which compares the relationships off all the organisms I had chosen.
As you can see in the phylogenetic tree, it has came to the conclusion that the leopard and the wild deer mouse seem to have the most similarities with each other. As seen in the phylogenetic tree the leopard and the mouse branched off of the tiger. This means that the leopard and the mouse share the most recent common ancestor between all three organisms. I believe my question of how the leopard and tiger are related to the wild deer mouse was answered, but I do not believe that my findings and the phylogenetic tree are an accurate representation of the evolutionary relationship between all three organisms. The tree shows that the tiger is the outgroup organism. The leopard and tiger should be more closely related to each other than to the wild deer mouse. I am basing this off of the fact the the leopard and tiger both share the same genus. But, by using the Agouti gene which codes for the color pattern in all three organisms, it is possible that the protein sequence of the leopard and the wild deer mouse are more similar to each other in that sense.
According to an article on www.dailymail.co.uk, scientists had discovered that the Agouti gene is responsible for the color pattern on the deer mice. In the mice, the Agouti gene is very active on the rodent's stomach where it causes a delay of the maturation of cells that produce pigment. Scientists believe that this gene is also responsible for the color patterns of other vertebrates, such as the spots on a leopard, and the stripes on tigers and zebras. Another article on www.blogspot.com states that the Agouti gene is found in variety of organisms that determines whether or not they have patterned fur. The gene causes a range of pigmentation, for example the darkening of patches and fur, as well as giving a tiger its stripes. Based on these articles, the phylogenetic tree that was made is an accurate representation of the relationship based on the Agouti gene of these three organisms. But, if this is the case then all three organisms should come off of the same branch point and share the same recent common ancestor. Again, the phylogenetic tree seems inaccurate in this sense.
Improvements that could have been made to ensure the accuracy of the evolutionary relationships shown in the phylogenetic tree could have been to use longer protein sequences. Using longer protein sequences could have been a make or break factor in the evolutionary relationships. Even though all of the protein sequences were not the same length, using longer sequences as well as sequences with similar number of proteins could have provided more balance between the organisms. Another improvement that could have been made is the addition of other organisms who also possess the Agouti gene. This also could have gave the phylogenetic tree some balance, possibly creating a variety of outcomes.
Works Cited
- The Blue Tiger Sightings - Unsolved Mysteries In The World. (n.d.). Retrieved October 24, 2014.
- Fiona Macrae for the Daily Mail. (n.d.). How the leopard REALLY got his spots: Scientists identify gene that determines patterns of colour on mice. Retrieved October 24, 2014.
Rana's Phylogenetic Analysis Article
Rana Srouji
AP Biology
Mr. Hammer
October 23, 2014
Relationships
of Organisms
Horses, domestic cats,
zebra fish and sheep are all living organisms but are never really classified
or thought of together. Possibly because they tend to live in different
habitats. The zebra fish live in water, domestic cats are raised in homes,
sheep are mainly found on farms, and horses are seen in wild grassy plains.
But according to the theory of evolution, they may be related through a
common ancestor. Which brings up the following question. Of horses,
domestic cats, zebra fish, and sheep, which are the most closely related?
In order to analyze
this, I researched a gene that all of these organisms had in common. All
of them contained the gene that controls pigmentation. It is the MC1R
gene, or officially known as the alpha melanocyte stimulating hormone receptor,
which supplies the instructions to make a protein called the melanocorotin 1
receptor. This receptor, which is located on cells that produce the
pigment melanin, plays a large role in normal pigmentation. The melanin
is what provides skin, hair, and eye color. Though I knew what gene to use as
comparison for each organism, I had to find their sequences of the MC1R gene.
To do so, I used the http://www.ncbi.nlm.nih.gov/ website.
