In this unit, we looked at how and why organisms evolve by modeling evolution with a hardware cladogram, researching the evolutionary history of an organism and studying why it evolved, and performed a lab to identify the ALU repeats in our genome.
EVidence
Hardware cladogram
Discovered: 2 Phyla, 6 new genera, 31 new species
A long time ago in a galaxy far, far away...
Two New Phyla
Metallum (stronger more durable cell structure) and Plasticus(Softer, more flexible cell material).
Metallum, slow and all terrestrial. Some carnivorous, others herbivorous. Plasticus, fast and completely herbivorous, often prey of carnivorous Metallum species.
6 New Genera
Plasticus (phylum as well as genus), Metallum (phylum as well as genus, only one species), Circum (defensive strong, grazing, herbivores), Acutis (predatory and venomous omnivores), Dente (highly aggressive apex predators), Planus (scavengers that act as decomposers, omnivorous)
31 new species
Plasticus
generalis:fast moving herbivore. Feeds off of low berry bushes
virga:rod like shape allows for consumption of hard nuts and faster movement
acutis:spines developed as a defensive mechanism against predators
Metallum
generalis:herbivore with a hard exoskeleton, that breeds very quickly
Circum
generalis:hard shelled grazing herbivore, feeds off grass, circular shape for defense
magna:massively increased size for predator deference
testa:increased thickness of exoskeleton and addition of a shell for increased predator
defense
flexus:Adapted musculature and skeletal structure for life in trees
contritum:Further adapted musculature and skeletal system as well as forming of tail for
tree life
poterant:Only predatorial Circum species, hunts other Circum species using
strengthened jaw muscle to crush through exoskeleton
dente:Adapted teeth for consumption of large nuts and tough leaves
clipeum:Circum Dente adapted with a shell like defensive protrusion
alas:Powerful wings for evasion and feeding off the treetops
Acutis
generalis:Lance-like stinger for neutralizing softer prey with venom
iacteret:Developed camouflage and thicker skin to more efficiently hunt prey
miniscule:Small sized adaptation, allows for bypass of larger shell structure in a pack
noncapitis:More streamlined head for speed and reduced vulnerability
bipedal:Further increased speed and an additional stinger for better hunting capabilities
and defense
tectumque:Head shape allows for amplification of communication cries over long
distances for pack hunting
sulcus:An evolutionary link between the Acutis and Dente genera, primitive tusks help
with hunting
Dente
generalis:Development of teeth allow for solitary hunting and piercing and chewing of
food, belongs to genus Dente, which are the apex predators
iactaret:Developed skin allows for counter defense and less risk from hunting larger
animals
mas-dente:More teeth allows for better chewing of tougher organisms for food
invisibilia:Camouflaged skin gives an advantage while hunting
noctis:Hunts at night to avoid competition and attack when prey is vulnerable, very small
numbers
fortis:Thickened skull allows for blunt-force attack to crush or bypass the exoskeleton of
stronger prey
cuniculum:Thick skull and developed posterior burrowing mechanism allow for
subterranean ambushes and striking prey from underbelly
longus:Long neck allows for hunting flying and tree dwelling organisms
Planus
generalis:A lack of stinger, but introduction of teeth, allows for consumption of nearly
anything, including nuts, leaves, berries, and carrion
fortis:Thick skull used as defensive mechanism for warding off predators
invisibilia:Camouflage used as a defensive mechanism against predators in addition to
a thick skull
A long time ago in a galaxy far, far away… there was a planet. This planet consists of large meadows with long grass useful for grazing. There are intermittent forests with large trees carrying strong nuts, swampy ground that harbors short berry shrubs. The Plasticus genus consists of small, fast herbivores that feed on the berries of the low berry bushes in the forests. They are the lowest level consumers in the forest. The Metallum genus consists of a single common grazing herbivore with a strong material structure allowing for potential predatory protection. This creature breeds very quickly, causing a high amount of genetic variation, and is the lowest evolutionary form and a common ancestor to all metallic species. These two phylums evolved differently because of a combination of geographic isolation and diet differences. The Circum genus consists of many round-built, slow, and armored herbivores that either graze in the meadows or feed of the trees in the forest. The species that live in the meadows are large, slow, and very heavily armored. The species in the forest, separated from the others by geographic isolation, are split into two leaf eating arboreal species, three nut eating bottom dwellers, and one flying species that feeds on the tops of the trees. These two Circum groups evolved differently due to geographic isolation. The Acutis genus contains venomous and carnivorous predatory species, some of which hunt in packs. They use venomous stingers to incapacitate and liquify the innards of their prey for either consumption or as a host for their larvae. This genus can be found in both the forest and the grassland, varying species to species. The Dente genus consists of solitary predators with many teeth, they are the apex predators. They hunt in the forest and on the meadows on the Plasticus, Circum, Acutis, and Planus genera. The Planus genus is a series of omnivorous scavengers that appear to eat almost anything, including nuts, berries, and carrion. They can be found in every environment where living creatures can be found. The Acutis, Dente, and Planus genera evolved differently due to behavior isolation (use of venom vs. teeth).
