26 Phylogeny Flashcards
What is phylogeny?
The evolutionary history of a species with a focus on how it is related to others.
What is systematics?
discipline focused on classifying organisms and determining their evolutionary relationships
What does a binomial name consist of?
The genus then the species
What are the ‘ranks’ of the Lennaean system?
Domain, Kingdom, Phlyum, Class, Order, Family, Genus and Species
What is each step i.e. class of the Linnaean classification called?
A rank
What is the plural of genus?
Genera
What is a genera?
It is the plural form of genus
What is a taxon?
named taxonomic unit at any level of the hierarchy is called a taxon (plural: taxa).
In the example of a Leopard, Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level
How is the evolutionary history of a group of organisms often represented?
A phylogenetic tree
What is a phylogenetic tree?
One that shows phylogeny by showing the relative time when species diverged.
What are the places where a phylogenetic tree diverges called?
Branch points
What are branch points?
The places where a phylogenetic tree diverges
What do branch points signify?
When one species diverged into two.
What is kit called when more than two species emerge from a branch point?
A polytomy
What is a polytomy?
A branch point from which more than two descendant groups emerge.
What is the significance of a polytomy?
It indicates that the precise evolutionary relationships i.e. who diverged first is not yet known
What does ‘extanct’ refer to?
A species that is still living i.e. not extinct
What are species that are still alive called?
Extanct
What are analogous structures that arose independently called?
Homoplasies
What are homoplasies?
Analogous structures that arose independently
What does ’molecular homologies’ refer to?
Similarities in DNA sequence. The more similar, the more closely related two species probably are.
This is because changes to genes i.e. insertions and mutations accumulate over a long period of time
What is molecular systematics?
The discipline that uses data from DNA and other molecules to determine evolutionary relationships.
What is a common approach to systematics and what does it entail?
Cladistics where common ancestry is the primary criterion used to classify organisms
What is cladistics?
An approach to systematics where common ancestry is the primary criterion used to classify organisms
What are ‘clades’?
A group which includes an ancestral species and all of its descendants
Based on phylogeny, what are the basic types of groups of organisms?
Monophyletic, paraphyletic and polyphyletic
What is a monophyletic group of organisms?
One that includes only an ancestral species and ALL of its descendant species.
This is also called a clade
What is a paraphyletic group of organisms?
One that consists of an ancestral species and some, but not all, of its descendants
What is a polyphyletic group of organisms?
One that contains species that do not have a single ancestral species.
Note that this is relative as all life diverged from a single organisim
What is a sister taxon?
Groups of organisms that share an immediate common ancestor (branch point) and hence are each other’s closest relatives
What is it called when a phylogenetic tree contains the common ancestor of all the species shown on the tree?
That phylogenetic tree is said to be ‘rooted’
What does ‘rooted’ refer to?
When a phylogenetic tree contains the common ancestor of all the species shown on the tree
What is a ‘basal taxon’?
A species that diverge early thus lies on a branch that originates near the common ancestor of the group.
What are species that diverged early form the common ancestor called?
Basal taxon.
How can traits of organisms be classed based on phylogeny?
As ’shared ancestral characters’ or as ’shared derived characters’
What are shared ancestral characters?
Traits that are present in all species of a clade but also in species outside the clade. This indicates that first ancestor with this trait emerged before the trait.
For example the presence of a backbone is a shared ancestral trait as all mammals have backbones but so do birds and reptiles
What are shared derived characters?
Thus present in all members of a clade and only those in a clade.
For example all mammals have hair and no non-mammals have it.
What is an ‘outgroup’?
A species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species whose phylogeny is being studied.
In this way it acts as a control of sorts
What is an ingroup?
The species that is begin studied as part of a phylogenetic analysis
Do phylogenetic trees indicate when species diverged?
Generally not. However in some a scale and proportional branch lengths are used to indicate this.
What is the fundamental assumption when determining phylogeny based on molecular data?
‘Maximum parsimony’
What is the idea that the most simple explanation is probably correct called?
Parsimony
What is parsimony?
The viewpoint that the simplest explanation that is consistent with the facts is most probably correct.
How is parsimony related to molecular systematics?
It is possible that two species appear closely related as gradual mutations caused the base sequences to diverge as normal but by random chance changed closer to the original.
However this is unlikely and thus not parsimonious so is probably untrue and thus can be ignored.
What is the ‘principle of maximum likelihood’?
The principal that states that given certain probability rules about how DNA sequences change over time, a tree can be found that reflects the most likely sequence of evolutionary events.
(Basically it is just the application of parsimony to molecular systematics)
What principle applies the idea of parsimony to molecular systematics?
The ‘principle of maximum likelihood’
What does ’phylogenetic bracketing’ refer to?
The idea that based on parsimony features shared by two groups of closely related organisms are probably present in their common ancestor and all of its descendants unless independent data indicate otherwise.
What is ‘brooding’?
When a parent warms an egg with its body i.e. by sitting on it
What are groups of related genes in a genome called?
Gene families
What are gene families?
Groups of related genes in an organism’s genome.
They often arise from gene duplication.
How can genes be grouped based on their history?
As orthologous genes or as paralogous genes
What are orthologous genes?
Those that are those found in different species, and their divergence traces back to the speciation events that produced the species.
For example many organisms have the same gene for haemoglobin with similar alleles.
They differ form paralogous genes in which a new gene originates WITHIN a species i.e. one gene in the species duplicates to form two.
What are paralogous genes?
Those that arise form from gene duplication; hence, multiple copies of these genes have diverged from one another within a species
What are methods to determine the age of divergence based on genetics called?
Molecular clocks
What are ‘molecular clocks’?
Methods to determine the age of divergence based on molecular methods.
What are the basic ideas behind molecular clocks?
- Parsimony
- Mutations occur at fixed rate
- Therefore rate of NEUTRAL change is fixed (‘Neutral theory’)
What is ’neutral theory’?
The idea that only neutral i.e. not harmful or beneficial mutations should be used in the determination of molecular clocks.
This is because many harmful mutations arise then quickly disappear
What mutations are analysed with molecular clocks?
Neutral ones because as per the “neutral theory” they are not subject to natural selection and are thus more reliable
What is the concept of the ‘ring of life’?
The idea that due to ‘horizontal gene transfer’ the origin of early life can not be represented on a phylogenetic tree as early organisms received genetic information from multiple species.
How is early life often represented in terms of phylogenetics?
As a ring i.e. the “ring of life”
What are the domains of life?
Bacteria, Archaea and Eukarya
