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Homology
Dr Avril [email protected]
Note: this talk contains animations which can only be seen by downloading and using ‘View Slide show’ in Powerpoint
Note: the ancestral eyeless gene may not have been involved in eye formation
• Slightly different versions of the eyeless gene control eye formation in many animals
• eyeless genes in different animals are homologuesie. they are homologous (related) genes that descended from an ancestral gene in the ancestor of all these animals
Human eyeless(PAX6 or aniridia)
Mouse eyeless
Tiger eyeless
Sea squirt eyeless
Drosophila eyeless
ancestral eyeless gene
Controls human eye development
Controls mouse eye development
Controls tiger eye development
Controls sea squirt eye developmentControls fruitfly eye development
Homologues
• Aside: this is a phylogenetic tree of eyeless genes in different animalsA representation of the evolutionary relationships between members of the eyeless gene familyExternal nodes represent existing genes in different speciesInternal nodes represent their ancestors (usually extinct)
Human eyeless(PAX6 or aniridia)
Mouse eyeless
Tiger eyeless
Sea squirt eyeless
Drosophila eyeless
ancestral eyeless gene
Time
The present100s of millions of years ago
Human eyeless
Sea squirt eyeless
Fruitfly eyeless
Mouse eyeless
Tiger eyeless
Fruitfly twin of eyelessan internal node (ancestor)an external node (existing gene)
Types of homology• Walter Fitch (1970) realised that there are different types of homologues• Orthologues are homologues in different species that arose due to the speciation event
Time
Human eyeless
Sea squirt eyeless
Fruitfly eyeless
Mouse eyeless
Tiger eyeless
Fruitfly twin of eyelessan internal node (ancestor)an external node (existing gene)
Types of homology• Walter Fitch (1970) realised that there are different types of homologues• Orthologues are homologues in different species that arose due to the speciation event
Time
Speciation event giving rise to human and mouse
eyeless in the human-mouse ancestor
The human and mouse eyeless genes are orthologues
• Paralogues are homologues that arose due to a gene duplication event within a species
Human eyeless
Sea squirt eyeless
Fruitfly eyeless
Mouse eyeless
Tiger eyeless
Fruitfly twin of eyeless
an internal node (ancestor)an external node (existing gene)
Time
eyeless in a fruitfly ancestor
Duplication event giving rise to twin of eyeless
The fruitfly eyeless and twin of eyeless genes are paralogues
Types of homology• Homologues (homologous genes) are genes that derive from a common ancestor-gene• Orthologues (orthologs) are homologous genes in different species• Paralogues (paralogs) are homologous genes in one species that derive from gene duplicationWhen one gene is duplicated, the duplication event results in two paralogous
genes (paralogues)Studies of paralogs have found that one paralogue of a pair often retains the
ancestral gene’s function, while the other paralogue is free to evolve and adopt new functions
Ancestral gene Paralogue 1 Paralogue 2Duplication event
• Homologues can differ because of mutations that occurred since their common ancestorSubstitution of one nucleotide for another eg.
Evolution of homologues
T→C substitution
ACTGTA...
ACTGCA...
Mouse eyeless gene
Human eyeless gene
Speciation event giving rise to human and mouse
eyeless in the human-mouse ancestor ACTGTA...
Insertion of nucleotides eg.
Deletion of nucleotides eg.Insertion of G
ACTGTA...
AGCTGTA...
Mouse eyeless
Human eyeless
Deletion of T ACGTA...
ACTGTA...
Mouse eyeless
Human eyeless
eyeless in the human-mouse ancestor ACTGTA...
eyeless in the human-mouse ancestor ACTGTA...
Human eyeless
• Comparing 2 sequences, we don’t know the ancestor’s sequence, so can’t tell in which species an insertion/deletion (indel) occurred eg. mouse ACTGTA... and human ACTGGTA...
They may have evolved by an insertion in human:
Alternatively, they may have evolved by a deletion in mouse:
Insertion of G
ACTGTA...
ACTGGTA...
Mouse eyeless
Human eyeless
ACTGTA...
ACTGGTA...
Mouse eyelessDeletion of G
eyeless in the human-mouse ancestor ACTGTA...
eyeless in the human-mouse ancestor ACTGGTA...
Further Reading• Chapter 3 in Introduction to Computational Genomics Cristianini & Hahn