A long time ago in a galaxy far, far away...
Two New Phyla
Metallum (stronger more durable cell structure) and Plasticus(Softer, more flexible cell material).
Metallum, slow and all terrestrial. Some carnivorous, others herbivorous. Plasticus, fast and completely herbivorous, often prey of carnivorous Metallum species.
6 New Genera
Plasticus (phylum as well as genus), Metallum (phylum as well as genus, only one species), Circum (defensive strong, grazing, herbivores), Acutis (predatory and venomous omnivores), Dente (highly aggressive apex predators), Planus (scavengers that act as decomposers, omnivorous)
31 new species
Plasticus
generalis:fast moving herbivore. Feeds off of low berry bushes
virga:rod like shape allows for consumption of hard nuts and faster movement
acutis:spines developed as a defensive mechanism against predators
Metallum
generalis:herbivore with a hard exoskeleton, that breeds very quickly
Circum
generalis:hard shelled grazing herbivore, feeds off grass, circular shape for defense
magna:massively increased size for predator deference
testa:increased thickness of exoskeleton and addition of a shell for increased predator
defense
flexus:Adapted musculature and skeletal structure for life in trees
contritum:Further adapted musculature and skeletal system as well as forming of tail for
tree life
poterant:Only predatorial Circum species, hunts other Circum species using
strengthened jaw muscle to crush through exoskeleton
dente:Adapted teeth for consumption of large nuts and tough leaves
clipeum:Circum Dente adapted with a shell like defensive protrusion
alas:Powerful wings for evasion and feeding off the treetops
Acutis
generalis:Lance-like stinger for neutralizing softer prey with venom
iacteret:Developed camouflage and thicker skin to more efficiently hunt prey
miniscule:Small sized adaptation, allows for bypass of larger shell structure in a pack
noncapitis:More streamlined head for speed and reduced vulnerability
bipedal:Further increased speed and an additional stinger for better hunting capabilities
and defense
tectumque:Head shape allows for amplification of communication cries over long
distances for pack hunting
sulcus:An evolutionary link between the Acutis and Dente genera, primitive tusks help
with hunting
Dente
generalis:Development of teeth allow for solitary hunting and piercing and chewing of
food, belongs to genus Dente, which are the apex predators
iactaret:Developed skin allows for counter defense and less risk from hunting larger
animals
mas-dente:More teeth allows for better chewing of tougher organisms for food
invisibilia:Camouflaged skin gives an advantage while hunting
noctis:Hunts at night to avoid competition and attack when prey is vulnerable, very small
numbers
fortis:Thickened skull allows for blunt-force attack to crush or bypass the exoskeleton of
stronger prey
cuniculum:Thick skull and developed posterior burrowing mechanism allow for
subterranean ambushes and striking prey from underbelly
longus:Long neck allows for hunting flying and tree dwelling organisms
Planus
generalis:A lack of stinger, but introduction of teeth, allows for consumption of nearly
anything, including nuts, leaves, berries, and carrion
fortis:Thick skull used as defensive mechanism for warding off predators
invisibilia:Camouflage used as a defensive mechanism against predators in addition to
a thick skull
A long time ago in a galaxy far, far away… there was a planet. This planet consists of large meadows with long grass useful for grazing. There are intermittent forests with large trees carrying strong nuts, swampy ground that harbors short berry shrubs. The Plasticus genus consists of small, fast herbivores that feed on the berries of the low berry bushes in the forests. They are the lowest level consumers in the forest. The Metallum genus consists of a single common grazing herbivore with a strong material structure allowing for potential predatory protection. This creature breeds very quickly, causing a high amount of genetic variation, and is the lowest evolutionary form and a common ancestor to all metallic species. These two phylums evolved differently because of a combination of geographic isolation and diet differences. The Circum genus consists of many round-built, slow, and armored herbivores that either graze in the meadows or feed of the trees in the forest. The species that live in the meadows are large, slow, and very heavily