pop gen 7 - human genetics Flashcards
When are Homo erectus specimens thought to be from
1.6 MYA to 0.3 MYA
When do homo sapiens fossils date back to?
0.4 MYA
Is evolution linear with no branches??
NO!!! countless branches, as well as species that diverged then went extinct
Two hypothesis for relationship between homo sapiens and homo erectus
- multiregional hypothesis
- out-of-africa hypothesis
Multiregional hypothesis
homo sapiens evolved from precursors throughout Africa and Asia, with gene flow keeping populations similar
Less genetic data to support
Out-of-Africa hypothesis
homo sapiens evolved recently from a population WITHIN Africa, which then migrated to Asia and Europe
Strongly supported by genetic data
Cann et al. 1987
Used mitochondrial sequences from 147 people to create a human phylogeny
Gives only female ancestors as mitochondria are only maternally inherited
What genetic evidence suggests Out-of-Africa hypothesis
Mitochondrial genomes are more diverse in Africa, according to Cann et al. 1987, indicating that homo sapiens evolved in Africa and other geographical regions include a subset of those lineages
Founder events, individuals moving out of africa and populating other areas
According to mitochondrial sequence, when was all human’s MRCA?
200,000 years ago
why are mitochondria good for studying human lineages?
No recombination
Inherited matrilineally so following one line
Human mitochondrial sequences are VERY similar, less than 1% different
according to Y chromosome, when was human MRCA?
50, 000 years ago (estimated by number of mutational differences)
Points from Y chromosome analysis
all Y chromosomes closely related by descent
Different Y lineages more common in different geographic regions
Differences in stories told by diff genes
details differ, but can get a better idea of whos more closesly related to who by looking at a wide array of different genes
Different individuals in the past were MRCA for different genes
What can human genetic similarities tell us?
Migration patterns of humans across the globe
How many generations does it take on average to reach the MRCA of a single allele in two individuals?
2N generations when N is population size before diverging
gene tree
Nodes represent a copy descending to multiple children, looking backwards the two copies “coalesce” into one at the nodes
how many generations back to MRCA of all alleles of a gene
4N where N is population size before diverging, bc for 1 allele 2N but two alleles of each so 4N
Key points in differences between gene trees for different genes
Linkage binds adjacent sections of the genome to have the same tree, but recombination breaks this up
Recombination can occur within genes, so different segments can have different trees
The further apart are two loci, the more different are their trees
Hybridization with Neanderthals
hybridization w/ Neanderthals happened in Eurasia, interbreeding with humans that left africa
For those regeions MRCA could go much further back in time, to MRCA of human and neanderthal
Adding up sequences in all people, recreate about 40% of neanderthal genome
hybridization with Desinovans
adding up all people, recreate less than 0.1% of genome
most common in oceania
Problems with human genomic data
Biased, giving a very skewed view of humanity and missing diversity in medical genetic studies
78.4% genomic data in GWAS (genome wide association studies) comes from europeans, 2% african
Loss of genetic diversity in humans
bottleneck event, roughly 10,000 individuals
genetic diversity lost in some populations due to founder effect as people spread across the globe
FST
A measure of how much allele frequencies differ between populations, relative to what is seen in the total population
If 0 - allele frequencies are similar, diff is within populations not between population
If 1(fixed differences) - variations is between populations not within
used by evolutionary biologists to understand how different populations are at the genetic level
Overall genetic similarity between individuals
Descended from a very small population only 200,000 years ago
On average two people differ at only 0.1% of genomes
Most sequence variants are found in all regions or AT LEAST some other regions
Structure Plot
For a given number of separate groups, a computer program estimates how best to place each human’s genome in the groups
Why does human ancestry matter?
diversity in people with different ancestors should be accounted for in study of genetic basis of diseases
hypothesized processes that determine human skin colour
Folate - important vitamin in DNA replication but degraded by UV radiation
Vitamin D - critical for skeletal growth production is UV catalyzed
Genes that most clearly differentiate human populations
SLC24A5 associated with skin pigmentation
HERC2 associated with eye colour
LCT associated with lactose tolerance
FADS cluster may be associated with dietary fat sources
Notes on Lactose Tolerance Gene
the lactase-phlorizin hydrolase enzyme determines human ability to digest lactose,
enzyme levels decrease in adulthood = lactase non-persistence vs if enzyme levels remain high lactase persistence
In humans, patterns of lactase persistence reflects historical patterns of dairy farming
Human differences: Immune Genes
Immunoglobulin genes, often under balancing selection to increase immunity
extremely deep divergence even predating our split from monkeys
Favoured to remain polymorphic
Trans-specific polymorphism
incomplete lineage sorting (ILS)
no one copy of an allele fixes before divergence, population remains polymorphic for a longer time thus one organism may appear more closely related to a less recent common ancestor than its true MRCA
complete lineage sorting
One allele rises to fix before species diverge, therefore sequencing one copy from each of 3 species would yield a normal phylogenetic tree with one branching off earlier
Is
