Evolution - Week 4: Human evolution

Human evolution
Ancestors, relatives & major transitions
Recent insights from genomics
What about today?
Monday, 14 October 13

Benton (2005)
Fig 10.47

Relatives and recent ancestors

New world
monkeys

“Higher primates” = Old world monkeys + Apes

PLATYRRHINI

CATARRHINI

Apes

CERCOPITHECOIDS

Old world
monkeys

SPIDER MONKEY

MACAQUE

HOMINOIDS

Great Apes

HYLOBATIDS

HOMINIDS

Lesser
apes

SIAMANG

GIBBON

ORANGUTAN

OURANOPITHECUS
PROCONSUL

GORILLA

DRYOPITHECUS
14 MYA

SIVAPITHECUS
16 MYA

HUMAN

9 MYA

CHIMPANZEE

Potential
common
6 MYA
ancestors
(Miocene)

19 MYA
25 MYA

40 MILLION YEARS AGO

simple chewing surfaces — a feeding apMonday, 14 October 13

FAMILY TREE of hominoids encompasses the lesser apes (siamangs and

gibbons), great apes (orangutans, gorillas and chimpanzees), and humans. Most
Miocene apes were evolutionary dead ends. But researchers have identiﬁed a handful
of them as candidate ancestors of living apes and humans. Proconsul, a primitive
Miocene ape, is thought to have been the last common ancestor of the living hominoids;
Sivapithecus, an early great ape, is widely regarded as an orangutan forebear; and either
Dryopithecus or Ouranopithecus may have given rise to African apes and humans.

© Scientiﬁc American

suspensory locomotion, especially in

east Asia. Most phylogenetic analyses

Proconsul

Some ape-like features
Some monkey-like
features

East African Rift Valley


Relatives and recent ancestors
PLATYRRHINI

CATARRHINI
CERCOPITHECOIDS

HOMINOIDS
HYLOBATIDS

SPIDER MONKEY

MACAQUE

SIAMANG

HOMINIDS

GIBBON

ORANGUTAN

GORILLA

HUMAN

CHIMPANZEE

6 MYA
OURANOPITHECUS
PROCONSUL

DRYOPITHECUS

9 MYA

14 MYA

SIVAPITHECUS
16 MYA
19 MYA

25 MYA

40 MILLION YEARS AGO

simple chewing surfaces — a feeding apparatus well suited to a diet of soft, ripe
fruits. They 13
Monday, 14 Octoberalso possessed shortened

Potential
common
ancestors
(Miocene)

FAMILY TREE of hominoids encompasses the lesser apes (siamangs and

gibbons), great apes (orangutans, gorillas and chimpanzees), and humans. Most
Miocene apes were evolutionary dead ends. But researchers have identiﬁed a handful
of them as candidate ancestors of living apes and humans. Proconsul, a primitive
Miocene ape, is thought to have been the last common ancestor of the living hominoids;
Sivapithecus, an early great ape, is widely regarded as an orangutan forebear; and either
Dryopithecus or Ouranopithecus may have given rise to African apes and humans.

suspensory locomotion, especially in
the elbow joint, which was fully extendable and stable throughout the full range

east Asia. Most phylogenetic analyses
concur that it is from Sivapithecus that
the living orangutan, Pongo pygmaeus,

© Scientiﬁc American

Major transitions in human
evolution
• Bipedalism
• Increased
• Use

(down from the trees)

brain size

of simple stone tools

• Fire, spears

& other sophisticated tools (stone, bone...)

• Language, complex
• Agriculture...

In which order?

culture

Million!
years!
Glacial cycles!
Homo!

P. robustus!

Arctic icecap!

Australopithecus africanus/!
A. afarensis!
Ardipithecus ramidus!

Antarctic icecap!

Orrorin tugenensis!
Cold! Warm!
Climate!

WP!

• Life

in trees.

• Occassionally
• New

go down

context required going down more often?

Why bipedalism?
Mid Miocene!

efﬁcient locomotion (for
distant food sources)

Late Miocene!

Climate!
cooling!

• Energy

• Less

Habitat!
fragmentation!

exposure to sun?

the hands? (for gathering/
hunting?)

Million!
years!

• Free

farther: Finding food &
avoiding predators?

Glacial cycles!
Homo!

• Seeing

P. robustus!
Australopithecus africanus/!
A. afarensis!
Ardipithecus ramidus!

• Sexual

or anti-predator
displays?

Arctic icecap!

Antarctic icecap!

Orrorin tugenensis!
Cold! Warm!
Climate!


Running
• sweating
• arched

for thermoregulation.

foot + achilles tendon

• head

stabilization

• early

Homo?

