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THE HISTORY OF LIFE: WORKING AT THE PATTERNS

CLADOGRAM/ DENDROGRAM “extant organisms (bacteria, humans, plants etc.) have


~branching representations of relationships functional characteristics that enabled their survival up to
Patterns that we see in cladograms this day”.
 Phylogeny: evolutionary history (taxon) *evolution is not progressive.
 Ontogeny: life history (stages of development) of “since the environment change, phenotype also changes
an organism/ individual. in order to adapt.
RECAPITULATION THEORY
“Ontogeny repeats phylogeny of the taxa”. Using trees for classification
 phylogenetic classification (human activity)
Cladograms: diagrams that represents a hypothesis  naming of clades
supported by evidences that can change/ arbitrary
(lengths are arbitrary) ORIGIN OF SCIENCE OF TAXONOMY
“all cladograms are hypothesis as systematics and Artificial (morphologically based)
taxonomy is developing/ evolving”. CURRENT STANDING/ INFORMATION
Natural (molecular & morphological based)
PHYLOGENIES
~represent postulated evolutionary history; TYPES OF CHARACTERS
branch lengths indicate the amount of character change a. APOMORPHIC. unique characteristics of a clade
Phylograms: lengths of branch describe the amount of b. SYNAPOMORPHIC. character of ancestor to all
change descendant in a certain clade
c. PLESIOMORPHIC. Shared ancestral character
TREE OF LIFE (dendrogram) d. SYMPLESIOMORPHIC. Characteristics shared by
Dichotomous splitting ancestor but not all descendants

TYPES OF CLADES/ GROUPS


a. MONOPHYLETIC
 share common ancestry & evolutionary
characteristics
 apomorphic characters (one clade)
b. PARAPHYLETIC
 share some symplesiomorphy
c. POLYPHYLETIC
 grouping with analogous sructures

IMPORTANT ASSUMPTION ON TREES


1. Any group of organisms is related by descent from a
common ancestor
PARSIMONY
 chooses the simplest scientific explanation that
Clade: includes common ancestor and all the possible fits the evidence
descendants  the best hypothesis is the one that requires
:defined at different levels fewest evolutionary changes used of trees
2. To make predictions about fossils
PHYLOGENETIC PITCHFORKS Ex. Ungulates – double pulley ankle mammals
Resulted from the lack of knowledge (in relation Whales have the remnants
to rate of evolutionary process) 3. To make prediction of poorly studied species
“In phylograms, the clustering is more important than the Ex. Taxus brevitalia – contains taxol, a drug that
position.” stabilizes the microtubules during mitosis which prevents
cancer. The gene was transferred by microbial
ADAPTIVE RADIATION: fast splitting of lineages endophytes through horizontal gene transfer. Became
 due to the availability of new niche endangered but was subjected to plant tissue culture.
 process enables variation to adapt
 leads to lesser intensity of completion HOMOLOGIES AND ANALOGIES
Phylogenetic tree is a hypothesis about
Rapid Speciation evolutionary relationships; we want to use characters
ex. cichlids (still a hypothesis) that are reliable factors indicators of common ancestry.

“diagrams are read as trees, not ladders as there are no HOMOLOGOUS CHARACTERS
hierarchy”  Common evolutionary history (via ontogeny)
 Ex. Bones of reptiles to eat are homologous to “Convergent evolution will never result
the bones used in hearing of mammals; wings of convergence of lineages”.
bats are homologous to the wings of birds.
HOMOPLASY
ANALOGOUS CHARACTERS
 Character shared by a set of secies but not
 Only looks at the structure
common in ancestors
Genetic Bricolage  Ex. evolution of the eye
~the hit or miss recruitment & adaptation of pre-
1
existing genes or materials for new functions. STRATIGAPHY
 Provides a sequence of events from which
1
existing sequence of nucleotides that code a particular
characteristic relative dates can be extrapolated based on
Recruited: loss of having new functions layers of deposited sediments.
“hit or miss” – fitness (depends of environment) RADIOACTIVE DATING
 Relies of half-life decay of radioactive
~recruitment of gene is advantageous, will then be
passed on for survival elements to allow scientists to date rocks
and materials directly
HOMOLOGY, ORTHOLOGY AND PARALOGY DENDROCHRONOLOGY
 Annual rings of trees to date
MOLECULAR CLOCKS
 Over the course of millions of years,
mutations may build up in any given stretch
of DNA ata reliable rate
 Example: the gene that codes for the proten
alpha-globin (hemoglobin) experiences
loose changes at a rate of 5.6

