- When did life originate on Earth?(1)
a. What were the first cellular life forms?(1)
b. When did eukaryotes emerge?(1)
c. How do you know organisms have a common ancestor?(1)
d. What is divergence?(1)
- Life originated on Earth about 3.5 BYA(1)
a. first cellular life forms: prokaryotes(1)
b. 2 billion years later: eukaryotes emerged(1)
c. enough residual similarities among living things ->common ancestor(1)
d. divergence -> great diversity among living forms(1)
What evidence does sequence analysis give?(1)
a. How do you obtain a consistent picture for higher organisms?(2)
b. Give 2 reasons why is it more difficult to classify microorganisms?(2)
1.Sequence analysis gives the most unambiguous evidence for the relationships among species
a. higher organisms: sequence analysis + classical tools (e.g., comparative
anatomy, palaeontology and embryology) usually give a consistent picture
b. classifying microorganisms is, however, more difficult
1. it is less obvious how to select the features on which to classify them
2. extensive lateral gene transfer threatens evolutionary tree entirely
3.How does the present chapter seek to discuss general approaches to comparative genomics in different species.?(2)
a. compare genomes in a way that illuminates the relationship between
humans and other species (already, we’ve done human vs. human: HapMap
project; gene variations within populations, i.e. cancer genomics)
- WHo first proposed the concept of classification as we currently know it?(1)
a. What is the classification hierarchical system of 7 levels? How are most organisms typically described?
b. How are relationships between living organisms can be illustrated?
c. Define genome sequences as a way to define species
d. How do sequences relate with microbial taxonomy and traditional morphological methods?
4.Carl Linnaeus – 18th century Swedish naturalist
a. classification hierarchy: kingdom, phylum, class, order, family, genus and
species; popular system follows binomial description: genus + species
b. for macroscopic organisms, the Linnaean classification is reinterpretable as a
phylogenetic tree: a set of ancestor–descendant relationships between species
- species are fundamentally discrete; cornerstone of biological thought
c. genome sequences: most general, detailed and consistent approach to definition
of species
d. sequences rule microbial taxonomy, but jostle for power with traditional
morphological methods in classification of plants and animals (see Box 7.1)
a. What do methods of classifying microbes involve?
b. What was a criterion for similarity before sequencing?(1) When did it occur?
c. What did Carl Woese develop?(1)
d. Disuss variations in 16S ribosomal RNA and other sequences
a, morphology (cell size + shape), biochem (cell staining, carbon + nitrogen sources,
fermentation products), physiology (growth temp. range and optimum, osmotic
tolerance) and immunological cross-reactivity (esp. infectious species)
b.before sequencing, hybridization of DNA from two different bacteria was a criterion for similarity – occurred only if base sequence similarity is >80%
c.Carl Woese-Carl (this time, Woese) developed
the technique of using DNA encoding 16S rRNA
d. variations in 16S ribosomal RNA (rRNA) and other sequences
- if 16S rRNA sequences differ by 2.5 – 3% then imply different species
- that’s because such difference corresponds to <70% similarity in overall
genome sequence
a. How has protein,RNA and DNA sequences helped?(1) For?(1)
a.Protein, RNA and DNA sequences have illuminated relationships between species, both for macroscopic organisms and microbes
Following the use various sequences (i.e.
protein, RNA and/or DNA) to delineate relationships between organisms, list the four key findings that have been made from many such studies.(4)
all life on Earth has enough general similarity to show that all life forms
had a common origin. Evidence for this came from:
-universality of basic chemical structures of DNA, RNA and proteins
- universality of general biological roles
- near-universality of the genetic code
- What did Carl divide living things into?
a. Are archae more closely related to eukarya or bacteria?
b. What was recently discovered? what gap does this bridge and how many eukarya genes does it contain?
c. Whch organism is the closest living organisms to the root of the tree of life?
On the basis of 16S rRNAs, Carl Woese divided living things into bacteria,
archaea and eukarya (see Fig. 4.2 on next slide!)
a. while archaea and bacteria are both unicellular organisms that lack nuclei, at the molecular level archaea are somewhat more closely related to eukarya than to bacteria
b. recently discovered Lokiarchaeum (complex prokaryote) – bridges gap between archaea and eukaryotes; contains ~175 eukarya genes
c. it is also likely that the archaea are the closest living organisms to theroot of the tree of life
figure 4.2, which shows the three lineages of bacteria (i.e. prokaryote) archaea and eukarya. What is the dashed red circle and what does it mean?
The dashed red circle is a common point for all three
lineages, meaning the common ancestor would be around that point