• ﬁrst: improved
• then

scavenging.

persistence hunting


H. neanderthalensis
H. sapiens

H. erectus

Australopithecines

Proconsulidae


Most lineages
went extinct

Australopithecines

Wikipedia

a

Taung child

Nature 1925

Australopithecus afarensis 2.5 mya

Lucy - Australopithecus afarensis

1978

3.2 mya

Australopithecines
30°

20°

10°

0°

10°

20°

30°

40°

50°

60°

30°

30°

20°

20°

A. Bahrelghazali
A. Afarensis

10°

10°

A. Gahri
P. Boisei

P. Aethiopicus

A. Anamensis
0°

0°

10°

10°

20°

A. Africanus
30°

(km)

0

Wikipedia
0

30°


10°

30°

3 000

(mi)
Projection de Lambert azimutale équivalente

20°

P. Robustus (Crassidens)

0°

2 000

10°

20°

30°

40°

50°

60°

Brain size: 35% of
modern human

Evidence for bipedalism in Australopithecines


Evidence for bipedalism in Australopithecines
• Pelvis

short & broad (like humans), not long & narrow (like gorilla)
• Hip & walking muscles arranged like in a bipedal organism
• Femur angled as in humans, not straight as in chimps
• Feet


Fossilized tracks at
Laetoli (Tanzania)
3.6Mya
Footprints preserved in
volcanic ash from: 3 hominids
(Australopithecus afarensis)
Numerous other mammals


Tool use?

• generally: only

great apes).

• but

simple tools (similarly to current non-human

Australopithecus garhi (2.5 mya) may have made stone
tools.


Summary: Australopithecines
• Major

group of early bipedal hominids (4mya to 1 mya)

• Small

brains

• Only

in Africa

• Many

forms/species


Homo habilis


Tool use

H. habilis made tools

Chimps and other animals
may use objects as tools.

Cutting
H. sapiens!

H. habilis! Australopithecine!

Scraping

Stages of human
evolution are deﬁned by
the style and
sophistication of stone
tools….

e.g.:
•Oldowan (2.5-1.5 mya)
•Achuelian (1.5-0.2 mya)


Oldowan tools
Hammerstone

Scraper

Choppers

Flakes

Brain sizes increase


Out of Africa - H. erectus


Acheulian tools
Handaxes!

Cleaver!

Handaxe
Pick!

Scraper!


Trimming ﬂakes!

Nariokotome/Turkana
boy

H. erectus
Found 1984 in Kenya. From1.5mya

H. erectus lifestyle

• Stone

tools (Acheulian)

• Fire
• Sociality
• Hunting


• …language?

Homo ﬂoresiensis “The Hobbit”

H. ﬂorensis vs. H. sapiens skull


Nature (2004) vol. 431, 1043-1044

Major transitions in human
evolution
• Bipedalism
• Increased
• Use

(down from the trees)

brain size

of simple stone tools

• Fire, spears

& other sophisticated tools (stone, bone...)

• Language, complex
• Agriculture...

culture

Neanderthal

600,000-30,000 years ago

Burial ritual?


Neanderthals - Summary
• Neanderthals

were morphologically and genetically distinct
from early H. sapiens

• disappeared

after H. sapiens arrived - possibly because they
were culturally less advanced.


H. sapiens out of Africa

• 50,000

years ago: fully “modern” with language, music, advanced
social intelligence, strategic planning etc.
• 70,000 years ago: began migrating out of Africa
• Simultaneous decline of other Homo species (erectus,
neanderthalensis...): competition?
• Superior cooperation & learning due to language?
• Agriculture ~ 10,000 years ago

Burial ritual in
early H. sapiens
• At

Sungir, Russia, around 28,000
years ago
• A 60 year old buried with an
elaborate collection of beads,
necklaces and bracelets


