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Assuming neutrality of molecular markers
If markers are under selection, this will provide a misleading
perspective on migration.
Figure 6.4
Multiple, independent loci should be used.
Case Study of Positive Darwinian Selection in Nature
Dennis Powers et al.
Fundulus heteroclitus
•Widely distributed baitfish (topminnow).
•Occurs in coastal waters (bays, inlets, marshes)
along the Atlantic Coast.
•Given the wide distribution, environmental variation
may be an important selective factor in Fundulus.
Lactate Dehydrogenase
Lactate
LDH
Pyruvate
LDH genes in vertebrates:
Ldh-A
Ldh-B
Ldh-C
Ldh-Ba
Fundulus
Ldh-Bb
Coastal Populations
Chesapeake Bay and Tributaries
Temperature Cline:
Coastal Waters
off the Atlantic Coast
LDH Bb has a higher catalytic efficiency at low temperature
Tree-based approach
mtDNA
haplotype network
Haplotype Network
1
2
6
3
5
4
1 = tttaga
2 = ttcagt
1
3 = ttcaga
4 = ttcact
3
2
5 = tccact
6 = tccact
4
5,6
Thus, there is genealogical concordance between
nuclear and mitochondrial genes
Figure 6.14
Genealogical Concordance Principles:
A conceptual framework for empirically distinguishing
historically deep (ancient) from shallow (recent) population
structures, based on levels of agreement between independent
genetic characters or data sets.
See Figure 6.13, 6.14
OUT OF AFRICA
Based upon 189 mt sequences from indigenous people
around the world.
OUT OF AFRICA
30 nuclear
microsatellite
Loci, 14 pops
Chimp / Human
Split
What is the Origin of Modern Human
Populations?
• Multiregional Hypothesis
– Homo sapiens evolved from an ancient
stock of Homo erectus that originated in
Africa (~ 1-1.8 mya)
• Out of Africa Hypothesis
– Homo sapiens evolved from a relatively
recent stock of archaic sapiens that
originated in Africa (~ 100-200,000 ya)
MULTIREGIONAL HYPOTHESIS
OUT OF AFRICA
How Can We Test These Hypotheses With
Archaic and Contemporary Morphological Data?
• Multiregional Hypothesis
– Predicts greater morphological
similarity between archaic and modern
Homo within regions
• Out of Africa Hypothesis
– Predicts greater morphological
similarity between modern forms from
different regions than between modern
and archaic forms within regions
Morphological Evidence Is Inconclusive
I. Morphological Support for Multiregional Hypothesis
Frayer et al. 1993. American Anthropologist 95:14-50.
Li Tianyuan and D.A. Etler. 1992. Nature 357:404-407.
II. Morphological Support for Out of Africa Hypothesis
Liberman, D.E. 1995. Current Anthropology 36:159-197.
Waddle, D.M. 1994. Nature 368:452-454.
How Can We Test These
Hypotheses With Molecular Data?
• Multiregional Hypothesis
– Predicts that Homo sapien “eve”
existed more than 1 mya.
• Out of Africa Hypothesis
– Predicts that Homo sapien “eve”
existed ~ 200,000 yr ago.
Molecular Clock
Basic Idea: Some proteins evolve at an
approximately constant rate over time
10 total AA in GeneX
Human : Ile Cys Ile Lys Ala ….Phe
ATA
TGT
ATA
AAG
GCA
TTT
Orang. : Lys Cys Ile Lys Ala ….Phe
AAA
TGT
ATT
AAG
GCA
Last Common
Fossil Ancestor
12 mya
TTT
Camelids: Lys Met Val Lys Ala ….Phe
AAA
AGT
GTT
AAG
GCA
TTC
Ruminants: Thr Ile Val Lys Ala ….Phe
ACA
ATT
GTC
AAG
GCA
48 mya
TAT
Carnivores: Lys Met Val Lys Ala ….Phe
AAA
AGT
GTT
AAG
GCA
TTC
Ungulates : Thr Ser Val Arg Ala ….Tyr
ACA
AGU
GTC
AGG
GCT
TAT
66 mya
Molecular Clock
Camelid-Ruminant
0.5
Number
Of
Amino Acid
Substitutions
Per Site
0.4
Carnivore-Ungulate
0.3
0.2
0.3/38 = 0.008/my
8 x 10-9 substitutions/site/yr
0.1
Human-Orang.
10
20
30
40
50
Millions of years ago
60
Molecular Clock Estimate of
Divergence Time of Modern Humans
Gene
Estimate
mt DNA
mt DNA
nuclear DNA
mt DNA
nuclear DNA
166-249,000
129-536,000
75-287,000
125-161,000
102-450,000
Reference
Vigilant et al., 1991
Ruvolo et al., 1993
Bowcock et al., 1994
Horai et al., 1995
Tishkoff et al., 1996
How Can We Test These
Hypotheses With Genetic Data?
• Multiregional Hypothesis
– Predicts similar allele diversity in
different regions of world
• Out of Africa Hypothesis
– Predicts higher allele diversity in Africa
GENETIC DIVERSITY AMONG GEOGRAPHIC REGIONS
• short-tandem-repeat
polymorphism
• repeat = TTTTC
• repeated 4 – 15 times = 12
alleles
MAJOR ROUTES OF EXPANSION OF MODERN HUMANS
OUT OF AFRICA
In each great region of the world, the living mammals are
closely related to the evolved species of the same region. It is,
therefore, probable that Africa was formerly inhabited by
extinct apes closely allied to the gorilla and chimpanzee: and as
these two species are now man's nearest allies, it is somewhat
more probable that our early progenitors lived on the African
continent than elsewhere.
-- Charles Darwin, The descent of man
1871
Finally, what about our
relationship to Neandertals?
PCR analysis of Neandertal
fossilized mtDNA suggest that
this was a species distinct
from Homo sapiens.
Tree-Based
Approach
Summary Statistic
Approach
Gene Trees
Polymorphism
Haplotype Networks
FST
Nested Clade Analysis
q
Strengths/Limitations of Tree-Based Methods
Graphical in nature
Not model based
Recombination may be hard to account for
A single gene inference may be misleading
Natural selection
Stochastic variance