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