Lecture 17: phylogenetics part 1: introduction Flashcards
phylogenetic trees (2)
-A data based branching diagram depicting inferred evolutionary
relationships among biological species or other entities based upon
similarities and differences in their physical or genetic characteristics.
-consider them hypotheses about evolutionary relationships
Like a tree (3)
-Phylo trees reflect relationships in branching order
-Branch points are called nodes
-Roots are called common ancestors
Strange things happen in evolution
Some trees are not great representations of evolutionary histories due to things like horizontal gene transfer, hybridization, and merging species, but are often still very useful tools
Phylogeny
-represents the inferred evo history of Taxa (species, genera, families …)
Why is phylogeny important (2)
- useful for classification
- Helps make mechanisms of evolution more clear
how are phylogeny’s Useful for classification (3)
If classification reflects genealogy/phylogeny:
-Helps us organize and communicate information about millions of species
-Helps us predict properties of organisms (e.g., according to properties of
closest relatives)
How do phylogeny’s help us clear up mechanisms of evolution?
-To see way in which characters change over time (e.g., direction and frequency of change)
-Ex Loss of limbs occurring independently in multiple vert lineages (Snakes, legless lizards etc)
Terminology (6)
-Species are grouped in HIERARCHIALLY
-Species are NESTED into more and more inclusive taxa with the higher levels being less inclusive and the lower levels being more inclusive
-King Philip came over for green soup = Kingdom, phylum, order, family, genus (or genera), species
-Binomial nomenclature = scientific naming of species (genus species). Italicized
-Taxon = a named taxonomic unit at any level (plural = taxa)
-Relatedness - how recently two taxa shared a common ancestor
Sister taxa
Sister taxa are each others closest relatives ie they shared an ancestor most recently
Evo trees are hypotheses (4)
-Evo history is rarley directally observed
-we can only estimate or infer evo history using clues left behind
-If classification is intended to reflect evo relationships, classifications will change as hypotheses about relationships change
-Hypothesized branching order is based on inferences about the order in which evo modifications (transitions) occurred
The logic of inferring evo trees (3)
-Descent with modification from a common ancestor
-Modifications = evolutionary novelties = derived characters
-Infer evolutionary history of a group of species from nested sets of shared evolutionary innovations/derived characters = synapomorphies
Key concepts in phylogeny inference (5)
- Evolutionary innovation = derived character = apomorphy
- Shared evolutionary innovations/derived characters = synapomorphies
- Pre-existing or ancestral character = plesiomorphy
- Each taxon with mixture of ancestral (plesiomorphic) and derived (apomorphic) characters
- Presence of synapomorphies (rather than retention of ancestral characters) tells us about branch order
Cladistics (2)
-Cladistics = hierarchical classification of species based on evolutionary ancestry
-Clade (“branch”) = monophyletic group = an ancestor and all of its descendants
Monophyly (3)
-Cladistics recognizes only taxonomic groups that are monophyletic.
Where same ancestor gave rise to all species in that taxon
and to no species in any other taxon
-For example picture a tree with animals ABCD on one side of a node and EFGH on the other. Cladistics would recognize ABCD as a clade but not CDEF because they are on different sides of the node (aka polyphyletic).
-Cladistics also doesnt recognize paraphyletic taxa, where taxa share a common ancestor but dont include all descendants of said ancestor. For example, Picture a tree with a split. On the left side of the split is baboons, on the right side the lineage continues, splitting off into orangutans, then Chimps and humans (sister taxa). You cannot group orangutans with the chimps because you are excluding humans, another descendent of the common ancestor between chimps and humans.
Traditional groups (2)
-many traditonal groups are paraphyletic
-Includes things like dinosaurs and reptiles (which should include birds to be Mono)
Polytomy
Nodes where lineages split into more than two descendent lineages at the same time (i.e. 3+ branches from a single node at a time)
Adaptive radiation
An event in which an ancestor gave rise to more than two daughter species at the
same time
Difficulties building trees (3)
- Characteristics of common ancestor often unknown
- Similar characteristics sometimes evolve independently in different lineages (convergent or parallel evolution)
- Sometimes evolutionary novelties are secondarily lost (reversals)
pleiomorphic vs apomorphic
traits that are ancestral (plesiomorphic) and that are derived (apomorphic)
Synapomorphy
a shared, derived trait that is present in an ancestral species and all of its descendants, but not in more distant ancestors. EX all mammals have hair and mammary glands
Homologous Traits
traits that are similar between species because they were inherited from a common ancestor. These traits might look different or serve different functions now, but they share an underlying structure or origin. EX the hands of bats vs whales vs horses vs humans
Convergence and Reversal (4)
-Only homologous characters say something meaningful about evolutionary history
-Similar characters that evolved independently (i.e., are homoplasious) would be misleading
-Convergence: different evolutionary path to similar derived trait
-Reversal: loss of derived trait
Homoplasious traits
Similar characters that evolved independently. EX fins in sharks, dolphins and penguins
causes of homoplasy (3)
Convergent evolution: bats & birds do not have a most recent common ancestor with wings
- Parallel evolution: elongate hind legs in arid adapted rodents in Africa & North America
*Evolutionary reversal e.g., “re-evolution” of streamlined body & fins of
aquatic whales & dolphins whereas sharks retained these traits from the ancestral condition
