Upload
others
View
13
Download
0
Embed Size (px)
Citation preview
Max Planck Institute for Evolutionary AnthropologyEvolutionary Genetics
Martin Kircher
Studying Modern Human Origins from Neandertal DNA
September 9 2010, Berlin
2
Studying Modern Human Origins from Neandertal DNA
• Closely related species and our own history
• Ancient DNA
• Importance of how high-throughput sequencing
• Insights from the Neandertal genome
3
Closest relatives
• Tell us:
– How evolution shaped our
• Genome
• Transcriptome
• Proteome
– When things changed
How we adapted to environmental changes
What makes us human!Steiper and Young (2006) Mol. Phyl. & Evol. 41(2):384
Old world monkeys
New world monkeys
~ Lemurs
Apes
4
Closest relatives
• Chimpanzees and Bonobosare our closest living relatives
• ~98.8% genome identical
Chimpanzee Steiper and Young (2006) Mol. Phyl. & Evol. 41(2):384
Old world monkeys
New world monkeys
~ Lemurs
ApesBonobo
5http://www.mnh.si.edu/anthro/humanorigins/index2.htm
Closest relatives
6
• Closest extinct relative
• Lived in Europe and West Asia~400 – 30ka
• Went extinct when modern humans spread in Europe & Asia
• Share ~99.9% of genome
Allow to distinguish recent changes from shared evolutionary history
Neandertal modern human
Neandertals
7
Recent changes ...
appearance of art
world-wide dispersion
agricultural and technological revolution
morphological changes
8
1 cm
Ancient DNA
DNA extract
~ 500 mg
• DNA can be extracted from blood, soft tissues as well as bones, hair and teeth
• Successful for up to 100ka old samples
9
Modern DNA
Ancient DNA
~1μg DNAper gram tissue
~0.0000001-0.001μg DNA per gram tissue
Two types of DNA?
Contamination
10
Minimizing contamination from handling (e.g. Sidron 1253)
Contamination avoidance
EL SIDRÓN (ASTURIAS, SPAIN)
11
Quantifying human contamination
• Neandertal mitochondrial genomes
fall outside of human variation
– 133 fixed differences can be used
as informative sites
Green et al. Cell 2008 / en.wikipedia.org
12
Quantifying human contamination
• Neandertal nuclear genome falls within human genomic variation
• No known fixed differences, other measures possible:
– Triallic sites
– X homozygosity
– Y chromosomal coverage
Green et al. Science 2010
13
Sampling ancient DNA
1.77% 0.86%1.60%
0.27% 0.40% 0.41%
4.17% 4.49% 2.17% 4.10%2.5% 1.7%
14
Neandertal libraries• Screened ~200 DNA extracts from at least 70 fossils from 16 sites
0 20 40 60 80 100 120 140
01
23
4
0 20 40 60 80 100 120 140
01
23
4
% o
f rea
ds
Length
Vi33.16Vi33.25Vi33.26Feld1Mez1Sid1253
Vindija 0.2 – 4.0%El Sidron 0.1 - 0.4%Neander Valley 0.2 - 0.5%Mezmaiskaya 0.8 - 1.5%
15
Feasibility: Neandertal genome
Nov. 2006Aug. 2007May. 2007Aug. 2007Sep. 2007Feb. 2008Jul. 2008
Bone (grams) Sequencing (runs)
20220.20.20.20.2
6.000 (454 GS20)6.000 (454 GS20)4.000 (454 FLX)4.000 (454 FLX)
700 (454 FLX)300 (454 Titanium)20 (Illumina GAII)
(“Proof-of-Principle”) Improved library prep454 FLX upgradeLibrary amplificationLibrary enrichmentTitanium upgradeIllumina/Solexa
1997 Sanger sequencing of hypervariable region of first Neandertal mitochondrial genome
2000 Two additional mitochondrial sequences2005 454 platform becomes available
Neandertal 1x genome project idea is born
16
Neandertal Illumina sequencing
• Improved base caller (Ibis)
• Ancient DNA aware
