Transcript Basic Molecular Biology Information

Human Evolution
Evolutionary Forces
• Darwin's original theory of evolution was based
on natural selection.
• Natural Selection: the most fit individuals
contribute more to the following generations so
their genetic influence takes over the population.
• "Fitness" is defined as
– the ability to survive and reproduce
– for the offspring to also survive and reproduce.
Neo-Darwinian Synthesis
• The is a refinement of Darwin's theory using the
knowledge of genetics gained from Mendel and
his followers. (Darwin had only a crude and
incorrect understanding of the mechanism of
heredity).
• In the neo-Darwinian model,
– the frequencies of alleles in the population are
examined.
– Many genes have multiple alleles, and their
frequencies are influenced by several factors,
especially including natural selection.
– The most important evolutionary event is speciation.
Speciation in the neo-Darwinian
model
• The creation of 2 distinct species from a
single species.
– This can occur when two groups within a
species are physically isolated.
– In this situation, allele frequencies change in
different ways in response to different
environmental pressures.
– If the allele frequencies change enough, the
two groups have become different species.
Sexual Selection
• If, after speciation has occurred, the two new species are
allowed to mate, their offspring will be less fit:
– sterile,
– weak,
– unable to survive.
• When this happens, there is a rapid period of sexual
selection.
• Sexual selection is where the two species evolve various
mechanisms to prevent mating between the species:
– behavioral,
– anatomical,
– biochemical.
Genetic Drift
• Genetic drift: random changes in allele
frequencies
• More recently, Kimura recognized that genetic
drift can have a major influence on evolution.
• Kimura’s theory is the neutral theory of
evolution:
– most alleles do not confer any selective advantage on
the individual,
– alleles frequencies change only in response to
random events.
Current Belief
• The current belief is that both selection and drift
are important in evolution.
• Genetic drift has the largest effects on small
groups:
– random events such as mate choices and
environmental disasters can radically alter allele
frequencies.
• In large groups these random events tend to
cancel each other out, making it hard to
significantly alter allele frequencies.
Molecular clock
• Mutations occur at random, but the rate of
mutation is relatively constant.
• Thus, on the average it is possible to gauge how
long ago two lineages split apart.
• This works best when synonymous mutations-mutations where the DNA is altered but the
amino acid sequence remains the same-- are
used. Such mutations are thought to be
selectively neutral.
• The molecular clock theory is the origin of the
dates used for the genetic evidence described
above.
Our History
• Starting at the beginning
• Big Bang: all matter and
energy in the Universe
suddenly appear as a single
point, extremely hot and
dense.
– Everything expands out form
this point, a process
continuing to this day.
– This is the starting point of
time also
– We have no scientific
evidence of anything before
this point
– There is strong evidence for
this scenario, but I am in no
way qualified to judge it.
More History
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Formation of the Earth: about
4.6 billion years ago.
– as judged from uranium
isotope dating of rocks from
the Moon and meteorites: 4.6
billion years is as old as they
get
– Condensation of gases and
dust out of a cloud: as
particles get larger, their
gravity attracts more
particles. The big get bigger,
etc.
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Hadean era: 4.6 – 3.8 billion
years ago. Many collisions
between large objects
periodically melt the Earth’s
surface, making life
impossible.
– the Moon is thought to have
formed when a very large
object (the size of Mars) hit
the Earth
Origin of Life
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When: there are things that look like fossil bacteria
and chemicals that may owe their origin to living
organisms is rocks that are 3.2 -3.8 billion years
old. Still controversial, but life seems to have
started on Earth shortly after the surface solidified.
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stromatolites: finely layered mounds built by
cyanobacteria living as a biofilm in the ocean and
precipitating calcium carbonate around themselves.
Seen in 3.5 billion year old rocks in Australia. They
are found from all eras, and there are stromatolites
living today (but they are rare).
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on Earth, the oldest known rocks are about 3.8 billion
years old. They are metamorphic: sediments that
have been processed by heat and pressure.
things that look like or seem to be derived from fossil
bacteria: can they be generated by non-living
processes?
However, the oldest ones remain controversial:
possibly the product of abiotic processes.
Greenland rocks roughly 3.7 billion years old have
microparticles of graphite that appear to be
depleted in 13C relative to normal 12C. Living
organisms do this routinely: enzymes slightly prefer
the isotope because compounds containing it are
lighter and move through the enzyme faster.
Molecular phylogenies of organisms living today
seem to require several billion years back to the
last universal common ancestor.
Origin of Life
• How: still a mystery: how to get both
genetics and metabolism going
simultaneously.
