Evolution continued

Molecular evidence for evolution

• Molecules common to living organisms include DNA and RNA (used to carry the genetic blueprint), many proteins (e.g., enzymes) and ATP, which provides energy for immediate use in cellular reactions.

• When we compare organisms at the molecular level, we first have to identify that the molecules are homologous.

• A specific protein in one organism is compared with the equivalent (homologous) protein in another.

• When we compare homologous molecules, we have evidence that enables us to reconstruct the evolutionary divergence of species from a common ancestral species, just as we have seen for the comparison of anatomical features.

• The advantage of studying molecules, however, is that it allows comparison across organisms that are anatomically very different; for example, a eucalypt tree and a kangaroo!

Amino acid sequences of proteins

• In the 1960s and 1970s, it was shown that humans and chimpanzees have identical amino acid sequences in the respiratory enzyme cytochrome c and in α- and β-haemoglobins, while they have one amino acid difference in myoglobin.

• Amino acid sequencing will not reveal all the differences in the DNA sequence between species.

• For this reason, and because it is now technically easier and cheaper to analyse nucleic acids than proteins, DNA comparisons are the preferred type of data.

Comparing DNA—DNA hybridisation

• Early comparison of the DNA of different organisms was based on a technique called DNA hybridisation.

• Molecular hybridisation can be a very useful tool in the investigation of the overall genetic similarity of organisms.

• A DNA molecule consists of two strands made up of a sequence of nucleotides.

• If DNA is heated, it unwinds and the two strands separate (dissociate), resulting in single strands.

• When the temperature drops, two complementary strands will pair up again to reform a double-stranded DNA molecule.

• This ability to separate strands and reform DNA molecules is the basis of a technique called DNA hybridisation.

DNA Hybridisation

1 DNA is extracted from tissues of two species (their double-stranded DNA molecules AA and BB). The DNA is cut up into manageable sized pieces. The double-stranded DNA from each two species is separated by heating.

2 The separated strands (As and Bs) of the two species can then be mixed together and will recombine to some extent as a hybrid DNA molecule (AB). Pairing of the single-strands A and B will occur where the two strands have a similar sequence. Where they are different, the strands will not pair up. Thus, the greater the similarity between the DNA of the two organisms, the greater the level of hybridisation that will occur

3 The level of similarity is measured by reheating the hybrid molecule (AB).

The temperature needed to dissociate half of these molecules is recorded as the melting temperature or thermal stability T s.

Thus, a difference in Ts of 2°C indicates that around 2% of the nucleotides do not pair; a difference of 3°C indicates that around 3% of the nucleotides do not pair and so on.

The higher the temperature, the greater the similarity between the two species. It is assumed that the greater the genetic similarity, the closer the two species are related in evolutionary terms.

4 As in all experiments, an experimental control is required. The DNA of each single species is dissociated and recombined with itself. The Ts required to melt these recombined molecules gives a measure within a species for comparison with hybridisation between the DNA of the different species.

Sequencing DNA

• Sequencing the order of nucleotides in DNA is now common practice. The data are recorded as the order of the specifi c bases A, T, C and G in each strand. (Remember a nucleotide is made up of a nitrogenous base, a 5-carbon sugar and a phosphate group.)

Sources of DNA • Sequencing can be carried out on any source of nucleic acid.

In bacteria (prokaryotes), DNA occurs as a single circular molecule or chromosome in the cytoplasm.

• In a virus particle (called a virion), DNA is coiled inside a protein coat. Some viruses, however, have an RNA molecule instead of DNA.

• In eukaryotes, there are three sources of DNA (genomes), each of which can be sequenced.

• All organisms (animals, fungi, algae and plants) have DNA in their nucleus (nuclear DNA) and in their mitochondria (mitochondrial DNA). Photosynthetic organisms, such as algae and plants, have an additional genome in the chloroplast (chloroplast DNA).

