BIOLOGY 1 REVIEWER - EVOLUTION TO GENETIC INFORMATION.pdf

Biology reviewer regarding evolution up to genetic information.

1. BIOLOGY CORE
First Quarter


Overview of Evolution
What is Evolution
-​The process of change in all forms of life over
generations
-​It is not linear
-​It is a branching process involving
gradual changes and diversification
-​∴ We didn’t evolve from apes; rather,
we share a common ancestor with
them
-​Evolution is a hypothesis, but it has evidence to
support it
-​One of the evidence is fossils
-​Lucy - Australopithecus afarensis
-​Considered as the LUCA of Humans
(Homo sapiens)
-​Developed bipedalism
-​Reason for change: environmental pressures
Charles Darwin in Galapagos
-​His observation of finches and other wildlife
provided crucial evidence for evolution
-​He thought that they evolved from one
species, as they all have similar traits
Evolution of the Limbless Body ​

Evolution relies on Natural Selection
-​Natural Selection - Organisms will survive and
reproduce if they have traits that give them an
advantage when competing for resources
-​∴ These traits will become prevalent over time
-​In simpler terms, it is the survival of the fittest
-​Speciation Event - when a group within a
species separates from other members of its
species and develops its unique characteristics
4 patterns of evolution
-​Divergent Evolution - occurs when a single
species or group with a common ancestor
evolves into two or more species
-​! Species with the same ancestor are
becoming extinct due to environmental
pressures and natural selection!
-​Convergent Evolution - unrelated species
evolve similar traits independently due to
similar environmental pressure
-​! Do not have common ancestries, just
similarities!
-​Parallel Evolution - independent evolution of
similar traits in related species that have already
diverged from a common ancestor
-​Coevolution - the reciprocal evolutionary
influence between two or more species that
interact closely
Types of Structures
-​Homologous - indicates shared developmental
pathway
-​Has a common ancestor, divergent
evolution
-​Analogous - structures that arise independently
due to environmental pressures
-​Different origin, convergent evolution





Hierarchical Classification

- Taxon - a taxonomic unit at any level of the hierarchy

Overview of Phylogeny
What is Phylogeny
-​Evolutionary history or patterns, and
relationships of species
Ontogeny vs Phylogeny
-​Ontogeny - the development of embryos
-​Individual growth and development of
an organism
Early Ideas Related to Phylogeny and Ontogeny
-​Von Baer’s Law
1 / made by jana

2. -​Structures that form early in
development are more widely
distributed among groups of organisms
than structures that arise late in
development
-​In embryo development, animals
initially appear similar, but as they
mature, they become increasingly
distinct. Early stages exhibit general
features, while later stages display the
specific characteristics of their species.

-​Biogenetic Law
-​Theory of Recapitulation
-​Theorized by Ernst Haeckel
-​Ontogeny recapitulates phylogeny
-​The growth of an organism
throughout its embryonic
stage follows the evolutionary
history
-​. An embryo’s development repeats the
evolutionary stages of its species. For
example, a human embryo may briefly
have features like gill slits, resembling
fish ancestors.


-​These laws have been debunked, as ontogeny
does not correlate with evolutionary history

Carl Woese
-​Using 16S rRNA, he found out that some Monera
didn’t have the characteristics of a true bacteria
in 1997
Phylogenetics
-​Hypothesis about the relationship represented
by tree diagrams
-​Dynamic discipline that aims to uncover
evolutionary processes behind the origin of
power
-​The hypothesis of evolutionary relationship is
represented by trees
-​Rooted: shows common ancestor and
LUCA
-​Tells the evolutionary path
-​Unrooted: does not show common
ancestors
-​Tells relations
-​Phylogenetic Systematics - reconstructing the
Evolutionary history by studying the patterns of
relationships between organisms
Phylogenetic Tree of Life

3 Domains of Life: Bacteria, Archaea, and
Eukarya
-​Rooted Tree - shows a single common ancestor
from which all life forms diverge
-​Animals - eukarya, closely related to fungi and
slime molds
Relationships to Other Disciplines
-​Comparative Biology - natural variation and
disparity to understand the patterns of life at all
levels
-​Systematics - study of the diversification of
living forms and the relationships among living
things through time
-​Taxonomy - a classification that organizes living
organisms and other entities


Taxonomy/Systematics Relates to Phylogeny
-​Taxonomic characters allow groupings
-​Homologies - character similarities attributed to
common ancestry
-​Morphological - deals with the form of
living organisms and the relationship
between their structure
-​Molecular - Biochemical
-​Chromosome, DNA, protein,
etc.
4 Eukaryotic Super groups after Reclasification
-​SAR clade (Chromalveolate + Rhizaria)
-​The new Supergroup
-​SAR:
1.​Stramenophile
2.​Alveolates
3.​Rhizarians
-​Unikonta (Ameobazoans + Opisthokons)
-​Where humans are