armored. The species in the forest, separated from the others by geographic isolation, are split into two leaf eating arboreal species, three nut eating bottom dwellers, and one flying species that feeds on the tops of the trees. These two Circum groups evolved differently due to geographic isolation. The Acutis genus contains venomous and carnivorous predatory species, some of which hunt in packs. They use venomous stingers to incapacitate and liquify the innards of their prey for either consumption or as a host for their larvae. This genus can be found in both the forest and the grassland, varying species to species. The Dente genus consists of solitary predators with many teeth, they are the apex predators. They hunt in the forest and on the meadows on the Plasticus, Circum, Acutis, and Planus genera. The Planus genus is a series of omnivorous scavengers that appear to eat almost anything, including nuts, berries, and carrion. They can be found in every environment where living creatures can be found. The Acutis, Dente, and Planus genera evolved differently due to behavior isolation (use of venom vs. teeth).
Description
For the hardware cladogram project, we first split the species based on material. One branch consisted of all the plastic organisms and the other consisted of all the metal organisms. The Plastic branch was much smaller so we made it one of the genera. Then, we split the metal branch into circular and non circular organisms. The circular organisms included all the washers and nuts and the other branch consisted of all the nails, screws and bolts and we called it "rod-like." That branch was then split into "teeth" and "without teeth." The latter branch had all the nails. The "teeth" branch was then split further into just "teeth", and "no stinger", which included all of the bolts. For the story, we envisioned a world with expansive meadows and swampy forests and gave all of our organisms niches in that environment.
species timeline project
Description
For the species timeline project, we researched Andrias Davidianus, the Chinese Giant Salamander. We traced its history back to the earliest chordate, Haikouichthys. Then we looked at the first jawed fish, Placodermi. Then Guiyu Oneiros, the first bony fish. After that, we researched Eusthenopteron and Ichthyostega, which completed the transition onto land. Then we traced the giant salamander lineage through the late Cenozoic and early Mesozoic, which included Cochleosaurus, Prionosuchus, and Brachyopoidea. Lastly we arrived at the Chinese Giant Salamander, which has stayed in its current form since the Cretaceous. For every organism, we explained how it evolved into the form that it took.
PCR lab report
Luis Jasper
Electrophoresis and PCR to find ALU repeats in our genome
Purpose
The purpose for this lab was to learn how to prepare DNA and perform PCR on it and to use agarose gel electrophoresis to find the genotype of our ALU repeats in our genome. Then we would use that information to figure out where on the Earth we are from.
Hypothesis
I think that my ALU repeats will show that I am from European descent after we analyze the results.
Procedure
Data/Observation
Day 1: On the first day, we did steps one through six. I noticed that my sample had a lot of cheek cells in it that the centrifuge didn’t properly condense, creating problems when I had to pour off the supernatant. On day two, we did steps seven through 12. I noticed that The tube didn’t look that different after the Chelex beads and that transferring liquids on the ice was difficult. On day three, we did steps 13 through 14. I noticed that our gel box was leaking. On day four, we did step 15 and gathered our evidence. I saw that our results were inconclusive because none of the DNA moved.
Electrophoresis and PCR to find ALU repeats in our genome
Purpose
The purpose for this lab was to learn how to prepare DNA and perform PCR on it and to use agarose gel electrophoresis to find the genotype of our ALU repeats in our genome. Then we would use that information to figure out where on the Earth we are from.
Hypothesis
I think that my ALU repeats will show that I am from European descent after we analyze the results.
Procedure
- Swish a saltwater solution in mouth to collect some cheek cells. Extract 1500 microliters and put into a microfuge tube.
- Centrifuge in a small tube for one minute to condense the cheek cells in a small pellet.