• RNA World idea
• Fe-S crystals: metabolism first
• Clay crystals
• top-down approach: design a minimal
prokaryote from sequenced genomes.
General Principles of Phylogeny
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Phylogeneticists theses days attempt to put
organisms into monophyletic groups: groups
that contain the last common ancestor and all
of its descendents. A monophyletic group is
also called a clade.
Paraphyletic groups : the group contains its
most recent common ancestor but not all
descendants of the last common ancestor are
included.
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Reptiles are a good example: since birds are
descended from reptiles, the last common
ancestor of all reptiles has birds as well as
reptiles among its descendants. Thus, reptiles
are a paraphyletic group.
Phylogeneticists argue about the value of
paraphyletic groups
Polyphyletic: the group does not contain its last
common ancestor
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for example, “warm-blooded animals”, which
would include birds and mammals but not
reptiles.
Discerning and separating polyphyletic groups is
a principle goal in phylogeny
A Tour through Phylogeny
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First stop: 3 domains of life:
Archaea, Eubacteria, and
Eukarya.
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Based on extensive sequencing
of 16S ribosomal RNA genes
(18S in eukaryotes).
largely confirmed by sequencing
other genes
but: prokaryotes do a lot of
lateral gene transfer, moving
genes between species.
Eukaryotes are closer Archaea
than to Bacteria. Divergence
time 3.6 billion years or so.
Green plants, along with red and
green algae branch off.
Fungi branch off later: we are
more similar to fungi than to
plants
Animals (=metazoans) are sister
taxa to choanoflagellates, a
group of protists that resemble
the collar cells of sponges and
have long been speculated to be
closely related to sponges.
Metazoan Phylogeny
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Sponges are the most primitive animals, with no
nervous system or muscles, no axis of symmetry,
and no real germ layers. Sponge development
reaches teh blastula stage but does not undergo
gastrulation.
Cnidarians (jellyfish) are diploblasts: only 2
embryonic germ layers (ectoderm and endoderm)
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All other animals have three germ layers,
including the mesoderm = triploblasts
Bilaterans all have bilateral symmetry at some point
in their life
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echinoderms (starfish for example) are
bilaterally symmetric as larvae
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bilaterans and triploblasts are (at least
roughly) the same organisms.
Another major split roughly 1 billion years ago:
protostomes vs. deuterostomes.
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based on whether the mouth or anus
develops first in embryonic life
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protostomes (mouth first): mollusks,
annelids, arthropods, nematodes, flatworms
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deuterostomes (anus first): echinoderms
and chordates
Chordates have a notochord, a rod of cartilage in
their back, at some point during development.
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in vertebrates the notochord is eventually
replaced by the vertebrae
Craniates have a skull enclosing the brain, eyes,
nose, and ears
Vertebrates have vertebrae: skeletal elements
flanking the spinal nervous system
Vertebrate Phylogeny
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Various kinds of fish
as opposed to terrestrial
vertebrates: amphibians,
reptiles, birds, and mammals
Amphibians: tetrapods (4
limbs): started with lobe-finned
fish.
Reptiles: the amniote egg,
which is resistant to
dessication, allowed animals to
lay eggs on dry land and thus
escape dependence on bodies
of water.
Birds branched off from the
reptiles
Mammals
Placental mammals (as
opposed to monotremes which
lay eggs and marsupials which
raise their young in a pouch
after a very early birth).
Primates: lemurs, tarsiers,
monkeys (old World and New
World), apes
Great apes: orangutans,
gorillas, chimpanzees (2
species), humans
Human Evolution
• The broad outlines of the story seem clear,
but the details are very hazy.
• In reality, we have only a few bones from
ancient times to examine.
• Anthropologists tend to create new
species names for almost every new find.
The Great Apes
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The primates can be divided into
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These days. the family Hominidae (the
hominids) are considered to include all of
the Great Apes. past and present, including
all human ancestors.
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the New World Monkeys,
the Old World Monkeys,
the Great Apes (including humans).
in former times, the Great Apes were
classified as Pongidae. Since humans share
a common ancestor with the Pongidae but
were put into the family Hominidae, the
pongids were a paraphyletic group.
About 20-30 millions years ago there as an
“adaptive radiation” of Great Ape species in
Africa: many species appeared rather
suddenly.
Most of them have long since died out
Great apes of today:
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chimpanzees
bonobos (pygmy chimps),
gorillas,
orangutans, and
humans
Hominin Species
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Hominin = a
subfamily,
species whose
living
descendants
are humans
only and not
other apes.
At some point
maybe 4
million years
ago one of
these species
evolved into
Australopithec
us, the first
hominin
species.