Examples of early H. sapiens tools


Lion man, Ulm - 40,000 years ago

Lascaux - 35000 years ago

Flute - 36,000 years ago

Recent insights from genomics


A Draft Sequence of the
Neandertal Genome
Richard E. Green,1*†‡ Johannes Krause,1†§ Adrian W. Briggs,1†§ Tomislav Maricic,1†§
Udo Stenzel,1†§ Martin Kircher,1†§ Nick Patterson,2†§ Heng Li,2† Weiwei Zhai,3†||
Markus Hsi-Yang Fritz,4† Nancy F. Hansen,5† Eric Y. Durand,3† Anna-Sapfo Malaspinas,3†
Jeffrey D. Jensen,6† Tomas Marques-Bonet,7,13† Can Alkan,7† Kay Prüfer,1† Matthias Meyer,1†
Hernán A. Burbano,1† Jeffrey M. Good,1,8† Rigo Schultz,1 Ayinuer Aximu-Petri,1 Anne Butthof,1
Barbara Höber,1 Barbara Höffner,1 Madlen Siegemund,1 Antje Weihmann,1 Chad Nusbaum,2
Eric S. Lander,2 Carsten Russ,2 Nathaniel Novod,2 Jason Affourtit,9 Michael Egholm,9
Christine Verna,21 Pavao Rudan,10 Dejana Brajkovic,11 Željko Kucan,10 Ivan Gušic,10
Vladimir B. Doronichev,12 Liubov V. Golovanova,12 Carles Lalueza-Fox,13 Marco de la Rasilla,14
Javier Fortea,14 ¶ Antonio Rosas,15 Ralf W. Schmitz,16,17 Philip L. F. Johnson,18† Evan E. Eichler,7†
Daniel Falush,19† Ewan Birney,4† James C. Mullikin,5† Montgomery Slatkin,3† Rasmus Nielsen,3†
Janet Kelso,1† Michael Lachmann,1† David Reich,2,20*† Svante Pääbo1*†
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe
and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal
genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the
Neandertal genome to the genomes of five present-day humans from different parts of the world
identify a number of genomic regions that may have been affected by positive selection in ancestral
modern humans, including genes involved in metabolism and in cognitive and skeletal development.
We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with
present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the
ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

T

he morphological features typical of Neandertals first appear in the European fossil
record about 400,000 years ago (1–3).
Progressively more distinctive Neandertal forms
subsequently evolved until Neandertals disappeared from the fossil record about 30,000 years
ago (4). During the later part of their history,
Neandertals lived in Europe and Western Asia
as far east as Southern Siberia (5) and as far
south as the Middle East. During that time, Neandertals 14 October 13
Monday,presumably came into contact with ana-

sumed ancestors of present-day Europeans.
Similarly, analysis of DNA sequence data from
present-day humans has been interpreted as evidence both for (12, 13) and against (14) a genetic
contribution by Neandertals to present-day humans. The only part of the genome that has been
examined from multiple Neandertals, the mitochondrial DNA (mtDNA) genome, consistently
falls outside the variation found in present-day
humans and thus provides no evidence for interbreeding (15–19). However, this observation

changed parts of their genome with the ancestors of these groups.
Several features of DNA extracted from Late
Pleistocene remains make its study challenging.
The DNA is invariably degraded to a small average size of less than 200 base pairs (bp) (21, 22),
it is chemically modified (21, 23–26), and extracts
almost always contain only small amounts of endogenous DNA but large amounts of DNA from
microbial organisms that colonized the specimens
after death. Over the past 20 years, methods for
ancient DNA retrieval have been developed (21, 22),
largely based on the polymerase chain reaction
(PCR) (27). In the case of the nuclear genome of
Neandertals, four short gene sequences have been
determined by PCR: fragments of the MC1R gene
involved in skin pigmentation (28), a segment of
the FOXP2 gene involved in speech and language
(29), parts of the ABO blood group locus (30), and
a taste receptor gene (31). However, although PCR
of ancient DNA can be multiplexed (32), it does
not allow the retrieval of a large proportion of the
genome of an organism.
The development of high-throughput DNA sequencing technologies (33, 34) allows large-scale,
genome-wide sequencing of random pieces of
DNA extracted from ancient specimens (35–37)
and has recently made it feasible to sequence ge1

Department of Evolutionary Genetics, Max-Planck Institute for
Evolutionary Anthropology, D-04103 Leipzig, Germany. 2Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA.
3
Department of Integrative Biology, University of California,
Berkeley, CA 94720, USA. 4European Molecular Biology
Laboratory–European Bioinformatics Institute, Wellcome Trust
Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
5
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
20892, USA. 6Program in Bioinformatics and Integrative Biology,
University of Massachusetts Medical School, Worcester, MA
01655, USA. 7Howard Hughes Medical Institute, Department
of Genome Sciences, University of Washington, Seattle, WA
98195, USA. 8Division of Biological Sciences, University of
Montana, Missoula, MT 59812, USA. 9454 Life Sciences,

2-4% of eurasian DNA comes from Neanderthals

wnloaded from www.sciencemag.org on March 24, 2013

RESEARCH ARTICLE

Strong reproductive isolation between human
Strong reproductive isolation between humans
and Neanderthals inferred from observed
Neanderthals inferred from observed
patterns of introgression
patterns of introgression
Mathias Currata,1 and Laurent Excoffierb,c,1
Mathias Currata,1 and Laurent Excoffierb,c,1
a
a Anthropology,