Mitochondrial DNA • Early sequencing work was done on animal

mitochondrial DNA (mtDNA). • Few studies have been done on plant mitochondria. • Mitochondria have a small, circular molecule of

double-stranded DNA.• It is only 16 000 nucleotides long in humans,

although larger in organisms such as yeast (75 000) and peas (110 000). In animals, mtDNA evolves relatively fast.

• Thus, mtDNA sequencing is only useful in animals that have diverged from one another in a relatively short time (about 20 million years).

Chloroplast DNA

• All chloroplasts have many copies of a small circular molecule of DNA (cpDNA).

• It includes about 160 genes, mostly for the function of photosynthesis, and is highly conserved (very slowly evolving).

Nuclear DNA • The nuclear genomes of eukaryotes vary greatly in size. In

humans with 46 chromosomes there are about 6 × 109 nucleotides (6 000 000 000), which represents a considerable amount of genetic information.

• However, only about 2% of the nuclear DNA of mammals, including humans, represents genes coding for proteins.

• The other 98% has a variety of functions, not all of which have been discovered.

• Thus, nuclear DNA offers the possibility of sequencing coding or non-coding regions (silent DNA).

• The choice of DNA region depends on what organisms are being studied and how far back in time they have diverged.

DNA coding for ribosomal RNA

• Ribosomal RNA genes evolve slowly.• Many studies of DNA have been made on ribosomal

RNA genes (rRNA genes), which exist in multiple copies.

• These genes encode for the RNA component of ribosomes.

• In vertebrates there are three rRNA genes (18S, 5.8S and 28S) that form an array (unit) that is repeated many times along a chromosome.

• This is called a repetitive DNA sequence.

• Within an array of ribosomal RNA genes, the genes are separated by internal transcribed spacer regions, called ITS1 and ITS2 for short.

• (ITS DNA is transcribed to RNA but does not result in mRNA). These spacer regions evolve at a faster rate than that of the gene.

Looking back in time- Ancient DNA

• DNA is a robust molecule and 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.

• Ancient DNA has contributed knowledge of early forms of humans, including Neanderthals, who lived up until approximately 30 000 years ago.

• DNA has been extracted from a fossil arm bone of a Neanderthal (Homo neanderthalensis) and a small segment amplified, using PCR, and sequenced.

• It proved to be significantly different when compared with DNA sampled from modern humans (Homo sapiens), supporting the idea that Neanderthals and our species did not interbreed.

Molecular clocks

• If we can determine the rate of base substitution in DNA over time, then we can use the degree of difference between the DNA of two organisms to estimate how long ago they diverged. This is the principle of a molecular clock. Calibration of the clock is based on knowing the age of the oldest fossil related to these two organisms, or is based on a geological event. For example, 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.

Gene flow and genetic drift

• There are other ways in which the frequency of genotypes present in a population can change when the influence of selection is not important.

Gene flow • Genetic variation can also result from gene flow

between populations• Gene flow is the movement of genes through

genetic exchange between populations.• In animals, this can result by their movement

from one population to another. • Individuals that migrate into a population may

mate with the local members, bringing particular genetic traits into the population.

Gene Flow

• In plants, gene flow results from the movement of seeds and pollen.

• Dispersed between populations by wind, water and animals, seed and pollen can significantly increase the amount of genetic variation present in a population.

• The effect of gene flow (wind-borne pollen) on the percentage of grass tolerant to heavy metals in populations from a mine and surrounding areas.

Gene Flow

• The influence of gene flow depends on migration rate (the proportion of migrants per generation) and the difference in allelic frequency between populations

• The greater each of these is, the greater the effect of gene flow.

• It is important to note that movement of individuals between populations is not sufficient to ensure gene flow.

• Migrants must interbreed with the population they enter and leave progeny if gene flow is to have an evolutionary impact.

Genetic drift

• Is the change in frequency of alleles from generation to generation caused by chance alone.

• Its influence is usually greatest in small isolated populations. In some circumstances, chance events can result in changes in a direction opposite to that expected under the influence of selection.

• For example, genetic drift may occur when a small number of individuals of a species colonises a new area and a new population is founded.

