Download HOMOLOGY CONDIDERED Bones in the forelimbs in mammals

HOMOLOGY CONDIDERED
Bones in the forelimbs in mammals provide one
standard example of anatomical homology.
Biology gets considerable mileage from the term "homology", but the word is used in different
ways by different groups of biologists. We need to explicitly sort this out.
"Homology" was originally introduced in 1843, as a concept in comparative anatomy, by the
notorious British anatomist Richard Owen. His definition was "the same organ in different animals
under every variety of form and function". Introductory biology
students invariably encounter the term homology in this
anatomical context when they learn about the evidence
supporting Darwinian evolution. Organs as seemingly different
as a bird's wing, a whale's flipper, a dog's paw and a human
hand have a common underlying structure of bones and
muscles because they all evolved from the same organ in the
common ancestor. This is contrasted with "analogous" traits:
similarities between organisms that were not present in the last
common ancestor of the taxa being considered, but arose
independently by convergent evolution.
Ironically, Owen defined homology more than a decade before
publication of Origin of Species, so Owen himself did not invoke
Richard Owen 1804-1892
evolution as the basis of homology. Instead, Owen proposed
that there is a common structural "archetype" or "plan" for all vertebrates. In fact, Owen became
an outspoken and implacable critic of Darwin and his supporters. Darwin uncharacteristically said
of Owen that "I used to be ashamed of hating him so much, but now I will carefully cherish my
hatred and contempt to the last days of my life".
Geneticists later conscripted the term homolgy to describe the
special relationship between equivalent chromosomes in a
pair inherited by diploid individuals from their 2 parents. As in
"homologous chromosomes pair during Meiosis I".
Homologous chromosomes (also called homologs) have
genes for the same characteristics at corresponding positions.
Homologs are usually very similar, but not identical, i.e. they
may carry different alleles of the same genes.
Our immediate concern right now is using homology as a term to describe a relationship among
DNA sequences. As with anatomical structures, DNA sequence similarity may be the result of
homology (common ancestry) or analogy (convergent evolution of unrelated sequences).
Unfortunately, the terms "percent homology" and "sequence similarity" are often used
interchangeably.
Here are some additional technical terms you would need to read, write, speak, or think about
genomic evolution in general, or the evolution of rRNA genes in particular.
paralog
ortholog
xenolog
Two homologous DNA sequences can have shared ancestry because of either a speciation event
(orthology) or a duplication event (paralogy). Homologous sequences are orthologous if they
were separated by a speciation event: when a species diverges into two separate species, the
copies of a single gene in the two resulting species are said to be orthologous. Orthologs, or
orthologous genes, are genes in different species that originated by vertical descent from a single
gene of the last common ancestor.
Homologous sequences are paralogous if they were separated by a gene duplication event within
a lineage: if a gene in an organism is duplicated to occupy two different positions in the same
genome, then the two copies are paralogous. Paralogs can be divided into in-paralogs
(paralogous pairs that arose after a speciation event) and out-paralogs (paralogous pairs that
arose before a speciation event). Between species out-paralogs are pairs of paralogs that exist
between two organisms due to duplication before speciation, whereas within species out-paralogs
are pairs of paralogs that exist in the same organism, but whose duplication event happened after
speciation.
Another term you may run across, particularly if you are doing bacterial genetics, is "Xenology".
Xenologs are homologous genes that exist in separate species due to horizontal gene transfer
from one of the species to the other.
From now on you should try using these terms appropriately to describe evolutionary
relationships among genes or DNA sequences.
EXERCISE
Consider the evolution of the Gene sequence "G" in the following scenario:
G1 G2
ancestral species
G
duplication
G
G
divergence
G1 G2
divergence
G1a G2a
duplication
species A
G1a G2a G2a'
speciation
G1 G2
divergence
species B
G1b G2b
1. A single copy of a gene G in an ancestral species.
2. Duplication of G in the ancestral species.
3. Divergence of the 2 copies of G to produce G1 G2 in the ancestral species.
4. A speciation event.
5. Divergence of the gene sequences following speciation produces G1a G2a in
species A and G1b G2b in species B.
6. A second duplication event involving G2a in species A produces G1a G2a
G2a'.
1. For each pair of contemporary sequences below, are they orthologous, inparalogous, out-parologous or xenologous?
• G1 and G2 in species A: ________________
• The G2a and G2a' in species A: ________________
• G1a and G1b: ________________
• The 7 copies of rrs in E. coli?: ________________
2. Which of the contemporary sequences (G2a, G1b, G2b) should have the
highest sequence similarity G1a?
3. Draw the phylogentic tree you would expect by comparing the sequences of
the 5 contemporary sequences from species A and B.