Lecture 22

Question 1

Gene Evolution

Answer 1

• genes evolve by assembly from domains of other genes and by modification of existing genes to new functions
• as precursor gene might already have a vital function this requires more than simple change in gene sequence
• gene duplication can also occur. the copy is free to lose functionality or evolve new function
• not limited to coding sequences. changes in regulatory elements can also be required for evolution of site, timing, or level of expression

Question 2

Gene Duplication

Answer 2

• gene duplicates and get mutation in new gene natural selection can then either have negative selection or positive selection
• negative selection means it selects for the gene without the duplication, so you have two of the original gene
• positive selection means it selects for the gene with the mutation that could have a beneficial function so you have the original and also the mutated gene

Question 3

Duplication and Divergence****

Answer 3

• can also evolve useful other new functions and sites of expression
• ex: Sox9 plays role in development of the body axis
• in zebrafish this gene has been duplicated to produce two similar versions, Sox9a and Sox9b and they have evolved distinct sites of expression in tissues along the body axis
• the three larval body tissues are the neural crest (gives rise to spinal nerve column), optic placodes (give rise to the eyes), and somites (give rise to muscles of body wall)
• when you look at staining of Sox9a you see lots in the neural crest, less in the optic placode and none in the somites
• Sox9b has no staining in the neural crest (no RNA so not stained) the optic placode and to somites are darkly stained
• evolution of two of the same gene operating in different versions?

Question 4

Divergence and Functionalization of Genes

Answer 4

• evolve novel functions
• one pair of duplicated genes can be under selection for a novel function while the other remains under selection for its original function
• ex: venoms that have evolved independently in many organisms generally from important bio-active but non-toxic proteins
• ancestral genes are those that have powerful physiological effects and thus are likely precursors for toxins
• saliva contains bio-active proteins

Question 5

Venom Genes

Answer 5

• can evolve convergently among different toxic creatures
• generally evolve from important bio-active non-toxic proteins
• lots of convergent evolution involving analogous gene duplication events that leave the organism with the original important function and with a novel one (a venom)

Question 6

Komodo Dragons

Answer 6

• hunt deer
• multiple venom glands and grooved teeth
• bite contains lethal mix of venoms
• have blood clotting blockers and other bio-active proteins
• wound deer and track till they die of shocks

Question 7

Platypus

Answer 7

• male platypus have poison spur on hind leg

- co-opted of 20 different peptides causing excruciating pain and drop in blood pressure

Question 8

Convergent Venom

Answer 8

-shrew and gila monster have convergently modified kallikrein (protease that regulates blood pressure) to a venom

Question 9

Toxin Evolution

Answer 9

• can happen independently to inhibit the same functions

- convergent evolution from a limited number of protein families

Question 10

Defensins

Answer 10

• example of single gene recruited again and again convergently to a venom
• small cysteine-rich proteins that act against viral bacterial and fungal infections by creating pores in pathogen cell membranes
• selection on modified alleles yield defensins toxic to neural cells
• some are not toxins but are used to make venoms

Question 11

Single Common Ancestor

Answer 11

• all genomes have evolved from this by divergence and symbiosis
• eventually three great kingdoms arose

Question 12

Genome Evolution

Answer 12

• genome exchange happens between organisms
• genomes contain more than just coding sequences
• genome size not directly related to effective gene number
• organismal complexity is not linked to either genomes size or gene number

Question 13

Genomes Contian

Answer 13

• genes
• non-coding DNA
• DNA encoding gene expression-regulatory RNAs (microRNA) involved in transcript processing
• coding sequences
• non-coding introns
• remnants of integrated DNA virus genomes

Question 14

Genome Size

Answer 14

• only partly related to organism complexity
• humans have 3.3 billion bp and 21,000 genes mice have 2.8 billion bp and 23,000 genes; norway spruce has 19.6 billion bp and who knows how many genes

Question 15

Human and Chimp Genome

Answer 15

-98.5% alike in DNA sequence

Question 16

What does it mean to be human?

Answer 16

• raw sequence similarity is not the complete story
• even if all coding sequences are alike, shape and behavior of two related species can be distinct if regulatory gene expression networks are different
• as regulatory regions are short, the number of nucleotide difference may be small and the effects large

Question 17

What can aDNA tell us about human evolution?

Answer 17

• if we can obtain sequenceable DNA from extinct relatives can potentially clarify relationships of H. sapiens to close relatives such as Neanderthals
• can ask questions like: were they our ancestors? If not, was there interbreeding? What’s the meaning of neanderthal genes present in some human populations? What happened as they approached extinction? inbreeding? can we sequence genomes of other extinct relatives?

Question 18

How long can DNA last in fossil record?

Answer 18

• less than we’d like-perhaps 100,000 years or less but more in cool dry climates
• the power of being able to examine DNA of any extinct species adds evolutionary information not obtainable any other way

Question 19

The Major Technical Issues That Plague Ancient Genome Studies

Answer 19

• degradation
• available preservation
• contamination with modern DNA
• tiny amounts recovered
• age limits
• available fossil material

Question 20

Causes of DNA Degredation

Answer 20

• autolysis: destruction of organisms tissues and cells by chemicals produced within organism
• microbial damage
• oxidation: water-derived hydroxyl and superoxide free radical molecules modify and cause loss of bases
• hydrolysis: OH and H molecules from water bond to nucleotides and cause breaking of DNA molecule
• deamination: nucleotides change
• Maillard reactions: DNA molecules becomes cross linked with another molecule (ex: a protein)

Question 21

Source Material of Preservation

Answer 21

• bones
• teeth
• hair
• feces

Question 22

DNA Preservation Factors

Answer 22

• source material
• temperature
• humidity and water levels
• soil pH and salt concentration
• microorganisms

Question 23

Methodological Issues: PCR Problems

Answer 23

• modified bases
• crosslinked macromolecules (Maillard products)
• co-extracted inhibitors of Tag polymerase

Question 24

Contamination

Answer 24

• from surrounding environment
• from people who handle specimen
• from lab personnel
• from DNA in lab chemicals or supplies
• from non-lab personnel

Question 25

Preventing Contamination

Answer 25

• work in isolated, dedicated aDNA lab
• wear protective clothing
• use DNA free chemicals and supplies
• destroy contaminants with UV light and bleach

Question 26

Detecting Contamination

Answer 26

• include blank extractions and PCR controls
• replicate results independently
• most PCR products should be <300 bp (because most sequences broke by degradation-longer DNA sign of contamination)
• results should make sense phylogenetically

Question 27

Nuclear Genomes of Two Individual Neanderthal Individuals From Different Areas Sequenced

Answer 27

• the second is a full genome
• comparisons show: Date divergence from us (ca 700,00 years)
• degree of hybridization with europeans and north asians about 20% of their genes in us but no single modern individual has more than ca 5%
• neanderthals share same FOXP2 allele as us
• neanderthals were highly inbred-likely very small local populations

Question 28

Discovery

Answer 28

• unknown major hominid that we share genes with
• no neanderthal DNA in modern Africans
• contributes to modern DNA
• called Denisovans-don’t have fossils yet to tell who they were
• interacting hominids leave marks on our DNA throughout time

Question 29

Take Home Message via Fabio

Answer 29

-macroevolution is just an extension of microevolution: the trait that evolves and goes to fixation is an isolating barrier(s), which is heritable and can become more frequent in populations (more easily in allopatric ones) due to selection or drift.
-species are formed just like beak evolution in
populations of finches!