Evolution Through Duplication Flashcards
two key ideas for how new genes emerge
- novel gene formation from ancestral genes
- de novo gene birth
how can novel gene formation from ancestral genes occur (5)
- duplication and divergence
- gene fusion
- gene fission
- horizontal gene transfer
- retroposition
duplication and divergence (3)
- genes are duplicated
- duplicated gene has less selective pressure and is free to change
- eventually the duplicated gene develops a new function
gene fusion
- a hybrid gene forms from 2+ existing genes
gene fission (2)
- singe gene separates to form two different genes
- could happen by duplication, followed by loss of different sequences
horizontal gene transfer
- genes transferred from one species ends up diverging in function in the new species
retroposition (2)
- mRNA transferred from one gene may reverse transcribed and inserted elsewhere
- creates an intron-less version of the original gene
at what genomic scale do duplications occur (6)
at all genomic scales:
- domain (exon)
- gene
- gene cluster
- segment
- chromosome
- genome
what are the characteristics of an unduplicated gene (3)
- 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
what are the characteristics of a duplicated gene (3)
- 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
how can duplicated genes evolve (2)
can evolve into:
- pseudogenes
- genes with new functions
pseudogenes (3)
- defintion
- examples of how they are created
- why they are created
- 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
duplicated genes with new functions (2)
- when random mutations provide selective advantage to the organism
- the new gene usually has a novel pattern of expression
duplication of entire gene
- many duplications of an entire gene can create multigene families
multigene family (3)
- 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
tandem gene family
- members of the multigene family are clustered on the same chromosome
dispersed gene family (2)
- members of the multigene family are on different chromosomes
- likely due to transposition and insertion events
multigene family examples (2)
- human olfactory genes
- Hox genes
how does unequal crossing over affect multigene families (3)
- can expand and contract gene numbers in multigene families
- creates more genetically variant gametes
- due to crossing over mistake in alignment during meiosis
gene superfamily (3)
- 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
gene superfamily example (2)
- 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
what terms are used to describe relationships between genes (3)
- homologs
- orthologs
- paralogs
homologs (2)
- genes with similar sequence
- an all encompassing term
ortholog (2)
- genes in different species that are similar by descent (ancestry)
- related genes in DIFFERENT species
paralog (2)
- homologous genes in same species, similar by duplication
- related genes in SAME species
synteny (2)
- definition
- provides evidence for…
- 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)
whole genome duplications
- many examples found in eukaryotes, followed by increase in complexity
polyploid in agriculture (3)
- 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
syntelog
- sets of gene derived from the same ancestral genomic region
diploidization
- conversion from a polyploid state back to a diploid one, due to divergence and loss of genes
fractionation and diploidization (2)
- whole genome duplication: polyploid
2. gene loss/fractionation leading to diploidization: conversion from polyploid to diploid chromosomes
paleopolyploidy (2)
- ancient genome duplications which occurred at least several million years ago
- ancient genome duplications are usually followed by diploidization over evolutionary time
if we want to find evidence for whole gene duplication, what will our prediction be in an experiment
- if whole genome duplication has occurred, then we should be able to detect evidence for it in genomes of closely related sequences
what strategies can we use for finding evidence of whole genome duplication (3)
- 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)
what will our findings look like if there is evidence of whole genome duplication in an experiment
- most regions of single genome organism matched to two regions of the double genome organism
model of whole genome duplication (5)
- after divergence from common ancestor, whole genome duplication can occur
- vast majority of duplicated genes underwent mutation and gene loss
- 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
- evidence comes from conserved order of duplicated genes across different chromosomal segments; intervening genes are unrelated
- only by comparing to single genome sister species, can you determine the interleaving genes from sister segments of the ancestral gene order
what are the four levels of gene duplication that have fuelled evolution of complex genomes (4)
- 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
