Download Evolution - Emmanuel Biology 12

Evolution
Support for the theory of evolution
Support for the theory of evolution
Testing of predictions arising from the Darwin–Wallace view of evolution has
changed its status from a hypothesis to a theory that is supported by evidence
from many sources.
Evidence for evolution comes from a variety of sources:
Palaeontology - identification and interpretation of fossils gives some of the most
direct evidence of evolution
Embryology – study of the embryonic development of different organisms
Comparative Anatomy – study of the structure of particular organs in different
organisms
Biogeography – study of the geographic distributions can indicate where species
may originally have arise
Artificial Breeding – selective breeding of plants and animals has shown that
certain phenotypic characteristics can be ‘selected for’ in offspring
Biochemistry – similarities and differences in the biochemical make-up of
organisms can closely parallel similarities and differences in appearance
Molecular Biology – sequencing of DNA and proteins indicates the degree of
relatedness between organisms
The Fossil Record
The term fossil refers to any parts or impressions
of a plant or animal that may survive after its
death.
The fossil record is incomplete.
The majority of organisms that have lived have
not been fossilised.
Many species that existed in the past have
probably not been fossilised at all.
Types of fossils
Fossil evidence may be:
direct evidence, such as bones, teeth, leaves and shells
indirect evidence, such as footprints, tooth marks, tracks, burrows and coprolites
(fossilised dung).
Indirect signs are called trace fossils and among the best known are sets of
dinosaur footprints, called dinosaur trackways.
Sometimes, all or part of dead organisms become covered by sediments that
later form sandstone or mudstone.
The organisms decay, leaving a cavity known as a mould or impression
fossil. When the cavity within a mould is later filled by other material, a threedimensional model of the organism, known as a cast, is formed.
Hard body parts are much more likely to fossilised, e.g. bones, teeth, claws,
shells, horns, wood. Soft body parts such as skin, muscle and internal organs
decay much more quickly, so they are less likely to be fossilised.
Types of fossils
Organisms, or parts of
organisms, may be fossilised
in an altered form.
This occurs when organisms
are compressed under layers
of sediment and their tissues
are replaced by a carbon
film, or by minerals, as can
be seen in petrified wood or
opalised wood or bone.
This process is referred to as
mineralisation.
Conditions required for fossilisation
For mineralisation to occur the organism’s remains need to be covered by
sediments such as mud or sand and remain undisturbed.
Cold temperatures and low oxygen levels make fossilisation more likely,
because decomposition will be slow.
Types of fossils that met this criteria include:
Insects preserved in amber (hardened sap)
Organisms frozen in permafrost or glaciers
Animals and plants that fell into tar pits e.g. fossils of the sabre-tooth cat in the tar
pits at La Brea in California
Animals that fall into peat. Peat is partially decomposed vegetation deposited in
cold, wet conditions over hundreds of years. Animals that fall into an acidic bog or
swamp can be well preserved, e.g. the ‘Bog’ people of Norway
Natural mummification. If an animal dies in the desert, its remains may dry out so
quickly that there is no time for decomposition of soft body parts.
What the fossil record tells us
Fossil species are often similar to, but may differ from, today’s
species
Fossil types often differ between sedimentary rock layers
Fossils can be dated to establish their approximate age
Older sediments have older fossils while more recent sediments
have younger fossils
Numerous extinct species are found as fossils
New fossils mark changes in past environments of the Earth
Modern day species can be traced through fossil relatives to
distant origins
Rates of evolution can vary, with bursts of species formation
followed by stable periods
Evidence for evolution from the
fossil record
If evolution has occurred and if
species can change over
geologic time, then it would be
predicted that the fossil record
would reveal changes starting
from an ancestral species that
evolved into one or more new
species that in turn evolved to
yet different species.
One example of evolutionary
change can be seen in the
evolution of the horse family.
Members of the genus Equus are
the only living representatives.
Structural differences in the horse family
Structural differences in the horse
family
First horse species (Hyracotherium)
Was about the size of a greyhound dog.
It lived about 38–54 Myr ago in a forest environment, walked on four-toed feet and
browsed soft leaves that it chewed with its small low-crowned molar teeth.
Modern horse (Equus caballus)
Much larger animal.
It lives on open grassy plains and can move rapidly on its single-toed feet.
It is a grazer that grinds tough grasses with its large high-crowned molar teeth that
provide for greater wear during a horse’s lifetime.
It is important to note that these changes are just samples of many different
lines that evolved over geological time from isolated populations of various
members of the horse family that lived under different environmental
conditions.
These changes do not represent a single line of evolution from Hyracotherium
to Equus.
Is a fossil a direct ancestor?