Genetics, and Peopling History Laboratory, Anthropology Unit, Department Genetics and Evolution, University of o
Anthropology, Genetics, and Peopling History Laboratory, Anthropology Unit, Department of of Genetics and Evolution, University G
1227 Geneva, Switzerland; bComputational and Molecular Population Genetics Laboratory, Institute Ecology and Evolution, Univers
1227 Geneva, Switzerland; bComputational and Molecular Population Genetics Laboratory, Institute of of Ecology and Evolution, Uni
3012 Berne, Switzerland; and cSwiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
3012 Berne, Switzerland; and cSwiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

Edited by Svante Pääbo, Max Planck Institute of Evolutionary Anthropology, Leipzig, Germany, and approved August 3, 2011 (rece
Edited by Svante Pääbo, Max Planck Institute of Evolutionary Anthropology, Leipzig, Germany, and approved August 3, 2011 (receive
May 10, 2011)
May 10, 2011)

Recent studies have revealed that 2–3% of the genome of nonRecent studies have revealed that 2–3% of the genome of nonAfricans might come from Neanderthals, suggesting a a more complex
Africans might come from Neanderthals, suggesting more complex
scenario of modern human evolution than previously anticipated. InIn
scenario of modern human evolution than previously anticipated.
this paper, we use a model of admixture during a a spatial expansion
this paper, we use a model of admixture during spatial expansion
to study the hybridization of Neanderthals with modern humans
to study the hybridization of Neanderthals with modern humans
during their spread out of Africa. We find that observed low levels
during their spread out of Africa. We find that observed low levels
of Neanderthal ancestry in Eurasians are compatible with a a very low
of Neanderthal ancestry in Eurasians are compatible with very low
rate of interbreeding (<2%), potentially attributable to a a very strong
rate of interbreeding (<2%), potentially attributable to very strong
avoidance of interspecific matings, aa low fitness of hybrids, or both.
avoidance of interspecific matings, low fitness of hybrids, or both.
These results suggesting the presence of very effective barriers toto
These results suggesting the presence of very effective barriers
gene flow between the two species are robust to uncertainties about
gene flow between the two species are robust to uncertainties about
the exact demography of the Paleolithic populations, and they are
the exact demography of the Paleolithic populations, and they are
also found to be compatible with the observed lack of mtDNA inalso found to be compatible with the observed lack of mtDNA introgression. Our model additionally suggests that similarly low levels
trogression. Our model additionally suggests that similarly low levels
of introgression in Europe and Asia may result from distinct admixof introgression in Europe and Asia may result from distinct admixture events having occurred beyond the Middle East, after the split ofof
ture events having occurred beyond the Middle East, after the split
Europeans and Asians. This hypothesis could be tested because it it
Europeans and Asians. This hypothesis could be tested because
predicts that different components of Neanderthal ancestry should
predicts that different components of Neanderthal ancestry should
be present in Europeans and in Asians.
be present in Europeans and in Asians.

To examine these issues and clarify the proce
To examine these issues and clarify the pro
between Neanderthals and modern humans, we
between Neanderthals and modern humans,
istic and spatially explicit model of of admixt
istic and spatially explicit model admixture
between modern humans and Neanderthals (3
between modern humans and Neanderthals
simulations, we have estimated the interbree
simulations, we have estimated the interb
between humans and Neanderthals as as well t
between humans and Neanderthals well as a
hybridization that is is compatible with the o
hybridization that compatible with the obs
Neanderthal ancestry in in contemporary huma
Neanderthal ancestry contemporary humans,
latter migrated out of of Africa into Eurasia 50
latter migrated out Africa into Eurasia 50 ky
Results
Results

Low Rates of of Interbreeding Between Huma
Low Rates Interbreeding Between Humans

Using spatially explicit simulations, wewe
Using spatially explicit simulations, hav
expected amount of of Neanderthal ancestry pr
expected amount Neanderthal ancestry in in
from Europe (France) and Asia (China) forfo
from Europe (France) and Asia (China)
admixture with Neanderthals and over variou
admixture with Neanderthals and over var
derthal ranges (Fig. 1).1). Under our model
derthal ranges (Fig. Under our model of
range expansion, we find that observed low leve
range expansion, we find that observed low l
introgression into Eurasians imply the existe
introgression into Eurasians imply the exi
strong barriers to gene flow between the two

