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Genetics and evolution > Lecture 2 > Flashcards

Lecture 2 Flashcards

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Biology 101 flashcards
1
Q

What is Phylogeny?

A

the evolutionary history of a group of related species

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2
Q

What is a phylogeny?

A

is an evolutionary tree which shows the evolutionary relationship between species

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3
Q

what is an internal node?

A

a branch point representing the divergence of two hypothetically common ancestors

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4
Q

What are the three phylogenetic groups?

A

Monophyletic
Paraphyletic
Polyphyletic

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5
Q

What is the only valid phylogenetic group?

A

Monophyletic

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6
Q

What are monophyletic groups?

A

includes all descendants of a most recent common ancestor

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7
Q

What are paraphyletic groups?

A

include only some descendants of a common ancestor, it does not include all descendants of a common ancestor

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8
Q

What are polyphyletic groups?

A

include only some distantly related descendants of a common ancestor and doesn’t include the most recent common ancestor of them all

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9
Q

What determines branching points on a phylogenetic tree?

A

defined by shared derived characteristics, either molecular (genetic) or morphological (phenotypic)

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10
Q

What can happen to derived characteristics?

A

they can be lost over generations

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11
Q

How to determine monophyletic groups?

A

comparing homologous characteristics

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12
Q

What are homologous characteristics?

A

similar traits inherited from a last common ancestor

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13
Q

What is convergent evolution?

A

a general term for the repeated evolution of similar traits

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14
Q

What could be a reason for characters not being homologous

A

convergent evolution

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15
Q

Two types of convergent evolution

A

analogy and homoplasy

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16
Q

What is analogy?

A

similar functional traits due to convergent evolution, not inherited from the last common ancestor

17
Q

Analogous traits

A

not homologous at the level of convergence

18
Q

What is Homoplasy?

A

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

19
Q

Morphological phylogenies

A

first a morphological matrix is built to record the presence/absence of compared traits, this matrix is used to infer a phylogeny

20
Q

Molecular phylogenetic

A

-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

21
Q

Variation in molecular sequences

A

some molecular sequences evolve faster than others

some sequences are more consistent while others have more sites that can vary

22
Q

Suitability of molecular sequences

A

different rates of mutation mean different MS will be suitable for different levels of phylogenetic analysis

23
Q

Uses of histone H4 in phylogeny

A

Histone H4 could be informative about very deep divergences such as species in different kingdoms (e.g plants and animals)

24
Q

Evolution of DNA

A

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

25
Q

Phylogenetic inference methods

A

compare the possible trees against the optimal criteria to see which is the best and most likely

26
Q

Two main types of phylogenetic inference:

A

maximum parsimony
maximum likelihood

27
Q

What is Maximum Parsimony?

A

the best tree is the one which requires the lowest number of changes (e.g least number of base substitutions)

28
Q

What is maximum likelihood?

A

the best tree is the one that is most likely to have produced the data given a model of evolution
-incoroporates evolutionary models

29
Q

What are evolutionary models?

A

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

30
Q

Jukes and Cantor model

A

assumes that the probability of any nucleotide changing to any other is equal

31
Q

Variation in gene phylogenies

A

different genes can imply different phylogenies
the best tree suggested by one gene may contrast the best tree suggested by another

32
Q

Why do genes suggest different phylogenies?

A

due to gene duplication or subsequent divergence

33
Q

What is Divergence?

A

means to split apart or move away from one another

two species evolving further away from their common ancestor

34
Q

Two types of homologous genes

A

orthologous
paralogous

35
Q

Orthologous genes

A

have shared ancestry due to inheritance following a speciation event (diverge after speciation)

36
Q

Paralogous genes

A

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

37
Q

Paralogous and Orthologous genes recording patterns of speciation

A

Orthologous record this more accurately than paralogous because paralogous genes show complex patterns of presence, absence and similarly among species

38
Q

What is Horizontal gene transfer?

A

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)

39
Q

Problems with horizontal gene transfer

A

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

Genetics and evolution (15 decks)

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