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Genetics and Human Skeletal VariationProf. Tim Weaver
1The screen versions of these slides have full details of copyright and acknowledgements
1
Genetics and Human Skeletal Variation
Prof. Tim Weaver
Department of Anthropology
University of California, Davis
Department of Human Evolution
Max Planck Institute for Evolutionary
Anthropology
2
Why Are We Interested in Skeletal Variation?
Early attempts to classify humans into races
have often emphasized differences in skull form
These were often to support racist or eugenicist agendas
Today, the interest in skeleton variation is because the
skeleton is the part of the phenotype that remains from
extinct human ancestors
The physical record of human evolution consists
almost entirely of bones and teeth
3
Quantifying human skeletal variation
Genetic (and environmental) basis of human skeletal variation
Three observations about human genetic variation
How do patterns of human cranial variation compare
with patterns of human genetic variation?
Which evolutionary processes shaped patterns
of human cranial variation?
How do humans compare with other taxa?
Outline
Genetics and Human Skeletal VariationProf. Tim Weaver
2The screen versions of these slides have full details of copyright and acknowledgements
4
Traditional Caliper Measurements
5
Landmarks and Virtual Objects
6
Quantifying human skeletal variation
Genetic (and environmental) basis of human skeletal variation
Three observations about human genetic variation
How do patterns of human cranial variation compare
with patterns of human genetic variation?
Which evolutionary processes shaped patterns
of human cranial variation?
How do humans compare with other taxa?
Outline
Genetics and Human Skeletal VariationProf. Tim Weaver
3The screen versions of these slides have full details of copyright and acknowledgements
7
Variation in Human Height
8
Ronald Fisher
Infinitesimal Model
Fisher demonstrated that it was
possible to reconcile Mendelian
inheritance with the continuous
nature of most phenotypic variation
Only recently the data had become
available to evaluate how well the
infinitesimal model describes the
genetic basis of real phenotypes
9
0.00
0.25
0.50
– – – + + +
Single Locus Produces Discrete Phenotypes
+ -
Genetics and Human Skeletal VariationProf. Tim Weaver
4The screen versions of these slides have full details of copyright and acknowledgements
10
0.00
0.09
0.19
0.28
0.38
– –– –
– –– +
– +– +
– ++ +
+ ++ +
Two Loci Produce More Phenotypes
11
– –– –– –
+ ++ ++ +
– –– –– +
– –– +– +
– +– +– +
– +– ++ +
– ++ ++ +
0.00
0.08
0.16
0.23
0.31
Three Loci Produce Fairly Continuous Phenotypes
12Wood et al. Nat Genet. 2014
Multi-Locus Basis of Variation in Height
“The results are consistent with a genetic architecture
for human height that is characterized by a very large
but finite number (thousands) of causal variants”
Genetics and Human Skeletal VariationProf. Tim Weaver
5The screen versions of these slides have full details of copyright and acknowledgements
13
Classical Quantitative GeneticsModel of Heredity
Genetic basis of a metric trait is many genetic loci
that contribute equally and additively
(i.e., no interactions among them)
to the measurement value
14
Phenotypic
Variance
Genetic
Variance
Environmental
Variance+ =
Genetic & Environmental Contribution to Phenotypic Variance
Between group variation can have a different cause
than within group variation
15Franz Boas
Genetics and Human Skeletal VariationProf. Tim Weaver
6The screen versions of these slides have full details of copyright and acknowledgements
16
Environment Can Influence Between-Group Variation in Head (Skull) Shape
Relethford JH. Am J Hum Biol. 2004
European-bornParents
US-bornOffspring
Cephalic Index
Bohemian
Hungarian
HebrewPolish
Italian
Scotch
Sicilian
86
84
82
80
78
Cephalic
Index (
%)
17
Outline
Quantifying human skeletal variation
Genetic (and environmental) basis of human skeletal variation
Three observations about human genetic variation
How do patterns of human cranial variation compare
with patterns of human genetic variation?
Which evolutionary processes shaped patterns
of human cranial variation?
How do humans compare with other taxa?
