Download Human Origins

Chapter 14
Human Origins
Why are we humans?
Where did we come from?
Which monkey is more related to us?
Using DNA to understand the
beginnings of humankind
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Contents
 Methods
 Comparing great-ape and human DNA
 Comparing genetic markers in living humans
 Recovering ancient DNA
 Insights




Phylogenetic relationships
Time and place of human origins
Prehistoric human migrations
Uncovering past social practices
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The morphometric approach
 Compare physical attributes of humans
 To living species
 To fossil record
 Degree of relatedness is determined by
physical similarities
 Starting point for 19th-century biologists: How
closely related are we to existing species?
 Speculated that humans and apes shared a
recent common ancestor.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The great apes
 Apes have no tails
 Great apes
 Excludes gibbon, a
type of Asian ape
 Orangutan is the only
great ape that does not
live in Africa
 Great apes
 Share high level of
cognitive ability
 But have very different
social behaviors
bonobo
chimpanzee
gorilla
orangutan
Look similar?
human
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Social behaviors of great apes



Gorillas live in harems dominated by a single male, while orangutans lead fairly
solitary lives.
Chimpanzee society is marked by a rigid separation of the sexes. Adult males
interact with females primarily for the purpose of mating. The males spend the rest
of their time in male-only groups that will occasionally wage war against other
chimpanzees.
Amazingly, the chimpanzee’s closest ape relative, the bonobo, shows very different
behavior. These apes are generally peace-loving and avoid the violence that is
typical of the other four members of the great apes. Bonobos relieve stress in their
social group by engaging in seemingly random sexual relations. Groups of bonobos
consist of both males and females with strong bonds to one another.
There are many similarities in great-ape behavior as well.
 All great apes appear to be very intelligent. For example, researchers have been
able to teach a crude form of sign language to gorillas, chimpanzees, and bonobos.
 Experiments have shown that all the great apes are able to recognize themselves in
mirrors, an ability that seems absent in the rest of the primate world.
 These studies do suggest that the great apes share something very special.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Phylogeny of great apes
Based on DNA sequences
Orangutan
Gorilla
Human
Chimpanzee Bonobo
~2.6
4–6
6–8
million years ago
13–15
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Reduced diversity in humans
(Based on 10 Kbp DNA sequence from
non-coding region of X chromosomes)
gorillas
orangutans
chimpanzees
bonobos
Less related
humans
Closely related so recent diversion
From 3,700 individuals 160,000 to 190,000 years ago
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
DNA comparisons among great apes
DNA/DNA hybridization
Great apes
Genomewide similarity to
humans
Human
100%
Bonobo and Chimpanzee
98.4% (DNA homology shows 95%)
Gorilla
97.7%
Orangutan
96.4%
(Protein genes 99% similar)
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Differences in gene expression levels
among the great apes
Disparity in cognitive abilities
1.3-fold
Human
Chimp
1.0-fold
Human
Chimp
Human
5.5-fold
Chimp
Liver
Rhesus
Blood
Rhesus
Brain
Rhesus
A microarray study of 12,000 human genes was used to analyze expression patterns
in rhesus monkeys, chimpanzees, and humans.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The FOXP2 language gene (TF)
People with mutations in FOXP2 are unable to articulate
properly and have serious grammatical and linguistic deficits.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Looking for positive selection in the
human genome
 Two types of nucleotide substitutions
 Nonsynonymous (dN)
 Results in amino acid changes
 Synonymous (dS)
 No change in amino acid sequence
 Null hypothesis
 dN = dS
 dN / dS < 1
 Positive-selection hypothesis
 dN / dS > 1
 Testing for positive selection
 Measure probability (or P-value) that null hypothesis
accounts for nucleotide differences in a set of genes
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Testing human–chimp–mouse
orthologs for positive selection
 Human and mouse genomes are fully
sequenced
 Look for orthologs in databases
 Find chimpanzee orthologs by using PCR
 Primers from human exonic regions are used
 Match resulting 7,645 chimpanzee genes to
human and mouse orthologs
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Human genes indicating positive
selection
 Notable categories of genes
showing positive selection
 Olfaction (Smell)
 Amino acid catabolism
 Genes involved in
Mendelian diseases
(OMIM)
 Hearing
 Neural development
 Skeletal development
 Homeotic transcription
factors (early development)
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The fossil record
 Fossils are broadly defined as any evidence of past life
 Can be dated by the following methods:
 Studying radioactive decay in specimen (C-14)(<50K)
 Comparing with other datable material found in the same
or similar geological layer
 Sometimes cannot date specimen at all
 Specimen’s habitat can be deduced from the following
information:
 Types of fossils found with specimen (Coexistence)
 Geological evidence indicative of climate (flora and
fauna)
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Australopithecines
 Australopithecines are
earliest hominids (apes)
“Lucy”
 Lived 1–5 million
years ago
 Inhabited eastern and
southern Africa
 Two types
 Gracile (e.g., “Lucy”)
 Robust
 Gracile forms may
have been human
ancestors
H. sapiens
A. afarensis
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Homo
 Modern humans belong
to the genus Homo
0
 H. sapiens
 Ancestors
 H. habilis (2.0–1.6 MYA)
 H. ergaster (1.8–0.3 MYA)
