assuming neutrality of molecular markers

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