Looking under the category of Nucleotide, I put into the search bar the
scientific name of each organism along with the shorthand gene name. The scientific
name of the horse is Equus caballus, the name of the zebra fish is Danio rerio,
the name of the sheep is Ovis aries, and the name of the cat is Felis
catus. To choose which ones to use for
the analysis, I looked for mRNA sequences of less than 1000 bases long, with
the scientific name of the animal, and the gene name. After finding all the
sequences necessary, I placed them onto a word document and then transferred
them onto a text document. From the text document I could then open the
sequences onto the program ClustalX 2.1, which would align the sequences.
The alignment of the sequences allows for examining the differences to
show evolutionary relationships among the organisms. Finally, once they
have been aligned, they were made into a tree. Using the program NJplot,
the horses, domestic cats, zebra fish, and sheep were put into a phylogenetic
tree showing their relationships using the MC1R gene.
Thus, the results of the
phylogenetic tree showed that the most closely related of the 4 organisms,
through their MC1R genes, are the domestic cat and horse. This is because
they have the most recent common ancestor. The zebra fish was used as the
Out-group in this lab because it was least related to any of the other
organisms. Since the zebra fish lives in water, while the other organisms live
all live on land and breathe air, it would have the most distant common
ancestor, as proven by the tree. The phylogenetic tree also represents
evolutionary relationships between the organisms. It does this by
connecting them through branches and branch points. The domestic cat and
horse have the closest branching points, then the sheep, and then the zebra
fish. A possible explanation for the
fact that the domestic cat and the horse are the most closely related is that
many horses are also domesticated.
To further explain this,
a small amount of research has been implemented on the topic of how closely
related the domestic cats and horses are.
Scientists have found that there are forelimb homologous structures in
the domestic cat and horse. Homologous
structures are structures with different functions but all were inherited from
the same common ancestor who had that body part. The forelimbs have different forms and
functions but the same bones are present in both organisms (Zimmerman 12). This provides evidence for what the
phylogenetic tree shows. That the domestic
cat and horse have a more recent common ancestor.
Of the Equus caballus,
Felis catus, Ovis aries, and Danio rerio, the most closely related are the
Equus caballus and the Felis catus. Evolution shows that all living organisms
are linked genetically through common ancestors. Many organisms evolve over time due to
different selection pressures such as Natural selection, and even adaptive
radiation. They may become new species
but still have diversified from the same original lineage. Which could have been the cause for the
relationship of the organisms that were studied in this experiment. The phylogenetic tree showed the
relationships of the 4 organisms. The
zebra fish least related to the rest of them, then the sheep, and the cat and
horse are the most related due to their positions on the tree.
Citations:
Zimmerman, Elwood C. "Possible Evidence of Rapid Evolution in Hawaiian Moths."Evolution 14.1 (1960): 137. Web. 23 Oct. 2014. <http://www.mhhe.com/biosci/genbio/raven6b/graphics/raven06b/other/raven06b_21.pdf>
Gene Sequences:
http://www.ncbi.nlm.nih.gov/nuccore/167621421?report=fasta
http://www.ncbi.nlm.nih.gov/nuccore/30725833?report=fasta
http://www.ncbi.nlm.nih.gov/nuccore/542133114?report=fasta
http://www.ncbi.nlm.nih.gov/nuccore/57163858?report=fasta
Phylogenetic Tree:
https://drive.google.com/file/d/0B2zcPPV2YgJ0TUxibm5oVEFWM28/view?usp=sharing
Gene information:
http://ghr.nlm.nih.gov/gene/MC1R
Jube's Phylogeny Anaylsis
Olajube Aladewolu
Mr.Hammer
Ap Biology
24 October 2014
Evolutionary Links Between Organisms
Hemophilia A is a coagulation disorder that has had a fatal effect on many animals for years (College, 1). It is a very serious disease, and it first emerged in the early 1900s. This is an inherited disease that can have similar, yet different effects on organisms. FVIII is the blood clotting protein which enables the blood to clot as soon as an animal begins to bleed. This topic is very interesting because the mutations that cause Hemophilia A to occur are very powerful. They can mean the difference between life and death. Hence, such diseases may entail remarkable evolutionary similarities between organisms that are relatively similar. Phylogenetic labs are helpful when determining evolutionary relations so I wanted to test exactly how similar humans, chimpanzees, and mouses are to one another. What accounts for their differences or similarities, if any, in the presence of a mutation in the FVIII gene?