• This is called the founder effect.

The founder effect

• An island population of an animal or plant may start when a low number of organisms, for example, a single mated female, or a seed, is washed ashore on a log.

• The female and its offspring, or the seed, will carry only a tiny sample of the various alleles present in the populations from which they came.

The founder effect

• All subsequent generations will have only the limited variation that the founder carries (and, of course, low levels of new variation due to mutation).

• For example, in Tasmania, many sufferers of Huntington’s disease can trace their ancestry to a woman who migrated from Britain in the nineteenth century.

In summary

• Not all evolutionary change is the result of selection.

• Gene flow is the migration of alleles from one population to another. Genetic variation may result from such genetic

• Genetic drift can cause evolutionary change in small, isolated populations, called the founder effect.

• Genetic drift is a random process.

Patterns of evolution

Divergent and convergent patterns of evolution

• In the previous chapter we investigated evolution in action at the level of populations.

• Through the action of natural selection, gene flow or chance effects (in small populations), allele frequencies in populations may change over time.

• Given enough time, isolated populations may become very different from one another and diverge to the extent that we recognise them as different species (divergent evolution).

• On the other hand, unrelated species may evolve similar adaptations and come to resemble one another (convergent evolution).

Divergent evolution

• Divergent evolution is the evolution of different species (populations) from a common ancestral species (population).

• As time passes, natural selection or genetic drift may lead to divergence of species or populations.

• Isolated species and populations accumulate genetic differences and their homologous features (e.g., tetrapod limbs) may become more and more different (diverge).

Darwin’s finches• Darwin’s finches are a classic example of

divergent evolution and natural selection. Charles Darwin collected specimens of finches from the Galapagos islands when he sailed on the voyage of HMS Beagle (1831–1836).

• There were 13 different species, and every island in the archipelago is home to a number of species (some have up to seven species).

• Once Darwin learned from Gould that the finches were related species, he realised that the species differences were a result of divergent evolution.

• Each species had become adapted to particular food types as they diverged from a common ancestor.

• For example, among the seed eating species, large birds with large beaks have an advantage in drought areas, and smaller birds are favoured in wetter areas.

• This is because different types and sizes of seeds are available under these different environmental conditions.

Adaptive radiation

• Rapid divergence of an evolutionary lineage from a recent common ancestor is called adaptive radiation.

• A cluster of related species is considered evidence of adaptive radiation.

• It is assumed that this type of evolution occurred among Darwin’s group of 13 species of finches.

• The species evolved relatively rapidly as they adapted to different habitats and different islands in the absence of competitors.

Convergent evolution

• Is the development of similar features separately in unrelated groups of organisms.

• Natural selection may lead to them evolving one or more similar features, which are analagous. The two species become more alike, or converge.

• Convergent evolution of several characteristics in unrelated species may occur if the two species have similar environments and have similar lifestyles in an ecosystem.

• The Tasmanian devil and the wolverine (of North America), although unrelated, are also similar in many ways as they have adapted to living the life of a carnivore in their environments. optic retina

Parallel evolution

• Parallel evolution occurs when related species evolve similar features independently.

• For example, within the eucalypts, a number of species have evolved a white, waxy coating on their leaves that protects them from frost damage at high altitudes.

Races and geographic variation

• Natural selection, genetic drift and gene flow explain how populations change over time and how different populations within a species come to have different frequencies of alleles.

• A species that is geographically widespread usually occurs in numerous local populations, each physically separated from one another.

• If the environment across the range of the species is variable, local populations will consist of genotypes and phenotypes adapted to the local environmental conditions.

• Populations within a species that show genetic differences across a geographic range are often called races or subspecies.

Forming new species

• How can genetic processes (phenotypic variation, natural selection, gene flow, genetic drift) and environmental factors (selection, geographic isolation) explain the origin of new species (the title of Darwin’s famous book)?

• Speciation is the division of one species into two new species, but what exactly is a species?

• We recognise organisms as belonging to the same species if they resemble one another more than they do other organisms.

