U4 Terms Flashcards
Phylogenies is what type of explanation?
Backwards looking
Phylogeny
A visual representation of the genealogical relationships of life
–> Like a family tree
–> “History of branching”
Phylogenies as a conceptual model:
Phylogenies integrate…
observations and inferences in order to help understand a lineage and gain new insights into life on Earth
Time representation on a phylogeny
Bottom of a phylogeny = Oldest
Top of phylogeny = Present
Branch
The unique history of each taxon (The line coming straight down from a taxon type)
Node
Location of where speciation occurs
(Where a color/character change occurs)
Common Ancestor
Term we apply to the SHARED history of particular lineages
Phylogenies depict…
the evolutionary relatedness of species (or other taxa)
Patterns of lineage splitting are produced by…
(What causes new branches to form?)
Speciation
New traits can appear in phylogenies if…
Heritable variation originates and becomes common within a species ( leading to speciation)
4 main uses of phylogenies
1) Help develop new crops to feed humanity
2) Identify new pathogens that make people sick
3) Conserve endangered species
4) Decide legal cases
Taxa
The groups of living things that we would like to build a phylogeny of
–> Refers to all the different living things on Earth
The # of taxa determines…
The # of phylogenic hypotheses concerning their relationships
Character
Any feature (or part) of an organism
(The data used to generate a phylogeny)
Features of a useful character (2)
1) Shows greater variation AMONG the taxa of interest rather than within each taxon
2) Variation is heritable and independent of other characters
Character State
Term that describes the types of variation we observe in our characters
Data Matrix
All the collected data on taxa, characters, and characters states compiled into a table
Outgroups
A more distantly related group of organisms (taxa) that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study
Ingroups
The taxa we are directly studying
What do outgroups tell us?
The direction of character state changes –> Inform us of the most likely path of character state change across taxa
Parsimony
(Occam’s Razor)
–> The simplest solution is the best solution
–> A central philosophical principle of all the sciences (NOT unique to phylogenetics)
Purpose of parsimony in phylogenetics
Used to QUANTIFY the QUALITY of each phylogenetic hypothesis using the data in the data matrix
Tree Length
The sum of the # of changes in a given hypothesis for each character state
Smallest Tree Length =
Most parsimonious = BEST hypothesis
Minimum # State Changes
The MOST parsimonious # of character state changes
(The best tree length possible)
Minimum # State Changes CALCULATION
MIN = SUM (# character states - 1) –> Sum of each character’s minimum state change]
Consistency Index
CI = (Min. # state changes) / (Tree length for a given hypothesis)
The > CI…
The better (more parsimonious) the hypothesis
Best possible hypothesis would have a CI = ….
1.0
Data used to test for the most parsimonious hypothesis (4)
1) Different phenotypic characters (than those used to build the hypotheses)
2) Genetic Data –> Comparing morphology and genetic data to see if they match
3) Data from fossil record
4) Data from geography
Testing phylogenetic hypothesis with:
Different phenotypic characters
We can use another character data (not already used in determining the most parsimonious hypothesis) to test the hypothesis
–> Map the new data onto the hypothesis and if the “old” and “new” data yield the same result, the hypothesis is supported
Testing phylogenetic hypothesis with:
Genetic data
Data of chromosomes, genes, alleles, SNPs, RNA, proteins can be used to test a phylogenetic hypothesis
–> If results of this test match that of the result of test with morphology data the hypothesis is supported
Testing phylogenetic hypothesis with:
Data from the fossil record
Does the order of branching match the fossil record? (Distribution of taxa in time)
–> Does the “lowest” taxa branch match with the lowest (deepest) fossil taxa in the rock layer?
–> Does this match for all taxa branches and their corresponding order in which they’re found in the rock layers?
Yes = supported
Testing phylogenetic hypothesis with:
Data from geography
Looks at how the different taxa differ in their place of habitat (distribution taxa in space)
Ex: Wouldn’t make a lot of sense for a freshwater fish to move continents (very hard for them to do) –> A hypothesis with these fish taxa in different continent would be less supported with this data
MRCA
Most Recent Common Ancestor
Similarity (in appearance for example) DOES NOT EQUAL…
Ancestry = …
relatedness
Intermediates
Extinct taxa
Rotating phylogenies
Phylogenies can be rotate around each node –> Any of these types of rotations produces the same hypothesis simply rotated
Purpose of rotation in phylogenies
Reminds us that evolution DOES NOT have a direction, goal, or trajectory
Uses of Phylogenies in Solving Problems (6)
1) Identify hosts of major diseases
2) Used to make predictions about evolution
3) Help to guide the conservation of endangered species
4) Used to accurately name species
5) Used to understand how traits assemble over time
6) Help correct naive explanation of traits
How do phylogenies help to:
Identify hosts of major disease?