Australopithecines
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The first well-known Australopithecus species is
Australopithecus afarensis.
A afarensis walked on 2 legs, as seen by a set of
3.4 million year old footprints.
The Australopithecines evolved into 2 branches:
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the robust Australopithecines, which had enormous
jaws and small brains. Also called Paranthropus
the gracile (lightly-built) Australopithecines, which had
large brains.
The robust Australopithecines (several species:
robustus, boisei, aethiopicus ) eventually died out.
The gracile Austraopithecines (afarensis, garhi,
amanensis, and perhaps africanus) evolved into
genus Homo.
A. africanus is well known in the fossil record, but its
position in the lineage is unclear: ancestral t
paranthropus? ancestral to Homo? Neither?
Both?
Homo species
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Several species described, and it’s
not clear which are actually our
ancestors, or even which are
actually separate species. e.g.
ergaster, antecessor, rudolfensis,
heidelbergensis
H. habilis
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The best known early Homo species.
Lived 2-4 million years ago in Africa.
made crude stone tools. Possibly the
first species to do this.
H. erectus
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Started about 2 million years ago.
Homo erectus left Africa and
colonized the entire Old World
(Europe, Asia, Africa).
Various forms evolved out of H.
erectus,
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including H. sapiens, our species,
which evolved in Africa about
100,000 - 200,000 years ago.
Other species, including the
Neanderthals, also arose from H.
erectus.
possibly survived until recently: the
“hobbit people” H. floresiensis lived
on a small island near Java until
15,000 years ago.
Neanderthals
• Originally found in 1864 in a limestone
quarry in the Neander Valley in Germany.
The first non-H. sapiens skeleton
recognized.
• Many other bones found in Europe and
the Middle East.
• Lived in Europe between 200,000 years
ago and 30,000 years ago
• Modern humans also lived in Europe for
the last 5000 years of this period.
• Physical description: short, stocky, heavy
build, large head, protruding brow ridges
and a large nose. Their brain was as large
or larger than ours. The oldest known was
40 years old when he died, and nearly all
Neanderthal skeletons show signs of
injury: healed bones.
What did Neanderthals Look Like?
Alternate Views
Neanderthal Behavior
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Could they talk? It’s a little late for a conversation!
An argument has been made that the structure of the
base of the skull would not have allowed the larynx
(voicebox) to produce the range of sounds that
modern humans have. Another contribution to this
controversy: in one skeleton, the hyoid bone in the
throat (connects the tongue to the lower jaw) has
been found. It is shaped like a modern human hyoid,
and not like the hyoid bone in gorillas and chimps.
Evidence for human-like behavior. Neanderthal
bones are sometimes found in what look like funeral
burials, arranged in a comfortable position. Some
evidence that flowers were used to cover one of
them. This evidence is controversial, however. In
one case, Shanidar (named after the site), the person
had had severe injuries, including destruction of an
eye socket. These wounds were healed, and they
were severe enough so that he wouldn’t have
survived without assistance.
A fragment of a flute has been found from
Neanderthal times (50 000 years ago) It is bone, with
holes spaced in a way that allows several modernstyle notes on it.
They definitely made stone tools and used fire.
What happened to the
Neanderthals?
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About 35,000 years ago, modern humans came into
their territory in western Europe. The modern humans
are sometimes called “Cro-magnon”, based on the first
archeological site they were found at. Although there is
no obvious evidence of conflict, after several thousand
years of co-existence, the Neanderthals apparently died
out.
Two competing theories. 1. The Neanderthals were the
same species as modern humans, and the distinctive
Neanderthal type disappeared by interbreeding. This
implies that people of today carry Neanderthal genes. 2.
Alternatively, the Neanderthals may have been an
entirely different species, unable to produce fertile
hybrids with modern humans. This implies that people
today carry no Neanderthal genes.
Theories are tied up in a larger context. The older
theory , called the “Multi-regional hypothesis”, says that
all of the human-like creatures that lived in the past two
million years or more (including Homo erectus, generally
considered to be our ancestral species) are part of the
same species, Homo sapiens, and that they evolved
worldwide from the primitive forms into the forms we see
today. The mechanism for the spread of new genes was
a slow process of interbreeding between neighboring
groups. This theory suggests that many of today’s
populations have lived in the same area of the world for
a very long time: the Chinese evolved in China, the
Africans evolved in Africa, etc.
The newer theory, called “Out of Africa” says that there
have been many different species of human-like
creatures, with Neanderthals just one of these species.
Modern humans evolved in Africa about 100,000 years
ago, then spread out from there. All other human
species were eliminated.