I chose to analyze the genome sequence data of the coagulated FVIII gene in the three animals. I used the scientific (genus-species) name to find the nucleotide sequences. The mouses were referred to as mus musculus; humans as homo sapiens, and chimpanzees as pan troglodytes. Furthermore, I used the NCBI website to ensure the validity of the sequences. I aligned the genes in clustalx and then used my findings to make a phylogenetic tree in the njplot program. This allowed me to see just how closely related the gene sequences of the pan troglodytes and homo sapiens were in comparison to the mus musculus.
My tree diagram shows how the pan troglodytes (chimpanzees) and homo sapiens (humans) diverged from a common ancestor. It also shows that the mus musculus (mice) diverged from the ancestor of the common ancestor of pan troglodytes and homo sapiens. Thus, it makes sense that they would all suffer from similar diseases such as hemophilia. However, the constructed phylogenetic tree also shows that the mus musculus diverged earlier than the pan troglodytes and homo sapiens so it’s expected that their gene sequences for the FVIII protein are not identical to one another. Essentially, the results from my phylogenetic tree supports the evolutionary links between all three species. It is a fact that chimpanzees and humans share 98.8% of the same DNA (DNA, 1). In fact, an experiment was conducted in which a chimpanzee's blood was analyzed. The results showed that the number of genetic differences between humans and chimps is ten times smaller than that between mice and rats. Hence , the data constructed from the experiment shows that there are close evolutionary ties between humans and chimpanzees. This also supports my phylogenetic tree because it shows that there’s a prevalent relationship between both species. Thus, the genome sequences of chimpanzees and humans in the presence of mutated FVIII genes do not contain many differences.Essentially, their differences in gene sequences in the presence of a mutated FVIII gene is caused by their different points on divergence because the most recent ancestor of chimpanzees and humans was not shared with the mice. The mice had their own ,distinct, evolutionary line of ancestors which allow them to be the way they are. Humans and chimpanzees suffer from similar problems as their bodies code in similar fashion for the most part. Generally speaking, my phylogenetic tree was very useful because it used the genome sequence of Hemophilia A to clearly show the different points of divergence between the three animals.
Furthermore, researchers also discovered that some classes of genes are changing unusually quickly in both humans and chimpanzees in comparison to other mammals (Chimps, 1). Although It remains evident that humans and chimpanzees share many of the same features, they share some evolutionary links with mice as well. However, mice do not have as many similarities due to their earlier evolutionary divergence. The chimpanzee immune system is a reflection of the human genome because viruses that cause diseases like AIDS and hepatitis can also infect chimpanzees (DNA, 1). However, researchers have found extraordinary consistency between gene expression profiles in the mouse and human immune systems in addition to their points of divergence. The majority of gene expression patterns, about 80 percent, were the same in mouse and human (HMS, 1). To sum up, humans and chimpanzees are a lot more closely related to each other than they are to mice. Mice are less complex because they diverged from their common ancestor at an earlier point while humans and chimpanzees came into existence more recently, according to evolutionary scales and models.
Works Cited
"Chimps, Humans 96 Percent the Same, Gene Study Finds." National Geographic. National Geographic Society, n.d. Web. 22 Oct. 2014.
"College of Veterinary Medicine - Cornell University." Hemophilia A. N.p., n.d. Web. 24 Oct. 2014.
"DNA: Comparing Humans and Chimps." AMNH. N.p., n.d. Web. 24 Oct. 2014.
"HMS." Comparing Mouse and Human Immune Systems. N.p., n.d. Web. 24 Oct. 2014.
"HMS." Comparing Mouse and Human Immune Systems. N.p., n.d. Web. 24 Oct. 2014.