Direct observation and birth records tell us about our parents, grandparents and earlier
ancestors.
We cannot get the same information from fossils.
It is scientifically impossible to know whether a particular fossil, such as B, is a direct
ancestor of a living organism C, or whether it is a close relative of C that became
extinct.
All a scientist can ever determine, based on the similarity of the structural features of a
fossil and its living counterparts is that they are close or distant relatives.
Transitional fossils
If new species arise by evolution from ancestral species, it would be predicted
that the fossil record should reveal some fossils that are intermediate between
forms.
An example of this is Archaeopteryx, the earliest known bird. Like modern birds,
Archaeopteryx showed the characteristic presence of feathers and a wishbone
(furcula). However, it also showed some reptilian features now lost in modern
birds.
There are many other examples of intermediate forms or ‘missing links’ that relate
an ancestral group with its descendants.
These include:
primitive amphibians that show a transitional stage between the simple pelvic (hip)
girdle present in fish and the complex pelvic girdle in later more advanced amphibians
fossil mammal-like reptiles that show a transitional stage between reptiles with simple
conical teeth and mammals with teeth differentiated into incisors, canines, pre-molars
and molars.
Archaeopteryx lithographica
The first unequivocal evidence of birds in
the fossil record occurs in the late Jurassic
period, about 150 Myr ago.
A fossil skeleton of the earliest known bird
Archaeopteryx lithographica was found in a
limestone quarry in Bavaria, Germany, in
1861.
The fine-grained limestone preserved the
faint impressions of feathers.
In the absence of feather impressions, these
organisms would have been Archaeopteryx
= ‘ancient wing’ classified as reptiles.
Like modern birds, Archaeopteryx showed
the characteristic presence of feathers and a
wishbone (furcula). However, it also showed
some reptilian features now lost in modern
birds:
Archaeopteryx had teeth in its beak, claws
on its wings, unfused (free) bones in its
‘hand’ and a long jointed bony tail
Skeleton of (a) Archaeopteryx and (b) a modern
flying bird.
Comparative Embryology
1828 – Karl von Baer formulated a law which stated that the
features common to all members of a group of animals are
developed early in the embryo, and that more special features,
which distinguish different members of a group, develop at a
later stage of development.
Features that characterise all vertebrates include the dorsal brain
and spinal cord, axial skeleton, gill or pharyngeal slits, and aortic
arches. These all develop early. Feathers, fur and fins which
distinguish different classes of vertebrates appear later.
Reinterpreted and renamed the biogenetic law by Ernst Haeckel
in 1868 after Darwin’s evolutionary theory.
Observation that features of ancient evolutionary origin appear
earlier in development than features of newer origin.
Comparative Embryology
These photographs have
been taken at similar
stages of development.
Top: a Fish Embryo
Next: a Chick Embryo
Next: a Pig Embryo
Bottom: a Human Embryo
Comparative Anatomy
(also known comparative morphology)
Basic similarities in anatomy
suggest a genetic similarity, which
in turn suggests a common
ancestor.
An example is the pentadactyl (five
digit) limb seen in many
vertebrates.
Basic anatomy of the limb shows
the same bone arrangement,
however the size and shape of the
bones varies in different species,
depending on what it is used for.
Comparative Anatomy
When comparing anatomy of organisms in relation to evolution,
two basic types of structures can be identified.
Homologous structures
Structures of organisms that show the same basic structure but may
perform different functions e.g. wings of birds and flippers.
Homologous structures suggest there is a genetic connection, and
therefore evolution from a common ancestor.
Analogous structures
Features of organisms that have the same function but different structure
e.g. eye structure of the octopus and mammals.
Analogous structures do not have a genetic connection, so they do not
indicate an evolution relationship.
Comparative Anatomy
Vestigal structures are reduced structures with no apparent
function but which provide evidence of an evolutionary
relationship.
Presumably these organs were important in some ancestral form
but became redundant in later species.
The selection pressure for their complete loss is weak so these
structures remain in a reduced form.
Examples:
pelvic bones in whales are not longer used for the attachment of hind
limbs
wisdom teeth of humans have little value in a chewing function
muscle in human ear which is the same as the one dogs use to wiggle
their ears
Biogeography
Is the study of plant and animal distribution.
Basic principle is that each plant and animal species originated only once –
the place where this occurred is the centre of origin
Regions that have been separated from the rest of the world for a long time,
e.g. Australia and New Zealand, often have a biota that is quite distinctive and
species that are found nowhere else (endemic species).
General principles about the dispersal and distribution of land animals are:
Closely related animals in different geographic areas probably had no barrier to
dispersal in the past
The most effective barrier to dispersal in land animals was sea levels.
