Who developed the nested classification system that we use today?
The traditional terms ‘fishes’ and ‘reptiles’ are not terms that encompass only evolutionarily related groups of species. What specifically is wrong about the ‘fishes’ in figure 1 of the handout? How about the so-called ‘reptiles’?
Who developed our modern classification system that classifies species based on shared derived evolutionary relationships? This system is now central to how most people draw evolutionary trees.
This classification system is called……………………………………..
A ‘phylogeny’ displays classification as trees. Why is this name appropriate?
What sorts of traits are fair game for classification. There are several.
The turtles used to be classified as a basal group among the reptiles. They are today argued to be more advanced, placed as you see them in figure 2. Why were they considered more ‘primitive’ in older classification?
Identify the root, nodes, and any taxon in a tree.
For any two species in a tree, indicate the exact common ancestor.
State what, if any, evolutionary relationships are changed in a tree if some branches are rotated around a node. How about if the tree is redrawn in a different style like wrapping it into a circle?
Some tree have uneven branch lengths. What is indicated by the different branch lengths in these trees?
A diagram showing genetic markers in human mitochondrial DNA informs us about the relative age and origins of different human populations. Which populations of humans are thought to be especially old? Which are more recent in origin? On what continent did our species originate according to this mitochondrial DNA tree?
A tree with extinct species rarely indicates an extinct species is a direct ancestor of a modern species. Why is this probably the safest way to draw such a tree?
If a particular group is pointed out, Indicate the closest related outgroup.
If a particular species or group is pointed out, indicate their sister taxon [Be sure the one you choose has an equal ‘rank’ in the tree].
Correctly circle a specific monophyletic group in a tree that fulfills a specifications such as for mammals, orchids, insects…. [Be sure to include their common ancestor and all descendant species !]
Identify an uncertainty of relationships in a tree. What is the term for uncertainty in a tree?
If I ask you to draw a simple polytomy, can you do it right?
Given a particular species, indicate a polyphyletic group that includes that species.
Given a particular species, indicate a paraphyletic group that includes that species.
Putting a root on a tree has what effect on the tree?
Given a species with an indicated trait, identify an example of a species with a trait that is synapomorphic to that.
Given a species with an indicated trait, identify an example of a trait that is plesiomorphic to that.
Given a species with an indicated trait, identify an example of a species with a trait that is homoplastic to that.
Most mammals have dichromatic vision. What does this mean? How did the early mammals probably become dichromatic?
What is different about color vision in old world primates versus new world primates? What is the accepted explanation behind these differences?
What did systematics predict about alligator lungs, simply because they were a sister taxon to birds?
Because non-venomous snakes are related to venomous snakes, and because snake venom is similar to lizard venom, what was found when researchers looked at some of the non-venomous snakes and lizards?
Inferring Phylogeny Study Guide
Given a tree, can you identify a species that shares the most traits with another species?
We build trees based on traits shared between members. The origin of a trait is an ‘event’, or ‘change’ in a lineage. Sometimes traits are lost in a group, and this too is an event or change. So… A tree that draws relationships between species with the fewest changes (origins or losses of traits) is the most tree.
What does parsimony mean?
Equate parsimony with ‘keep it simple’!
The tree of bilateral animals now seems pretty stable, and is not likely to be significantly changed. In the lecture I used the chordates to talks about this. They are of course a subset of bilateral animals. When researchers use an assembly of derived traits within the chordates (and with other bilateral animals), they can build a tree. What can happen to the tree if they use an assembly of different traits?
[Note: Although I do emphasize that trees can get revised from time to time, that does not mean we know nothing about phylogeny! The basic phylogeny of life on earth is pretty well settled science now-a-days, although the ‘tips’ of the branches (species, sub-species) do get revised. There are a couple significant parts of the tree of life that has continued to challenge us, however. One major example is the tree for the entire animal kingdom, hence the assignment below.]
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Video assignment: Competing Phylogenies in the Animal Kingdom. Watch the video. This video was developed by one of two competing groups, and they have proposed different trees based on the use of numerous characters including anatomy, cell types, and genetics. They each came up with different ‘most parsimonious’ trees.
In one of the two competing trees, the earliest animals most closely resembled ……………………………., and in the other tree the earliest animals most closely resembled ……………………………
In the first model, what organ systems would have appeared one time in the remaining animals?
In the second model, what group would then have had to lose these organ systems to be like they are today?
The video then goes on to say it supports which model? I want to add that just because that is so, that does not mean that the other model is ‘wrong’. It really depends on what is used to make the tree, and I don’t think it is really decided yet.