Helps to see where/how new diseases/illnesses fall within other lineages
–> From understanding its relation to other lineages, a prediction can be made about the host of the new disease based on the hosts of the related lineages
How do phylogenies help to:
Make predictions about evolution?
Through a phylogeny, we can create potential explanations for how the related taxa are related (what they have in common)
–> This produces hypotheses and predictions of evolution that can then be tested to determine whether they are supported or not
Examples: Whale and HIV cases
How do phylogenies help to:
Help to guide the conservation of endangered species?
Phylogenies can show the various lineages of a specific family, genus, etc.
–> This can then help us to determine where to set up reserves to supply a reserve in each region that has one or more of these lineages to maintain this genetic diversity
Ex: Spotted leopard
How do phylogenies help to:
Accurately name species?
Biologists want all biological names to reflect ancestry –> Naming based off of monophyletic groups
–> Makes it easier to look for genetic relatives of different taxa or lineages
Monophyletic Groups
An ancestor and ALL of its descendants (branches)
Common Species Naming Mistakes (2)
1) Excluding a taxon from a monophyletic group
2) Include members of a group from 2 different ancestors
How do phylogenies help to:
Understand how traits assemble over time?
Helps us to answer the question of: which character came first, second, etc.?
–> We can analyze how characters have changed over time and between taxa
Ex: In birds, order of development of feathers, wings, and flight
How do phylogenies help to:
Correct naive explanation of traits?
Naive Explanations = Only focus on the CURRENT function of a trait, as it exists today, as the primary explanation for its existence (Ex: Birds have wings because they need them to fly)
–> Phylogenies highlights ancestry and takes the origins/history of traits into consideration when explaining the presence of a trait in a living taxon
Things that can be fossils (7):
1) DNA
2) Embryos
3) Pollen
4) Hard parts and skeletons
5) Footprints and traces
6) Proteins and lipids
7) Soft tissues
Types of rocks
1) Igneous rocks
2) Sedimentary rocks
3) Metamorphic rocks
Igneous Rocks
Liquid rock that hardens when cooled (Volcanic origins)
Metamorphic Rocks
Sedimentary rocks subjected to heat and pressure (“cooked rocks”)
Sedimentary Rocks
Formed from erosion of igneous rocks that is then cemented into rock
What rock is the most common source of fossils? Why?
Sedimentary
–> Igneous: Fossils would get vaporized
–> Metamorphic: Fossils are melted or deformed by heat and pressure
Superposition
Younger rock layers are deposited over older rock layers
–> central to interpreting fossil age by rock layer
Phylogenies as predictive tools (in terms of fossils)
Important tools for predicting (geographically) where and when (in time) fossils should exist for a given taxon
(Tells us where fossils are most likely located)
What do phylogenies and the fossil record show about character/state assembly
Phylogenies and the fossil record help to reveal how characters + character states were assembled in a lineage (How/when did character transitions occur?)
Tiktaalik Example
Tiktaalik is an extinct tetrapod
–> The first fossil with a neck present (demonstrating the shift from fish to amphibians)
How do phylogenies and the fossil record reveal ecological relationships?
Together they help to reveal stability and change in ecological relationships
Ex: Amber (tree resin) can preserve creatures in action which can be compared to the same creature’s actions today to see if there is any difference
EX: Ants and scale insects
How do phylogenies and the fossil record help to understand mass extinctions?
I dont’t know, they just do Sarah
Extinction
Death of a taxon or lineage
Extinction is a _______ process that is ______ happening on Earth in __________ _________
1 ) NATURAL
2) ALWAYS
3) LOW LEVELS
Background Extinction
“typical” rates of extinction
Mass Extinctions
Significantly higher rates of extinction (many species going extinct pet one unit of time)
What taxa tend to have greater chances of surviving mass extinctions?
Geographically widespread taxa
Factors that impact survival (natural selections during normal times…
may NOT promote survival during mass extinctions
How do mass extinctions impact natural selection?
These extinctions change the playing field again and again making it hard for natural selection to produce better and better taxa over time
