. University of southern California
, : . , , , , , , .
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, DNA ResearchToward high-resolution population genomics using
archaeological samplesIrina Morozova, Pavel Flegontov, Alexander
Mikheyev, Hosseinali Asgharian, Petr Ponomarenko, Vladimir
Klyuchnikov, GaneshPrasad ArunKumar, Sergey Bruskin,Egor
Prokhortchouk, Yuriy Gankin, Evgeny Rogaev, Yuri Nikolsky, Ancha
Baranova,Eran Elhaik, Tatiana V. Tatarinova
, , , , , . , .
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Speech gene FOX2P
http://www.nature.com/nature/journal/v418/n6900/fig_tab/nature01025_F2.html
http://www.sciencedirect.com/science/article/pii/S0960982207020659Extremely
conserved among mammalsAll humans have two functional amino-acid
changesThis gene has been the target of selection during recent
human evolution.Neanderthals have the same variant of FOX2P as
modern humans6
6
6
It looks like the forming of lactase persistence started in
Bronze Age
http://www.nature.com/ncomms/2014/141021/ncomms6257/full/ncomms6257.html
Lactase persistence gene is absent in Neolithic but present in
Bronze
Age.7http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html
Response to the artificial environment: Lactase persistence
http://mideats.comMostmammalsnormally cant produce lactase
afterweaning, but some human populations have developedlactase
persistence into adulthood. Domesticated cattleMilkingLactase
persistence8Geographic distribution of the lactase persistence
allele in contemporary EuropeansCattle breeds (blue dots) sampled
across Europe and TurkeyDiversity in cattle milk genes
Limits of the geographic distribution of early Neolithic cattle
pastoralist (Funnel Beaker Culture)
http://www.nature.com/ng/journal/v35/n4/full/ng1263.html
8
Lactase persistence: Gene-culture co-evolution9
LDC = lactose digestion
capacityhttps://www.msu.edu/course/eng/473/johnsen/LDC.pdfMilking
evolves first, and evolution of high LDC is highly dependent on
milking.
10Industrial Revolution: Changing in microbiotic ecosystems
Industrial revolution (17-19th cent.):New technologies:Industrially
processed flour and sugar Changes in oral
microbiotahttp://www.nature.com/ng/journal/v45/n4/full/ng.2536.html
Industrial Revolution: Changing in microbiotic ecosystems
http://www.nature.com/ng/journal/v45/n4/full/ng.2536.html
Mesolithic hunter-gatherers Farming - distinct shift in early
Neolithic more caries- and periodontal diseaseassociated
taxaConsistency in the composition of bacteria through the medieval
periodToday's oral environment is much less biodiverse and is
dominated by potentially cariogenic bacteria11Decrease of
diversity
Domination of cariogenic bacteria
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Rychkov et al. 2014 .
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. . . 2013; . . 2013
K11K22334455667788991010111112_113214315416_51761871982092110K2211
. . 2013; . . 2013 , .
16
. . 2013; . . 2013
Der Sarkissian. University of Adelaide. 2011
, . .
VIII-III ...
Keyser et al. Hum. Genet. 2009 : . , , , .
.., ..
Der Sarkissian. University of Adelaide. 2011; Rychkov et al.
2014 .
Keyser et al. Hum. Genet. 2009; Der Sarkissian. University of
Adelaide. 2011 ( < 20 )
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Amelogenin gene in females and males:Different lengthDifferent
sequence
TATCCCAGATGTTTCTCCATCCCAAATAAAGTG...
Amel XAmel Y
Amel XAmel YX+ Y-X+Y+
NGS Genetic methods24
Sex determinationGenetic methodsFemaleX+Y-FemaleX+Y-MaleX+Y+
25
mtDNA (48,000-30,000 ), , : 3 , ?
?