18
1) Among-region differences typically account
for a small percentage of the genetic variance
2) The genetic distance between groups increases
with the geographic distance between them
3) Within-group genetic variance decreases
with distance from sub-Saharan Africa
Three Observations about Human Genetic Variation
Genetics and Human Skeletal VariationProf. Tim Weaver
7The screen versions of these slides have full details of copyright and acknowledgements
19
Between-groupvariance
Total varianceWithin-group
variance
Partitioning Variance
20
Genetic Differentiation of Major Geographic Regions
(e.g. Eastern Asia vs. Europe)
90% within regions(10% between regions)
Within region
Barbujani et al. 1997
Autosomal STRs
87% within regions(13% between regions)
Within region
Autosomal SNPsFischer et al. 2006
94% within regions(6% between regions)
Within regionThe Apportionment of
Human Diversity (1972)
R. C. Lewontin
21
Three Observations about Human Genetic Variation
1) Among-region differences typically account
for a small percentage of the genetic variance
2) The genetic distance between groups increases
with the geographic distance between them
3) Within-group genetic variance decreases
with distance from sub-Saharan Africa
Genetics and Human Skeletal VariationProf. Tim Weaver
8The screen versions of these slides have full details of copyright and acknowledgements
22
Relationship between Genetic Distance (Based on STRs) and Geographic Distance
Ramachandran et al. PNAS. 2005
0 5000 10000 15000 20000 25000
0.0
0
0.1
0
0.2
0
FS
T
Great circle geographic distance using waypoints (km)
23
Three Observations about Human Genetic Variation
1) Among-region differences typically account
for a small percentage of the genetic variance
2) The genetic distance between groups increases
with the geographic distance between them
3) Within-group genetic variance decreases
with distance from sub-Saharan Africa
24
Great circle geographic distance using waypoints (km) from Addis Ababa, Ethiopia
Exp
ecte
d h
ete
rozyg
osi
ty
0 5000 10000 15000 20000 25000
0.5
0.4
0.3
0.2
0.1
0.0
Expected Heterozygosity and Geographic Distance
Ramachandran et al. PNAS. 2005
Genetics and Human Skeletal VariationProf. Tim Weaver
9The screen versions of these slides have full details of copyright and acknowledgements
25
Outline
Quantifying human skeletal variation
Genetic (and environmental) basis of human skeletal variation
Three observations about human genetic variation
How do patterns of human cranial variation compare
with patterns of human genetic variation?
Which evolutionary processes shaped patterns
of human cranial variation?
How do humans compare with other taxa?
26
William W. Howells’Present-Day Cranial Sample
>2,500 individuals30 groups
27
Genetics vs. Skull Form
86%within region
Relethford 1994
87%within region
Fischer et al. 2006
=
Genetics and Human Skeletal VariationProf. Tim Weaver
10The screen versions of these slides have full details of copyright and acknowledgements
28
Geographic distance (km)Geographic distance (km)
Sim
ilarity
Sim
ilarity
Genetics Cranial Form
Relationship with geographic distance
Relethford J H. Hum Biol. 2004
0 10,000 20,000 30,000
0.250
0.150
0.050
-0.050
0 10,000 20,000 30,000
0.050
0.025
0.000
-0.025
29
>4,500 individuals105 groups
Tsunehiko Hanihara’sPresent-Day Cranial Sample
30Betti et al. Proc. R. Soc. B 2009
Decrease Within Group-Cranial Variance With Distance from Sub-Saharan Africa
Distance from sub-Saharan Africa (km)
Within
-gro
up v
ariance
(Male
s)W
ithin
-gro
up v
ariance
(Fem
ale
s)
0 5000 15,000 25,000 35,000
1.2
0.8
0.4
1.2
0.8
0.4
Genetics and Human Skeletal VariationProf. Tim Weaver
11The screen versions of these slides have full details of copyright and acknowledgements
31
The structure of human cranial variation is similar
to the structure of human genetic variation
However, the relationships between geography and
cranial variation are much weaker than those
between geography and genetic variation
Structure of Human Cranial Variation
32
Outline
Quantifying human skeletal variation
Genetic (and environmental) basis of human skeletal variation
Three observations about human genetic variation
How do patterns of human cranial variation compare
with patterns of human genetic variation?
Which evolutionary processes shaped patterns
of human cranial variation?
How do humans compare with other taxa?