HNS Protein – histone-like nucleoid structural


protein
Stabilizes DNA
Protein where DNA coils

CONVERGENT EVOLUTION
 Process in which two distinct lineage evolve
a similar characteristic independently of on
another.
 Often occurs because both lineages faced
similar environmental challenges and
selctive pressures.
PHENETICS
phenotypes; form not function each taxonomic rank, and identifying the clusters
(morphological characteristics) that are distinct at the cut level as the taxa of that
numerical taxonomy; quantified rank.

FUNDAMENTAL POSITIONS OF NUMERICAL ADVANTAGES OF NUMERICAL TAXONOMY


TAXONOMY  Numerical taxonomy has the power to
1. The greater the content of information in the integrate data from a variety of sources,
taxa of a classification and the more such as morphology, physiology, chemistry,
characters on which it is based, the better a affinities between DNA strands, amino acid
given classification will be. sequences of proteins, and more.
2. A priori, every character is of equal weight  Through the automation of large portions of
in creating taxa the taxonomic process, greater efficiency
3. Overall similarity between any two entities is promoted.
is a function of their individual  The data coded in numerical form can be
similarities in each of the many integrated with existing electronic data
characters in which they are being processing systems for the creation of
compared. descriptions, keys, catalogs, maps, and
4. Distinct taxa can be recognized because other documents
correlations of characters differ in the  Being quantitative, the methods provide
groups that are being compared greater discrimination along the
5. Phylogenetic inferences can be made spectrum of taxonomic differences and
from the taxonomic structures of a group are more sensitive in delimiting taxa
and from character correlations, given  Ex. 6 is greater than 5, unlike
certain assumptions about evolutionary color which has no greater or
pathways and mechanisms lesser value
6. Taxonomy is viewed and practiced as an  The creation of empirically derived data
empirical science tables has already forced workers in this
7. Classifications are based on phenetic field to use more and better-described
similarity characters
PHENETIC METHODOLOGY PROBLEMS OF ESTIMATING PHENETIC
 Phenetic classification starts with the RELATIONSHIPS
collection of raw measurement data on  Different life history stages and sexual
the choasen set of morphs, called dimorphism
Operational Taxonomic Units, or OTU's  Differences in estimates of relationships
 The data may then be transformed in produced by different similarity coefficients
some manner to remove redundancy, and (different kinds of statistical analysis)
to normalize the values to a common  Possible effects of parallelism and
scale. convergence on taxonomic judgments
 Numerical based on estimates of phenetic
 Categorical relationships
 A measure of similarity or dissimilarity is
computed for each pair of OTU's
(correlation coefficient)

A clustering method is used to group


OTU's that are most similar. The agglomerative
clustering algorithms involve joining the two most
similar OTU's into a new, compound, OTU, and
recomputing the similarity measure for the resulting
cluster. This is repeated until all OTU's have been
merged into one

