Lecture 40 Flashcards
What is gene tree?
A diagram which shows the genealogy of genetic variants (i.e. the family tree of a gene)
Which can be used to estimate (but is not the same as) a species tree
Why are a species and gene tree different?
The branching events in a gene can either pre or post date the speciation event
The process of divergence in a gene is subject to neutral evolution so the process can be very random
What is the polyphyly phase of a gene tree?
When there is a genetic variant that is the same but comes from different lineages
What is the paraphyly phase of a gene tree?
When the all but a few of the descendents of a single ancestor have the same genetic variant
What is coalescence?
When the genealogy of modern genetic variants is considered then going back in time the lineages join resulting in them theoretically they will all eventually coalesce to a single lineage
(Other lineages will have existed at this time but they went extinct)
What are the two theories on the ancestry of modern humans?
The multiregional theory where there was gene flow between human populations in many regions and they all developed into modern human lineages
The out of africa theory where there was a much more recent common ancestor (200,000 years ago) of modern humans in africa which then travelled outside of africa and took over the regions already occupied by other hominid species
What evidence supported the out of africa theory?
A phylogenetic tree of mtDNA revealed african haplotypes scattered among clades throughout the tree suggesting a common african ancestor Using chimpanzees (and later gorillas) as an outgroup the mtDNA evolution rate was calibrated allowing an estimate of a common ancestor between 150-200,000 years ago
What were the issues found with the dating of a common modern human ancestor of 200,000 years ago and how were they refuted?
There were suggestions it was a non-uniform rates of evolution among human populations (corrected by using mt protein coding DNA) and along human and chimpanzee lineages (corrected by using gorillas as an outgroup)
The rate of mutations was so high that there were multiple mutations in the same site (corrected by using an analysis method which corrects for this or by using sites with lower rates of substitution)
How is the rate of molecular evolution calculated?
Rate=K
K= difference between outgroup and comparison group/(2*estimate time of divergence)
This allows unknown dates to be estimated through dividing the largest difference between two individuals within the species and dividing it by twice the rate obtained and
How can the Y chromosome be used to prove phylogenetic estimates?
Through ignoring the section of Y that can undergo recombination we get an effective population about the same size as mtDNA which is vulnerable to genetic drift
Geographical patterns can be influenced by male behaviour (patrilocal vs matrilocal societies) with patrilocal showing more clustering of the Y chromosome
What does evidence from the Y chromosome say about the out of africa theory?
There are no ancient Y lineages greater than 200,000 years anywhere in the world so there is no evidence of genetic contribution of ancient homo species
The phylogeny roots in africa so supports the out of africa theory
What does the evidence say about if there was hybridisation between modern humans and neanderthals?
The mitochondrial genomes of modern humans are not derived from neandertal which is strong evidence against measurable hybridization
However whole genome sequencing of both species revealed that there is a large similarity between neandertals and humans with larger similarities between non-africans when compared to africans
Implying gene flow between neandertals and the ancestors of all non-africans or ancient genetic variation in africa persisted from the divergence of neanderthal and man until the ancestors of the non-africans left africa
