Molecular phylogenetics & population genetics (lectures 18&19)

Question 1

how old are eukaryotes?

Answer 1

first animal fossils appear 750 million years ago
first eukaryotic fossil (Tappania) is 1.6 billion years old
eukaryotes are younger than bacteria

Question 2

what did Charles Darwin think about he origin and tree of life?

Answer 2

all life was depended from a common ancestor

pathway from the descendant was tree-like

Question 3

what is small subunit (SSU) ribosomal RNA used for?

Answer 3

a complex chronometer
in bacteria = 16S SSU rRNA
in eukaryotes = 18S SSU rRNA

Question 4

how do we go from molecules to evolutionary trees?

Answer 4

1) make an alignment of the gene or protein sequences
2) measure the similarities between sequences
3) convert sequence similarity to evolutionary distance estimates using a mathematical model
4) draw a tree that best fits the pair-wise distance estimates between sequences

Question 5

what are the 3 fundamental domains?

Answer 5

bacteria
archaea
eukarya

archaea and eukarya share a common prokaryotic ancestor not shared with bacteria

Question 6

how can we root the universal tree?

Answer 6

by using an outgroup - a species which is not a member of any of the groups to be rooted

Question 7

what are the complications of trying to root the universal tree?

Answer 7

it isn’t possible to find an outgroup species for the tree of all cellular life

overcome this by using ancient gene duplications that occurred in the last common ancestor of life (LUCA)

rooting spits the tree into 2

Question 8

how is the universal tree split into 2?

Answer 8

all cellular life has 2 types of protein translation elongation factor

Ef-Tu
Ef-G

duplication happens before the rooting

Question 9

do all of the genes in our DNA have the same evolutionary history?

Answer 9

No
mitochondria are fundamentally important

mitochondrial genes have bacterial origin
contain hundred of proteins but the mitochondrial genome is very small - biggest encodes only 67 proteins

Question 10

what is mitochondria heat shock protein 70 (Hsp70)?

Answer 10

crucial for mitochondrial function
helps import protein into the mitochondria
plays a role in assembly of Fe-S clusters
electron transport chain doesn’t work without Fe-S

it is encoded by the eukaryotic nucleus but is of bacterial origin - lateral gene transfer

Question 11

what are the 2 main theories for the origin of modern humans?

Answer 11

the multiregional model

the out of Africa hypothesis

Question 12

what does the multiregional model propose?

Answer 12

proposes that modern human populations arose independently from isolated populations of Homo Erectus

Question 13

what does the out of Africa hypothesis propose?

Answer 13

proposes that modern humans originated in Africa
members of this species moving into the rest of the world displacing the descendants of Homo Erectus that they encountered

Question 14

how can we test these hypotheses?

Answer 14

compare the sequences of modern humans in different populations

once isolated, small communities rapidly accumulate genetic differences by drift
these differences allow us to map relationships between populations and patterns of gene flow (interbreeding)

mitochondrial DNA is often used as its sequence changes relatively quickly

Question 15

did neanderthals and modern humans interbreed?

Answer 15

Neanderthals are descendants of the original Homo erectus populations that left Africa 1 million years ago
they lived in Europe between 300,000 and 30,000 years ago

out of Africa hypothesis states modern humans displaced them when they reached Europe without any interbreeding

Question 16

how can we test if neanderthals and modern humans interbred?

Answer 16

PCR

neanderthal sequence falls outside the cluster of modern human sequences

Question 17

do any modern populations contain neanderthal DNA in their genomes?

Answer 17

yes

tested by comparing SNPs