Orthology
speciation events
Paralogy
gene duplication
Xenology
HGT event, DNA from a completely different lineage, very rare
can make a gene history not match species history
Which of these subclasses are of use when trying to infer phylogenetic history? (gene tree = species tree)
Orthology, paralogous can be used when lined up in data set
Convergence in New Wolrd and Old World vultures
Filling same niche
Lineage sorting
history of alleles in the population doesn't trace the species history
idea that allelic diversity, aslong as coalescence happens faster than speciation occurs then there is no lineage sorting (?)
key for lineage sorting is the amount of time it takes for speciation and allele fixation.
What are the two processes that would make lineage sorting more likely?
when coalescence is slow and speciation time
What are the three things that can cause a gene tree to conflict with a species tree (even when both trees are reconstructed accurately?)
Gene duplication, HGT, and coalescence/lineage sorting
Gene duplication
w/ paralogy
Horizontal Gene transfer
xenology
Strict consensus tree
two, three, or more trees that are trying to describe together, very little resolution
Majority rule consensus tree
>50% is shown on tree
Review genera example and opsin ex in video in unit 2.7.2
how they relate to paralogy/orthology issue
something about chiken 4 opsins and humans have 3 while chimps/apes have 2 i think idk.
Pseudogene
duplicated gene still in genome but no longer functional
Neofunctionalization
duplicated gene that functions differently from its original function
Anagenesis
process of developing new potential and diversity within species, species changing over time
Cladogenesis
process of speciation, new clades / lineages form a singular ancestor popualtion