Genetic studies of early human populations Flashcards
when was H. erectus in africa vs when in Eu/asia
- 9mya
1. 8mya
when was H. neaderthalensis in Eu
200-30kya
when did Homo sapiens in Afr
195kya
when did homo sapiens in eu
65kya
how do genetic studies study human pre history
look at modern pops to make sense of ancient
how is genetic diversity found in modern pops and how has this changed
dna seq
used to be only mt DNA and y chr dna
now whole genome
what are some methods for infering deviersity evolution
phylogenetics - patterns of div as tree/network
dating - method assign dates to key positions in an ev scheme
phylogeographic - interpret diversity of pop migr
what are the problems with the methods for infering the diversity evolutio
do they produce anything real or just a narrative
lots of diff way data can be interpreted
lots of data - lot of computer power required
why is mtdna good to study
most rapidly ev part of genome
easy seq
what is the d loop
the most variable part of mt dna
lot of ev here as no sel pressure as there are no genes on this bit of dna as it is the origin of replication
most early studies used dloop amplified by pcr
what has next gen seq meant for mt dna studies
now look at whole genome of mt dna not just d loop
put into haplogroups
what arehaplogroups
275
diff groups assoc with diff parts of the world
not distinct seq but related seq
have subsitututions which categorise
what are haplogroups made up of
haplotypes - mixture of seq
share subsitiutions of haplogroup
but have own distinct substitutions that define (these allow the ev relationships between haplotypes to be worked out)
if haplotypes are rare this shows
the result of recent mut
how are networks built
compare subsitutions
want maximum parsimony
trees are diff ypothesis that make sense of the data
networks - lots of diff trees
what is a principal node
many have this haplogroup
the defining subsitutions
what is an empty node
unknown haplotype in modern human pop
or existed in past and now extinctqqqq
what shape do netowrks form in expanding pops
starburst
in a network what shown by peripheral node
have own unique substitutions
what does coalescent analysis reveal
date the origin of the haplogroup
expresses date in generations
what is founder analysis
an extension of the coalescent analysis
use diversities of haplogroups to estimate time of pop split
eg study bottleneck - group that leaves bottleneck decr gen div-but overtime incr in div and then compare w source pop
allows effective pop size of bottleneck to be calculated
what is the problem with past study on mtdna and y chr
narratives
small bit of genome
animal studies no longer use
why is whole genome seq preferred over mtdna / y
more sophisticated as more snp/ recomb between pat v mat dna
what is the issue with whole genome seq
dont yet knwo how to analyse rigourously
what thought to occur between 130-190kya to homo sapiens
bottleneck
what genetic ev is there for homo sapien bottleneck
low gen div - about 25% of other hominids#
mito eve dated 190kya - suggest pop expand then
coalescence analysis of 50 nuc genes suggested a effective pop size of 2000 at 130kya
what archaeological evidence is there for a bottle neck in homo sapiens
decr in dwellings around the time predicted to occur
what are the three hypothesis for the affect of climate change on human pops
- founder hypothesis , pop contracts/argue that only one pop of h.sap survived and we all descended from this one pop
- fragmentation hypo - human pops in afr divided into sep grps w no gene flow between . aridity severe caused
- no bottleneck
why studies of pot bottleneck use modern afr seq
aas carry mat/pat lineages of some of the deepest clades in mod humans
what was the main finding of Sjodin et al., 2012
model doesnt support bottleneck
found that the option of the no bottleneck most liekly model for all afr pops looked at (at least 79%)
therefore the bottleneck is illusory
why is the conc of bottleneck being illusory paper importnat
reconsider the refugia pleistocene hypo
shows mtLCA not enough
what did the paper by yi & dublin find ev for based on 2 yoruba genomes
pop expansion during 190-130kya
what explains the low diversity
selecive sweeps throughout genome
what are selective sweeps
env pressure puts sel on many genes
aar these genes less diverse as adpative
allele therfore selected and incr in pop
recomb decr lenth of segments subject to sel
aar mut and dna on either side becomes fixed and dating thus inaccurate as this not been taken into aacocutn