Clarifications :
-​Broken lines = extinct or undefined
-​This means that there is still confusion
-​“Pitchfork” or Polytomy = many descendants
-​This means that there is still confusion



2 / made by jana

3. 4 Eukaryotic Supergroups after Reclassification
(Images)​

Importance of Studying Phylogeny
-​Gaining insight into the possible functional and
adaptive significance of hypothesized
evolutionary changes
-​Conservation of endangered species
-​Enriches our understanding of how genes,
genomes, and more evolve
-​Cladograms - a classification of life reflecting
evolutionary history
How do Natural Selection and Speciation relate to
Phylogenies?
-​Natural Selection - a process where individuals
with advantageous traits survive and reproduce
successfully
-​Speciation - the process by which new, distinct
species arise
-​Natural selection leads to speciation

Comparing Systems of Classification
and Trees
Systems in Classifying Species
1.​Phenetics
-​Based on physical attributes,
regardless of ancestry
-​Total of all shared characteristics
-​Types:
-​Natural - more than one
character
-​Artificial - one character
-​Dendogram: Phenogram
2.​Phylogenetics
-​Based on evolutionary history and
relationships
-​Types:
-​Cladistics - based on
evolutionary history
-​Total of derived
characteristics
-​Phyletics - based on the
genealogy
-​Genealogy - traces
the descendants of
one person
-​Dendogram: Cladogram/Phylogram
Trees used in Depicting Relationships:
1.​Phenogram
3 / made by jana

4. -​Based on phenetics or phenotypic
similarities
2.​Cladogram
-​The hypothetical relationship between
taxa and their common ancestor
3.​Phylogram
-​Similar to a cladogram, except the
branch length represents
evolutionary time
-​Uses molecular data, fossil data, and
morphology





Anatomy of Phylogenetic Trees

-​Node - recent common ancestor
-​Branch Point - common ancestor
-​Basal Taxon/Outgroup - diverged early
-​Meaning it has characteristics more
similar to the LUCA
-​Sister Taxa - common ancestor not shared by
anyone
-​Broken line - branches that went extinct or were
not sampled
-​Polytomy - more than two descendants
-​There is still ambiguity



Topology
-​Topology - the branching pattern of trees
​
-​Nodes can be rotated as node rotation doesn’t
affect the relationships indicated.
-​As long as the relationship between the
organisms doesn’t change, the nodes
can rotate.


Types of Tree
●​Rooted Tree - a diagram that shows the last
common ancestor of the groups
●​Unrooted Tree - shows the relationship between
the organisms with showing the common
ancestors
○​Central Branch - unrooted tree with
four external branches


4 / made by jana

5. Phylogenetic Trees as Representation of
Evolutionary History
●​Character - observable traits
●​State - value of the traits
Types of Character State Similarities:
1.​Homology - similar characteristics due to a
shared common ancestor
-​Happens due to Divergent Evolution
-​Same structure and origin, different
function
2.​Analogy - similar characteristics due to
convergent evolution
-​Evolves independently
-​Same function, different structure and
origin


Examples of Homologous and Analogous Traits
1.​Homologous
-​Forelimbs of Vertebrates - Human arms
vs Bat Wing vs Whale flipper
-​Leaves of a pine tree - spine of a cactus,
needles of a pine, maple leaf
-​Mouthparts of Insects - grasshopper
jaws, butterfly proboscis, mosquito
stylet
-​Vertebrate Skull bones - reptile
jawbones, mammal ear bones, fish gill
arches.
2.​Analogous
-​Wings of birds and insects
-​Flippers of Penguins and Fins of Fish
-​Eyes of Octopuses and Eyes of Humans
-​Streamlined body shape of dolphins
and sharks
-​Wings of Bats and Wings of a Butterfly

Phyletic Groups:
●​Monophyletic (“Single Tribe”) - ancestors with
all of the descendants
●​Paraphyletic (“Beside the Tribe”) - ancestors
with some of the descendants
●​Polyphetic (“Many Tribes”) - two convergent
descendants but not the common ancestor.


