Lec 3 Flashcards
Phylogenetics
Reconstruction of evolutionary history and relationships among groups
Natural Selection and adaptation
Individuals with alleles best suited to their environment survive and reproduce
The complexity of nature
Nature is complex, confusing, and disorienting
We have a great interest in imposing some sort of order
But - classifying living organisms is challenging
Classification Systems: Carolus Linnaeus
1707-1778
First scientist to develop a taxonomic system to classify living organisms based on similarities
- hierarchical classification
- NOT based on evolutionary biology (Linnaeus is pre-Darwin)
- He encountered some problems: should whales be classified as fish or mammals?
Classification systems: Willi Henning
1913-1976
Revisited the problem of taxonomy using Darwin’s ideas and proposed a classification system based on evolutionary relationships
Phylogenetic Systematics
Field of science that reconstructs evolutionary history and studies the patterns of relationships among organisms
Classification of organisms must reflect evolutionary history
What is a phylogeny?
Phylogenies are how we show shared relationships
A phylogeny shows the branching relationships of populations as they give rise to descendant populations over evolutionary time
We can reconstruct phylogenies across multiple scales, from populations within a species to all life on earth
Reading trees: Branches and Times
Trees can be written in different ways
Each “tip” of the tree is a taxon
Points where the tree splits are called NODES
-Nodes are branching events
Nodes represent EXTINCT common ancestors
All taxa arising from a particular node are descendants of that ancestor
Reading trees: Finding common ancestors
Interior nodes represent COMMON ANCESTORS
To find the common ancestor of any two taxa, we just track backwards on the tree to find the splie
Which node represents the common ancestor of mammals and lungfish? (From phylogeny)
a) Teal node
b) Purple node
c) Green node
d) Orange node
e) Red node
d) Orange node
Reading trees: Divergence Times
Nodes near the “tips” of the tree indicate more recent splits
Nodes farther towards the base (“root”) of the tree are older splits
More recent common ancestor =
More recent divergence
For example:
- Mammals and lizards diverged more recently than mammals and amphibians
- Amphibians and mammals diverged more recently (share a more recent common ancestor) than amphibians and lungfish
Reading trees: Relationships among branches
Rotation of a node results in a tree representing the SAME relationships
Which pair of species diverged most recently? (From phylogeny)
a) Tapirs and rhinos
b) Tapirs and horses
c) Elephants and hyraxes
d) Cetaceans and pigs
e) Pigs and ruminants
a) Tapirs and rhinos
Types of groups: Clade
Group of species that share a single recent common ancestor
Types of groups: Monophyletic
Group composed of all descendants of the groups’ most recent common ancestor (and no other groups)
Equi. to clade
Types of groups: Paraphyletic
Group composed of organisms sharing a common ancestor in which NOT all of the descendants of the common ancestor are included
Types of groups: Sister groups
Two lineages or taxa derived from a common ancestor that are each other’s closest relative on a tree
Fish (is, is not) a monophyletic group
Is NOT because it does not include all descendants of the common ancestor of its members
Tetrapod vertebrates (is, is not) a monophyletic group
IS because it includes all descendants of the common ancestor
Which group on this tree is paraphyletic?
a) Elephants and manatees
b) Manatees, tapirs, rhinos
c) Tapirs, rhinos, horses
d) Cetaceans, hippos, ruminants
b) Manatees, tapirs, rhinos
Paraphyly in mammals
Elephants, manatees and hyraxes are MONOPHYLETIC
Pachyderms: elephants, rhinos, and hippos are NOT monophyletic
This is a case where classification based on character similarity does NOT reflect true evolutionary relationships
Which taxa are SISTER on this tree?
a) Arthropods and Echinoderms
b) Flatworms and sponges
c) Nematodes and Annelids
d) Cnidarians and Ctenophorans
d) Cnidarians and Ctenophorans
How do we build a phylogeny?