?After the death of an organism, all of its biomolecules are
degraded either by host enzymes released from their proper
compartments or by saprobic microorganisms. Therefore, compared to
modern DNA, aDNA has lower concentration; it is fragmented (may be
down to 50-70 nt long fragments), contaminated, and chemically
modified.Relative preservation of DNA in old samples depends on
environmental circumstances, such as temperature, humidity, pH, or
oxygen, rather than the absolute age of the sample. For instance,
DNA samples extracted from frozen remains dated thousands or even
hundreds of thousands years can be of better quality than much more
recent samples. Recent studies showed that the age of readable (by
current methods) aDNA products is restricted to about 11.5 million
years. At present, the 560780 thousand years old Middle Pleistocene
horse is the most ancient organism from which reliable aDNA data
have been procured
DNase enzymes
Sawyer et al. 2012
Ancient DNA is often contaminated with some level of exogenous
DNA (e.g., DNA from ancient or modern saprotrophic bacteria or
fungi), postmortem juxtaposition of organisms, or modern human DNA
from the researchers themselves
in the 1990s a large number of papers were published reporting
DNA sequences from extremely ancient remains such as Miocene plant
fossils, amber-entombed organisms, 250-million-year-old bacteria in
salt crystal, and dinosaur bones and eggs. In one such case,
researchers reported successful extraction and amplification of
mtDNA cytochrome b fragment from a dinosaur. The sequences differed
from all modern cytochrome b sequences. This led the authors to
believe that they had sequenced authentic DNA from
80-million-year-old bones. It was later discovered that those mtDNA
sequences were not close to avian and reptilian mtDNAs, as would be
expected from their phylogenetic history, but rather to mammalian
(including human) mtDNAs. It was thereby suggested that the alleged
dinosaur DNA was contaminated, presumably by modern human DNA. A
similar course of events occurred in the study of ancient bacterial
DNA supposedly preserved in 250-million-year-old salt crystals,
which turned out to be modern bacterial DNA. In addition to these
examples, several other aDNA projects have been impeded by
contamination of ancient samples.
To prevent contamination, the experiment must be properly
managed, including special requirements for sample collection,
sterilization of the working area, DNA authentication, and
independent reproducibility. mechanical removal of the upper layer
and UV and/or bleach treatment of the sample.sample incubation in
an extraction buffer and its subsequent removal. this step alone
increases the fraction of endogenous DNA several fold.a substantial
fraction of the reads comes from contamination with environmental
DNA from bacteria and fungi. Microbial sequences should be easily
flagged by a standard BLAST search against the NCBI non-redundant
nucleotide database. This strategy, however, fails to discover most
of the microbial sequences that have yet to be sequenced.
Therefore, it is not surprising that a large fraction of reads in
many aDNA libraries is labeled as unknown or unclassified, mainly
due to the unidentified microbial content.
. ? ( ) (). ?
6 , % ~1% ~99%, 5 8001600 0% 100%
Der Sarkissian et al. 2015
http://mammoth.psu.edu/hair.html
Transitions vs transversionsComparison of modern and ancient
humansPost mortem base modification in aDNA often involve C to U
(T) and A to G transitions, contamination with external DNA can be
reliably estimated using transversion or indel counts
Base modifications are often observed in the 57 final bases of
DNA fragments and are thought to occur more readily in terminal,
single-stranded overhangs
U? U U C A->G An excess of CT (and GA) transitions in
modern-ancient alignments provides an estimate of base
modification
Base Calling De-multiplexing:
Trim adapters at both ends,Clip low quality sequences,Stitch
overlapping reads
Mapping and Realignment
Mapping and Realignment
Estimating post mortem damage and contamination Variant Calling
Reduction of Heterozygosity/ Homozygosity
( ) ,
Ancestry SNP chipFaster and cheaper as compared to whole genome
sequencingWell-designed SNP chips contain carefully selected
markers
To infer population structure from genotype data, it is
necessary to first reduce the dimensionality of the dataset due to
the thousands of SNPs it encompasses. From SNPs to Admixture
Thousands of SNPs
North EastAsianMediterranianSouth AfricanSouth West AsianNative
AmericanOceanianSouth East
AsianNorthernEuropeanSub-SaharanAfricanHGDP00985
0.52530.020200.22220.04040.01010.01010.17170HGDP010940.040.0400.030.8300.010.050HGDP009820.01020.15310.03060.07140.040800.01020.20410.4796
ADMIXTURE
Admixture proportions in geographically adjacent populations,
such as Italian and Greeks, and populations sharing similar
history, like British and Germans, are similar.43
603 unrelated individuals representing 54 worldwide populations
and subpopulations with ~15 samples per population. The results of
the admixture analysis exhibit spatial patterns for individuals of
the same genetic background that decreased in similarity with
distance. In few places, the distribution of admixture proportion
in geographically adjacent populations, such as Italian and Greeks,
and populations sharing similar history, like British and Germans,
overlapped.
