EvolutionEvolution

Support for the theory of evolution

Support for the theory of evolutionSupport 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 evolutionEmbryology – study of the embryonic development of different organismsComparative Anatomy – study of the structure of particular organs in different organismsBiogeography – study of the geographic distributions can indicate where species may originally have ariseArtificial Breeding – selective breeding of plants and animals has shown that certain phenotypic characteristics can be ‘selected for’ in offspringBiochemistry – similarities and differences in the biochemical make-up of organisms can closely parallel similarities and differences in appearanceMolecular Biology – sequencing of DNA and proteins indicates the degree of relatedness between organisms

The Fossil RecordThe 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 fossilsTypes of fossils

Fossil evidence may be:direct evidence, such as bones, teeth, leaves and shellsindirect 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 three-dimensional 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 fossilsTypes 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 fossilisationConditions 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 glaciersAnimals and plants that fell into tar pits e.g. fossils of the sabre-tooth cat in the tar pits at La Brea in CaliforniaAnimals 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 NorwayNatural 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 usWhat the fossil record tells us

Fossil species are often similar to, but may differ from, today’s speciesFossil types often differ between sedimentary rock layersFossils can be dated to establish their approximate ageOlder sediments have older fossils while more recent sediments have younger fossilsNumerous extinct species are found as fossilsNew fossils mark changes in past environments of the EarthModern day species can be traced through fossil relatives to distant originsRates of evolution can vary, with bursts of species formation followed by stable periods

Evidence for evolution from the fossil recordEvidence 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

Structural differences in the horse familyStructural 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?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 fossilsTransitional 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 amphibiansfossil 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 lithographicaArchaeopteryx 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 EmbryologyComparative 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 EmbryologyComparative Embryology

These photographs have been taken at similar stages of development.

Top: a Fish EmbryoNext: a Chick EmbryoNext: a Pig EmbryoBottom: a Human Embryo

Comparative Anatomy(also known comparative morphology)

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 AnatomyComparative 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 structuresFeatures 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 AnatomyComparative 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 limbswisdom teeth of humans have little value in a chewing functionmuscle in human ear which is the same as the one dogs use to wiggle their ears

BiogeographyBiogeography

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 originRegions 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 pastThe 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 DriftContinental 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 DriftContinental Drift

Biogeography of the Camel FamilyBiogeography 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 CunhaBiogeography: 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 onesThis is probably due to the predominant westerly trade winds from the direction of South America.

Phylogenetic treesPhylogenetic 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 treesPhylogenetic trees

Consider three vertebrates: fish, bat and seal.Theoretically, there are three possible ways that these organisms are related, and thus three possible phylogenetic treesTree 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 groupsGenetic 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 togetherThe 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 chromosomeHuman chromosome 6 and Cat chromosome B2Human chromosome 1 and Cat chromosome C1Human chromosome 12 and Cat chromosome B4

Molecular evidence for evolutionMolecular 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 hybridizationDNA hybridization

One way to reconstruct the evolutionary history of a species is using DNA hybridizationIn this technique DNA from different species is ‘unzipped’ and recombined to form hybrid DNAHeat 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 hybridizationDNA 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 2.4% differenceHumans cf gibbon 5.3% differenceHumans cf green monkey 9.5% difference

DNA SequencingDNA 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 SequencingAmino Acid Sequencing

Closely related species have proteins with similar amino acid sequencesAmino acid sequences are determined by inherited genes and differences are due to mutationsThe 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 and haemaglobins. The problem with amino acid sequencing, other then expense, is that it does not detect silent mutations in the DNA.

Immunological TechniquesImmunological Techniques

Immunology indirectly measures the degree of similarity of proteins in different species.Example:

Develop anti-human antibodiesAdd this to the blood of other speciesGreater 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 DNAAncient 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 ClocksMolecular 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 clockCalibrating 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.

(a) 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

In the case of the haemoglobin protein, the molecular clock passes this test

Cautions about molecular clock dataCautions 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.