Tree
Tree
https://docs.google.com/document/d/1Cz0VdYtFnuLb5ZrgBCOjr96jGTMjFTFBYP4QOWo5cts/edit
Thursday, October 23, 2014
Jazmean's Phylogenetic Analysis Article
Jazmean Williams
AP Biology
Phylogenetic Analysis
How Closely Related are
Dogs to Humans?
The basis of this
Phylogenetic Analysis revolves around the domestication of dogs
(Canis lupus familiaris) by humans (Homo sapiens). While there is no
clear date as to when dogs were domesticated by humans, scientists
know that dogs have been domesticated for a long time. Scientists
also know that early human hunter-gatherers used dogs to perform many
roles such as hunting, herding, and providing protection. This leads
to the conclusion that humans domesticated dogs in order to improve
their style of living. But why dogs? Why not choose another animal to
domesticate? The answer lies within the idea of companionship. Dogs
are known today as being man's best friend, however, becoming
someone's best friend takes time and an immense amount of effort.
Could it be that early humans were willing to put forth the effort in
order to find another species they could relate to besides their own?
Could the domestication of dogs begun with the intention of
companionship instead of the completion of menial labor and
protection?
To figure this out, three
genes that exist in both dogs and humans will be analyzed and
compared on a Phylogenetic Tree to see how closely related dogs and
humans are. The closer in relation the dog and human are in the tree,
the more alike they are, and the more likely they are to develop a
bond with each other. The three genes that will analyzed are the
PHOX2A gene, the TGIF1 gene, and the PROP1 gene. The PHOX2A gene
deals with the development of the nervous system which affect bodily
functions such as heart rate and breathing. The TGIF1 gene provides
instructions to develop the front part of the brain. The PROP1 gene
helps the pituitary gland release hormones that aid in growth and
reproduction (along with other bodily functions). If the nervous
system and front part of the brain develop in a similar fashion ,
then one an infer that there will be similar bodily and brain
functions between the human and the dog. This applies too if the
human and the dog grow and reproduce in a similar fashion. Also, in
the tree, an outlying animal (the Zebrafish) will also be used to
further help compare the dog with the human on the tree.
After doing the
Phylogenetic Tree for each gene, it shows that the dog and the human
share a recent common ancestor. Because both the dog and human share
a more recent common ancestor, they share common structures and even
patterns of behavior. All three animals share a common ancestor, but
it is the dog and human that is most closely related due to both
species having a more recent common ancestor with each other.
The results and inferences
of this Phylogenetic Tree Analysis is similar to the information
presented in scholarly articles. In the National Geographic, Jane J.
Lee wrote an article about how the dog and human genomes evolved
together in parallel evolution. Weiwei Zhai, a genetics researcher
Lee references in their article, used genes that helped in the
transport of neurotransmitters and cholesterol processing to compare
the two species. He found that those genes were selected for in both
humans and dogs. Zhai also found that there are cancer-related genes
that are evolving together in humans and dogs. Weiwei Zhai believes
this parallel evolution occurred due to the fact that dogs and humans
lived closely together in the same environment. There is still debate
however on whether the parallel evolution between humans and dogs are
unique or if they exist in other domesticated animals as well.
The Huffington Post also
reported an article about how dog brains process voices and emotions
like humans which further supports the idea of humans and dogs being
alike. Attila Andics, the researcher cited in this article, proposes
that voice recognition between humans and dogs can explain why
communication between the two species is so successful. He also
proposes that this discovery can lead to an explanation of the
“unique bond” humans and dogs have together.
The evidence provided from
the Phylogenetic Tree and from the researchers aforementioned can
solidify the possibility that dogs were domesticated with the
intention of companionship and not labor. The companionship between
the dog and the human could then lead off to a symbiotic relationship
between the two species which is shown to have happened due to
present day conditions. This way of thinking supports the idea that
two species that live in the same environment will not always result
to competition, but can work together to form a relationship that
benefits the both of them.
Primary Sources for Discussion
Gene Sequences Used
Software Used
Subscribe to:
Posts (Atom)