Neanderthal-H. sap interbreeding
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Multi-regionalists think that
Neanderthals extensively interbred
with modern humans, that they were
essentially one species.
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evidence from “intermediate” fossil
bones
including apparent recognition of
“Chinese” features in H. erectus
skeletons found in China and dated to
300,000 years ago
Out of Africa types have believed that
Neanderthals and modern humans
were two separate species who never
interbred
Mitochondrial DNA evidence from
about 10 different Neanderthals
shows that the lineages diverged
roughly 300,000 years ago, well before
the appearance of modern humans.
There is currently a project to
sequence the entire Neanderthal
genome.
Microcephalin
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Recent work (Evans et al., 2006) on genes
involved with brain development has found a gene
that has several alleles, microcephalin. Patterns of
variation among alleles at this gene have been
examined in light of the molecular clock theory.
There are two rather different groups of alleles of
this gene, called D and non-D.
The variations among the D group alleles are very
slight, implying a common ancestor about 37,000
years ago. D alleles are found in about 70% of
humans today, implying a very rapid spread through
the population caused by a significant selective
advantage.
The non-D alleles are much more variable.
The differences between D alleles and non-D alleles
imply a separation of about 1.1 million years.
The origin of D alleles is not certain, but the times
suggest Neanderthals.
There may be other genes that fit this pattern—
ongoing research
Does not imply a thorough mixing of modern
humans and Neanderthals, but rather a rare or
unique event, compatible with the two being
different species.
Current Human Speciation Theory
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Current thought on speciation: usually occurs in a small isolated group as a result of
genetic drift and natural selection.
This event can be thought of as
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a "bottleneck"
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"founder effect“
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the allele frequencies are quite different from the original population,
many alleles are fixed--only one allele in the population for a given gene.
Much genetic evidence points to a bottleneck in the human species between 100,000
and 300,000 years ago.
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where a new species starts out with just a few members.
In both cases,
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the population of a species is reduced to a small number and then builds up
we are very different in appearance from the other Great Apes
our genes, both nuclear and mitochondrial, have relatively few neutral alleles compared to
other Great Apes.
This period probably represents the origin of Homo sapiens.
An amusing theory about the cause: the Toba supervolcano in Indonesia erupted
about 70,000 years ago with a force about 3000 times greater than Mt. St. Helens.
This was enough to lower the Earth’s temperature by 3-4oC and possibly trigger an
ice age, which killed most of the humans alive at that time.
mtDNA
•Evidence for the Out of Africa theory
•recall that mitochondrial DNA is inherited
through the mother only
•thus mtDNA can be considered as
a single haplotype
•when mitochondrial haplotypes are
compared, the people with the largest
amount of variation, and the most
distantly related variants are subSaharan Africans. This implies an
African origin for modern humans.
•Molecular clock theory implies a
common ancestor for mtDNA about 100150,000 years ago.
•“mitochondrial Eve”
•there were other humans alive at
that time, but their mtDNA lineages
didn’t make it into the current
population.
•Similar results for the Y chromosome
(which also doesn’t recombine):” Y
chromosome Adam”
•largest amount of variation among
Africans
•most distantly related lineages
among Africans
Beginning of civilization
• About 30,000 years ago,
is as good a point as any
to mark the beginning of
civilization
– a great flowering of art and
culture
– perhaps associated with
the development of
language? A big mystery,
really.
– maybe that microcephalin
gene
– seen most vividly in the
cave paintings in France.
Human Migrations
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Started in Africa
Spread to Asia and Australia
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much later spread to Americas
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getting to Australia requires boats, 40-60,000 years ago
a bit of controversy: very clear archeological sites dating to about 12,000 years ago. But possibly some older ones? Population
must have been very sparse.
started at Bering Strait which was dry land then, and spread over both continents in less than 2000 years
last settlements:
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Iceland settled around 800
Pacific islands weren’t completely populated until 1500
Madagascar was settled from Asia around 600 from Asia as part of teh same migration that populated the Pacific islands
Azores Islands in the Atlantic weren’t discovered until 1432
Race
• What is the genetic basis for distinct sub-groups in the
human species?
– Studies of allele frequencies among different ethnic groups
shows that about 85% of all variation is seen between groups,
and
– only about 10% is limited to a single group.
– these numbers vary a bit because of difficulty objectively defining
different ethnic groups,
• Thus, most human traits are shared among all groups,
and the idea of a strong racial identity is not supported
by genetics.
• trying to establish groups based solely on DNA variation
generates 5 major groups: sub-Saharan Africa,
Europe+Middle East+South Asia+North Africa, East Asia,
American Indians, and Pacific Islanders.