Characters: Any observable characteristics of an organism (any part of its phenotype). Example = coat color
Traits: The state of the character (brown vs. tan coat)
DNA sequences: Now that we can “observe” these, these are the most common CHARACTERS used in phylogenies
Building trees based on traits
Build an initial tree based on the similarity of sequence data
Sequences that are more similar are more closely related (diverged from a common ancestor more recently)
This discovery was a huge source of support for evolutionary theory
Mapping traits on trees
Map different characters onto tree
By looking at where a trait maps on a tree, we can make hypotheses about WHEN and HOW that trait evolves
Trait mapping: Opsin evolution
Vertebrate ancestors had 4 opsin pigments, which persist in lizards and birds
Opsins were LOST on the mammal lineage, potentially due to nocturnality
Primates gained a new opsin due to a gene duplication + divergence in the long wavelength option = helps us see red
Phylogenetic trees are HYPOTHESES
These are testable hypotheses about the relationships among populations and species (“lineages”)
As we acquire more data, we REVISIT these hypotheses. If the hypothesis is no longer supported by our data, we REVISE it
Trees are ALTERNATIVE HYPOTHESES
Placental and marsupial mammals are “sister taxa”
Ingroup (blue lines) = group you are interested in studying
Outgroup (green line) = external group used for comparison and character polarization
Reptiles are the outgroup to the MAMMAL CLADE here
Are mammals monophyletic on this tree? YES
In an alternative hypothesis, marsupials and monotremes are sister taxa
Which two groups diverged most recently on the second tree (B)?
a) Monotremes and placentals
b) Marsupials and placentals
c) Marsupials and monotremes
d) Placentals and squamate reptiles
c) Marsupials and monotremes
Polytomies indicate ______________-
Uncertainty on trees
Ecological analogues
Similar adaptations in unrelated organisms
Unrelated organisms display similar adaptations to the same ecological niches - kangaroos and cows both have two stomach chambers for fermenting grasses and other plants
Analogy
Correspondence in function or position between traits of DISSIMILAR evolutionary origin (i.e. the wing of a bat is ANALOGOUS to the wing of a bird)
Homology
Similarity between species that results from inheritance of traits from a common ancestor - often the ancestral structure has taken on new functions or lost its function
Homology: Jaws and Ears
The mammalian inner ear bones are derived from reptile jaw bones
Analogies: Body shape in Marine animals
These species [shark (fish), ichtyosaur (reptile), and dolphin (mammal)] INDEPENDENTLY evolved similar shapes that are well suited to their environments
Analogous traits reflect CONVERGENT EVOLUTION
2 or more populations or species become similar to one another when exposed to SIMILAR ENVIRONMENTS
Divergent Evolution
Occurs when closely related populations or species diverge from one another because natural selection operates differently
Lizards and mice in different environments are experiencing divergent evolution
Detecting homologies and analogies
Long legs for a MONOPHYLETIC CLADE - suggests HOMOLOGY from a single ancestor with long legs
Long tails occur far apart on the tree - suggests ANALOGY (independent origins)
We can map wings onto a phylogenetic tree of tetrapods
The most likely scenario is that wings evolved independently in bats and birds - a result of convergent evolution
Wings are therefore ANALOGOUS TRAITS - they are not descended from a shared common ancestor with wings and have separate evolutionary origins
However, wings derive from HOMOLOGOUS STRUCTURES - they are both modified forelimbs. So bats and birds did not inherit wings from a common ancestor with wings, but they DID inherit forelimbs from a common ancestor with forelimbs
Phylogenetic trees are ____________________________ to detect homologies and analogies
The most powerful tools
Detecting homologies is fundamental for understanding evolutionary relationships
Based on this tree, would you hypothesize that striped tails are homologous?
Yes, striped tails form a monophyletic group
How do we describe traits on trees? Derived Traits
Evolved from other traits
How do we describe traits on trees? Ancestral traits
State of the base of the tree
Synapomorphy
A shared, derived trait
Help uncover evolutionary relationships on trees
Present in ALL descendants but in NO ancestors
Means that trait has evolved and everyone AFTER shares that trait and no one before does
Limbs is a __________ for tetrapods
Synapomorphy
Which is a synapomorphy (shared derived trait) in the Sauria?
a) Determinate growth
b) Extensive changes in skeleton
c) Hole in skull below eye socket
d) Hole in skull in front of eye socket
b) Extensive changes in skeleton
Homoplasy
Trait similar in two or more species that is absent in a common ancestor (analogy on a tree)
Homoplasies can be misleading on trees, because we may think things that have similar traits are more closely related to each other than they actually are
-i.e. pachyderms
Symplesiomorphy
An ANCESTRAL, shared trait
VERY RECENTLY DERIVED TRAITS obscure true phylogenetic relationships
Is coat patterning a useful trait for building a phylogeny in the Felidae?
