This document discusses the concept of homology in molecular evolution. It defines homology as similarity between structures or organisms inherited from a common ancestor, distinct from analogy which refers to similarity due to convergent evolution. Sequence alignment is used to identify homologous regions and relationships by maximizing matches between sequences. There are different types of homology depending on the level being considered, from individual characters and positions within sequences to genes, developmental processes, and entire organisms.

1. Role Of
Homology In
Molecular
Evolution
PRESENTED BY : ALESHBA FATEMA
RIAZ

2. What is homology ?
 Homology is a concept in comparative biology
that refers to the similarity between different
organisms or structures that is due to
inheritance from a common ancestor.
 Homology implies that the similar features in
different organisms or structures are derived
from a shared ancestral feature, and that they
have been modified over time through
evolution.
 Homology is distinct from analogy, which refers
to similarity between different organisms or
structures that is due to convergent evolution
rather than inheritance from a common ancestor.

3. Homology and similarity are two related but distinct
concepts in comparative biology
 Homology implies that the similar features in different
organisms or structures are derived from a shared ancestral
feature, and that they have been modified over time
through evolution. Homology is a multidimensional
concept, with potentially different interpretations being
relevant to different biological studies, such as evolution,
function, and development.
 Similarity, on the other hand, refers to the degree to which
two or more things are alike. Similarity can be based on any
number of shared characteristics, such as appearance,
behavior, or function. Similarity does not necessarily imply
homology, as similar features can arise through convergent
evolution or other mechanisms.
 For example, the wings of birds and bats are similar in
function, but they are not homologous because they
evolved independently in the two groups

4. What is a character
?
 In the context of comparative biology, a
character is a feature or trait that can be
compared across different organisms or
structures. Characters consist of two or more
different attributes, or character states, that
are found in two or more specimens and can
be considered alternate forms of the same
thing.
 For example, the presence or absence of
wings is a character that can be used to
compare different species of insects. In the
context of molecular data and sequence
alignment, characters refer to specific
nucleotide positions or amino acid residues
that are aligned across different sequences.

5. What is a taxon
?
 In the context of comparative biology, a
taxon is a group of organisms that are
classified together based on shared
characteristics and evolutionary
relationships. Taxa can be at different levels
of biological organization, such as species,
genus, family, order, class, phylum, and
kingdom.
 In the context of molecular data and
sequence alignment, taxa refer to the
different sequences or organisms that are
being compared.

6. How is homology
done ?
 sequence alignment is a method used in
molecular biology and bioinformatics to
compare and identify similarities and differences
between two or more nucleotide or amino acid
sequences.
 The goal of sequence alignment is to identify
regions of similarity that may be a consequence
of functional, structural, or evolutionary
relationships between the sequences.
 Sequence alignment involves arranging the
sequences in a way that maximizes the number
of matching characters, while minimizing the
number of mismatches or gaps.

7.  There are two main types of sequence alignment:
 pairwise alignment, which compares two sequences at a
time,
 multiple sequence alignment, which compares three or
more sequences at a time
 In sequence alignment, the sequences being compared
are arranged in a matrix format, with the sequences
aligned in rows and the positions of the nucleotides or
amino acids aligned in columns. Each row represents a
different sequence, and each column represents a
position in the alignment.
 Homology search is to find such homologous sequences
with the sequence in question, called as the ‘query’
sequence.

8. As genome sequences of many
organisms have been determined, there
is a high chance to find homologous
sequences in those stored in the target
database with a query sequence picked
up from the newly determined genome
sequences.
CURRENTLY THE MOST
FREQUENTLY USED
HOMOLOGY SEARCH SYSTEM
IS BLAST WHICH IS ACRONYM
OF “BASIC LOCAL ALIGNMENT
SEARCH TOOL”

9. Software Query sequence & their
Target databases :
 BLASTN
Nucleotides - Nucleotides
 BLASTP
Amino acids - Amino acids
 BLASTX
Nucleotides* - Amino acids
 TBLASTN
Amino acids - Nucleotides*
 TBLASTX
 Nucleotides* - Nucleotides*
 * Automatically translated into amino acids

13. dynanmic programming first developed by
Needleman and Wunsch an algorithm for pairwise
alignment based on dynamic programming

15. Multiple Alignment
 “Multiple Alignment using Fast Fourier
Transform’ – MAFFT
 MISHIMA, developed by Kryukov and
Saitou is acronym of “Method for
Inferring Sequence History In terms of
Multiple Alignment”

17. Genomewide
Homology Viewers
 VISTA and multiVISTA produce the result
of homology search visually. Figure is an
example output of Vista for the Hox A
cluster region of human and chicken,
which is roughly corresponding to Fig.
15.11.
 Red colored parts are conserved
noncoding sequences (CNSs) showing
high evolutionary conservation. VISTA
server also prepared their own genome
sequence data
 Light violet colored parts are protein
coding region, light blue colored parts are
untranslated region (UTR) of exons, and
red colored parts are CNSs

19. The goal of sequence alignment;
 To identify regions of
similarity between the
sequences, which are
represented by matching
characters in the same
column.
 The alignment can also
include gaps, which are
represented by a dash or a
space, to account for
insertions or deletions in the
sequences. The alignment
matrix can be visualized as a
table or a graphical
representation, such as a
sequence logo or a heat map.
The alignment matrix is used to calculate various
measures of sequence similarity or distance, such as
percent identity, percent similarity, or evolutionary
distance

20. Alignments
versus
phylogenies
 homology is about relationships among characters, whereas a
phylogeny is about relationships among taxa (represented by
nucleotide sequences).
 That is, homology does not apply to whole organisms but to parts of
organisms, and yet, we use homologies to derive phylogenies of whole
organisms.
 Inference of homology involves deriving a plausible scenario for
molecular change among the set of sequences. This scenario may
involve a different set of details for each character (alignment column)
or it may involve events common to groups of characters (contiguous
blocks of columns in the alignment).
 Once this scenario has been derived, reconstructing a phylogeny is
simply a matter of drawing a connected line graph that reflects the
scenario.

21. Types of
homology :
 Evolutionary homology = phylogenetic homology
 Nucleotides that are descended by chains of inheritance
from a common ancestral nucleotide; this differs from the
other types in that it is not experimentally testable
 Character-state homology = transformational homology
 Optimised character-state transformations are determined
as synapomorphic on the best tree(s) and are thus inferred
as homologous; a result of the concept that homology
equals synapomorphy
 Character homology = positional homology
 A site occupying an homologous position in a sequence;
this refers to a vertical column in a sequence alignment
matrix; the position has a unique evolutionary trajectory

22.  Regional homology = locus homology
Sequential positional homologies; blocks of
sequence that share unaltered positional
relationships and an evolutionary trajectory; can
move in a genome due to recombination
 Structural homology = functional homology
Structural features of a macromolecule that are
conserved due to function requirements and are
present in all copies of that molecule; examples
include RNA helices and protein active sites
 Genic homology
Orthologous copies of a gene; undisturbed by
recombination, translocation, or xenology and
sharing an evolutionary trajectory

23.  Developmental homology = deep
homology
Structures that share unaltered developmental
sequences (includingthe controlling gene
regulatory networks) and an evolutionary
trajectory
Organismal homology = taxic homology
Correspondence of features between sister
groups because the organisms being
compared share a common ancestor;
synapomorphies must always be taxic
homologues; this goes all the way back to the
origins of life