“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
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.
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”.
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
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
BIOINFORMATICS