Finally, although it is not shown in this video, the different models also looked at the Placozoa, which I mention in lecture, which are incredibly simple animals. Interestingly, both models say that the Placozoa are about in the ‘middle’ of the tree, and that they used to have muscles and nervous systems! This is according to the genes they carry.
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Distance methods are also used to build trees. Be sure to practice building a tree with the distance method described in class. Being able to do this is a significant question on the next exam. Practice practice practice.
According to a large amount of data and combinations of different algorithms for building trees, which of these groups are now strongly considered to be sister taxons: Egg laying mammals, Marsupials, and Placental mammals.
Let me set this up. Consider a region of DNA with genes, DNA between genes, introns, exons, promoters, other DNA regulatory regions, and DNA triplets that code for mRNA codons like …ACA.TGG.CGA.AAA… Note that these triplets include a 1st base, a 2nd base, and a 3rd base.
In terms of looking at a DNA region with the above things now, we expect that that this sort of DNA has had a history of mutations that are distributed without clear bias. That is, some mutations had occured in genes, in DNA between genes, and inside of genes some mutations hit exons and others hit introns, and so on.
After a mutation comes selection. A given mutation can have three possible effects. It might either increase fitness, in which case selection would seek to increase its frequency, or it might decrease fitness. In this case selection could cause its frequency to decrease in populations. The third effect is that the mutation might be neutral (or close to neutral) to selection. In this case, its fate is controlled by random chance and here it might increase or decrease in frequency by chance. This is genetic drift. Remember that selection cannot cause neutral mutations to increase or decrease in frequency. We will learn a lot more about neutral genetic drift later, but for now here is this fact: Some neutral mutations increase in frequency and become very common totally by chance, even though they are not selected for. Other neutral mutations decrease in frequency and maybe they go extinct. Don’t worry now about how that happens right now, just remember that it really does happen (quite a lot, actually). So..
a) Look at each of the above DNA structures in bold, and tell me: is a mutation in that structure likely to be selected against? If so, then we can look for it to be removed by selection and its as if the mutation did not happen. Such DNA structures are said to ‘evolve slowy’ because over time we see very little if any change in it– that being b/c most mutations were selected out. Some DNA regions in fact are at a virtual standstill; not changing appreciably for billions of years in most species!
b) Look again at those remaining DNA structures in bold, and tell me: is a mutation in that structure likely to be selected for, or (more likely!) be neutral to selection? Such DNA structures are said to ‘evolve quickly’ because mutations that hit them can stick around since natural selection does not drive them out of the population. Neutral mutations actually increase in frequency about 50% of the time, by genetic drift, and even take over that area of DNA in a population or entire species (!) The point for these DNA structures, then, is that they ‘evolve quickly’ because their rate of change is close to 50% of the original rate of mutation. Even closely related species will, as we consider things, quickly accumulate several differences in these regions over time.
c) An important detail: I wrote above about mutations and then there is selection or drift in either ‘fast’ or ‘slow’ evolving areas of DNA. Here is a question: Does a ‘fast’ evolving region of DNA get more original mutations than a ‘slow’ evolving region? Think about it!
d) A common thing that I ask about all of this is to have a drawing of a DNA region with the various structures (genes, parts of genes, DNA between genes), and I simply ask for you to identify regions that evolve fast or evolve slowly. I also ask if these different regions are more or less likely to get mutations.
What were the general trends in evolution of horses? How did their diet change over 10s of millions of years? What were their changes in habitat? How did the morphology of legs and teeth change during this time?
The first species of horses were small forest species. All horses today had their earliest ancestors on what continent? How do we know that they lived in forests and ate shrubs, etc.? What was their general size, form of teeth, and # of toes?
Later species of horses included the specialist grass feeders. What was their size, form of teeth, and what was the trend of change in the # of toes? On what continent did fairly ‘modern’ looking horses first appear? What was their pattern of spread? What was the pattern of extinction?
How did ancient people in Asia and Europe and North America eventually acquire horses (the story is pretty dramatic! Think of how the history of human civilization might be very different had the story of the horse been just a little bit different!
Who were the first peoples to domesticate horses? Where were they living? All domesticated horses are descended from this stock.
When humans first arrived in the Americas, many thousands of years ago, they may have seen fossils of large, modern-looking horses. But did they see live horses? Who were the first people to use horses in the Americas?
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From the reading on Fossil Horses:
I asked above about the ‘trends’ of horse evolution. I like this article b/c it shows the story is a bit more complicated.
The original evolutionary tree of horses from the 1800’s was considerably different from the tree we know today. Back then, how would one describe the branchyness of the horse evolutionary tree?
What is Copes’ rule? I recommend that you Google this.
So does the trend of horse evolution follows Copes’ rule overall, or only in some lineages?
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