Evolution Through Duplication

Question 1

two key ideas for how new genes emerge

Answer 1

• novel gene formation from ancestral genes

- de novo gene birth

Question 2

how can novel gene formation from ancestral genes occur (5)

Answer 2

• duplication and divergence
• gene fusion
• gene fission
• horizontal gene transfer
• retroposition

Question 3

duplication and divergence (3)

Answer 3

• genes are duplicated
• duplicated gene has less selective pressure and is free to change
• eventually the duplicated gene develops a new function

Question 4

gene fusion

Answer 4

• a hybrid gene forms from 2+ existing genes

Question 5

gene fission (2)

Answer 5

• singe gene separates to form two different genes

- could happen by duplication, followed by loss of different sequences

Question 6

horizontal gene transfer

Answer 6

• genes transferred from one species ends up diverging in function in the new species

Question 7

retroposition (2)

Answer 7

• mRNA transferred from one gene may reverse transcribed and inserted elsewhere
• creates an intron-less version of the original gene

Question 8

at what genomic scale do duplications occur (6)

Answer 8

at all genomic scales:

• domain (exon)
• gene
• gene cluster
• segment
• chromosome
• genome

Question 9

what are the characteristics of an unduplicated gene (3)

Answer 9

• retains original function and therefore has few base substitutions
• functions are critical to cell function and for survival to be maintained
• mutations/modifications of this gene would be harmful and selected against

Question 10

what are the characteristics of a duplicated gene (3)

Answer 10

• this gene is free to accumulate new mutations and thus diverge from original gene
• new functions are free to develop
• some of these new functions may provide a survival advantage

Question 11

how can duplicated genes evolve (2)

Answer 11

can evolve into:

• pseudogenes
• genes with new functions

Question 12

pseudogenes (3)

• defintion
• examples of how they are created
• why they are created

Answer 12

• nonfunctional genes that result from random mutations in a duplicated genes
• loss of regulatory function, substitutions at critical amino acids, premature termination, frame-shift mutation, altered splicing patterns
• accumulate mutations at a fast pace as there is no selection acting on it

Question 13

duplicated genes with new functions (2)

Answer 13

• when random mutations provide selective advantage to the organism
• the new gene usually has a novel pattern of expression

Question 14

duplication of entire gene

Answer 14

• many duplications of an entire gene can create multigene families

Question 15

multigene family (3)

Answer 15

• set of genes descended by duplication and diversification from one ancestral gene
• often have related functions and structures due to shared history
• can be clustered together or dispersed on several chromosomes

Question 16

tandem gene family

Answer 16

• members of the multigene family are clustered on the same chromosome

Question 17

dispersed gene family (2)

Answer 17

• members of the multigene family are on different chromosomes
• likely due to transposition and insertion events

Question 18

multigene family examples (2)

Answer 18

• human olfactory genes

- Hox genes

Question 19

how does unequal crossing over affect multigene families (3)

Answer 19

• can expand and contract gene numbers in multigene families
• creates more genetically variant gametes
• due to crossing over mistake in alignment during meiosis

Question 20

gene superfamily (3)

Answer 20

• large set of related genes that is divisible into smaller families
• genes in each family are more closely related to to each other than to other members of the super family
• gene families within a superfamily arise from several rounds of repeated gene duplication events following by divergence

Question 21

gene superfamily example (2)

Answer 21

• globin gene superfamily
• consists of three families in all vertebrates: beta-like multi-gene family, alpha-like multi-gene family, or a single myoglobin gene

Question 22

what terms are used to describe relationships between genes (3)

Answer 22

• homologs
• orthologs
• paralogs

Question 23

homologs (2)

Answer 23

• genes with similar sequence

- an all encompassing term

Question 24

ortholog (2)

Answer 24

• genes in different species that are similar by descent (ancestry)
• related genes in DIFFERENT species

Question 25

paralog (2)

Answer 25

• homologous genes in same species, similar by duplication

- related genes in SAME species

Question 26

synteny (2)

• definition
• provides evidence for…

Answer 26

• presence of segments of DNA with the same gene sequences (usually a groups of genes found together) that are found in two different species
• provides evidence that multiple chromosomal rearrangements of originally similar chromosomes has been an important feature of evolutionary change (one common ancestor)

Question 27

whole genome duplications

Answer 27

• many examples found in eukaryotes, followed by increase in complexity

Question 28

polyploid in agriculture (3)

Answer 28

• 1/3 of all known flowering plant species are polyploid
• often results in increased size and vigour
• many polyploid plants have been selected for agricultural cultivation

Question 29

syntelog

Answer 29

• sets of gene derived from the same ancestral genomic region

Question 30

diploidization

Answer 30

• conversion from a polyploid state back to a diploid one, due to divergence and loss of genes

Question 31

fractionation and diploidization (2)

Answer 31

1. whole genome duplication: polyploid

2. gene loss/fractionation leading to diploidization: conversion from polyploid to diploid chromosomes

Question 32

paleopolyploidy (2)

Answer 32

• ancient genome duplications which occurred at least several million years ago
• ancient genome duplications are usually followed by diploidization over evolutionary time

Question 33

if we want to find evidence for whole gene duplication, what will our prediction be in an experiment

Answer 33

• if whole genome duplication has occurred, then we should be able to detect evidence for it in genomes of closely related sequences

Question 34

what strategies can we use for finding evidence of whole genome duplication (3)

Answer 34

• whole genome sequencing of two species
• annotate the gene sequences found in each
• align the sequences: identify orthologs and see if there are larger conserved regions between species (synteny)

Question 35

what will our findings look like if there is evidence of whole genome duplication in an experiment

Answer 35

• most regions of single genome organism matched to two regions of the double genome organism

Question 36

model of whole genome duplication (5)

Answer 36

1. after divergence from common ancestor, whole genome duplication can occur
2. vast majority of duplicated genes underwent mutation and gene loss
3. sister segments retained different subsets of original gene set, keeping 2 copies of only a small minority of duplicated genes, which were retained for functional purposes
4. evidence comes from conserved order of duplicated genes across different chromosomal segments; intervening genes are unrelated
5. only by comparing to single genome sister species, can you determine the interleaving genes from sister segments of the ancestral gene order

Question 37

what are the four levels of gene duplication that have fuelled evolution of complex genomes (4)

Answer 37

• exons duplicate or shuffle
• entire genes duplicate to create multi-gene families
• multi-gene families duplicate to produce gene superfamilies
• entire genome duplicates to double the number of copies of every gene and gene families