The clustering diagram is then converted


into a classification by selecting a cut level for
MOLECULAR SYSTEMATICS
Issues in Taxonomy METHODS IN DNA-BASED SYSTEMATICS
 Retiring taxonomists are leaving numerous  Isolation of genetic material from N, C, M
“orphan” behind  Genomic – bacteria
 Few students are entering the field ~chromosomes (chromosomal), wound
 Environmental impact assessment require around protein; usual activities of the cell
accurate taxonomic information ~larger, complex, more info
 Conservation managers critically need  Plasmic – bacteria (multiple copies)
precise species data ~codes DNA for stressful conditions (pH,
heavy metals)
Solution ~naked; no histone-like proteins
 Molecular Systematics  Nuclear
~speeds up the process of  Mitochondrial
describing species and living species.  Chloroplastic
 Consortium for the Barcode of Life
(CBOL) Nuclear, Chloroplastic & Mitochondrial Genome
~CO1 gene (cycloxygenase 1) for Genome
Origin Inheritance Shape
all organisms. Size (kbp)
cyanobacteria
~specimen identification but also the C 135-160
(via alga)
Maternal Circular
determination of species boundaries engulfed
M 200-250 Maternal Circular
bacteria
Fungi over a
N genetic history Biparental Linear
Similarity is less than 95% - not related million
95% - 97% - congeneric
97% - 100% - conspecific Molecular clocks help track evolutionary time
 A molecular clock uses constant rate of
Why DNA? evolution in some genes to estimate the
 Many more molecular characters available absolute time of evolutionary change
for analysis than morphological ones  To extend molecular phylogenies beyond
Internal Transcribed Spacer (ITS) the fossil records, we must make an
~400-600 base pairs vs. in assumption about how change [in the
morphological characteristics in sequence of nucleotides] occurs over time
fungi
 Identity is easier to define: ATCG vs Each gene mutates at a different rate
whether the flower color is pink or white.  Genes coding for vital enzymes or structure
 An organism’s evolutionary history is tend to be more conserved
documented in its genome (recall  Slow rate of mutation – for older groups
Recapitulation Theory).  Fast rates of mutation is used to assess
relationships in closely related populations
Taxonomic Issues addressed by DNA
 Resolving species boundaries Neutral Theory
Morphological differences between  States that much evolutionary changes in
the species may be very subtle; difficult to gene & protein has no effect on fitness and
describe and applicable only to life history is not influenced by natural selection
stages or only one gender.  It states that the rate of molecular change in
DNA sequences is a very rich these genes & proteins should be regular
source of additional data like a clock
 DNA sequences help assign species names
to tissues Gene Mutation Problems
Many biological tissues are collected  If a gene is mutating very slowly, the level of
but only a fraction can be identified to variation approaches the sequencing error
species rate and inferences become unreliable
Quarantine solutions for  If a gene is mutating very quickly,
conservation and food safety. parallelisms and reversals accumulate so
fast that all phylogenetic information is lost
MOLECULAR MARKERS IN GENOME ANALYSIS

1. Restriction Fragments Length Polymorphism


o Extraction of DNA
o Restrict/ cut using restriction enzyme
o Subject to gel electrophoresis2 4. Denaturation
2
chromatography; bigger fragment nearer to  The gel is placed in sodium hydroxide
the well as it has more base pairs; negativity (NaOH) solution for denaturation so that
caused by the phosphodiester bonds. single stranded DNA are formed.
 is an enzymatic procedure for separation 5. Blotting
and identification of desired fragments of  The single stranded DNA obtained are
DNA. transferred into charge membrane i.e.
 Using restriction endonuclease enzymes, Nitrocellulose paper by the process called
fragments of DNA is obtained and the capillary blotting or electro-blotting
desired fragment is detected by using 6. Baking and blocking
restriction probes.  The nitrocellulose paper transferred with
 May be used to differentiated two organism DNA is fixed by autoclaving. Then the
by analysis of patterns derived from membrane is blocked by using bovine
cleavage of their DNA. serum albumin or casein to prevent binding
Considerations for the use of RFLP of labeled probe nonspecifically to the
 Relatively slow process. charged membrane.
 Use of radioisotopes has limited RFLP use 7. Hybridization and visualization
to certified laboratories (but non-radioactive  The labeled RFLP probe is hybridized with
labeling systems are now in wide use) DNA on the nitrocellulose paper. The RFLP
probes are complimentary as well as
 Co-dominant markers; often species-
labeled with radioactive isotopes so they
specific; highly locus-specific
form color band under visualization by
 Specific to a single clone/restriction enzyme
autoradiography.
combination
 Need high quality DNA
2. Random Amplified Polymorphic DNA
 Need to develop polymorphic probes
 Subjected to polymerase reaction (addition
 Expensive of DNA primers)
 Extract DNA from sample
STEPS OF RFLP TEST
 Denaturing stage
1. Collection of sample
 Annealing stage
 DNA is extracted from the tissues samples
2. Restriction digest  Extending stage
 The DNA in each sample is digested with
3. Amplified Fragment Length Polymorphism
the same restriction enzyme(s).
 Uses restriction enzymes
 The enzyme RE has specific restriction site
on the DNA, so it cut DNA into fragments.  amplify
Different size of fragments are generated  gel electrophoresis (polyacrylamide gel)
along with the specific desired fragments. All use banding pattern in a gel

4. DNA sequencing (Sanger Method)


a. Denature DNA with heat
b. Make multiple copies of a segment (PCT
cut)
3. Gel electrophoresis c. Attach primer to sequences
 The digested fragment are run in d. Add to four polymerase solution (A, T, C, G)
polyacrylamide gel electrophoresis *diedeoxynucleotides – restricts
(agarose) or Agarose gel electrophoresis to connections
separate the fragments on the basis of
length or size or molecular weight.
‘OMIC TECHNOLOGY OF SYSTEMATICS

