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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. - PowerPoint PPT Presentation
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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
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.
Dennis Powers et al.
Lactate Dehydrogenase
LDHLactate Pyruvate
LDH genes in vertebrates:
Ldh-ALdh-BLdh-C
Ldh-Ba Ldh-BbFundulus
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 approachmtDNA
haplotype network
1 2
3
4
5
6
5,6
1 = tttaga 3 = ttcaga 5 = tccact 2 = ttcagt 4 = ttcact 6 = tccact
1 3 2 4
Haplotype Network
Thus, there is genealogical concordance betweennuclear and mitochondrial genes
Figure 6.14
Genealogical Concordance Principles:
A conceptual framework for empirically distinguishinghistorically deep (ancient) from shallow (recent) populationstructures, based on levels of agreement between independentgenetic 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 nuclearmicrosatelliteLoci, 14 pops
Chimp / HumanSplit
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 modernand archaic forms within regions
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.
Liberman, D.E. 1995. Current Anthropology 36:159-197.Waddle, D.M. 1994. Nature 368:452-454.
II. Morphological Support for Out of Africa Hypothesis
Morphological Evidence Is Inconclusive
• 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.
How Can We Test These Hypotheses With Molecular Data?
Molecular ClockBasic Idea: Some proteins evolve at anapproximately constant rate over time
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
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 TTT
Last CommonFossil Ancestor
12 mya
10 total AA in GeneX
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 TAT
48 mya
Molecular Clock
NumberOf
Amino AcidSubstitutions
Per Site
Millions of years ago10 20 30
0.1
0.2
0.3
40 50 60
0.4
0.5
Human-Orang.
Carnivore-Ungulate
Camelid-Ruminant
0.3/38 = 0.008/my8 x 10-9 substitutions/site/yr
Molecular Clock Estimate of Divergence Time of Modern Humans
Gene Estimate Reference
mt DNA 166-249,000 Vigilant et al., 1991 mt DNA 129-536,000 Ruvolo et al., 1993 nuclear DNA 75-287,000 Bowcock et al., 1994 mt DNA 125-161,000 Horai et al., 1995nuclear DNA 102-450,000 Tishkoff et al., 1996
• Multiregional Hypothesis– Predicts similar allele diversity in
different regions of world
• Out of Africa Hypothesis– Predicts higher allele diversity in Africa
How Can We Test These Hypotheses With Genetic Data?
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 Neandertalfossilized mtDNA suggest that
this was a species distinctfrom Homo sapiens.
Tree-BasedApproach
Summary StatisticApproach
Gene Trees Polymorphism
Haplotype Networks FST
Nested Clade Analysis
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