Human origins and evolution
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Human origins and evolution. Gil McVean, Department of Statistics, Oxford. Questions about human origins. What defines a human? What does the fossil record tell us? What are the genetic changes that make us human? What are the genetic changes that make people(s) different?.

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Human origins and evolution

Human origins and evolution

Gil McVean, Department of Statistics, Oxford


Questions about human origins

Questions about human origins

  • What defines a human?

  • What does the fossil record tell us?

  • What are the genetic changes that make us human?

  • What are the genetic changes that make people(s) different?


What makes us human

What makes us human?

  • Upright posture, bipedalism

  • Advanced tool-making capability

  • Big brain, relative to body size, and small canine teeth

  • Global dispersal

  • Use of fire to modify environment

  • Language and ‘consciousness’ (self-awareness)

  • Complex culture


Human brain size

Human brain size

  • Humans have an encephalisation quotient of about 6.5 – 8.0

    • The biggest of any mammal!

Mammals:

Ebrain = 0.12 x Mbody 2/3


What is culture

What is culture?

  • Language

  • Beliefs

  • Rituals

  • Law

  • Morality

  • Manners

  • Visual arts


Great ape phylogeny

Great ape phylogeny

  • Human and chimp ancestors split about 6 MYA

Hacia JG (2001)


A recent x

A recent X?

  • Suggestion of a more recent divergence time for X chromosome

    • Patterson et al (2006)


Some terminology

Some terminology

  • Hominid is a term used to describe Humans and any lineages that share a common ancestor with humans more recently than the human-chimp split


An overview of the fossils

An overview of the fossils

Origin of H. sapiens sapiens

Human – chimp split


Australopithecus

Australopithecus

  • 3.9 – 3 MYA

  • Both gracile and robust forms (latter called Paranthropus)

  • Evidence for sexual dimorphism within these species

Australopithecus robustus

Australopithecus africanus

Australopithecus afarensis (Lucy)

Australopithecus boisei


The laetoli footprints

The Laetoli footprints

  • First evidence of bipedalism

  • 3.7 MYA

  • Three sets of tracks in volcanic ash


Human origins and evolution

Lucy

  • 3.2 MYA from Ethiopia

  • Lucy was bipedal, an adaptation for travel across savannah woodlands and grasslands

  • Big teeth, still not a big brain.


Early homo species

Early Homo species


Homo habilis

Homo habilis

  • 2.6 – 1.4 MYA

  • Some, but not all, have slightly bigger brains

  • Maker of tools (Oldowan tools)


Striding out standing tall and at last a big brain

Striding out, standing tall, and at last, a big brain

  • Turkana boy (1.5 million years ago): the earliest individual with estimated brain size (909cc) significantly above primate allometry curve.

  • Homo ergaster

Brain size versus height


H ergaster lived in eurasia at same time as in africa

H. ergaster lived in Eurasia at same time as in Africa

  • Dmanisi fossils date to 1.7 mya

  • Caucasus Mountains, Republic of Georgia (well north of the tropics)

  • Associated Oldowan tools

  • H. ergaster is the first species of hominin adapted for endurance running.


Why leave africa the role of pleistocene climate change

Why leave Africa? The role of Pleistocene climate change

  • Middle Pleistocene climate: colder and more variable; long cold glacial periods punctuated by short, warmer interglacials

  • Migrations of many species between Africa and Eurasia during interglacials

Warm

Onset of Lower Pleistocene glaciations at ~2 million years ago with formation of permanent ice sheets and sharp cooling. Africa becomes drier.


What is life in the pleistocene like for early homo species

What is life in the Pleistocene like for early Homo species?

  • Hunting game as well as scavenging

  • Control of fire

    • Possibly from 2MYA

  • Improving the tool kit

    • more elaborate Acheulean stone tools: e.g. handaxe for butchering

  • Increasingly complex social behaviour


Homo erectus did cross sea barriers

Homo erectus did cross sea barriers

  • Archaeology on Flores, dates to 840,000 years ago

  • H. florensiensis (Hobbits) on Flores date to as recently as 20,000 yrs ago

Hobbit on left compared with modern human


Homo sapiens neanderthalensis

Homo sapiens neanderthalensis

  • From H. heidelbergensis (0.75 – 0.25 MYA)

  • Only found in Europe and near East

  • Diverged from AMH lineage about 0.8 MYA

  • More robust than AMH, but shared many features of culture

    • Music

    • Jewellery

    • Complex tools

    • Ritual (burial of dead)

    • Language ability?


