Lecture 6: Cladistics Flashcards
Cladistics
an approach for systematics to classify organisms using ancestral relationship as the primary criteria
Clades
Groups of organisms which
are classified together
You can put any organisms into a
clade, but that does not mean the
grouping is ‘correct’ (i.e., reflects close evolutionary relatedness)
Monophyletic group
- A clade where all members are descendants of their most recent common ancestor
- Once again, this concept is relative to the reference point
Paraphyletic group
- A clade where all members are descendants of their most recent common ancestor but there are more descendants of that ancestor which were not included
- A paraphyletic group is an incomplete representation of organisms with close evolutionary relatedness
Paraphyletic group Ex
- Birds are closely related to lizards and dinosaurs
- The monophyletic group ‘Reptile’ include lizards, dinosaurs and birds
- However, birds were initially thought to be un-related to dinosaurs
- The original ‘Reptile’ clade used to be a paraphyletic group which excluded birds
Polyphyletic group
A clade which includes members belonging to a different evolutionary lineage
Para/and polyphyletic clades are also relative
Algae
Eukaryotic photoautotrophs which is not a plant. Historically, many non- plant photoautotrophs were labelled ‘algae
Now we know that ‘Algae’ is a ___
polyphyletic group
Algal species are found in many, independent taxa
Classification using cladistics
Organize organisms into groups with ancestry as your priority
Guidelines when classifying
- Keep track of shared ancestral and shared derived characters as they get passed on from the ancestor to descendants
- Very complicated traits, shared across organisms, usually do not occur due to convergent evolution
Ingroup
organisms you want to classify (frog, cow, dog)
Outgroup
a species closely related to the ingroup, but does not share any common trait (fish)
Creating a table to classify organisms relatedness
- Identify homologous traits, shared by the ingroup, to use for classification
- Summarized in a character table
- 0= organism does not have the trait
- 1= organism has the trait
Build a phylogenetic tree assuming these traits arouse only
once during evolution
Making the phylogenetic tree
- First, split your outgroup from the ingroup
- The outgroup (fish) is the most different from the ingroup
- The common ancestor splits into the ‘fish’ lineage and the ‘frog/cow/dog’ lineage
- After diverging:
- The ancestor of ‘fish’ lineage did not evolve four legs. That’s why fish does not have four legs.
- The ancestor of ‘frog/cow/dog’ lineage evolved four legs. That’s why its descendants have four legs.
- After splitting the outgroup, keep on splitting off members of ingroup, starting from the most different one
- Lastly, the cow/dog group diverged into animals with canines and animals without canines
- Now, all members of ingroup are resolved in the simplest evolutionary pathway
Maximum parsimony
- When there are multiple ways to describe a phenomena, the simplest explanation is most likely the correct one
- Organisms are classified with maximum parsimony as the guiding principle
Classification using genes
- Genes are classified using with cladistics and maximum parsimony
- Evolution (mutation) of the gene at every base (sites) are analyzed separately
Maximum parsimony and classification using genes
- To resolve the discrepancy, evolution events for all sites are mapped onto all possible scenarios
- The scenario which requires the least number of changes overall is the most parsimonious explanation
Computers are essential for molecular genetics
- Amount of calculation required to resolve the tree increase drastically with more species
- Resolving 3 species is simple, there are only 3 possible scenarios (trees) to resolve this
- Resolving 4 species have 15 possible trees
- Resolving 10 species have 34,459,425 trees
- Also, the not all mutations (such as A-to-C or T-to-G) happen at the same frequency
Maximum likelihood
resolve molecular phylogenetics while taking into account the different chances of mutations
Horizontal gene transfer (HGT)
Genes (which represent morphological and biochemical traits) can jump from one lineage to another unrelated lineage
Fundamental assumption during classification using traits
a trait gets transferred from ancestor to descendant via reproduction
Why does the concept of HGT make it harder to map evolutionary relationships
Horizontal gene transfer breaks this assumption and makes it much harder to discern relationships between organisms