ARTICLE

Nature 2010
doi:10.1038/nature09710

Genetic history of an archaic hominin
group from Denisova Cave in Siberia
David Reich1,2*, Richard E. Green3,4*, Martin Kircher3*, Johannes Krause3,5*, Nick Patterson2*, Eric Y. Durand6*, Bence Viola3,7*,
Adrian W. Briggs1,3, Udo Stenzel3, Philip L. F. Johnson8, Tomislav Maricic3, Jeffrey M. Good9, Tomas Marques-Bonet10,11,
Can Alkan10, Qiaomei Fu3,12, Swapan Mallick1,2, Heng Li2, Matthias Meyer3, Evan E. Eichler10, Mark Stoneking3,
Michael Richards7,13, Sahra Talamo7, Michael V. Shunkov14, Anatoli P. Derevianko14, Jean-Jacques Hublin7, Janet Kelso3,
¨¨
Montgomery Slatkin6 & Svante Paabo3

• Only

known remains(all found since 2010): phalanx (ﬁnger
bone), three teeth, a toe bone. From 41,000 years ago.

• Amazingly

well preserved DNA (Siberia; average temperature
sequenced the genome.

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an
archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with
Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however,
the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate
this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene
epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth
shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans
have an evolutionary history distinct from Neanderthals and modern humans.

0°C).

• Common

ancestor with Neanderthal: 600,000 years ago

• Interbreeding

with Homo sapiens: 4-6% of Melanesian
Less than 200,000 years ago, anatomically modern humans (that is, mitochondrial (mt)DNA sequences have been determined from
genomes are from present-day humans)
humans with skeletons similar to those of Denisovan. Neanderthals . This has shown that all Neanderthals studied so
9–17

appeared in Africa. At that time, as well as later when modern humans
appeared in Eurasia, other ‘archaic’ hominins were already present in
Eurasia. In Europe and western Asia, hominins defined as Neanderthals
on the basis of their skeletal morphology lived from at least 230,000
years 14 October 13
Monday, ago before disappearing from the fossil record about 30,000 years

far share a common mtDNA ancestor on the order of 100,000 years
ago10, and in turn, share a common ancestor with the mtDNAs of
present-day humans about 500,000 years ago10,18,19 (as expected, this is
older than the Neanderthal–modern human population split time of
270,000–440,000 years ago estimated from the nuclear genome8). One

H. neanderthalensis
H. sapiens
Denisovan
H. erectus

Australopithecines

Proconsulidae


Most lineages
went extinct

Stoneking & Krause 2011 Nature Reviews Genetics

? No additional admixture detected despite probable overlap
! detected admixture (location uncertain)

Stoneking & Krause 2011
Figure 4 | Dispersal of modern humans from Africa. A map illustrating the


African ori
of mtDNA
lations have
of our spec
the deepest
sity 14,62–65. G
view 7–9, and
humans ind
within mod
from south
mately 115
humans fir
divergences
35–50 kya13
of a strong
our genome
close correla
in a populat
ulation from

A WINDING PATH

H. sapiens spread from Africa to
western Asia and then to Europe and
southern Asia, eventually reaching
Australasia and the Americas.

After early modern humans left Africa around 60,000 years ago (top
right), they spread across the globe and interbred with other
descendants of Homo heidelbergensis.
0

Homo sapiens
Denisovans

Homo floresiensis

Neanderthals

Homo erectus

0.4

Million years ago

Homo heidelbergensis
0.8
Homo antecessor

1.2

Homo erectus
1.6

2.0

H. floresiensis originated
in an unknown location
and reached remote
parts of Indonesia.

H. heidelbergensis
originated from
H. erectus in an
unknown location
and dispersed across
Africa, southern Asia
and southern Europe.

H. erectus spread to western Asia, then
east Asia and Indonesia. Its presence
in Europe is uncertain, but it gave rise
to H. antecessor, found in Spain.
Wavy branch edges suggest presumed fluctuations in population.

PATCHWORK PLANET
Most people’s genomes contain remnants of archaic DNA from ancient interbreeding3–6.

2%

98%

2.5%

97.5%

2.5%

5%

92.5%

Genes*
African
Unknown archaic
African source
Neanderthal
Denisovan
*Figures are approximate,
and for Africa, based on


Stringer 2012 Nature

What about today?
Does natural selection (still) act on humans?


But...
Triple (?) misunderstandings:
1. Evolution (ie genetic change) is not only through natural
selection
• Drift
• Sexual selection
• ...
2. Medicine can reduce effect of deleterious traits.
• OK many are ‘‘alive who otherwise would have perished’’
• But many have limited access to medicine.
3. Even with the best medical care
• there are differences in reproductive success


Some examples


Pathogens/disease
• “Spanish” Flu

population


pandemic of 1918 killed 1-3% of the world’s

Pathogens/disease
• “Spanish” Flu

population

pandemic of 1918 killed 1-3% of the world’s

• AIDS
• Dengue, Typhus, Malaria...


