Lecture 26 - Phylogenetic's (using trees)

Question 1

What is a gene tree?

Answer 1

A visual representation of genetic relationships among individuals or species, showing how genes are inherited through ancestors.

Question 2

How do gene trees reflect mitochondrial inheritance?

Answer 2

Mitochondrial genes are maternally inherited and do not undergo recombination, tracing back to a single maternal ancestor (e.g., ‘Mitochondrial Eve’).

Question 3

What does “Human mtDNA variation reflects African origin” mean?

Answer 3

It indicates that all human mitochondrial DNA traces back to a common ancestor in Africa about 200,000 years ago.

Question 4

What is the role of genetic drift in mtDNA?

Answer 4

Genetic drift can fix mitochondrial variants in populations, leading to the fixation of a single maternal lineage.

Question 5

Why does SARS-CoV-2 have a unique gene tree topology?

Answer 5

It has a very low recombination rate, and gene regions (e.g., spike protein) show distinct evolutionary paths.

Question 6

How are recombination clades detected in SARS-CoV-2?

Answer 6

By analyzing differences in gene tree topology.

Question 7

What are recombination breakpoints?

Answer 7

Locations in the genome where recombination events create switches in ancestry, leading to variation in gene trees.

Question 8

What influences gene tree variation?

Answer 8

Most variation arises from genetic drift rather than selection.

Question 9

What is incomplete lineage sorting?

Answer 9

A phenomenon where gene trees do not align perfectly with species trees due to random genetic drift in ancestral populations.

Question 10

What does monophyly mean in gene trees?

Answer 10

It refers to a group of organisms that share a common ancestor, evolving over time due to genetic drift.

Question 11

How does hybridization affect species evolution?

Answer 11

Hybridization introduces genetic material between species, which can lead to adaptive introgression or hybrid speciation.

Question 12

What is adaptive introgression?

Answer 12

The incorporation of beneficial alleles from one species into another through hybridization, enhancing survival or adaptation.

Question 13

What is homoploid hybrid speciation?

Answer 13

Formation of a new species through hybridization without genome duplication, as seen in the Italian sparrow.

Question 14

What is allopolyploid speciation?

Answer 14

A form of speciation where hybridization between two species results in a new species with duplicated genomes, common in plants.

Question 15

How does hybridization create genetic mosaics?

Answer 15

Recombination between hybrid species produces varied gene tree topologies across the genome.

Question 16

What role does selection play in hybrid species?

Answer 16

Selection removes incompatible allele combinations (BDMIs), leaving only viable genetic mixes in hybrids.

Question 17

What is represented by each internal node of a gene tree?

Answer 17

An ancestor.

Question 18

Why does human mitochondrial variation reflect an African origin?

Answer 18

The African clade is the deepest, and the most recent common ancestor (Mitochondrial Eve) lived in Africa ~200,000 years ago.

Question 19

Why do mitochondrial sequences form a single tree?

Answer 19

No recombination occurs in mtDNA.

Question 20

What leads to variation in gene tree topologies along the genome?

Answer 20

Recombination events and genetic drift.

Question 21

What is the typical breakpoint rate per generation in sexual organisms?

Answer 21

~1 breakpoint per chromosome per generation.

Question 22

What does incomplete lineage sorting reflect?

Answer 22

Random variation in ancestral populations, often seen in young species.

Question 23

How does monophyly evolve?

Answer 23

Over time and due to genetic drift, resulting in shared ancestry at different points for different genes.

Question 24

What is adaptive introgression?

Answer 24

The transfer of beneficial alleles through hybridization between species.

Question 25

What are possible outcomes of hybridization?

Answer 25

Merging species, hybrid zones, introgression of specific genes, or forming new species.

Question 26

What is the key feature of allopolyploid speciation?

Answer 26

Genome duplication from hybridization between two species.

Question 27

How does homoploid hybrid speciation differ from allopolyploidy?

Answer 27

It involves hybridization without genome duplication.

Question 28

How can hybridization impact species evolution?

Answer 28

It can introduce beneficial variation, adaptive introgression, and speciation.

Question 29

What is the significance of gene tree variation?

Answer 29

It highlights recombination events and the complex ancestry of genomes.