The discontinuous distribution of modern species may be explained by movement
out of the area they originally occupied, or by extinction.
Oceanic islands often have species that are similar to, but distinct from, those
on neighbouring continents. The occurrence of these species suggest that
they were island colonizers that evolved in isolate differently to their ancestors
on the mainland.
Continental Drift
Is the theory that continents ride on crustal plates that gradually
move.
In the southern hemisphere, continents once came together and
formed the super-continent Gondwana.
When Gondwana broke up, ancestral groups of organisms
became separated and subsequently evolved on the different
land masses.
Australia broke free of Antarctica about 45 million years ago,
drifted north and eventually came into contact with the Oriental
region in South-East Asia.
The geographic distributions and evolutionary age of plants and
animals can be correlated with the time of separation of land
masses.
Continental Drift
Biogeography of the Camel Family
The camel family
consists of 6
modern day species
that have survived
on 3 continents.
There are no
surviving species on
their continent of
origin – North
America.
Biogeography: Tristan da Cunha
The island of Tristan da Cunha, in
the Southern Atlantic Ocean,
provides good evidence of the
evolution of new species from old
ones.
Plants species on the island are
either of South American origin,
African origin or both (universal
origin)
Despite the fact that Africa is
considerably closer, more species
show South American affinities than
African ones
This is probably due to the
predominant westerly trade winds
from the direction of South America.
Phylogenetic trees
Phylogenetic trees are branching diagrams showing how
organisms are related and how they have diverged during
evolution.
Each branch point represents a common ancestor.
Phylogenetic trees based on different information will
show different relationships between organisms.
Phylogenetic trees
Consider three vertebrates: fish, bat and seal.
Theoretically, there are three possible ways that these organisms are related, and thus
three possible phylogenetic trees
Tree 1 suggests that the seal and fish are most closely related relative to the bat, based on their
similar body shape, which suits their aquatic lifestyle.
Tree 2 indicates that the seal and bat are the two most closely related. They have similar bones in
their forelimbs, have hair, suckle their young, are endotherms, and share many other features.
Tree 3 has little to support it because the bat and fish have few features in common (other than the
fact that they are vertebrates as is the seal).
Genetic Comparisons:
Genetic linkage groups
A genetic linkage group is a group of genetic loci close together
on the same chromosome.
Because they are so close together, they rarely segregate and as
a result they are inherited together
The similarity of genetic linkage groups between species
provides evidence that species have a common ancestry.
For example, humans and cats are both mammals and therefore
share a common ancestry. This is reflected by common linkage
groups on some chromosomes.
Linkage groups common to humans and cats are found on:
Human X chromosome and Cat X chromosome
Human chromosome 6 and Cat chromosome B2
Human chromosome 1 and Cat chromosome C1
Human chromosome 12 and Cat chromosome B4
Molecular evidence for evolution
Molecules common to living organisms include DNA
and RNA, many proteins (enzymes) and ATP, which
provides energy for immediate use in cellular reactions.
When we compare organisms at a molecular level, we
first have to identify that the molecules are homologous.
A specific protein or gene in one organism is compared
with the equivalent (homologous) protein in another.
Comparing homologous molecules provides evidence
that enables us to reconstruct the evolutionary
divergence of species from a common ancestral
species.
DNA hybridization
One way to reconstruct the evolutionary history
of a species is using DNA hybridization
In this technique DNA from different species is
‘unzipped’ and recombined to form hybrid DNA
Heat can be used to separate the hybridized
strands – the amount of heat required to do this
is a measure of how similar the two DNA strands
are (% bonding)
DNA hybridization
A difference in melting temperature or thermal stability
(Ts) of 2°C indicates that around 2% of nucleotides do
not pair.
The higher the temperature, the greater the similarity
between the two species, leading to the assumption that
the greater the genetic similarity, the closer the two
species are related in evolutionary terms.
Humans cf chimpanzee
Humans cf gibbon
Humans cf green monkey
2.4% difference
5.3% difference
9.5% difference
DNA Sequencing
Sequencing DNA allows us to determine the order of bases in a particular region of
DNA.
This information can be used to construct phylogenetic trees.
Closely related species show the greatest levels of base sequence similarity.
The choice of which region of DNA to sequence depends on the types of organisms
being compared because different DNA regions evolve at different rates.
Regions of DNA, such as spacer regions between genes where base substitutions
accumulate rapidly, are useful for studying the phylogeny of closely related organisms.
Mitochondrial DNA (mtDNA) evolves relatively fast in animals, and therefore
sequencing of mtDNA is only useful in animals that have diverged from one another in
a relatively short time (about 20 million years)
Highly conserved regions, such as nuclear genes that encode ribosomal RNA, can be
used to study organisms that have evolved over longer periods of time.