aligner (ANFO)
• Paired End sequencing:
reconstruction of original molecule
• Deep sequencing: PCR duplicate consensus
17
Improved base calling: Ibis
0 20 40 60 80 100Position in read
0.000.01
0.020.03
Estim
atederrorrate
BustardIbis
GA I (26nt)
GA II (51nt, v1)
GA II (77nt, v2)
GA II (76nt, v3)
GA IIx(101nt, v4)
Perfect 11.3% 39.8% 9.19% 51.52% 62.60%Error 7.1% 2.0% 2.74% 0.89% 0.41%Perfect 23.4% 60.2% 36.58% 58.90% 65.05%Error 5.4% 1.1% 0.73% 0.65% 0.33%
Bustard
Ibis
GA I (26nt)
GA II (51nt, v1)
GA II (77nt, v2)
GA II (76nt, v3)
GA IIx(101nt, v4)
Perfect 11.3% 39.8% 9.19% 51.52% 62.60%Error 7.1% 2.0% 2.74% 0.89% 0.41%Perfect 23.4% 60.2% 36.58% 58.90% 65.05%Error 5.4% 1.1% 0.73% 0.65% 0.33%
Bustard
Ibis
18
Ancient DNA aligner: ANFO
• Short, erroneous and
damaged reads are
difficult to align
• Ancient DNA damage
model, substitutions
and indel aware aligner
• Highr resolution mapping quality: search for second best alignment
Correct alignments: important for downstream analyses
Modified from Briggs et al. NAR 2010
19
Paired End read merging
Position in read0 20 40 60 80 100
Reverse read Forward read
Err
or p
rofil
e
20
Paired End read merging
0 50 100 150
0.0
0.1
0.2
0.3
Insert size
Seq
uenc
ing
erro
r on
read
s [%
]
Average of raw reads (no merging)
Error-informative scores
Position in read0 20 40 60 80 100
Reverse read Forward read
21x error reduction
21
Neandertal Genome ConsortiumMax Planck Institute for Evolutionary Anthropology
* Adrian Briggs * Anne Fischer* Jeffrey Good * Ed Green * Janet Kelso * Johannes Krause* Martin Kircher * Michael Lachmann * Tomislav Maricic* Matthias Meyer * Svante Pääbo * Kay Prüfer * Susan Ptak* Qiaomei Fu * Susanna Rankin * Rigo Schultz * Udo Stenzel * Johann Visagie * Hernan Burbano
Sequencing group at MPI EVA:* Aximu Ayinuer-Petri* Anne Butthof* Barbara Höber * Barbara Höffner * Madlen Siegemund* Antje Weihmann
Museo Nacional de Ciencias Naturales, Madrid* Javier Fortea* Carles LaLueza-Fox* Marco de la Rasilla* Antonio Rosas
Rheinisches Museum/University of Tübingen* Ralf Schmitz
Broad Institute/ MIT * David Reich* Nick Patterson* Chad Nussbaum* Eric Lander
Whitehead Institute* Steve Rozen * Jen Hughes * Helen Skaletsky
LBL* Gavin Crookes
NIH/NHGRI* Jim Mullikin
Uppsala University* Siv Andersson
Oxford University* Daniel Falush
European Bioinformatics Institute (EBI) * Ewan Birney * Paul Flicek * Ben Paten * Michael Hoffmann * Daniel Zerbino
Croatian Academy of Sciences and Arts * Maja Paunovic* Dejana Brajkovic* Jadranka Mauch Lenardic* Zeljko Kucan * Ivan Gusic * Pavao Rudan
Slatkin Lab: UC Berkeley * Hua Chen * Philip Johnson * Anna-Sapfo Malaspinas * Josh Pollack * Montgomery Slatkin * Rasmus Nielsen
U. of Washington, Seattle* Evan Eichler
EMBL, Heidelberg* Peer Bork
CSHL* Greg Hannon * Emily Hodges * Zhenyu Xuan * Michelle Rooks
Cornell University* Andy Clark * Kirk Lohmueller * Carlos Bustamante
454 Life Sciences Inc * Jan Berka * Brian Desany * Lei Du * Michael Egholm * Xavier Gomes * Jerry Irzyk * Clotilde Perbost * Jason Affourtit
22
Science 328, May 2010
2323
Neandertal genome• 454 data from Vindija extracts (206 million reads; 1.4 Gb hominid)
• Illumina data (214 lanes; 2.5 billion raw reads; 4.1Gb hominid)
• ~ 1.5x: coverage for ~63% bases of human genome
24
Browse the genome...
