Phylogeny Flashcards
Microevolution
Generational timescale
evolution within a population or species; occurs on a generational timescale
- examines need breeding population, evolution, and reproductive isolation
Macroevolution
Geological timescale
evolution across species; occurs on a geological timescale
- examines reproductive isolation, new species, and biodiversity - not in terms of time but in terms of geologic(different species are different rates of generations)
Systematics(macroevolution)
study of biological diversity and its origins / history
GOAL: Reconstruct evolutionary history
PROBLEM: Cannot directly observe evolutionary history
SOLUTION: Infer history using deductive logic
HOW: Phylogenetics – a tool used to study evolutionary history
What are phylogentic trees?
Phylogeny – pattern of lineage branching that represents the evolutionary history of different organisms. Akin to a family tree.
Terminology
1. root - basal common ancestor(farthest back in time we are looking at) 2. branch - edge - one line 3. node - common ancestor 4. terminal node - usually modern day(not always) 5. common ancestor 6. extant species 7. Internal node - the last common ancestor before the terminal node - an “X” means the species went extinct - nodes can be rotated so be wary of how you read them
What are phylogenies based on?
Synapomorphy – shared derived character. In other words, characters that are derived by a distant ancestor and shared by all of those ancestors decedents.
NOTE: Phylogenies are hypotheses based on all of the available data (see the Prologue for more detail on scientific hypotheses).
Synapomorphies can be obtained from the following types of data:
- Fossil Record
- Morphology
- Molecular/genetic data
- Behavior
- Ecological
Synapomorphies:
Fossil Record
for fossils to be useful, they must be dated.
Dating the fossil record
- Radiometric analysis of surrounding rocks
- igneous(cooled magma) – provides absolute age
- sedimentary(in aged layers not for radioactive dating) – provides relative age
- provides relative and absolute age
- metamorphic - often not useful
- Index fossils – fossils that had a brief existence in geologic time and a wide geographic distribution. Allows unknown fossils found in the same or nearby rock strata to be age via correlation analysis.
- e.g Ammonite fossil
- if its below this fossil layer then older etc
- Magnetism –Iron in lava aligns along magnetic force lines as lava cools. Earth flips its magnetic poles every 500,000 years, changing the orientation of iron in the rock.
Synapomorphies:
Morphology
- can look at something like how the skeleton has morphed over
Synapomorphies:
Molecular/genetic data
- takes a lot of data
Synapomorphies:
Behavior
just know its one of them
Synapomorphies:
Ecological
just know its one of them
Homologous (synapomorphies) versus analogous (homoplasy) traits
Homologous traits – those that are derived from the same common ancestor (i.e. synapomophic)
Analogous traits – similar looking traits that evolved independently and were NOT derived from a common ancestor. This phenomenon is also known as homoplasy (i.e. homoplasious traits).
Homoplasy is due to:
1. Convergent evolution – phenomenon where two (or more) distinct species independently evolve similar (analogous / homoplasious) traits. Results from similar environmental challenges.
Something can have both analgous and homologous traits
Classification and phylogeny
Linnaean Hierarchal classification system:
- Kingdom, Phylum, Class, Order, Family, Genus, Species - King phillip conqueror of france got smacked - Furthest related-----------closest releated
Binomial – official species name comprised of the genus and species
- Genus capitalized, species lower case - Italicized or underlined - Classification should reflect evolutionary history (but not always)
Taxonomy follows logically from phylogeny but not always
Kingdom, Phylum, Class, Order, Family, Genus, Species
King phillip conqueror of france got smacked
Synapomorphy vs. plesiomorphy
Terms are relative to the clade currently under investigative
- synapomorphy – shared derived character(new)
- plesiomorphy – ancestral character. In other words, lineages not included in the group of interest also possess this homologous character(old)
- autapomorphy – unique character
- phylogenetically uninformative
- if no other node has the trait then we can not build a phylogeny from it
The importance of outgroups
When constructing a phylogeny, one should identify the outgroup.
Outgroup - serves as a reference to help determine the evolutionary relationships among the group of interest (the ingroup).