• Furthermore, members of different species do not usually interbreed in the wild. In genetic terms, a species may also be thought of as a collection of genes or a gene pool, isolated from the gene pools of other species.

Speciation

• Speciation involves two steps: – 1 Physical isolation of populations. Isolated

populations accumulate genetic differences due to different selection pressures and genetic drift.

– 2 Divergent evolution, which occurs over time.

Two models of speciation

1 The gradual model is a case where the entire population of the original species is split into two smaller, approximately equal populations, by a physical barrier. The parts of the population gradually diverge into races and then into new species. This is Darwin’s model.

2 The rapid model is a way that speciation can occur quickly. A small founder population on the periphery of the range of the original species is physically separated. Since advantageous mutations can increase rapidly in frequency in a small population as the result of natural selection, divergence is rapid. Genetic drift can also occur, leading to divergence of populations in the absence of natural selection.

Geographic isolation—allopatric speciation

• Usually the physical isolation that begins the process of speciation is due to geographic isolation. Geographic speciation is also called allopatric speciation. A shift in the path of a river may divide and isolate two halves of a population of small animals that cannot cross a water barrier.

In summary• Divergence between races may lead to speciation. Species do not

usually interbreed. In a genetic sense, a species can be thought of as a collection of gene pools isolated from the gene pools of other species.

• There are two general models of speciation: the gradual and rapid model.

• The gradual model involves the geographic split of an ancestral population by a barrier. The two separated populations, of similar size, gradually diverge because their environments differ and thus they are under different selection pressures.

• The rapid model involves a small peripheral population being isolated. Through natural selection, founder effect and genetic drift, the isolated population may diverge rapidly from its sister population.

Reproductive isolation

• In time, the extent of genetic divergence between separated races leads to reproductive isolation. Reproductive isolating mechanisms prevent the interbreeding of members of different species when they come into contact. Reproductive isolation results from mechanical, behavioural and ecological isolation as well as hybrid sterility.

Isolating mechanisms• Mechanical isolation results from structural

differences in the genitalia of two species, making interbreeding physically impossible.

• Behavioural isolation results from differences in the behaviour of related animal species. its mother.

• Ecological isolation occurs when two related species have evolved different ecological requirements.

• Hybrid sterility or hybrid inviability also isolates species from one another. Mating occurs, but offspring are either infertile or die because of chromosome or gene incompatibility.

Polyploidy

• If reproductive isolation arises suddenly, speciation is also sudden. This can occur by polyploidy, where organisms, such as many ferns, have multiple sets of chromosomes.

• During meiosis, if paired chromosomes fail to separate and remain in the same cell, gametes with a diploid set of chromosomes will form. Usually diploid gametes (2N) fuse with haploid gametes (N) to produce a sterile triploid plant (3N).

• A tetraploid can mate with another tetraploid and produce viable offspring, but it cannot do so if it mates with a diploid. The tetraploid is a new species suddenly formed.

Hybrids and polyploidy

• Speciation also occurs when a hybrid (an individual from a cross between two different species) has a doubling of its chromosomes.

• Hybrid sterility usually occurs because hybrids have single copies of two sets of chromosomes (one from each parent species) that do not pair at meiosis.

• For example, if a plant with a diploid number of 10 chromosomes crosses with a plant with a diploid number of 20 chromosomes, the hybrid offspring will have 15 chromosomes, 5 from one parent and 10 from another which cannot pair off at meiosis.

Species don’t exist forever

• We have been studying how new species come into being through evolutionary processes.

• On the other hand, the fossil record is clear evidence that species and groups of species eventually die out naturally—the evolutionary process of extinction.

Background extinction

• Species disappear as environments change and through competition.

• The average rate of natural loss of species is called the background extinction.

• The average life of a species varies depending on the type of organism, but is generally a few million years.

• Based on the fossil record, some marine animals appear to have lived for 5–10 million years, while mammals average 1 million years.

Mass extinction

• The fossil record also indicates that at times there has been a substantial and rapid loss of many species and groups, called a mass extinction.