433/15/2016
QuestionHow to link genetic and geographic divergence?44
Input: geneticsSamples with known origin45SAMPLE IDNORTH
EASTASIANMEDITERRANIANSOUTH AFRICASOUTH WEST ASIANNATIVE
AMERICANOCEANIANSOUTH EAST
ASIANORTHERNEUROPEANSUB-SAHARANAFRICAChinese10.7188260.0004190.000010.000010.000010.000010.2806950.000010.00001Chinese20.7349670.000010.000010.000010.0010610.000010.2639120.000010.00001Chinese30.746930.000010.000010.000010.0102710.0032440.2395050.000010.00001Chinese40.6712090.000010.000010.000010.000010.000010.3287210.000010.00001Chinese50.7256140.000010.000010.000010.000010.000010.2743160.000010.00001Chinese60.720710.000010.000010.0010980.016650.000010.2614920.000010.00001Chinese70.6957010.000010.000010.000010.000010.000010.3042290.000010.00001Chinese80.7097670.000010.000010.000010.000010.000010.2901630.000010.00001Chinese90.7158080.010560.000010.000010.000010.000010.2735720.000010.00001Chinese100.7320430.000010.000010.000010.0126940.000010.2552030.000010.00001Chinese110.6559950.000010.000010.000010.000010.000010.3439350.000010.00001Chinese120.7126070.000010.000010.000010.000010.000010.2873230.000010.00001
Input: geographyFor every reference population find the
corresponding coordinates.
LatitudeLongitudeChinese39.55116.2Russian55.7537.62Tatar55.5550.93
Moscow46
Relationship between genetic and geographic distances
We correlated the admixture patterns with geography, by
calculating two distance matrices between all populationsFor all
reference samples, compute genetic and geographic distance between
samples47
QuestionKnowing relationship between geographic and genetic
distances, is it possible to find a geographic origin of a person
of known genotype?
We decided to try a simple approach48
AB
X
First step: calculate mean admixture vectorsFor every reference
population, calculate mean admixture vectorsNORTH
EASTASIAMEDI-TERRANIASOUTHAFRICASOUTHWESTASIANATIVEAMERICAOCEANIASOUTHEASTASIANORTHERNEUROPESUB-SAHARANAFRICAChinese0.7116810.0009231.00E-050.0001010.0033960.000280.2835891.00E-051.00E-05Russian0.0688670.2652220.0012410.2246590.0350110.0086220.0318440.3631070.001419Tatar0.157940.2098971.00E-050.2109570.0119020.0026050.0057030.4009751.00E-05
49
Dealing with individuals of unknown originNORTH
EASTASIAMEDI-TERRANIASOUTHAFRICASOUTHWESTASIANATIVEAMERICAOCEANIASOUTHEASTASIANORTHERNEUROPESUB-SAHARANAFRICAUnknown0.7116810.0009231.00E-050.0001010.0033960.000280.2835891.00E-051.00E-05
Find distances between the Unknown vector and all reference
vectorsSort reference populations by distance from smallest to
largest50
Example
Unknown samples52
Accuracy of the GPS algorithmLeave-one-out approach
GPS1 maps 80% of the individuals to their countries of origin,
and 60% of all individuals to their exact inner-country region. The
assignment accuracy was largely affected (r=0.45) by the genetic
diversity of the reference populations as estimated by the standard
deviation of their admixture proportions.54
GPS1 accurately assigned: ~100% of all individuals to their
continental regions 80% of all individuals to their country of
origin 60% of all individuals to their inner-country region55
Populations for which inner-country data was available are
marked with *. The average accuracy is calculated across
populations given equal weights.
553/15/2016
Application of GPS to aDNA (Bronze Age)
30 out of 100 Bronze Age samples (Allentoft et al 2015) had over
500 of ancestry informative markers.We applied GPS algorithm to
find the closest modern population.
/ (, 23 ) rs262555, ? ?
Phenotype prediction from aDNAProblem: coverage is low, and
reliability of each individual SNP is meagerSolution: Consider
population, group SNPs by diseases and rank diseases by the number
of SNPs
Phenotype
Links can be taken from HGMD or ClinVar databases
Conditions with the highest/lowest number of SNPs in Bronze Age
EuropeAdenomatous polyposis coliLiver glycogenosisMuir-Torre
syndromeHaemoglobin variantCongenital disorder of glycosylation
1aThalassaemia alphaVon Willebrand disease 2aDiabetes, permanent
neonatalShort statureDiabetes, neonatal
F3 X, Y Z (), Y1 Y2 X ()F3(Z;x,y)>0 X,Y Z