Other examples


tans maintain normal aero- gories). The XP-EHH (light
e profound arterial hypoxia blue) and iHS (dark blue)
EGLN1
H
D
REPORTSchanges in selection candidate sets in- C
he existence of
system. For example, ele- clude genes in the top 1%
evels increase vasodilation of the empirical distribuwhich, when combined with tions of XP-EHH and iHS re13), may increase the avail- sults, respectively, excluding
ells (4). Collectively, these those with evidence of posi*
*
that Tibetans have adapted tive selection in neighboring
igh-altitude conditions. The 1populations (see SOM). The D. Huff,1 Haixia Yun,2* Ga Qin,2*
Tatum S. Simonson, Yingzhong Yang,2* Chad
daptation, however, remains intersection of functionalFelipe R. Lorenzo,3 Jinchuan Xing,1
David J. Witherspoon,1 Zhenzhong Bai,2* candidates with selection canLynn B. Jorde,1† Josef T. Prchal,1,3† RiLi Ge2*†
didates (outlined in black) is
enriched for regions containenetics, University of Utah School
Tibetans have lived ating genes that contribute thousands of years, and they have a distinctive
very high altitudes for to
UT 84112, USA. 2Research Center
suite of physiological local adaptation to them to tolerate environmental hypoxia. These phenotypes
traits that enable hypoxia in Tibetans. The genes in the intersection of functional
e, Qinghai University Medical
are Republic the result selection candidates still exhibit genetic their genetic the population. (B to D) C
of adaptation to this environment, but variability in basis remains
0001, People’s clearly of China.
Department of Pathology (ARUP), genome-wide scans that reveal positive selection selection scans. The that and bo
unknown. We report Tibetan and CHB-JPT genomic regions identified in in several regions top
Medicine and VAH, Salt Lake City,
figure represent chromosome regions in the adaptation. Positively selected
contain genes whose products are likely involved in high-altitude Tibetan (number of chromosomes
haplotypes of EGLN1 populations (62 randomly drawn chromosomes from 90 individuals), respectively, f
and PPARA were significantly associated with the decreased hemoglobin
gh-Altitude Medicine initiated the
EGLN1, and (D) HMOX2 genes identified in XPEHH, both genes provides
phenotype phenotyp- unique to this highland population. Identification of thesescans, and iHS, respectiv
that is
imarily responsible for
support for previouslywith the highest iHS and XP-EHH scores (indicated by and asterisk) were desi
hypothesized mechanisms of high-altitude adaptation an illuminates the
haplotype pathways in humans.
e should complexity of hypoxia-response for each genomic region. All haplotypes were sorted to the horizontal m
be addressed. E-mail:
based on the length of uninterrupted matches to the reference sequence. See fig.
B.J); josef.prchal@hsc.utah.edu
the remaining seven regions and details about these regions.
.com (R.L.G.)
We used two intersecting criteria to identify
he Tibetan highlands are one of the most
extreme environments inhabited by hu- genes potentially involved in high-altitude adapmans. Many present-day Tibetan popula- tation: First, a priori candidates for adaptation to
2 JULY 2010 VOL 329 SCIENCE www.sciencemag.org
tions are thought to be descendants of people high-altitude hypoxia were chosen because of

Genetic Evidence for High-Altitude
Adaptation in Tibet

T


59.6
REPORTS
22.1
8.6
4.6
2.3

35613
27061
10175
25619
44408

1069
1815
2438
8784
26255
40846

33.3
14.9
4.2
2.9
1.7

Deep Human Genealogies Reveal a
Selective Advantage to Be on an
Expanding Wave Front
SLSJ

25.4
1.79***
43.2
1.48***
tracing back the founding events of new localities.
72.9
2.07***
As shown in Fig. 1, the inferred colonization pro49.9
1.58***
cess is a mixture of long-distance settlements
creating an irregular wave front, followed by fur27.7
1.38***
ther, more progressive, short-range expansions,
40.2
which then filled gaps and created a more reg-