• These may be global in extent, associated with a major geological event.

• A major event was the coming together of all the continents during the Permian period.

Humans cause extinctions• The dodo was a species of bird. The last dodo was

killed on the island of Mauritius more than 300 years ago.

• The North American passenger pigeon was once the most common bird in the world. A hundred years ago a migrating flock could contain as many as two billion birds. But the pigeons were tasty and whole flocks were hunted and killed for food. The last passenger pigeon died in Cincinnati Zoo in 1914.

• The Tasmanian tiger was hunted until no more animals could be found. The Tasmanian Government placed a bounty on the species in 1888 because it was believed to be a killer of sheep and poultry. The last captive specimen died in the Hobart Zoo in 1934.

Human evolution and intervention

Humans are primates

• Humans are eukaryotes and members of the animal kingdom.

• Among animals, humans are mammals, with the characteristics of body hair and ability to suckle young.

• Among mammals, humans are also primates, having a grasping hand, bicuspid teeth, short nose and well- developed eyes and brain.

• Humans are also in the same family as the great apes, which all lack a tail and have similar skeletal and skull features.

Being human

• Humans, as Homo sapiens, are a species that:– is bipedal —walks fully upright – has fewer, smaller teeth than apes – has a flat face and lacks heavy brow ridges– has a large cranial capacity, which is a measure of

brain size, ranging from 1200 to 1500 cm3 compared with 350–500 cm3 in apes

– makes tools – uses languages and art – is self-aware.

• Because chimpanzees and gorillas occur in Africa, fossil hunters have focused on Africa as a likely place to find evidence of our origins. South-East Asia, where our more distant relatives (orang-utans and gibbons) live, also reveals evidence of fossil species of Homo.

Hominid evolution

• Findings from samples of similar geological age allow us to put the pieces of a jigsaw together.

• Among the fossils that are recognised as hominids, meaning human-like, scientists generally recognise four genera: Sahelanthropus, Australopithecus, Paranthropus and Homo.

• None of these fragments of fossils can be identified as a direct ancestor, and are best depicted as extinct relatives.

• A hominid is human-like, walks upright and is classified in the family Hominidae.

Homo

• Fossils that have been classified as Homo, the same genus to which we belong, were gracile hominids; that is, less heavy boned.

• Homo fossils had a relatively large brain case and reduced jaw size. Like Paranthropus, they were also tool-makers.

Within the genus Homo, up to eight species are recognised by scientists today:

• Homo rudolfensis• Homo habilis • Homo ergaster• Homo erectus

Younger fossils than these are much more like modern humans. They include:

• Homo heidelbergensis• Homo neanderthalensis• Homo floresiensis• Homo sapiensboth

Origin of modern humans

• Cave paintings and carvings show that images and symbols became part of the culture of Homo sapiens.

• Culture is the accumulated knowledge passed on to the next generation by communication.

• A very important step for the human species was the development of language and the ability to record information.

• Indeed, study of the relationships of different languages, together with DNA data, provides evidence of the evolution of the different races of Homo sapiens living today in different geographic regions.

Different theories on the origin of modern humans

• In addition to the study of fossils, scientists have been studying molecules in modern human populations across the geographic range of our species.

• As a result, there is much controversy about the geographic origin of modern Homo sapiens due to differences in interpretation of the fossil record and the use of molecular clocks

There are two major competing hypotheses:

• Out-of-Africa hypothesis: modern humans from a single origin.

• Parallel evolution hypothesis: modern humans having multiple origins.

Out-of-Africa hypothesis

• Supporters of this theory argue that modern humans evolved in a discrete African population within the last 200 000 years, then migrated in relatively recent times throughout Africa, Europe and Asia, displacing more primitive Homo erectus and Homo ergaster populations.

• This theory is also referred to as the Replacement theory. Mitochondrial DNA evidence Those who argue for the Out-of-Africa hypothesis base their reasoning on mitochondrial sequence data.