Terms used to describe Relatedness:
-​Plesiomorphy - ancestral character
-​Apomorphy - derived character state
-​Modified from the primitive state
-​Synapomorphy - shared derived character
-​Shared by more than one species or
group
-​Autapomorphy - uniquely derived character
-​Modified from the ancestral
-​Symplesiomorphy - shared ancestral character
-​Homoplasy - analogy
-​Same function




Clarifications on Phylogenetic Trees
1.​It is the hypothesis of Evolutionary Relationships
-​There are many possible ways in
constructing and representing
phylogenetic trees
5 / made by jana

6. -​Most parsimonious = fewer
assumptions
2.​Phylogenetic Trees are based on Various Data
sources:
a.​Internal and external characteristics
b.​Physiology
c.​Behavior
d.​DNA sequences
Morphological and Molecular Data from
Phylogenetics
●​Data set for inferring phylogeny
★​Character - observable feature or trait
★​Character State - value of the character
○​Ex: Hair - Character ; Present - State
Morphological Data
-​Solely on physical attributes
-​Comparing fossil evidence and the degree of
complexity
-​More similar elements in 2 complex
structures are LIKELY homologous
-​Delineating homologous structures is used
●​Analogous (Homoplasy) - features share similar
function but not ancestry
●​Homologous - share common ancestry but not
necessarily similar functions
Molecular Data
-​Use of DNA, RNA, and protein
-​DNA sequencing
-​Adenine (A), Guanine (G), Cytosine (C), and
Thymine (T) - basis
-​Able to know the degree of relatedness
-​Frame shift - shift of basis


●​Molecular homologies - homologies based on
DNA sequencing
​
Sources of Molecular Data apart from rRNA:
1.​Cytochrome c oxidase I (COI) gene
-​Used in animal barcoding
-​An important role in the electron
transfer chain in animals
2.​Cytochrome b gene
-​Used in animal barcoding
-​Useful in the recovery of phylogenetic
relationships of closely related taxa
3.​Rbcl gene & matK gene
-​Used in plant barcoding


Examples of Morphological Data




6 / made by jana

7. Examples of Molecular Data



Data Types
1.​Characters - any observable feature
a.​Character State = value
2.​Distances
-​Fraction of mismatches at aligned
positions
-​Quantitative statement concerning the
disimilarity
-​Higher: distantly related
-​Lower: closely related
Methods in Comparing Distances
1.​UPGMA (Unweighted Pair Group Method in
Arithmetic Mean)
-​Rooted tree
-​Total branch length from the root to the
leaf is equal
-​For closely related
-​Assumes evolution rates are the same
in all lineages
2.​NJ (Neighbour Joining)
-​Unrooted tree , direction of evolution is
unknown
-​Used for date sets with large, varying
rates of evolution and large datasets
-​More accurate and reliable
Inferring Evolutionary History and Relationships of
Organisms
●​Phylogenies as hypotheses
○​We can make and test hypotheses
●​Phylogenetic bracketing - we can predict a
feature shared by two groups of closely related

Trends of Evolution
●​Symmetry
●​Segmentation - body cavities (coelom)
○​Came from germ layers (endoderm,
ectoderm, mesoderm)
●​Ecdysis - shedding/molding of exoskeletons
What are metazoans
-​Any group that comprises all animals having a
body composed of cells differentiated into
tissues and organs, and usually a digestive
cavity lined with specialized cells.
1.​Protozoans - a single-celled organism of a
group of phyla of the kingdom Protista
2.​Eumetazoan - a group of animals characterized
by having true tissues
Origin of Body Cavities
-​Originated during embryonic development as
spaces within the body, formed primarily from
the folding and rearrangement of germ layers
●​Acoelomate - no body cavity
○​The space between the gut and the
body wall is filled with tissue
●​Pseudocoelomate - have a body cavity but not
derived from mesoderm
○​The cavity is a remnant of the
blastocoel (embryonic cavity)
●​Coelomates - possess a true coelom
○​A fluid-filled cavity completely lined by
mesoderm
○​The mesoderm lining forms the
peritoneum, which suspends and
supports the internal
Groups of bilaterally symmetrical animals
●​Protostomes - blastopore develops into the
mouth
●​Deuterostomes - blastopore develops into the
anus
Ecdysis - the process of shedding old skin
Nuclear vs Mitochondrial DNA
●​nDNA - Found within the cell's nucleus and
carries the majority of the organism's genetic
information.
○​Large and complex genome
○​Biparental inheritance
○​Recombination
●​mtDNA - Found within the mitochondria
(organelles in the cell's cytoplasm) and is
inherited maternally
○​Maternal inheritance (less
recombination)
○​High mutation rate
○​High copy number
○​Small genome size
●​In short:
○​mtDNA is best for maternal lineage,
population genetics, and degraded
samples.
○​nDNA is best for understanding full
heredity, genetic diversity, and
disease-related studies
Overview on Bioinformatics
●​Bioinformatics - application of techniques from
computer science to problem from biology using
DNA and amino acids sequences
Why is it Interesting?
1.​Important problem
2.​Massive quantities of data
3.​Desperate need for an efficient solution
7 / made by jana