Genomics DNA
transcription
Transcriptomics RNA functional
translation genomics
Proteomics Protein
enzymatic reaction
Metabolomics Metabolite

TRANSCRIPTOMES
Genome: all of hereditary information encoded in
the DNA (or RNA)
Transcriptome: set of all mRNAs (“transcripts”)
produced from a genome
The term can be applied to:
 Complete set of transcripts for a given
organism
 Specific subset of transcripts present in a
particular cell type or under specific growth
conditions
“Transcriptome varies because it reflects genes
that are actively expressed at any given time”.

Primary metabolites – housekeeping genes


Secondary metabolites – response to
environmental stress

DNA Microarrays Show Differences in Gene


Expression
 Microarray chips contain fragments from
genes in the group to be analyzed (full
genome of bacteria or yeast, or protein
families from larger genomes)
 mRNA or cDNA from different samples are
differentially tagged
 Analysis on the same chip shows
differences DNA Microarrays: Applications
 DNA array contains tags for genes that can DNA microarrays allow simultaneous
be possibly expressed by the organism of screening of many thousands of genes: high-
interest throughput screening
 Genome-wide genotyping
TRANSCRIPTOMICS
◦ Which genes are present in this
 Experiments performed under different individual?
conditions
 Tissue-specific gene expression
 Determines effect of conditions on
expression ◦ Which genes are used to make
 Produces huge amount of data proteins?
 Lots of repeats required (expensive)  Mutational analysis
◦ Which genes have been mutated?

Adaptations to PCR
Reverse Transcriptase PCR (RT-PCR)
 used to amplify RNA sequences
 first step uses reverse transcriptase to
convert RNA to DNA
Quantitative PCR (Q-PCR)  SDS-PAGE performed (sodium
 used to show quantitative differences in dodecylsulfate polyactylemyde gel
gene levels electrophoresis)
 Separates proteins according to pI and
mass

PROTEOMICS
Proteome
Proteome – set of all proteins produced under a
given set of conditions
Mass Spectrometry
 Term can be applied to:
 protein sample is ionized and exposed to
 Complete set of proteins for a given electrical field
organism
 ions travel according to size (indirect r’ship)
 specific subset of proteins present in a
 MALDI-TOF gives good estimates of
particular cell type or under specific
molecular weights
growth conditions
 Can be used to identify a few proteins within
 Proteome varies because it reflects genes
a mixture
that are actively expressed at any given tim
 Proteomics analyses many samples using
2D-electrophoresis and mass spectrometry
 High-throughput, but less than
transcriptomics

Gel Electrophoresis
 Electrophoresis separates molecules by
size.
 Resolution is limited
Isoelectric Focusing
 Electrophoresis across a pH gradient
 Proteins migrate to their isoelectric pH
Proteomic Analysis by Mass Spectrometry
 proteins separated by 2D electrophoresis
 single proteins eluted
 digestion with trypsin will give fragments
with unique set of sizes
 sizes identified by mass spectrometry and
matched to database
 allows identification of unknown proteins

Two-dimensional Gel Electrophoresis


 Protein sample initially fractionated in one
dimension by isoelectric focusing
 All of these should be incorporated into a
coherent profile that will contribute to the
systematics of the taxon of interest.
 Goal: Phylogeny reconstruction based on
character evolution.

Transcriptomics vs Proteomics
 Transcriptomics and proteomics are both
very powerful
 Differences in their practical application:
o Transcriptomics is robust, relatively
cost-effective and user-friendly
o Proteomics still relatively limited –
problems can remain with purification
and stability of proteins
 Increasing potential to combine and
compare data sets

Metabolomics
 Mass spectrometry can be used to measure

Bioinformatics
Goal:
 To enable the discovery of new biological
insights as well as to create a global
perspective from which unifying principles in
biology can be discerned

Wet lab Biological problems

BIOINFORMATICS

combinatory machine data


challenges

 Theory of evolution as the basis of


biological understanding
“nothing in biology makes sense except in the light
of evolution”
Goal for systematics:
 Phylogeny reconstruction based on
character evolution

Polyphasic approach to systematics


 This approach includes phenetic, genotypic,
transcriptomic, proteomic, and metabolomic
evidences

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