 H. heidelbergensis
(0.4-0.8 MYA)
Million years ago
1
2
3
 Dead ends
 H. erectus
 H. neanderthalis (0.150.3 MYA)
4
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
http://anthro.palomar.edu/homo/glossary.htm#hominid
Homo erectus the species of humans that followed Homo habilis and preceded Homo sapiens in
our line of evolution. Homo erectus evolved in East Africa nearly 2 million years ago. They were the
first humans to expand their range into Asia and Europe. By at least 400,000 years ago, they were
beginning a transitional evolutionary phase that would eventually lead to archaic Homo sapiens. .
Homo ergaster
An early form of the species Homo erectus from East Africa. In an alternate interpretation, some
researchers consider Homo ergaster to be the species that immediately preceded Homo erectus in
our line of evolution. Homo ergaster fossils date about 1.8-1.5 million years ago.
Homo habilis
a transitional species between the australopithecines and Homo erectus. Homo habilis may have
first appeared by 2.5-2.4 million years ago and continued until about 1.5 million years ago. They
lived in East and possibly South Africa.
Homo heidelbergensis
A very early form of archaic Homo sapiens in Europe and North Africa that lived from about 800,000
to 200,000 years ago. In an alternate interpretation, some researchers consider Homo
heidelbergensis to be a separate species. Homo heidelbergensis may have been the ancestor of the
Neandertals.
Homo rudolfensis
An early form of the species Homo habilis. In an alternate interpretation, some researchers consider
Homo rudolfensis to be the species that immediately preceded Homo habilis in our line of
evolution. Homo rudolfensis fossils date 2.4-1.9 million years ago.
Homo sapiens
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Limitations of fossil record
 Complete fossils are very difficult to find
 Distribution of fossils may not correlate to
range of species
 Difficult to estimate duration of species on
planet, based on small number of individuals
 Differences in morphology cannot be well
correlated to genetic differences, which more
accurately reflect course of evolution
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Sequences unique to the hominid lineage
 Yp11 (4 MBP), on Y
chromosome found only in
humans
 Derived from Xq21.3, on X
chromosome
 Xq21.3 not inactivated,
meaning males and females
have two functional copies
 Xq21.3 and Yp11 contain
genes involved in
development of nervous
system
Yp11
Yp11
Y
Y
Xq21.3
X
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Multiregional evolution vs.
“out of Africa”
H. sapiens
H. sapiens
H. neanderthalensis
H. heidelbergensis
H. erectus
H. erectus
H. ergaster
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Multiregional evolution
 Extinct hominids are
direct ancestors of
modern humans
 Neanderthals gave rise
to Europeans, H. erectus
to Asians, etc.
 Extinct hominids
interbred
 Humans are the product
of extensive gene flow
between different
hominid types
H. sapiens
H. erectus
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
“Out of Africa”
 Single-origin hypothesis
 Modern humans arose
very recently
 Modern humans are
distinct from other
hominids
 Neanderthals and H.
erectus were not direct
ancestors of humans but
extinct expts.
 Modern humans
displaced other groups
H. sapiens
H. neanderthalensis
H. heidelbergensis
H. erectus
H. ergaster
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Africans & non-Africans
Africans
 1987: A phylogenetic tree
based on mtDNA restriction
maps was constructed
 12 enzymes used 195
polymorphisms
 mtDNA inherited maternally
 Deepest node shows one
branch exclusively African,
the other both African and
non-African
 Suggests humanity’s
maternal ancestor lived in
Africa
Ancestor
Mitochondrial Eve (Rebecca Cann et al)
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Genomics and mitochondrial Eve
Based on 53 mt Sequences (2000)
171,500 ± 50,000
52,000 ± 27,500 years ago left Africa
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The Y chromosome’s story (2001)
163 African and Asian populations
(Nuclear genes?)
The Y chromosome was selected because it does not undergo the process of chromosomal recombination
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
More explanation
 All of the Asian individuals used in the study were found to have
polymorphisms (YAP, M89, and M130) that could be traced to a
single mutation (M168) found in Africa. The M168 mutation was
estimated to be only 35,000 to 89,000 years old, thus supporting
evidence that modern humans spread from Africa in the last
100,000 years. The phylogenetic tree in the slide shows how the
different Y-chromosome haplotypes are related. Red branches
represent African-only haplotypes, green branches represent
African and Asian haplotypes, and blue branches represent Asianonly haplotypes. The map shows how some of these markers may
have spread through Asia. These findings are supported by another
study that looked at a greater number (43) of Y-chromosome
markers in 50 worldwide populations of men and also found strong
evidence for the “out of Africa” hypothesis.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
What happened to the other
hominids?
Neanderthals, our closest hominid relatives.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Neanderthals
Neanderthal
Human
Neanderthal
Human
1200–1750 ml
1200–1700 ml
Hardware for higher cognitive
functions was at least present
so could they speak? not clear!
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The Neanderthals were sophisticated
 Neanderthal culture
 Burial of the dead
 Tools
 Fire
 Why did they go
extinct?
 Absorption into
modern human gene
pool? Ancestors of
Europeans
 Replacement by
modern humans?
Neanderthal tools
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Retrieving ancient DNA
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Properties of ancient DNA
 Postmortem DNA degradation