Parallel evolution hypothesis

• The idea is that Homo sapiens originated independently in different parts of the world from Homo erectus populations that had migrated from Africa around one million years ago.

• It was presumed that, although there was some geographic isolation of populations, there was some contact and hybridisation, and hence mixing of gene pools.

• The recent find of the fossil Homo floresiensis isolated on the Indonesian island of Flores strengthens the case for the parallel evolution model.

• This is because the fossil seems to be a separate line of evolution that became extinct recently.

Early humans in Australia

• Early humans entered Australia from South-East Asia. The oldest fossil skeleton provides a date of 40 000 years ago, but evidence of fire suggests this may be earlier, about 100 000 years ago.

• In Pleistocene glacial periods, low sea level exposed land bridges, assisting the migration of humans in Australia.

• Activities of early Australians, together with glacial climate change, led to changes in the Australian environment.

Human intervention in evolution

• Hunting, clearing of habitats, farming and over exploitation of species has led to an increased level of extinction of species.

• Humans have also intervened in the course of evolution through domestication and breeding of agricultural crops and by the addition of chemicals, such as deildrin into the environment, resulting in the evolution of chemical resistance in insect pests

Bacterial resistance to antibiotics

• Bacteria have a number of criteria that makes them likely to evolve resistance to drugs (bacterial resistance). They have populations of huge numbers, a short generation time and an unusually flexible genetic system, including plasmids. Genes on the bacterial chromosome may make the bacteria resistant to some antibiotics; however, resistance is often due to the presence of plasmids in bacteria.

• Plasmids are genetic elements that are capable of replicating independently from the chromosome. They may occur in the bacterial cell independent of the chromosome, or may be incorporated into the chromosome. Plasmids carrying genes that confer antibiotic resistance are called R plasmids.

• R plasmids may be passed between different bacterial species.

• Hence, resistance can be selected in a relatively harmless species and passed to a harmful one.

• An example of this occurs in the transfer of plasmids between Escherichia coli and Shigella dysenteriae. E. coli is found in the digestive system of humans and other animals. In normal circumstances it is harmless but, because it is present in the gut, it is exposed to the antibiotics used to control other harmful bacteria.

• It has been found that R plasmids from E. coli have passed to S. dysenteriae, resulting in strains of S. dysenteriae that show high levels of drug resistance and are therefore difficult to control.

Selective breeding

• The aim of animal and plant breeding programs is to produce a new variety or to increase the yield of an old one through selective breeding—choosing which individuals are allowed to breed.

• For example, agriculturalists may wish to increase the oil content of sunflower seeds for use in the manufacture of margarine and related products, or horticulturists may wish to produce a new flower (such as the blue rose) as a valuable commercial variety.

How might technology affect human evolution?

• Reproductive technology and genetic screening :– With increased knowledge of the molecular

structure of genes and their positions on chromosomes, scientists are able to predict the likelihood of inheriting a disease or whether a pregnant woman is carrying a girl or boy.

– A parent could potentially choose not to carry a particular fetus.

• In IVF, embryos may be screened for genetic disorders (genetic screening) and not implanted if found to be carrying an undesirable trait.

• If a healthy embryo is not implanted it could potentially be a donor of embryonic stem cells. These are cell lines derived from early embryos that can theoretically be made to differentiate into any human tissue type.

• This may be the only chance of survival for an already afflicted child in the family.

Gene therapy and ethical issues

• It is possible to treat serious inherited disorders by inserting the ‘normal’ gene into a patient who has a mutant allele. This is called gene therapy. For example, a person suffering from haemophilia could receive the gene that produces the missing blood-clotting factor.

• One technical problem is how to get the normal gene into the target tissue. Should viruses be used as the vector to carry the DNA? What if the patient’s immune system reacts to the virus vector? Is the patient facing an increased risk of dying from the therapy?

• A social and ethical issue is whether the gene should be inserted only into somatic tissue and not the germ line, which could affect the patient’s offspring. Do we want to increase the frequency of such genetic disorders in future generations?