ular wave front.
On the basis of the computation of a wave
7.4 Claudia Moreau,1 Claude Bhérer,1 Hélène Vézina,2 Michèle Jomphe,2
39
15
2.6
99.6 (WFI) (21), we find that the ancestors
2.8***
front index
1,3
1,4,5
* Laurent
of the Saguenay and the Lac-Saint-Jean people
4.6 Damian Labuda, 15444 Excoffier *4420
3.5
62.3
1.3***
lived more often on or close to the wave front
2.4 Since their origin, human populations have colonized the whole planet, but the demographic
35777
19726
1.8
30.9
1.3***
than expected by chance (WFI, P < 0.001 in both
regions) (fig. S1). Indeed, the very high WFI of
processes governing range expansions are mostly unknown. We analyzed the genealogy of more
24161
45.1
than one million individuals resulting from a range expansion in Quebec between 1686 and 1960 0.75 observed in Lac-Saint-Jean corresponds to
a situation in which half of the Lac-Saint-Jean
and reconstructed the spatial dynamics of the expansion. We find that a majority of the present
ancestors had lived directly on the wave front and
Saguenay Lac-Saint-Jean population can be traced back to ancestors having lived directly on or
close to the wave front. Ancestors located on the front contributed significantly more to the current the other half just one generation away from it.
gene 2. Age of from the range core, likely due to a of larger effective fertility of from In in the period 1840 lower in the
Table pool than thosereproduction and number 20%children of women women SLSJcontrast, WFI is significantlyto 1900.
Charlevoix region (P = 0.003) (fig. S1). These
on the wave front. This fitness component is heritable on the wave front and not in the core,
Note thatthat this table only includes women with known birth dates, such that age at marriage can be
this life-history trait evolves during range expansions.
results are consistent with different colonization
implying
dynamics of SLSJ and Charlevoix. The wave
computed.
front was always widespread in SLSJ where new
ost species go through environmental- Quebec parish registers that document the recent localities were continuously settled, whereas it was
Mean no. of
ly induced range expansions or range temporal and spatial expansion of the settle- much smaller in Charlevoix where most localities
Marriage
Mean of ment of the Charlevoix Saguenay Lac-Saint- remained in the range core until the 20th century
no. of
shifts (1), promoting the evolution
Mean age at FS ratio EFS ratio
married
No. of
traits associated with dispersal and reproduction Jean (ChSLSJ) region, northeast of Quebec City, (Fig. 1). New immigrants from outsideratio
age ChSLSJ
children
WF/RC
WF/RC
women
prime example of a marriage
recent, fast, and constituted an important minority of the people
(2). Humans likely colonized the world by a Canada: a children
WF/RC
(FS) well-documented range expansion (17) (Fig. 1). getting married, with a greater proportion of imseries of range expansions from Africa (3), pos(EFS)
sibly with episodes of interbreeding with now The European colonization of Quebec was ini- migrants settling on the wave front than on the
with
extinct
Waveand hominins (4, 5), clines from entry points tiatedand 16084.9 was well establishedQuebec range core, especially before 1900the range core)
front (WF) leading to allele frequen- City, in the colony the foundation of by the the wave front and up to 10% in (up to 20% on
2663
9.1
20.5
cy
heterozygosity
1.15*** 1.20***
0.95***
into several continents [e.g., (6, 7)]. Range7.9 end of the 17th century (18). The peopling of the (table S2). Generally, more male than female imexRange core (RC) 1783
4.1
21.6
pansions can also lead to drastic changes in allele Charlevoix region started from Baie-Saint-Paul, migration occurred in all regions, and this bias
***,frequencies, differencemimicking the effect P < 0.001 a rapid demographic growth and the de- toward males is significantly higher in the core
t test of sometimes between means; of and both
positive selection in recently colonized habitats velopment of the timber industry promoted further than on the wave front (table S3). Nevertheless,
(8, 9),
neutral through a process called gene surfing (9). a expansions afterof region (SLSJ) (19,River The of reproduction (frontbeen largely colsurfing or even deleteriousalso to the Lac-Saint-Jean upspatial location the newby people of SLSJ have or core)
process but mutations net effect 1838 the Saguenay 20). and onized territories recruited directly on the wave
Neutral, favorable,
can surf selection frequency (10, 11),
(P < 0.001 for of front effects) not that there is range
positive and increase inon the front. im- spatial and temporal dynamics of the peopling the twoor next to it, butby people from the no

s
ll
n
d
at
e
s
n
s
r
r
J
eMonday, 14 October 13

M

Natural selection in a contemporary
human population
c
Stephen C. Stearnsa,1
Sean G. Byarsa, Douglas Ewbankb, Diddahally R. Govindarajuc, and Stephen C. Stearnsa,1
a

New Haven, CT 06520-8102; bPopulation Studies Center,
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8102; bPopulation Studies Center, U
Boston University School of Medicine, Boston, MA 02118-2526
Philadelphia, PA 19104-6299; and cDepartment of Neurology, Boston University School of Medicine, Boston, MA 02118-2526

approved September 16, 2009 (received for review June 2
Edited by Peter T. Ellison, Harvard University, Cambridge, MA, and approved September 16, 2009 (received for review June 2