No, patterning is a homoplasy
Patterning is NOT a synapomorphy because then all would have it (some may evolutionary lose the trait, but there are too many without patterns for it to be a synap)
Building trees: Statistical inference
What do we do when we need to build a big phylogeny?
What do we do when traits are variable?
What do we do when it seems like there are many possible trees?
Answer to all: STATISTICS
The basic ideas underlying phylogenies
We assume there is ONE true evolutionary history
We then need to use all the data we have available NOW to reconstruct that past history
Some of our data will conflict (if there are homoplasies or symplesiomorphies)
We therefore need to figure out the MOST LIKELY phylogeny
Parsimony
The preference for the LEAST COMPLEX explanation for an observation
The preferred phylogenetic tree under parsimony is the tree that requires the smallest number of evolutionary changes/steps
Inferences under parsimony are stronger with multiple characters and characters shared between multiple species
If a trait is only present in one species, it can evolve via one evolutionary change, or step. This is NOT helpful for resolving a tree!
Parsimony: Practice
Imagine we look at coat color, which we map onto our 2 hypothesized phylogenies based on the trait values of our 4 species
In our 4 species, we notes that species 1 and 4 have yellow coats, and species 2 and 3 have brown coats
One tree has species 1 and 2 as sister taxa and species 3 and 4 as sister taxa
The other tree has species 2 and 3 as sister taxa, and the clade composing species 2 and 3 sister to species 4; this tree is MORE PARSIMONIOUS because it required fewer evolutionary “steps” (yellow is ancestral, brown only evolves one time in clade leading to species 2 and 3)
Parsimony: Adding multiple characters
We look at each character in turn, and then map them onto the tree with fewest possible changes
Say we start with 3 characters (green, blue, and purple)
We then put those characters with their states (light or dark) on our hypothesized tree
We then mark down where changes in trait states would have occurred if we assume the FEWEST possible changes, one trait at a time
We then summarize these changes by marking the branches of the tree
Note that these changes are not unique - we could have light purple be the ancestral state, with one change to dark purple
Once we have added each character to our proposed tree with the minimum number of changes, we give it a parsimony score based on the total number of changes required
We then REPEAT this process for a DIFFERENT hypothesized tree
A different tree is one where the species all have the same character states, but the pattern of branching (the evolutionary history) is different
We then choose the tree with the FEWEST total changes as the “most parsimonious” evolutionary history for our group
Which tree is more parsimonious?
Tree 1, because there are fewer changes in character state
Tree 1 can explain the patterns of trait variation we see with fewer changes, and is therefore the more likely (more parsimonious) evolutionary history
Molecular phylogenies
We can use DNA sequence data the exact same way we use traits - we just count up numbers of differences between the DNA sequences of different species
Below we have ALIGNED the DNA of 8 different species - this means we sequences the same part of the DNA and looked at differences
-i.e. same genes, introns, etc.
Think of each location as a nucleotide, different character
We have marked the sequence changes on this tree the same way we marked traits
Phylogenetic Methods
Sometimes with parsimony we will get multiple, equally parsimonious trees
We have a couple of different rules for choosing a “consensus tree”
Parsimony is a comparatively simple method for tree construction, and most scientists now use Maximum Likelihood or Bayesian models
Often multiple methods will be used to examine the same group, and agreement across methods increases support for a particular evolutionary hypothesis
We now have very sophisticated models to build phylogenies, which can incorporate mutation rates, population size, and other important variables
Biogeography
The study of patterns of species distributions and the processes that result in such patterns
Biogeography adds additional information to phylogenetic inference
Interpreting branch lengths: Cladograms vs. Phylograms
A Cladogram has the branch tips aligned and indicates only the EVOLUTIONARY RELATIONSHIPS among species
A Phylogram indicates evolutionary relationships AND represents the amount of sequence change along each branch by differing horizontal branch lengths
- The longer the branch, the faster the evolution
- More sequence change per unit time = faster evolution
Why is amount of sequence change important?
