chapter 7- phylogeny Flashcards
phylogeny
A hypothesis of ancestor descendent relationships.
Phylogenetics
the study of ancestor descendent relationships. The objective of phylogeneticists is to construct phylogenies
Phylogenetic tree
a graphical summary of a phylogeny
All life forms are related by common ancestry and descent. The construction of phylogenies provides explanations of the ———– seen in the natural world.
diversity
Phylogenies can be based on ——– data, ———– data, ——– data or all three. Today, phylogenies are usually constructed using ———-
morphological, physiological, and molecular,
DNA sequence data
We use —— to construct phylogenies. A ——- is any attribute of an organism that can provide us with insights into history (shared ancestry).
characters
character
In molecular phylogenies, characters are typically ———— in a gene sequence, and each position can possess four CHARACTER STATES: A,C, G, or T
nucleotide positions
Plesiomorphy
refers to the ancestral character state
Apomorphy
a character state different than the ancestral state, or DERIVED STATE
Synapomorphy
a derived character state (apomorphy) that is SHARED by two or more taxa due to inheritance from a common ancestor: these character states are phylogenetically informative using the parsimony or cladistic criterion
Autapomorphy
a uniquely derived character state
Monophyletic
a group that includes ALL of the descendants of a common ancestor. Monophyletic groups are also known as CLADES
Non Monophyletic
Any case that does not satisfy the above, such as:
Paraphyletic
Polyphyletic
Paraphyletic
A group that includes some, but not all of the descendants of a common ancestor
Polyphyletic
assemblages of taxa that have been erroneously grouped on the basis of homoplasious characters (eg “vultures”) -we will return to this
Homology
A character state that is shared between two DNA sequences or taxa may be so because they inherited it from a common ancestor, or it is HOMOLOGOUS (a homology/ synapomorphy)
homoplasy
the shared character might occur because they were evolved independently, in which case they are called a HOMOPLASY
Why can Homoplasy Occur
- parallel evolution
- convergent evolution
- secondary loss
parallel evolution
independent evolution of a similar feature from the same ancestral condition
convergent evolution
independent evolution of the same feature from different ancestral condition
secondary loss
revision to ancestral condition
Homoplasy results in ————, polyphyletic groupings
such as “vultures”
erroneous
what happened with the old world vulture and new world vulture ?
- they were thought to be from the same common ancestor due to morphological similarities, both looked similar, ate dead animals
- through further research, molecular data it was shown that they don’t come from common ancestors
- new world vulture common ancestor storks and their relatives
- old world vulture common ancestor birds of preys
relationship b/w new world vulture and old work vulture
polyphyletic - grouped together due to mistake, was believed to be derived independently
Vultures are a—————-. New world and old world
vultures provide an example of homoplasy resulting from ———————–.
polyphyletic group- grouped together due to a mistake, as a result of homoplasy
convergent evolution - independent evolution of similar feature from different ancestral condition
Three Spine Stickle Back
- 3 spine stickle back species pairs have evolved independently in coastal lakes of British Columbia
- Lake A have 3 spine stickle back , independently evolved similar feature from same ancestral condition : marine ancestors
- Lake B have 3 spine stickle back : independently evolved similar feature from same ancestral condition : marine ancestors
Mutation can cause ————
synapomorphies
———– can remove synapomorphies
reversals (back -mutations)
We use ————— to construct phylogenetic trees and to identify groups that are monophyletic; synapomorphies are ———————
homologous characters (synapomorphies) phylogenetically informative
We want to avoid using ——————– to construct phylogenies
homoplasious characters
The Principle of Parsimony
- simple explanations are preferred over more complicated ones.
- In terms of phylogenetic trees, less evolutionary steps are better than more steps to explain relationships. The tree with the least number of steps is the most parsimonious.
The parsimony method ———- the total number of evolutionary changes required to explain relationships
minimizes
outgroup
- When constructing a phylogeny for a group of organisms, we need to employ an outgroup, which is not part of the group of interest (the ingroup), but also not too distantly related to it.
- The outgroup is used to polarize the character states, or infer change. The character state possessed by the outgroup is defined a priori as ancestral (pleisiomorphic)
Bootstrap Method
- Assessing Confidence in Phylogeny
- Computational technique for estimating the confidence level of a phylogenetic hypothesis
- Randomly generates new data sets from the original set (1000 replicates is most common)
- Computes the number of times that a particular grouping (or branch) appeared in the tree
Taxonomic groups can be
Monophyletic – contain all descendants of a common ancestor
Paraphyletic – contain some but not all descendants of a common ancestor, or polyphyletic (erroneous homoplasious groupings)
The goal of ——— is to only recognize monophyletic groups as valid taxa, but traditional taxonomy has not always done this
cladistic taxonomy
Cladistics
the use of parsimony to construct evolutionary relationships
cladistic taxonomy is equal to
= evolutionary taxonomy
Coevolution
- The process where evolutionary changes in the traits of one species drives evolutionary changes in the traits of another species. Coevolution can involve predators and prey, hosts and parasites, and mutualisms, such as aphids and their endosymbiotic bacteria (above).
- Coevolution can result in co-speciation.