Our aims were to demonstrate that natural selection is operating
on contemporary humans, predict future evolutionary change for
specific traits with medical significance, and show that for some
traits we can make short-term predictions about our future evolution. To do so, we measured the strength of selection, estimated
genetic variation and covariation, and predicted the response to
selection for women in the Framingham Heart Study, a project of
the National Heart, Lung, and Blood Institute and Boston University that began in 1948. We found that natural selection is acting
to cause slow, gradual evolutionary change. The descendants of
these women are predicted to be on average slightly shorter and
stouter, to have lower total cholesterol levels and systolic blood
pressure, to have their first child earlier, and to reach menopause
later than they would in the absence of evolution. Selection is
tending to lengthen the reproductive period at both ends. To
better understand and predict such changes, the design of planned
large, long-term, multicohort studies should include input from
evolutionary biologists.

|

|

|

evolutionary rates heritability Homo sapiens medical traits

identify factors that contribute
sity to identify factors that contribute
It is the longest running multigenera
longest running multigener
history. The people originally enrolled
The people originally enrolled
dominantly European ancestry (20%
dominantly European ancestry (20%
Ireland, 10% Italy, 10% Quebec). T
10% Italy, 10% Quebec). T
5,209) has been examined every 2 ye
has been examined every 2 y
between 1948 and 2008. The offspring
1948 and 2008. The offsprin
been examined approximately every 4 y
examined approximately every 4 y
between 1971 and 2008 (4). There is
1971 and 2008 (4). There i
cohort (n = 4,095) that is not included ii
= 4,095) that is not included
in it have not yet completed reproduct
not yet completed reproduct
many physical and blood chemistry tr
physical and blood chemistry tr
questionnaire is administered, yielding
questionnaire is administered, yielding
are deidentified by the FHS and de
deidentified by the FHS and d
Institutes of Health dbGaP database
of Health dbGaP database
loaded them for analysis. In this study
them for analysis. In this study
individuals who were measured three o
individuals who were measured three o

5000 people &
their kids;
70 traits measured
every 2-4 years
since 1948.

Measuring Selection in a Multicohort
Measuring Selection in a Multicohort
Natural selection has been measured
selection has been measured
populations of animals and plants (5) u
populations of animals and plants (5) u

NATURE REVIEWS | GENETICS

VOLUME 11 | FEBRUARY 2010 | 137

How culture shaped the human
genome: bringing genetics and
the human sciences together
Kevin N. Laland*, John Odling-Smee‡ and Sean Myles§ ||

Abstract | Researchers from diverse backgrounds are converging on the view that human
evolution has been shaped by gene–culture interactions. Theoretical biologists have
used population genetic models to demonstrate that cultural processes can have a
profound effect on human evolution, and anthropologists are investigating cultural
practices that modify current selection. These findings are supported by recent analyses
of human genetic variation, which reveal that hundreds of genes have been subject to
recent positive selection, often in response to human activities. Here, we collate these
data, highlighting the considerable potential for cross-disciplinary exchange to provide
novel insights into how culture has shaped the human genome.
Accounts of human evolution frequently assume that
the selective events that shaped us were changes in the

adult lactose tolerance12,13,15,16. Estimates for the number
of human genes that have been subject to recent rapid

Genetics of our behavior?


Evolutionary Psychology
• Generosity

higher if
affects reputation

• Pheromones


help identify our mates

Summary

• Human
• (just


evolution is complicated but fascinating!

like any other species!!)

For more info
• http://humanorigins.si.edu/
• PBS

(Smithonian Institution)

Nova Becoming Human (on youtube)

• Stoneking

& Krause. Learning about human population history
from ancient and modern genomes. Nature Reviews Genetics
2011.


Any questions
About ﬁrst lectures?


http://qmplus.qmul.ac.uk/course/view.php?id=3972
Semester A: Evolution

Week 1: YW – Introduction, Historical context, Neo Darwinism
Week 2: YW – Geological Aspects, Drivers of Evolution, Levels of Evolution
Week 3: YW – Fossils, DNA and Molecules
Week 4: YW – Human Evolution
Week 5: DH – Evolution of Sex, Sexual Selection
Week 6: AH – Genetic Basis of Evolution
Week 7: Mid semester break, no lectures.
Week 8: AH – Founder Effects, Genetic Drift
In Jean Smith’s Timetable;
+ Computer Practical (tues or thurs afternoon)
not yet on “SMART”
Week 9: AH – Mutation, Selection and Gene Selection
Week 10: DH – Systematics, Speciation
Week 11: DH – Evolution of Parasites, Antibiotics
Week 12: DH – Convergence, Revision Session

Final Grade:
20% Workshop

80% Exam

Evolution - Week 4: Human evolution

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