More sequence change per unit of time = faster evolution
In herbaceous plants, branch lengths tend to be longer and rates of sequence change faster
This is because short-lived species have MORE GENERATIONS per year
Rates of evolution and biogeography of the SARS-CoV-2 virus
Since the beginning of the pandemic, scientists have been sequencing the DNA of thousands of SARS-CoV-2 samples from all over the world
We can use these samples to build phylogenies that allow us to track rates of mutation as well as biogeography of the pandemic
All of this information is available in an interactive format at nextstrain.org
Above is a phylogeny of several flowers in the genus Phox. When you find all these flowers outside, you assume that red P. drummondii are more distantly related to the other species, because they are red but all other species are purple. However, when you build a phylogeny based on DNA sequence data, you find the tree above. Red color is therefore most likely to be a:
a) Symplesiomorphy
b) Synapomorphy
c) Homoplasy
d) Analogy
a) Symplesiomorphy
In the PHYLOGRAM above, what is true about strains with comparatively longer branch lengths?
a) They have slower rates of evolution, potentially due to short generation times or strong selection
b) They have faster rates of evolution, potentially due to short generation times or strong selection
c) They have slower rates of evolution, potentially due to longer generation times or weak selection
d) They have faster rates of evolution, potentially due to longer generation times or weak selection
b) They have faster rates of evolution, potentially due to short generation times or strong selection
Why is it best to build trees based on synapomorphies (shared, derived traits) if possible?
a) These traits are present in all descendants of a common ancestor and are absent in all non-descendant groups
b) These traits are absent in all descendants of a common ancestor and are present in all non-descendant groups
c) These traits are present in some, but not all, descendants of a common ancestor
d) These traits are present in all descendants and all ancestors of a group
a) These traits are present in all descendants of a common ancestor and are absent in all non-descendant groups
Why are traits that are only present in one species not useful for resolving trees under parsimony?
a) These traits require only one evolutionary step, and could therefore be produced by an evolutionary history
b) These traits are not variable enough to accurately resolve evolutionary history
c) These traits are too variable to accurately resolve evolutionary history
d) These traits require many evolutionary steps, and resolving the correct evolutionary history is too complex
a) These traits require only one evolutionary step, and could therefore be produced by an evolutionary history
Which are sister taxa on this tree?
a) Ruminants and pigs
b) Tapirs and horses
c) Manatees and hyraxes
d) Elephants and manatees
d) Elephants and manatees
What does a phylogeny illustrate?
a) The hypothesized evolutionary relationships among groups of organisms
b) The end goal of natural selection
c) The confirmed evolutionary relationships among organisms
d) The progression from more simple to more complex organisms
a) The hypothesized evolutionary relationships among groups of organisms
The figure above shows a phylogeny of the SARS-CoV-2 virus on the left, and the biogeography of transmission in early February on the right. Based on this figure, which is true about the status of the outbreak in North America in February?
a) There were three recognizable clades of the virus, and transmission were coming in to North America only from Asia
b) There were three recognizable clades of the virus, and transmissions were coming in to North America only from Europe
c) There were three recognizable clades of the virus, and the transmissions were coming in to North America from Europe and Asia
d) There were two recognizable clades of the virus, and transmission were coming in to North America from Europe and Asia
c) There were three recognizable clades of the virus, and the transmissions were coming in to North America from Europe and Asia
Above are four alternative hypotheses for the evolution of shape (circle or square) and color (gray or black). Which tree is most parsimonious?
Tree 1: 3 changes
Tree 2: 3 changes
Tree 3: 2 changes
Tree 4: 3 changes
a) Tree 1, because the black square is the most different phenotype
b) Tree 3, because the black square is the most derived phenotype
c) Tree 2, because it has two sets of monophyletic sister taxa
d) Tree 4, because the black square is the most derived phenotype and the gray square is the ancestral state
e) Tree 3, because it requires the fewest character transitions
e) Tree 3, because it requires the fewest character transition
Based on this tree, which species are most closely related?
a) Dholes and Ethiopian wolves
b) Side-striped and black-backed jackals
c) Golden jackals and side-striped jackals
d) Gray wolves and coyotes
b) Side-striped and black-backed jackals
Which node indicates the common ancestor of amphibians and coelacanths?
a) 3
b) 2
c) 1
d) 4
a) 3
