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First year B > L46-47: Phylogenetics > Flashcards

L46-47: Phylogenetics Flashcards

1
Q

Phylogeny

A

The evolutionary history of species or group of related species.

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2
Q

Phylogenetic tree

A

A branching diagram that represents a hypothesis about the evolutionary history of groups of organisms.

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3
Q

Topology of a phylogenetic tree

A

The branching pattern

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4
Q

Features of a phylogenetic tree

A
  • Branches
  • Nodes
  • Roots
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5
Q

Features of a phylogenetic tree: Branches

A

Can be Internal or external

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6
Q

Features of a phylogenetic tree: Nodes

A
  • External nodes: Operational Taxonomic Units (OTUs)
  • Bifurcations: Internal node with exactly 2 daughter branches
  • Polytomies: Internal node with more than 2 daughter branches
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7
Q

Features of a phylogenetic tree: Roots

A

first lineage divergence of OTUs described in the tree

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8
Q

Systematics

A

A scientific discipline focused on classifying organisms and determine their evolutionary relationships.

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9
Q

Binomial Nomenclature

A

-The two-part scientific name of a species is called a binomial.

part:

1) genus
2) specific epithet

whole name italicised and first letter of Genus is Capitalised.

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10
Q

Linnaean Hierarchical Classification

A

1) domain
2) kingdom
3) phylum
4) class
5) order
6) family
7) genus
8) species

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11
Q

Linnaean Hierarchical Classification: Domain

A

Archaea, Bacteria and Eukarya

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12
Q

Problem with LinnaeanHierarchical Classification

A

Linnaean classification and phylogeny can differ from each other

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13
Q

Systematists Classification system

A

-Only recognises groups that include a common ancestor and all its descendants

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14
Q

Phylogenetic tree: Branch point

A

Represents the divergence of two evolutionary lineages from a common ancestor

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15
Q

Phylogenetic: Sister taxa

A

Groups that share an immediate common ancestor that is not shared by any other group

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16
Q

Phylogenetic tree: Monophyletic Group (clade)

A

Group that includes an ancestral species and all of its descendants

17
Q

Phylogenetic tree: Paraphyletic Group

A

Groups are distinguished from paraphyletic groups by the fact that they do not include the most recent common ancestor

18
Q

Phylogenetic tree: Polyphyletic group

A

avoid fining polyphyletic groups and instead reclassify organisms if evidence suggests they are polyphyletic.

19
Q

Phylogenetic tree: Parsimony meaning

A

A hypothesis of relationships that requires the smallest number of evolutionary changes is most likely to be correct

20
Q

Phylogenetic tree: Likelihood

A

based on probability rules about how DNA changes over time and assumes a tree can be found that reflects the most likely sequence of evolutionary events.

21
Q

Which is more accurate for determining a phylogenetic tree: Parsimony or Likelihood?

A

Likelihood = more accurate

It is completely probabilistic, therefore uses well established statistical methods

-Parsimony methods do not use all the available information

22
Q

Application if Phylogenies

A
  • Provide information about similar characteristics of closely related species
  • A phylogeny was used to identify the species of whale from which “whale meat” originated to discover if the whale was harvested illegally.
23
Q

Molecular Clock

A

A method for estimating the time required for a given amount of evolutionary change, based on the observation that some regions of genomes evolve at constant rates.

24
Q

Calibrating Molecular Clocks

A

Genetic differences due to mutation are graphed against dates of evolutionary branch points that are known from fossil records

The genetic differences in sequence data obtained from two species can be compared with fossil evidence to indicate the time of divergence from a common ancestor.

25
Q

Issues with molecular clocks

A
  • The clock is stochastic: changes happen at random intervals rather than regularly
  • Different proteins (or their regions) have “their own clocks”, i.e., evolve under different rates
  • Rate constancy may not hold globally but applies to groups of species
  • Fossil calibrations always involve uncertainties:
26
Q

Issues with molecular clocks: Stochastic changes

A

There are differences in the speed at which genes mutate:

  • Selectively neutral mutations in genes have a regular rate of evolution
  • Most mutations in genes which have an amino acid sequence critical for survival will be harmful, fewer neutral mutations -> slow rate of change.
  • amino acid sequence Less critical for survival will have fewer harmful mutations and more neutral mutations -> faster rate of change.
27
Q

Issues with molecular clocks: : Fossil calibrations

A
  • error in fossil dating
  • incomplete fossil record
  • errors in assigning a fossil on the phylogeny
28
Q

Give an example of an application of molecular clocks

A

Dating the origin of HIV infections in humans.

  • Originated from viruses infect chimpanzees and other primates.
  • Virus spread to humans more than once, therefore multiple strains of the virus exist and precise dating of when the first cases of HIV in humans occurred is not clear.

However a comparison of HIV samples shows that the virus evolved in a very clocklike way, therefore molecular clock data can be extrapolated backwards and this indicates HIV-1 was the first strain to pass to humans, estimated to have occurred in 1910.

29
Q

Definition of homologies

A

Phenotypic and genetic similarities due to shared ancestry

30
Q

Definition of morphogenesis

A

The development of the form of an organism and its structures

31
Q

Orthologous genes

A

Homologous genes that are found in different species because of speciation

*only 1 single copy in a genome

32
Q

Paralogous genes

A

Homologous genes that are found in the same genome due to gene duplication

33
Q

xenologues genes

A

Genes resulting from horizontal gene transfer

First year B (11 decks)

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