Assuming neutrality of molecular markers

1. 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.

2. 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.

3. Lactate Dehydrogenase LDH Lactate Pyruvate LDH genes in vertebrates: Ldh-A Ldh-B Ldh-C Fundulus Ldh-Ba Ldh-Bb

4. Coastal Populations Chesapeake Bay and Tributaries

5. Temperature Cline: Coastal Waters off the Atlantic Coast

6. LDH Bb has a higher catalytic efficiency at low temperature

7. Tree-based approach mtDNA haplotype network

8. Haplotype Network 2 3 6 5 4 1 = tttaga 3 = ttcaga 5 = tccact 2 = ttcagt 4 = ttcact 6 = tccact 5,6 4 2 1 3

9. 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

10. OUT OF AFRICA Based upon 189 mt sequences from indigenous people around the world.

11. OUT OF AFRICA 30 nuclear microsatellite Loci, 14 pops

12. Chimp / Human Split

13. 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)

14. MULTIREGIONAL HYPOTHESIS

15. OUT OF AFRICA

16. 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

17. 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.

18. 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.

19. 10 total AA in GeneX Last Common Fossil Ancestor Human : Ile Cys Ile Lys Ala ….Phe ATA TGT ATA AAG GCA TTT 12 mya Orang. : Lys Cys Ile Lys Ala ….Phe AAA TGT ATT AAG GCA TTT Camelids: Lys Met Val Lys Ala ….Phe AAA AGT GTT AAG GCA TTC 48 mya Ruminants: ThrIleVal Lys Ala ….Phe ACA ATT GTC AAG GCA TAT Carnivores: Lys Met Val Lys Ala ….Phe AAA AGT GTT AAG GCA TTC 66 mya Ungulates : ThrSerValArg Ala ….Tyr ACA AGUGTC AGG GCT TAT Molecular Clock Basic Idea: Some proteins evolve at an approximately constant rate over time

20. 0.3/38 = 0.008/my 8 x 10-9 substitutions/site/yr Molecular Clock Camelid-Ruminant 0.5 Number Of Amino Acid Substitutions Per Site 0.4 Carnivore-Ungulate 0.3 0.2 0.1 Human-Orang. 40 50 60 10 20 30 Millions of years ago

21. Molecular Clock Estimate of Divergence Time of Modern Humans GeneEstimateReference 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., 1995 nuclear DNA 102-450,000 Tishkoff et al., 1996

22. 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

23. GENETIC DIVERSITY AMONG GEOGRAPHIC REGIONS • short-tandem-repeat polymorphism • repeat = TTTTC • repeated 4 – 15 times = 12 alleles

24. MAJOR ROUTES OF EXPANSION OF MODERN HUMANS

25. 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

26. Finally, what about our relationship to Neandertals? PCR analysis of Neandertal fossilized mtDNA suggest that this was a species distinct from Homo sapiens.

27. Summary Statistic Approach Tree-Based Approach Gene Trees Polymorphism Haplotype Networks FST Nested Clade Analysis q

28. 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