Endogenous nucleases
Oxidation
Background radiation
Hydrolytic damage
 Limits of ancient DNA retrieval
 mtDNA almost always used because of multiple
copies per cell
 Under ideal circumstances, it may be possible
to extract DNA as old as 1.0 million years
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Analysis of Neanderthal mtDNA
human–Neandertal
human–human
human–chimp
Therefore, humans are only distantly related to Neanderthals.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Neanderthal phylogeny (mtDNA)
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Human migrations
 Hominid species existed in Africa, Europe, and
Asia for hundreds of thousands of years, but…
 H. sapiens is the first hominid to arrive…
 in Australia (60,000 y.a.)
 the Americas (18,000–30,000 y.a.)
 Polynesia (3,000–1,000 y.a.)
 Vast migrations occurred in prehistoric times
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The Cavalli-Sforza approach (1960s and
1970s)(blood proteins and PCA)
Fertile
crescent
The spread of agriculture? in Europe
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Using Y chromosomes to uncover
European migrations (2000)
 1,007 European and Middle Eastern Y
chromosomes were genotyped
 19 Y-chromosome haplotypes characterize
European and Near Eastern men
 10 key mutations account for > 95% of
European samples
 Most European haplotypes dated to before the
spread of agriculture
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Y-chromosome haplotypes in Europe
Yellow and red
associated
with agriculture
spread
Mediterranean populations were far more affected by the arrival
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
of migrants from the Middle East than the rest of Europe was
Inferences about European migrations
 Haplotypes associated with rise of agriculture
account for 22% of European Y chromosomes
 Corroborated by mtDNA study
 Results match those of original blood-marker
study
 Models of migration consistent with Ychromosome data
 Two preagriculture migrations
 One migration during the rise of agriculture
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Populating the Americas
 Standard hypothesis
 Ancestors of indigenous people arrived via land bridge
connecting Alaska to Siberia 13,500 years ago
 Archaeological and DNA evidence collected since
early 1990s indicates otherwise
 Much earlier migration
 Possibly 20,000 years ago or earlier
 Multiple waves of migrants
 Possibly of different ethnic origins
 Some may have arrived by boat
 More diverse than thought previously
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Phylogeny of America’s
indigenous people (544 native
Americans’ mt DNA)
Two ways of making trees
Three language groups
Native Americans crossed into North America from Siberia
30-40,000 years ago.© 2005
This
happened twice.
Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Polynesian migrations
 Polynesia
 Isolated islands scattered across 4,500 km
 Last area of world to be colonized by humans
 Where did Polynesians come from?
 Started their journey 3,000 years ago
 Express-train hypothesis: Ancestors of
Polynesians began in Taiwan, bypassed
adjacent Melanesia for more distant Polynesia
 Sequence data from mtDNA of contemporary
Polynesians support the express-train
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Polynesian Y-chromosome
markers
These data prompted scientists to adopt the “slow-boat hypothesis,” which states that Austronesian
migrants settled in Melanesia, mingled with the local population, and then grew in number before
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
heading for the Polynesian islands.
Insight into ancient social
practices from DNA
 Inheritance of mtDNA ( maternal) and Y
chromosome (paternal) provide separate
genetic histories of the sexes
 Comparison of mtDNA and Y-chromosome
markers can yield insight into marriage and sex
practices
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Mobility of men vs. women
 Who spread their genes over a greater distance,
men or women?
 Comparison of mtDNA and Y-chromosome
genetic markers suggest that women moved
farther
 Consistent with observation that women in
traditional societies leave their homes to be with
their husband’s family when they marry
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Caveats of using DNA to uncover
human origins (disclaimer)
 Statistical assumptions vs. biological reality
 Intermingling populations create
complications
 Challenges to the assumption of a steady
molecular clock
 Genetic drift (small populations isolate)
 Selection
 Model vs. model-free results
 The paucity of data
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Summary
 The fossil record has uncovered the remains of
extinct hominid species
 Analysis of human DNA complements, but
does not replace, the value of the fossil record
 DNA comparisons of humans with other great
apes lend insight into what makes humans
unique
 Analysis of extinct-hominid DNA elucidates
our evolutionary past
 Genetic comparisons between extant humans
reveal ancient origins and behavior
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
New slides updated
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Paleogenomics
 New sequencing technique requires no primers for
extraction of ancient DNA
 Successfully used to extract 28 million base pairs from
woolly mammoth!
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Analyzing the ancient DNA
 13 million base pairs from mammoth
 Nuclear and mitochondrial
 98.55% sequence similarity with modern
elephant
 Remaining DNA
 Endogenous micro-organisms
 Small amount of human contaminants
 Success signals beginning of “paleogenomics”
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
First Draft of Chimpanzee Genome
 Published September, 2005
 3.5X coverage
 Comparisons to human genome