Amino Acid Sequencing
Closely related species have proteins with similar amino acid
sequences
Amino acid sequences are determined by inherited genes and
differences are due to mutations
The degree of similarity of these proteins is determined by the
number of mutations that have occurred – with distantly related
species having more time for differences to accumulate.
Humans and chimpanzees have identical amino acid sequences
for cytochrome C and a and b haemaglobins.
The problem with amino acid sequencing, other then expense, is
that it does not detect silent mutations in the DNA.
Immunological Techniques
Immunology indirectly measures the degree of similarity of
proteins in different species.
Example:
Develop anti-human antibodies
Add this to the blood of other species
Greater antibody-antigen reaction (more precipitation) indicates greater
similarity between humans and the species whose blood is being tested
Evolutionary relationships established on the basis of
immunology are generally well supported by phylogenies
developed from other areas of biology – biogeography,
comparative anatomy, morphological studies, fossil evidence and
DNA/amino acid sequences
Ancient DNA
Because DNA is a reasonably robust molecule, it is sometimes preserved as ancient
DNA or fossil DNA.
Fragments of DNA have been amplified using PCR and sequenced from samples of
soft or hard tissue that have been dehydrated and mummified.
Likewise, DNA may be preserved for long periods when frozen in permafrosts or in cool
cave sediments.
DNA has been sequenced from plants and animals up to 400000 years old.
Ancient DNA has contributed knowledge of the early forms of humans, and sequence
data has been shown to support the idea that Neanderthals and our species did not
interbreed.
Molecular clocks can be used to estimate the time of divergence of groups of
organisms based on knowing the age of the oldest fossil related to these two
organisms.
The number of base differences between the two organisms is divided by the age of
the fossil to calculate the average rate of change per year.
Molecular Clocks
It was recognised that the number of
differences in the proteins of two species
might indicate the time that had elapsed
since these species diverged from their
most recent common ancestor.
This is the concept of the molecular clock.
Assume that a specific protein is estimated
to change at the rate of one amino acid
sub-unit per million years. This protein from
species A, B and C is compared and four
differences are found between B and A and
ten differences between B and C.
From these data, we may infer that the
divergence of the various species from
common ancestors may be as shown on
the right.
Calibrating the molecular clock
Assuming a particular protein changes over time at approximately the same rate in
each evolutionary line, it would be possible to use the molecular clock to identify
evolutionary relationships and to estimate when various modern species last shared a
common ancestor.
Looking at living organisms can assist us to infer evolutionary relationships, so the
present helps us to interpret the past.
The molecular clock can be calibrated against the fossil record provided adequate
fossils exist.
In setting the time scale, it must be recognised that, when the percentage differences
between the proteins of various species are large, these differences are
underestimates.
Why? Because, over long periods of time, some early changes can be reversed by
later changes so that the evidence of the change is lost.
A mathematical correction is made to take this into account.
To test data from the molecular clock, three species are required:
two that are closely related (such as two mammals, M1 and M2)
a third species for reference (R) that diverged before species M1 and M2 diverged, such as a
reptile.
The timing indicated by the molecular clock is valid if the difference between M1 and R
is similar to the difference between M2 and R.
In the case of the a haemoglobin
protein, the molecular clock passes
this test
Evolutionary relationship based on
percentage differences in the alpha
chain of haemoglobin of various
vertebrates. The horizontal lines do not
identify the time span of existence of the
modern species but identify the time
span of the line leading to the modern
species.
(b) Uncorrected time scale based on two
points, 0.0 and 53 per cent, where the
latter is equated to 350 Myr, the time of
the fi rst appearance of the shark line in
the fossil record
(c) Time scale corrected for the fossil record
appearance of all groups concerned
(a)
Cautions about molecular clock data
A molecular clock based on percentage differences between corresponding
genes or proteins does not keep perfect time and care must be taken in
making inferences.
Research has shown the following limitations can apply to the use of the
molecular clock:
The molecular clock ‘ticks’ at different rates for different proteins.
The alpha haemoglobin protein appears to change at the rate of about one amino
acid every 5 to 6 Myr, while a particular histone protein changes at the rate of only
one amino acid every 5000 Myr.
It is not valid to draw conclusions by combining the rates of change in different
proteins.
The rates of change in the same protein can differ in different groups.
For example, the rate of change in a protein from plant groups has been shown to
be slower than the rate for the same protein in animal groups.
Can be problematic because calibration based on the known age of a fossil or the
geological age of rocks is not always reliable.
The molecular clock remains a powerful technique provided it is used with
appropriate care.