33
Neutral Evolutionary Processes (Mutation and random genetic drift)
Neutral evolutionary processes are generally thought to play
an important role in shaping patterns of human genetic variation
It is often difficult to decide among neutral vs. adaptive
explanations for patterns of variation - hard to know exactly
how important neutral evolutionary processes were
in shaping human cranial form
Neutral evolutionary processes can’t ignored when trying
to understand patterns of cranial variation
Genetics and Human Skeletal VariationProf. Tim Weaver
12The screen versions of these slides have full details of copyright and acknowledgements
34
Between-group percentage of variance
0.00
Pro
bability
0.10 0.20 0.30 0.40
0.03
0.05
0.08
0.10
Nose Shape vs. Genetic Loci
Roseman and Weaver Am J Phys Anthropol. 2004
35
Geographic Distribution of Nasal Index
Leong and Eccles Clin Otolaryngol. 2009
Nasal index 65- 66-70 71-75 76-80 81-85 86-90 91-100 +100
36
Outline
Quantifying human skeletal variation
Genetic (and environmental) basis of human skeletal variation
Three observations about human genetic variation
How do patterns of human cranial variation compare
with patterns of human genetic variation?
Which evolutionary processes shaped patterns
of human cranial variation?
How do humans compare with other taxa?
Genetics and Human Skeletal VariationProf. Tim Weaver
13The screen versions of these slides have full details of copyright and acknowledgements
37
Pan troglodytes verus
Pan troglodytes troglodytes
Pan troglodytes schweinfurthii
Pan paniscus
West / Central Africa
3838
Region sub-S. Africa Europe E. Asia
sub-S. Africa 0.12 0.09
Europe 0.09
E. Asia
Region sub-S. Africa Europe E. Asia
sub-S. Africa 0.14 0.15
Europe 0.09
E. Asia
Present-day humans: craniometrics
Present-day humans: autosomal DNA (Fischer et al. 2006)
Weaver Am J Phys Anthropol 2014
FST Comparison for Humans
39
Region Eastern Central Western Bonobo
Eastern 0.02 0.08 0.18
Central 0.06 0.18
Western 0.21
Bonobo
Region Eastern Central Western Bonobo
Eastern 0.09 0.32 0.54
Central 0.29 0.49
Western 0.68
Bonobo
Chimpanzees: craniometrics
Chimpanzees: autosomal DNA (Fischer et al. 2006)
FST Comparison for Chimpanzees
Weaver Am J Phys Anthropol 2014
Genetics and Human Skeletal VariationProf. Tim Weaver
14The screen versions of these slides have full details of copyright and acknowledgements
40
Region sub-S. Africa Europe E. Asia
sub-S. Africa 0.44 0.32
Europe 0.52
E. Asia
Region Eastern Central Western Bonobo
Eastern 0.08 0.09 0.10
Central 0.07 0.12
Western 0.07
Bonobo
h2 Required for Match
Chimpanzees
Present-day humans
Weaver Am J Phys Anthropol 2014
41
Modern human(Cro-Magnon1)
Cranial Differences between Neanderthals and Humans
Neanderthal(La Chapelle-aux-Saints)
How does cranial divergence between Neanderthals
and modern humans compare with genetic divergence?
42
Morphological Split Time Estimator
Weaver et al. PNAS 2008
Difference between
group means
Measures of the degree of departure from mutation-drift equilibrium
Additive genetic variance from
mutations
Genetics and Human Skeletal VariationProf. Tim Weaver
15The screen versions of these slides have full details of copyright and acknowledgements
43
Split Times
H. sapiens
H. neanderthalensis
P. paniscus (Bonobo)
P. troglodytes schweinfurthii(Eastern common chimpanzee)
P. troglodytes troglodytes(Central common chimpanzee)
P. troglodytes verus(Western common chimpanzee)
0.5
1.5
0.6
7.0
Split times in millions of years ago
44
Neanderthal vs. modern human
P. t. verus vs. other P. t.
Split time
259,000 or 383,000depending on assumptions
27,000 or 151,000depending on assumptions
Morphological Split Time Estimates
Cranial differentiation constrained in chimpanzees
relative to modern humans and relative to Neanderthals
45
Human cranial variation tends to be structured similarly
to human genetic variation in that:
Among-region differences typically account for a small
fraction of the morphological variance
The morphological distance between groups increases
with the geographic distance between them
Within-group morphological variance decreases
with distance from sub-Saharan Africa
Neutral evolutionary process mediated by population history
appear to have played an important role in structuring
human cranial variation
Summary
Genetics and Human Skeletal VariationProf. Tim Weaver
16The screen versions of these slides have full details of copyright and acknowledgements
4646