Lecture 26 - Phylogenetic's (using trees) Flashcards
What is a gene tree?
A visual representation of genetic relationships among individuals or species, showing how genes are inherited through ancestors.
How do gene trees reflect mitochondrial inheritance?
Mitochondrial genes are maternally inherited and do not undergo recombination, tracing back to a single maternal ancestor (e.g., ‘Mitochondrial Eve’).
What does “Human mtDNA variation reflects African origin” mean?
It indicates that all human mitochondrial DNA traces back to a common ancestor in Africa about 200,000 years ago.
What is the role of genetic drift in mtDNA?
Genetic drift can fix mitochondrial variants in populations, leading to the fixation of a single maternal lineage.
Why does SARS-CoV-2 have a unique gene tree topology?
It has a very low recombination rate, and gene regions (e.g., spike protein) show distinct evolutionary paths.
How are recombination clades detected in SARS-CoV-2?
By analyzing differences in gene tree topology.
What are recombination breakpoints?
Locations in the genome where recombination events create switches in ancestry, leading to variation in gene trees.
What influences gene tree variation?
Most variation arises from genetic drift rather than selection.
What is incomplete lineage sorting?
A phenomenon where gene trees do not align perfectly with species trees due to random genetic drift in ancestral populations.
What does monophyly mean in gene trees?
It refers to a group of organisms that share a common ancestor, evolving over time due to genetic drift.
How does hybridization affect species evolution?
Hybridization introduces genetic material between species, which can lead to adaptive introgression or hybrid speciation.
What is adaptive introgression?
The incorporation of beneficial alleles from one species into another through hybridization, enhancing survival or adaptation.
What is homoploid hybrid speciation?
Formation of a new species through hybridization without genome duplication, as seen in the Italian sparrow.
What is allopolyploid speciation?
A form of speciation where hybridization between two species results in a new species with duplicated genomes, common in plants.
How does hybridization create genetic mosaics?
Recombination between hybrid species produces varied gene tree topologies across the genome.
What role does selection play in hybrid species?
Selection removes incompatible allele combinations (BDMIs), leaving only viable genetic mixes in hybrids.
What is represented by each internal node of a gene tree?
An ancestor.
Why does human mitochondrial variation reflect an African origin?
The African clade is the deepest, and the most recent common ancestor (Mitochondrial Eve) lived in Africa ~200,000 years ago.
Why do mitochondrial sequences form a single tree?
No recombination occurs in mtDNA.
What leads to variation in gene tree topologies along the genome?
Recombination events and genetic drift.
What is the typical breakpoint rate per generation in sexual organisms?
~1 breakpoint per chromosome per generation.
What does incomplete lineage sorting reflect?
Random variation in ancestral populations, often seen in young species.
How does monophyly evolve?
Over time and due to genetic drift, resulting in shared ancestry at different points for different genes.
What is adaptive introgression?
The transfer of beneficial alleles through hybridization between species.
What are possible outcomes of hybridization?
Merging species, hybrid zones, introgression of specific genes, or forming new species.
What is the key feature of allopolyploid speciation?
Genome duplication from hybridization between two species.
How does homoploid hybrid speciation differ from allopolyploidy?
It involves hybridization without genome duplication.
How can hybridization impact species evolution?
It can introduce beneficial variation, adaptive introgression, and speciation.
What is the significance of gene tree variation?
It highlights recombination events and the complex ancestry of genomes.