- Pour off the supernatant so that only 100 microliters of saline solution are left and flick the tube to suspend the cells.
- Obtain a tube of 5% Chelex.
- Transfer the cell suspension to the Chelex tube.
- Place the tube in a heat block.
- Centrifuge the tube for one minute.
- Transfer the supernatant into a new tube and leave the Chelex beads behind.
- Refrigerate the DNA until ready for PCR.
- Put 20 microliters of Master Mix, 20 microliters of Primer Mix, and 10 microliters of the DNA into a new PCR tube.
- Put the tube in a thermal cycler to start PCR reaction.
- Create agarose gel in a tub with combs to make the wells.
- Put loading dye into PCR tube.
- Load DNA into the wells for electrophoresis.
- After electrophoresis, collect observations.
Data/Observation
Day 1: On the first day, we did steps one through six. I noticed that my sample had a lot of cheek cells in it that the centrifuge didn’t properly condense, creating problems when I had to pour off the supernatant. On day two, we did steps seven through 12. I noticed that The tube didn’t look that different after the Chelex beads and that transferring liquids on the ice was difficult. On day three, we did steps 13 through 14. I noticed that our gel box was leaking. On day four, we did step 15 and gathered our evidence. I saw that our results were inconclusive because none of the DNA moved.
Analysis/Discussion
We were unable to analyze our data because it was inconclusive, we only had the BP ladder produce results and one small spot that was probably a mistake. If we had gotten results, we could see if we had the +/+ genotype, the +/- genotype, or the +/+ genotype. A +/+ genotype is homozygous and would look like one line at 715 base pairs long. A -/- genotype is homozygous and would look like one line at 415 base pairs long. A +/- genotype is heterozygous and would look like two lines, one at 715 base pairs long, and one at 415 base pairs long.
Conclusion
I conclude that something happened during the experiment that caused me to not get results, like transferring incorrect amounts of liquids or accidentally destroying the DNA at some point. If I had transferred incorrect amounts of the Primer and Master Mixes, or the Chelex beads, The DNA may not have been cleaned or gotten the proper amounts of primers, polymerase, or other required substances. It could have happened that the DNA had been accidentally destroyed during handling. This would obviously have hindered the ability to observe my ALU repeats. If I were to repeat this lab, I would be more careful with my DNA, and I would make sure that I am adding the correct amounts of liquid.
COntent
Evolution - The very slow process in which a living species' traits can change and adapt to its circumstance through heredity, genetic mutations, and natural selection.
Genetic Variation - Diversity in the genes of a population, a large factor of evolution.
Heredity - The fact that traits of an organism get passed down to its offspring.
Natural Selection - The process in which some members of a species are more likely to survive because of advantageous traits, and then pass those traits on to their offspring. Over time, only the advantageous traits remain in the population. Natural selection can by modeled by four stages. Mutation: traits are introduced to a population, Competition: individuals have to compete for resources to survive, Survival: individuals with the most advantageous traits survive, Reproduction: those individuals can then reproduce and pass the advantageous traits on to their offspring.
Taxonomy - The study of classifying organisms and evolutionary lineages.
Taxonomic levels - Organisms are grouped in to eight types of groups and subgroups.
Domain - a grouping of organisms based on their very basic cell structure (cell membrane vs. no cell membrane and DNA vs. RNA).
Kingdom - a grouping of organisms based on specific cell structures.
Phylum - a grouping of organisms based on their genetic and morphological relations.
Class - a grouping of organisms based on more specific genetic and morphological relations.
Order - a grouping of organisms based on food type or relative body characteristics or specific characteristics depending on class and phylum.
Family - a further subdivision with no real scientific consensus on definition.
Genus - a small grouping of very similar organisms.
Species - The largest grouping of organisms that reproduce with one another and produce fertile offspring.
Speciation - The process in which new species are formed.
Allopatric Speciation - When a species gets physically separated and then speciates.
Sympatric Speciation - When new species develop without being physically separated.
Reproductive Isolation - A form of sympatric isolation when a population is split because they can't mate with one another.
Behavior Isolation - Species differentiated by behavior during mating, such as mating rituals or calls.
Temporal Isolation - When a population is split because they are active or mate at a different time.
