Lecture 2 Flashcards
What is Phylogeny?
the evolutionary history of a group of related species
What is a phylogeny?
is an evolutionary tree which shows the evolutionary relationship between species
what is an internal node?
a branch point representing the divergence of two hypothetically common ancestors
What are the three phylogenetic groups?
Monophyletic
Paraphyletic
Polyphyletic
What is the only valid phylogenetic group?
Monophyletic
What are monophyletic groups?
includes all descendants of a most recent common ancestor
What are paraphyletic groups?
include only some descendants of a common ancestor, it does not include all descendants of a common ancestor
What are polyphyletic groups?
include only some distantly related descendants of a common ancestor and doesn’t include the most recent common ancestor of them all
What determines branching points on a phylogenetic tree?
defined by shared derived characteristics, either molecular (genetic) or morphological (phenotypic)
What can happen to derived characteristics?
they can be lost over generations
How to determine monophyletic groups?
comparing homologous characteristics
What are homologous characteristics?
similar traits inherited from a last common ancestor
What is convergent evolution?
a general term for the repeated evolution of similar traits
What could be a reason for characters not being homologous
convergent evolution
Two types of convergent evolution
analogy and homoplasy
What is analogy?
similar functional traits due to convergent evolution, not inherited from the last common ancestor
Analogous traits
not homologous at the level of convergence
What is Homoplasy?
repeated evolution of the same state of the same character on a phylogenetic tree
-this can be considered a type of homology because there is a path of common ancestry though it shows independent evolution so some argue its not homology
Morphological phylogenies
first a morphological matrix is built to record the presence/absence of compared traits, this matrix is used to infer a phylogeny
Molecular phylogenetic
-bases on molecular characters are reconstructed
-molecules are sampled and sequences
-sequences are aligned using computer algorithms to make a molecular character matrix
-alignment is used to infer phylogeny
Variation in molecular sequences
some molecular sequences evolve faster than others
some sequences are more consistent while others have more sites that can vary
Suitability of molecular sequences
different rates of mutation mean different MS will be suitable for different levels of phylogenetic analysis
Uses of histone H4 in phylogeny
Histone H4 could be informative about very deep divergences such as species in different kingdoms (e.g plants and animals)
Evolution of DNA
Non-coding DNA sequences generally evolve faster than protein-coding
Nucleotides evolve faster than the corresponding amino acids
The 3rd position base in a codon is usually the fastest because it is least likely to effect amino acid coded for
Phylogenetic inference methods
compare the possible trees against the optimal criteria to see which is the best and most likely
Two main types of phylogenetic inference:
maximum parsimony
maximum likelihood
What is Maximum Parsimony?
the best tree is the one which requires the lowest number of changes (e.g least number of base substitutions)
What is maximum likelihood?
the best tree is the one that is most likely to have produced the data given a model of evolution
-incoroporates evolutionary models
What are evolutionary models?
models of the probability of different evolutionary events such as DNA substitution models which model the probability of mutation or substitution from one base to another
Jukes and Cantor model
assumes that the probability of any nucleotide changing to any other is equal
Variation in gene phylogenies
different genes can imply different phylogenies
the best tree suggested by one gene may contrast the best tree suggested by another
Why do genes suggest different phylogenies?
due to gene duplication or subsequent divergence
What is Divergence?
means to split apart or move away from one another
two species evolving further away from their common ancestor
Two types of homologous genes
orthologous
paralogous
Orthologous genes
have shared ancestry due to inheritance following a speciation event (diverge after speciation)
Paralogous genes
result from gene duplication, found in more than one copy in the genome. copies can diverge within the genome that carries them and evolve new functions
Paralogous and Orthologous genes recording patterns of speciation
Orthologous record this more accurately than paralogous because paralogous genes show complex patterns of presence, absence and similarly among species
What is Horizontal gene transfer?
a process which can lead to gene trees which don’t precisely match species trees
it is the transfer of genes between co-existing species not through common decent (e.g plasmids and viral replication)
Problems with horizontal gene transfer
can lead to rapid and wide transfer of genes so patterns of presence and similarity in genes that have been horizontally transferred may not accurately record speciation