Homo sapiens sapiens

Homo sapiens sapiens

  • Anatomically modern humans (AMH)

  • Modern anatomy at 200,000 years ago (Ethiopia – Omo I and II)

  • Out-of-Africa event 70,000 years ago


Out of africa diversity among early modern homo sapiens

Out of Africa: diversity among early modern Homo sapiens

  • Skhul 5, Israel, 90,000 Yrs

  • Cro-Magnon 1, France, 23-27 KYrs

  • Kow Swamp, robust Aboriginal Australian, 9-13 KYrs

Shared features: Cranial vault height high and domed, brow ridges lighter or absent, chin present


Dispersal of amhs out of africa

Dispersal of AMHs out of Africa

  • Into Middle East by 90,000 years ago, and then retreat. (Neanderthal distribution expands)

  • Reach Australia by 60,000 years ago, apparently via south Asian coastal route.

  • 40,000 years ago: substantial presence of moderns in Europe and Asia (little evidence in archaeological record at earlier dates)

  • Last Neanderthals about 25,000 years ago

  • Bottleneck in dispersal out of Africa - implicated by genetic data

    • Note that this bottleneck is not associated with speciation, only with modest structure between sub-Saharan and other human populations.


What does genetic variation tell us about human evolution

What does genetic variation tell us about human evolution?

  • Modern humans appear in the fossil record about 200K years ago

  • The mitochondrial Eve dates back to about 150K years ago

  • The Y-chromosome Adam dates back to about 70K years ago

  • AMHs left Africa about 70KYA

  • For most of our genome, however, the common ancestor is about 500K – 1M years ago

    • This predates the origin of Homo sapiens considerably


Did early humans interbreed with neanderthals

Did early humans interbreed with Neanderthals?

Neanderthals

mtDNA sequences say no…

Ovchinnikov et al (2000)


Human origins and evolution

But…

  • There is some evidence for this in the presence of unusual haplotypes found in Europe composed of SNPs not found in non-European populations

Plagnol and Wall (2006)


Deeper trees in the human genome

Deeper trees in the human genome

  • There is growing evidence that some regions of our genome have truly ancient common ancestors

  • Dystrophin has an ancient haplotype found primarily outside Africa suggesting a colonisation of >160KYA

  • There is an inversion found primarily in Europeans that is roughly 3MY old

Haplotype 1

Haplotype 2

Stefansson et al (2005)


What are the genetic differences that make us human

What are the genetic differences that make us human?


Chromosomal changes

Chromosomal changes

  • Human chromosome 2 is a fusion of two chromosomes in great apes

  • There are several inversion differences between the chromosomes

Feuk et al (2005)


Gene loss

Gene loss

  • Loss of enzymes that make sialic acid

    • Sugar on cell surface that mediates a variety of recognition events involving pathogenic microbes and toxins

  • Myosin heavy chain

    • Associated with gracilization

Wang et al (2006)


Gene evolution

Gene evolution

  • FOXP2 is a highly conserved gene (across the mammalia), expressed in the brain. Mutations in the gene in humans are associated with specific language impairment

  • Across the entire mammalian phylogeny, there have only been a very few amino acid changing substitutions

  • However, two amino acid changes have become fixed in the lineage leading to modern humans since the split with the chimpanzee lineage

Enard et al. (2002)


What are the genetic differences that make people and peoples different

What are the genetic differences that make people and peoples different?


How do we differ let me count the ways

How do we differ? – Let me count the ways

  • Single nucleotide polymorphisms

    • 1 every few hundred bp

  • Short indels (=insertion/deletion)

    • 1 every few kb

  • Microsatellite (STR) repeat number

    • 1 every few kb

  • Minisatellites

    • 1 every few kb

  • Repeated genes

    • rRNA, histones

  • Large inversions, deletions

    • Y chromosome, Copy Number Variants (CNVs)

TGCATTGCGTAGGC

TGCATTCCGTAGGC

TGCATT---TAGGC

TGCATTCCGTAGGC

TGCTCATCATCATCAGC

TGCTCATCA------GC

≤100bp

1-5kb


Detecting recent adaptive evolution

Detecting recent adaptive evolution

  • Let’s look closely at the dynamics of the fixation process for adaptive mutations

  • The fixation of a beneficial mutation is associated with a change in the patterns of linked neutral genetic variation

  • This is known as the hitch-hiking effect (Maynard Smith and Haigh 1974)

  • Looking for the signature of hitch-hiking can be a good way of detecting very recent fixation events


Diversity is not evenly distributed across genes ii

Diversity is not evenly distributed across genes II

  • Adaptive evolution ‘wipes out’ diversity nearby due to the hitch-hiking effects of a selective sweep

    • e.g. Duffy-null locus in sub-Saharn africa, protects against P. vivax

FY*O mutation

African

Pop1

Pop2

European

Ancestral allele

Derived allele

Hamblin and Di Rienzo (2000)

Missing data


Long haplotypes

Long haplotypes

  • A selective sweep at the Lactase gene in Europeans


Strong population differentiation

Strong population differentiation

  • SLC24A5

Lamason et al (Science 2005)


Classes of selected genes

Classes of selected genes

Voight et al. (2005)


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