Base pair level
Duplications
Deletions
Evidence of selective pressures
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Base pair comparisons
 Divergence of 1.23%
 Agrees with other
recent studies
 Lowest divergence in Xchromosome
 Highest divergence in Ychromosome
Reprinted by
permission from
Macmillan Publishers
Ltd: Nature, (437: 69-87)
From Figure 1 in The
Chimpanzee
Sequencing and
Analysis Consortium
“Initial sequence of the
chimpanzee genome
and comparison with
the human genome”
(2005).
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Segmental differences
 Magnitude of differences in genomes
 Due to base-pair divergence: 1.2%
 Due to indels (insertions deletions): 3.0%
 Due to segmental duplications: 2.7%
 Duplicated complete and partial genes
 177 found in human, but not chimpanzee
 94 found in chimpanzee, but not human
 Duplication rate since divergence
 4-5 megabases per million years
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Evidence of selection
 Estimating the level of positive selection




Examine coding regions
KA: rate of non-synonymous substitutions
KI: rate of synonymous substitutions
Low KA/KI
 Strong selective constraints
 High KA/KI
 Weak selective constraints
 Evidence for positive selection
 Highest KA/KI genes
 Involved in reproduction and immunity
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Primate genomes on the horizon
 Gorilla
 Sequencing begun in October, 2005
 Orangutan
 Draft sequence expected in 2006
 Gibbon (lesser ape)
 Some sequencing planned
 Rhesus monkey (old world monkey)
 Due soon
 Marmoset
 Draft sequence expected in 2006
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Recombination hotspots in humans
and chimpanzees
 Compare orthologous sequences in human and
chimpanzee
 Sequence similarity greater than 98%
 Linkage disequilibrium (LD) reveals
recombination hotspots
 Little match between hotspots in human and
chimpanzee
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Conclusions
 Recombination rates change in a way that is
disproportionate to the high level of sequence
similarity between humans and chimpanzees
 How do recombination rates differ when
chimpanzee and human sequences are so
similar?
 Epigenetic effects?
 SNP differences between the two species are
sufficient to cause different patterns of
recombination?
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Homo floresiensis
 New species of Homo
 Found in Indonesia
 18,000 years old
 Shared planet with H.
sapiens
 Physical attributes
 ~1 meter tall
 Small brain
 Skeleton like H.
erectus
From Figure 2 in Mirazon, M and Foley, R (2004)
“Palaeoanthropology: Human evolution writ small”
Nature 431: 1043-1044.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
The Chimpanzee Genome
 Motivation for sequencing
 Medical applications
 Evolutionary studies
 Informative differences




Insertions/Deletions
Difference in regulatory regions
Different genes
SNPs
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Progress in sequencing the
chimpanzee genome
 December 2003
 First draft completed
 May 2004
 Chimpanzee chromosome 22 sequenced to
same accuracy as human genome
 Chimpanzee chromosome 22 homologous to
human chromosome 21
 Trisomy 21 in humans results in Down’s
syndrome
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Differences between human and
chimpanzee chromosomes
 Nucleotide substitutions for 1.4% of sequence
 68,000 indels
 Range in size: 30 bp to 54,000 bp
 Human insertions of ~300 bp due to Alu element
 47 protein-encoding genes estimated to have significant
structural differences
From Figure 1a in The International Chimpanzee Chromosome 22 Consortium (2004)
“DNA sequence and comparative analysis of chimpanzee chromosome 22”
Nature 429: 382-388.
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458