http://neandertal.ensemblgenomes.orghttp://genome.ucsc.edu/Neandertal
25
Time of last common ancestor
x 6.5 ma Neandertal: 12.7% 825,000 yrs
French: 8.0% 520,000 yrsHan: 8.4% 550,000 yrs
Papua: 9.3% 605,000 yrsYoruba: 9.4% 610,000 yrs
San: 10.3% 670,000 yrs
~6.5 Myr
12.7%
5 human HGDP samples,sequenced to ~6-8x (Illumina GAII)
Reference human
26
Catalog of novel featuresfixed in the human genome
• 78 amino acid substitutions
• 45 fixed changes in 5‘ UTRs and223 fixed changes in 3‘ UTRs ofprotein-coding genes
• 1 fixed change in seed region of hsa-mir-1304
....
5 genes with two amino acid changes since Neandertal split:RPTN Epidermal matrix proteinSPG17 Sperm axonemeCAN15 Optic lobe homologTTF1 RNA pol. I termination factorPCD16 Ca-dep. fibroblast adhesion
Burbano et al. Science 2010
27
Adaptive evolution• Adaptive changes spread fast in a population
• Regions will show recent SNPs not known to Neandertal
Haplogroups before selection Regaining diversityAfter selection
28
Positive selection
Top 20 candidate regions:
Type II diabetes
Schizophrenia
Autism
Cleidocranial dysplasia
Down syndrome
Green et al. Science 2010
29
Cleidocranial dysplasia (CCD)• RUNX2 only gene associated with CCD, a skeletal dysplasia
CCD patient Normal rib cage
Ancestral state
30
Neandertals interbreed with modern humans?
• Neandertal mitochondrial DNA outside of known human
variation: No maternal decendents of Neandertals
• Arguments for Neandertal admixture in Europe for
morphological and geographical/temporal reasons: Is
there gene flow detectable in the nuclear genome?
31
Neandertals interbreed with modern humans?
Green et al. Science 2010
13 non-african haplotypes: 10 are shared with Neandertal
32
Neandertals interbreed with modern humans?
1-4% admixture in all (tested) out-of-Africa populations
% Neandertal matching to H2 –% Neandertal matching to H1
-1
0
1
2
3
4
5
6
7
Z-Sc
ore
HGDP01029 (San) HGDP01029 (Yoruba)HGDP01029 (San) HGDP00521 (French)HGDP01029 (San) HGDP00542 (Papuan)HGDP01029 (San) HGDP00778 (Han)HGDP01029 (Yoruba) HGDP00521 (French)HGDP01029 (Yoruba) HGDP00542 (Papuan)HGDP01029 (Yoruba) HGDP00778 (Han)HGDP00521 (French) HGDP00542 (Papuan)HGDP00521 (French) HGDP00778 (Han)HGDP00542 (Papuan) HGDP00778 (Han)
33
What next?
• Higher coverage genome (~20x?)
• Targeted analyses of genomic
regions and candidates
• Functional characterization
of changes!
• Other human forms?
34
Denisovans ...
Contact
PhD or PostDoc at MPI EVA?
– Viola Mittag (Assistant to Svante Pääbo)[email protected]
– Bioinformatics (Janet Kelso)[email protected]
Max Planck Institute for evolutionary AnthropologyEvolutionary GeneticsDeutscher Platz 6D-04103 Leipzig