Outgroups possess numerous plesiomorphic traits, which help to identify synapomorphies.
- doesn’t have the traits of the ingroup - serves as the reference point to what is happening in the in group - choose the node as close to the ingroup as possible without entering the in group
Phylogenetic groups
Monophyletic(Clade) – group consisting of an ancestor and ALL of its descendants.
- This group is known as a clade. - count the total number of branch points we determine the number of Monophyletic groups
Paraphyletic – group consisting of a single ancestor and MOST of its descendants
- reptile is paraphyletic since it excludes birds which are actually reptiles
Polyphyletic – a group consisting of multiple ancestors.
- marine mammals - they independently evolved their aquatic nature but are typically grouped together
Types of Phylogenetic trees
Cladograms – branch length arbitrary
- Shows who is related to who and that’s it
Phylogram – branch length indicates number of differences
- Longer path = more generations = more quickly evolved
Ultrametric – branch length indicates time since divergence
- Phylogram with a timeline at bottom
The Rule of parsimony
The best phylogenetic hypothesis is the most parsimonious hypothesis
Parsimony – a phylogenetic tree building rule that states the phylogeny with the least number of evolutionary changes is the correct phylogeny
- based on the philosophy of Occam’s Razor
Building a tree based on genetic data
- Create all the possible phylogenies for the species in question
- Obtain a gene sequence for species under investigation.
- Align the gene sequences so that the position of the nucleotide sites match
- For each nucleotide position, identify nucleotides that are different. These differences are inherited genetic mutations.
- Place the mutation event onto all potential phylogenies
- After all mutations have been placed, identify the phylogeny with the smallest number of mutational events. This is the most parsimonious tree.
NOTE: see figure 26.15 for a detailed description of this method.
Homoplasious traits create misleading phylogenies
Must be careful with homoplasious
- Figure 26.19
Molecular Clocks(continuation of VII)
If mutations occur at a steady rate, then we can use the number of mutations accumulated within a lineage to estimate how long ago that lineage split from another lineage.
- Genes have a timeclock of a probability to mutate in a population - Fairly linear relationship
Molecular clock – the technique used to relate the mutational differences between lineages to their absolute time since divergence. This allows you to construct an ultrametic tree.
Modern use of Phylogenies
- Reveal changes not captured by the fossil record
- Resolve evolutionary hypotheses
- Identify illegal activity
- Track the origins and spread of infectious disease
- HIV
- Bird flu
- West Nile Virus
extant
= living
synapomorphy
shared derived character(new)
plesiomorphy
ancestral character. In other words, lineages not included in the group of interest also possess this homologous character(old)
autapomorphy
unique character
- phylogenetically uninformative - if no other node has the trait then we can not build a phylogeny from it
Monophyletic(Clade) Group
group consisting of an ancestor and ALL of its descendants.
- This group is known as a clade. - count the total number of branch points we determine the number of Monophyletic groups
Paraphyletic Group
group consisting of a single ancestor and MOST of its descendants
- reptile is paraphyletic since it excludes birds which are actually reptiles
Polyphyletic
a group consisting of multiple ancestors.
- marine mammals - they independently evolved their aquatic nature but are typically grouped together
Cladograms
branch length arbitrary
- Shows who is related to who and that’s it
Phylogram
branch length indicates number of differences
- Longer path = more generations = more quickly evolved
Ultrametric
branch length indicates time since divergence
- Phylogram with a timeline at bottom
Igneous Rock
Cooled magma
Can be radioactive Decay aged
Absolute aging
Sedimentary Rock
Sediments deposited in aged layers
Most fossils here
provides relative age and absolute age
Metamorphic Rock
altered igneous and sedimentary rock.
serves to confuse and frustrate geologist/paleontologist.
Index fossils
fossils that had a brief existence in geologic time and a wide geographic distribution. Allows unknown fossils found in the same or nearby rock strata to be age via correlation analysis.
- e.g Ammonite fossil - if its below this fossil layer then older etc
Magnetism
Iron in lava aligns along magnetic force lines as lava cools. Earth flips its magnetic poles every 500,000 years, changing the orientation of iron in the rock.