Geographic Isolation - A form of allopatric isolation where a species is geographically isolated.
Genetic drift - Basically speciation through natural selection and mutation.
Biotechnology - The use of living things to create products or to do tasks for humans.
DNA - structure in which the information for our bodies is stored, encoded on Adenine, Guanine, Cytosine, and Thymine.
RNA - a structure similar to DNA except simpler, encodes information on Adenine, Guanine, Cytosine, and Uracil.
Gene - a sequence of DNA that encodes information for and organism.
Cladogram - A diagram that shows the cladistic relationships between different organisms.
Genetic Variation - Diversity in the genes of a population, a large factor of evolution.
Heredity - The fact that traits of an organism get passed down to its offspring.
Natural Selection - The process in which some members of a species are more likely to survive because of advantageous traits, and then pass those traits on to their offspring. Over time, only the advantageous traits remain in the population. Natural selection can by modeled by four stages. Mutation: traits are introduced to a population, Competition: individuals have to compete for resources to survive, Survival: individuals with the most advantageous traits survive, Reproduction: those individuals can then reproduce and pass the advantageous traits on to their offspring.
Taxonomy - The study of classifying organisms and evolutionary lineages.
Taxonomic levels - Organisms are grouped in to eight types of groups and subgroups.
Domain - a grouping of organisms based on their very basic cell structure (cell membrane vs. no cell membrane and DNA vs. RNA).
Kingdom - a grouping of organisms based on specific cell structures.
Phylum - a grouping of organisms based on their genetic and morphological relations.
Class - a grouping of organisms based on more specific genetic and morphological relations.
Order - a grouping of organisms based on food type or relative body characteristics or specific characteristics depending on class and phylum.
Family - a further subdivision with no real scientific consensus on definition.
Genus - a small grouping of very similar organisms.
Species - The largest grouping of organisms that reproduce with one another and produce fertile offspring.
Speciation - The process in which new species are formed.
Allopatric Speciation - When a species gets physically separated and then speciates.
Sympatric Speciation - When new species develop without being physically separated.
Reproductive Isolation - A form of sympatric isolation when a population is split because they can't mate with one another.
Behavior Isolation - Species differentiated by behavior during mating, such as mating rituals or calls.
Temporal Isolation - When a population is split because they are active or mate at a different time.
Geographic Isolation - A form of allopatric isolation where a species is geographically isolated.
Genetic drift - Basically speciation through natural selection and mutation.
Biotechnology - The use of living things to create products or to do tasks for humans.
DNA - structure in which the information for our bodies is stored, encoded on Adenine, Guanine, Cytosine, and Thymine.
RNA - a structure similar to DNA except simpler, encodes information on Adenine, Guanine, Cytosine, and Uracil.
Gene - a sequence of DNA that encodes information for and organism.
Cladogram - A diagram that shows the cladistic relationships between different organisms.
reflection
hardware cladogram
I think that my group did an overall good job on the hardware cladogram. We included all of the things that we had to and even a little more. Two things that we did well was the format of our cladogram and the complexity of our story. We stuck to the format of a cladogram almost perfectly and put the all the labels in the correct places. We made sure of this by double checking everything. Our story was also very complex. We didn't just include the environment of the organisms but also their diets and how they interacted with one another in this environment. Despite all this, their are also some things that we could have done better, like some small classifications changes and explanations of the evolutionary histories of the organisms. After we finished, we noticed that some of the hardware pieces that we thought were made out of plastic were actually made out of metal. If we were to do this project again, we would change that. Also, we didn't explain the evolutionary histories of the organisms. We didn't have to do this anyway because a cladogram is meant to show the relationships of living species but it would have been an interesting touch.
Species timeline
I think that my partner and I did a good job on the species timeline. We thoroughly explained all the evolutionary steps in the history of the Chinese Giant Salamander and formatted our presentation correctly. Two things that we did well was our research and the format of our slideshow. Our research was good because we spent a lot of time on it and made sure that we had the right information. Then we made sure that our slideshow was easy to understand and consistent. Two things that we could have improved on were our presenting and how far back we traced the salamanders evolution. We read the slides a lot during our presentation and I want improve on that in my next project. Also, we could have gone back even further than the first chordate and show more of the evolutionary history.