What is a Homolog?
Homolog is a broad term that describes any gene that shares a common evolutionary ancestor with another gene.
This term includes both Orthologs and Paralogs and is defined independently of function.
Genes are considered homologous when they share a common evolutionary ancestor, even if their functions have changed over time.
What are Orthologs?
Orthologs are genes in different species that diverged from a common ancestral gene as a result of a speciation event.
What are Paralogs?
Paralogs are genes that have diverged through gene duplication within a genome, they may gain new functions or become non-functional over time.
There are two types of paralogs:
In-paralogs: occur as a result of duplication after a speciation event.
Out-paralogs: occur as a result of duplication before a speciation event.
An example with HOX genes
HOX genes code for transcription factors that help determine the body plan of animals by regulating gene expression during embryo development.
In the fruit fly Drosophila melanogaster, HOX genes specify segment identity along the body axis, determining whether a segment develops into part of the head, thorax or abdomen.
Drosophila melanogaster is an ideal model for studying HOX genes as its genome contains a well characterised set of HOX genes that are functionally and evolutionarily related to those found in vertebrates.
Orthologs – between species
HOX genes in Drosophila have homologs in vertebrates.
These genes are orthologs, because they descend from the same ancestral HOX genes that existed before the divergence of insects and vertebrates.
Although HOX genes have broadly conserved roles, their specific functions and expression patterns have diverged to match a variety of species-specific body plans.
Paralogs – within genomes
Within the Drosophila genome, HOX genes such as Ubx, abd-A, and Abd-B are paralogous to each other.
They arose through ancient gene duplication events followed by divergence in function.
Similarly, vertebrates carry multiple HOX clusters (HOXA, HOXB, HOXC, HOXD), which arose through two rounds of whole-genome duplication events (2R-WGD) in early vertebrate evolution.
HOX genes at corresponding positions in these clusters (e.g. HOXA1 and HOXB1) are also paralogs.
It’s important to note that observing similar structure, function or expression patterns in genes does not always guarantee homology, as similar traits can also arise through convergent or parallel evolution.
Next, we’ll explore how different types of homologs and our assumptions about them influence phylogenetic analysis.