8. 4.​Success is rewarded


Internet and Bioinformatics
●​The Internet plays an important role in retrieving
biological information
●​Bioinformatics emerging new dimension of
Biological science
●​The computational part of bioinformatics used
to optimize the biological problems
​

Bioinformatics tools
●​There are software programs that are designed
for extracting meaningful information from
biological databases and carrying out sequence
or structural analysis
●​Major categories of Bioinformatics tools:
○​Homology and Similarity Tools
○​Protein Function Analysis
○​Structural Analysis
○​Sequence Analysis
Importance of Bioinformatics for?
-​Used in various fields of biology and medicine
●​Genomics - the study of genomes
●​Proteomics - the study of proteins
●​Transcriptomics - the study of genome
activation patterns
●​Metabolomics - the study of
metabolites
Collecting Molecular Data From
Databases
●​NCBI (National Center for Biotechnology
Information)
○​Houses a series of databases relevant
to biotechnology and biomedicine
○​Important resources for bioinformatics
tools and services
○​Major databases:
■​GenBank - DNA sequences
■​PubMed - a bibliography
database for biomedical
literature
○​Popular NCBI Databases
■​BLAST (Basic Local
Alignment Search Tool)
-​Compares nucleotide
or protein sequences
to sequence
database and
calculates the
statistical
significance of
matches
-​Used to infer
functional and
evolutionary
relationships
■​Entrez Gene
-​Searchable database
of genes
-​Defined by sequence
and/or located in the
NCBI Map Viewer
■​Nucleotide
-​Collection of
sequences from
several sources
-​Provide the
foundation for
biomedical research
and discovery
■​Protein Databases
-​Collection of
sequences from
several sources
-​Protein sequences -
the fundamental
determinants of
biological structure
and function
■​Pubmed
-​A bibliographic
database of more
than 19 million
citations for
biomedical literature
Molecular Clocks and Evolution
●​Molecular Clocks - uses mutation rates to
estimate the time that two species have been
evolving independently
8 / made by jana

9. ●​Neutral Mutation as “Ticks”
○​Neutral mutations occur at a steady
rate
○​More difference, the longer the
separation
●​Calibrating the Clock
○​Genes accumulate mutations
at different rates
○​Compare the number of
mutations in a particular gene
in species whose age has been
determined by other methods
●​Hox Genes and Evolution
○​Small changes in Hox gene
activity during embryological
development = large changes
in adult animals



●​Tree Distances
○​Evolutionary (sequence distance) =
sequence dissimilarity
Evolutionary History and An Organism’s
Genome
-​Comparisons of Nucleic Acids/Other molecules
can be used to deduce relatedness
-​Different genes can evolve at different rates
Evolutionary History from Organisms’ Genome
●​Evolutionary events from a hundred years ago
○​Uses DNA that changes slowly
○​Usually codes for important/critical
functions
●​Recent revolutionary events
○​Uses a DNA segment that evolves
rapidly
Types of Homology
●​Homologues (Homologous genes) - genes that
derive from a common ancestor gene
○​Orthologues (Orthologs) -
homologous genes in different species
■​Related by speciation and
preferably by function
○​Paralogues (Paralogs) - homologous
genes in one species that derive from
gene duplication
■​Related by gene duplication

Gene Duplication
-​Increase the number of genes in the genome
-​More opportunities for evolutionary changes
-​Gene Families - result of repeated gene
duplications
-​Duplicated genes can be traced to a
common ancestor
Gene Evolution
-​Othologous genes - widespread and extend
across many widely varied species
-​Gene number and the complexity of an organism
are not strongly linked
-​Humans can only have four times as
many genes as yeast
Overview of Molecular Clocks
What are Molecular Clocks
-​Used by evolutionary biologists to deduce how
species evolve and to fix the data when two
species diverged on the evolutionary timeline
-​Measures time from random changes
(mutations) in DNA
-​Features of an Ideal Molecular Clock:
1.​Rate constancy through time
-​Characters that have evolved
at a relatively constant rate
are most suitable
2.​Rate homogeneity across lineages
3.​Taxonomic breadth and applicability
4.​Accessibility of the data
9 / made by jana

10. Example of a Molecular Clock
●​The gene that codes for the protein
alpha-globin experiences base changes at a
rate
○​If this rate is reliable, the gene could be
used as a molecular clock
Contributions as New Evidence of Evolution
-​Used to determine how closely two species are
related by calculating the number of differences
in DNA sequences or amino acids
-​All living things share the same biochemical
building blocks

Assumptions of Using a Molecular Clock
●​It is based on the assumption that the regions of
the genome being compared evolve at constant
rates


10 / made by jana