To prepare for taking Quiz 2, I strongly review the following contents:
1. https://www.ncbi.nlm.nih.gov/books/NBK21112/Links to an external site. (***)
2. https://www.ncbi.nlm.nih.gov/books/NBK26836/Links to an external site. (*)
3. Homolog, paralog, and ortholog. (**)
4. Worksheet 3 (***)
5. Your presentations about review articles (**)
6. The review article about evolution by gene loss (one MCQ to cover the key points)(*)
7. Methods to study genome evolution: phylogenetic tree and comparative genomics (*)
8. LGT vs. VGT (**)
9. Common types of LGT and their differences (**)
10. Consequences, implications and significance of LGT (*)
11. GMO plants or GMO animals on human genome (*)
12. Gaps to study LGT in eukaryotes (*)
13. EGT vs. Hetero-EGT vs. Hetero-EPT (*)
Purifying selection: selection that eliminates individuals carrying mutations that interfere with
important genetic functions.
A phylogenetic tree: also known as a phylogeny, is a diagram that depicts the lines of evolutionary
descent of different species, organisms, or genes from a common ancestor. Phylogenies are useful
for organizing knowledge of biological diversity, for structuring classifications, and for providing
insight into events that occurred during evolution. Furthermore, because these trees show descent
from a common ancestor, and because much of the strongest evidence for evolution comes in the
form of common ancestry, one must understand phylogenies in order to fully appreciate the
overwhelming evidence supporting the theory of evolution.
(https://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956/Links
to an external site.)
Comparative genomics: Comparative genomics is a field of biological research in which researchers
use a variety of tools to compare the complete genome sequences of different species. By carefully
comparing characteristics that define various organisms, researchers can pinpoint regions of
similarity and difference.( https://www.genome.gov/about-genomics/fact-sheets/Comparative-
Genomics-Fact-SheetLinks to an external site.)
My study Note:
Hitchhiker Effect: When a neutral or harmful gene increases in frequency because it's linked to
a beneficial gene.
Antagonistic Pleiotropy: When one gene controls multiple traits, benefiting one while harming
another.
WNT Gene: A family of genes involved in cell signaling, crucial for development and cell fate.
HOX Genes: Genes that determine body plan and segment identity during embryonic
development.
Gene Ontology: A framework for classifying gene functions across species into categories like
biological process, cellular component, and molecular function.
Baker’s Rule: The idea that self-fertilizing species are more likely to colonize new habitats
successfully.
Most likely primary cause of increased gene numbers: Mechanism: Unequal crossing over,
unequal sister chromatid exchange, DNA amplification and Replication slippage.
In humans the O alleles has evidence that it helps protects from P. falciparum malaria
Neutral Evolution Hypothesis: neither beneficial nor harmful.
Driven by genetic drift, especially in small populations or where selection is weak.
parasitic and symbiotic organisms
In multicellular organisms
Adaptive Gene Loss Hypothesis
Definition: Losing a gene increases an organism’s fitness under specific conditions.
positively selected
free-living unicellular organisms
Sickle cell disease results from a genetic mutation (Glutamate, GAG is replaced by
valine, GTG) affecting Hemoglobin in red blood cells.
How it gets complicated to transfer bacterial gene to human,
(i) germ cell lineage,
(ii) insertion into a chromosome or as extrachromosomal elements. selective
advantage
(iii) transcriptional and translational controls that are quite different, functional
assimilation would be difficult.
Other compelling propositions
- Limitations of methods for data generation and analysis - gene distribution patterns
across taxa.
Essentially statistical one - inherent impossibility of observing events that may have
occurred in the distant past.
- Non identification bacterial source
- Some of the genes predicted to be horizontally transferred into the vertebrate lineage
appear to be involved in important physiological functions and so probably have been
fixed and maintained during evolution because of the increased selective
advantage(s) they provide. e.g. gene products involved in metabolism of xenobiotics
or stress response.
4.1. What are two ways in which new genes could be acquired by a genome?: LGT
and Gene duplication
4.2. What are roles of non-coding DNA in genome evolution?
-regulatory functions in gene expression.
transposable elements and introns are predicted to have functional roles in
genome evolution.
Neutral mutations spread slowly through drift, while beneficial ones spread via
natural selection
*Eukaryotic vs. Prokaryotic genome: Size, location, arrangement(linear, circular),
Chromosome number, intron, plasmid, gene density, origin of replication, Repetitive
element.
How Genomes Evolve
Ocean gas content: methane and ammonia instead of O2
