Gene tree and species tree

A gene tree is a model of how a gene evolves through not only nucleotide substitution, but also other
mechanisms that act on a larger scale, such as duplication, loss, and horizontal gene transfer. As a gene
at a locus in the genome replicates and its copies are passed on to more than one offspring, branching
points are generated in the gene tree. Because the gene has a single ancestral copy, barring
recombination, the resulting history is a branching tree. Sexual reproduction and meiotic recombination
within populations break up the genomic history into many small pieces, each of which has a strictly
treelike pattern of descent. Thus, within a species, many tangled gene trees can be found, one for each
non-recombined locus in the genome.

A species tree depicts the pattern of branching of species lineages via the process of speciation. When
reproductive communities are split by speciation, the gene copies within these communities likewise are
split into separate bundles of descent. In order to assess the evolutionary relationship among species,
data from multiple gene/protein families has been used because a phylogenetic tree derived from a
single gene/protein may give complex results.

Homology and analogy

Since a phylogenetic tree is a hypothesis about evolutionary relationships which use characters that are
reliable indicators of common ancestry to build that tree. Homologous characters is commonly used —
characters in different organisms that are similar because they were inherited from a common ancestor
that also had that character.

An example of homologous characters is the four limbs of tetrapods. Birds, bats, mice, and crocodiles all
have four limbs. Sharks and bony fish do not. The ancestor of tetrapods evolved four limbs, and its
descendants have inherited that feature — so the presence of four limbs is a homology.

Not all characters are

homologies. There are structural dissimilarities which suggest that certain characters were not inherited
from a common ancestor.

For example, birds and bats both have wings, while mice and crocodiles do not. When the bird wings
and bat wings is closely examine, there are some major differences. Bat wings consist of flaps of skin
stretched between the bones of the fingers and arm. Bird wings consist of feathers extending all along
the arm.
Bird and bat wings are analogous — that is, they have separate evolutionary origins, but are superficially
similar because they have both experienced natural selection that shaped them to play a key role in
flight. Analogies are the result of convergent evolution.

Interestingly, though bird and bat wings are analogous as wings, as forelimbs they are homologous.
Birds and bats did not inherit wings from a common ancestor with wings, but they did inherit forelimbs
from a common ancestor with forelimbs.

Orthology
Sequence that evolved from a single ancestral structure is said to be homologous.
Orthology means that two structures or sequences are similar after a speciation.
Orthologous structures or sequences in two organisms are homologs that evolved from same features in
their last common ancestor as the evolution of orthologs represents organismal evolution.
Eg. Human orthologs in other genome.
The draft human genome sequence contains homologs 61% of proteins found in drosophia43% of
protein found in C elegans. 46% of proteins found in Saccharomyes cerevisae

Paralogy
Homologs where evolution represent or reflects, give duplication events are called paralogs.
Paralogy derived from from duplication events.
For example, β chain of haemoglobin is a paralog of both haemoglobin chain and myoglobin, because
they evolved from same ancestral globin gene through repeated gene duplication events

Xenology
It denotes for homologs that were acquired by an organism through horizontal gene transfer.
Eg. Pieces of DNA that were originally proliferated by some virus. A retrovirus procreates by integrating
its genetic material into host’s DNA. If the virus find a way into some species germline, then two
seemingly unrelated species can become xenologous.

Tree Construction Methods:

The three main methods used for extracting phylogenetically useful information from 1. Distance based
methods
1. Distance based methods
2. Maximum Parsimony
3. Maximum Liklihood,

1. Distance based methods

DBM or distance matrix methods require the distance between pair of sequences and build a
phylogenetic tree. The sequence distance represents evolutionary distance between sequences and
calculated from differences in sequence positions. The evolutionary distance used for this purpose is
usually an estimate number of nucleotide or amino acid substitution per site. Sequences with minimum
number of changes between sequence characters are termed as neighbors. Several distance based
methods have been developed for constructing phylogenetic tree. Some of them are given below:
a. Unweighted pair group method with arthimetic mean (UPGMA)
The UPGMA is one of the simple, hierarchical clustering, tree-making method which produces the
rooted tree. It requires a distance matrix whose value represent dissimilarities between taxa under
consideration.
b. The neighbor joining (NJ) method
NJ method is a distance clustering method. It begins by choosing the two most closely related sequences
and then adding the most distant sequence as a third branch to the tree.

Maximum parsimony (MP)

MP is a character based method to estimate species or gene phylogenies from aligned sequence. It takes
care of insertions and deletions of sequence characters which often give significant polygenetic
information. It looks for all possible trees and select trees with fewest evolutionary changes.
It finds trees that produce the smallest number of changes overall for all identified sequences positions
are identified. It is optimal method for sequences that are quite similar and required small number of
sequences for analysis of nucleic acid program.

Maximum likelihood (ML) method

ML method is the most statistically robust method for phylogenetic inference.
In their simplest form, they begin by listing all possible models and then calculating the probability that
each model would generate the data actually observed. With enough sequence data and an appropriate
model of sequence evolution, the ML always produces the correct topology of the tree. ML method is
one of the most computationally intensive methods because each possible topology has to be assessed
separately and as the number of sequence increase, the number of tree topologies to be examined also
increases.