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A Level Biology Unit 5 page 1 Heckmondwike Grammar School Biology Department Edexcel A-Level Biology B Contents Classification ............................................................................ p3 Phylogenetics ........................................................................... p5 Five Kingdoms ......................................................................... p8 Three Domains ....................................................................... p10 Natural Selection .................................................................... p12 Speciation.................................................................................. p17 Biodiversity............................................................................... p21 Conservation ........................................................................... p24 These notes may be used freely by biology students and teachers. I would be interested to hear of any comments and corrections. Neil C Millar ([email protected]) June 2016 Y12 Unit 1 Biochemistry Unit 2 Cells Unit 3 Reproduction Unit 4 Transport Unit 5 Biodiversity Unit 6 Ecology Y13 HGS Biology A-level notes Unit 7 Metabolism Unit 8 Microbes Unit 9 Control Systems Unit 10 Genetics NCM/2/16 A Level Biology Unit 5 page 2 Biology Unit 5 Biodiversity Specification Classification The classification system consists of a hierarchy of domain, kingdom, phylum, class, order, family, genus and species. The limitations of the definition of a species as a group of organisms with similar characteristics that interbreed to produce fertile offspring. Why it is often difficult to assign organisms to any one species or to identify new species. Phylogenetics DNA sequencing, gel electrophoresis and bioinformatics can be used to distinguish between species and determine evolutionary relationships. Classification Models The evidence for the three-domain model of classification as an alternative to the five-kingdom model and the role of the scientific community in validating this evidence. Natural selection Evolution can come about through natural selection acting on variation bringing about adaptations. Organisms occupy niches according to physiological, behavioural and anatomical adaptations. There is an HGS Biology A-level notes evolutionary race between pathogens and the development of medicines to treat the diseases they cause. Speciation Reproductive isolation can lead to allopatric and sympatric speciation. The role of scientific journals, the peer review process and scientific conferences in validating new evidence supporting the accepted scientific theory of evolution. Biodiversity Biodiversity can be assessed at different scales: within a species at the genetic level by looking at the variety of alleles in the gene pool of a population. within a habitat at the species level using a formula to calculate an index of diversity Conservation The ethical and economic reasons (ecosystem services) for the maintenance of biodiversity. The principles of ex-situ (zoos and seed banks) and in-situ conservation (protected habitats), and the issues surrounding each method. NCM/2/16 A Level Biology Unit 5 page 3 Classification There are millions of different types of organisms on the planet, from large animals and plants to microscopic fungi and bacteria, and each type is unique. We call each different type a species. Biologists have so far found and named around 1.5 million different species, and the more we find, the more we realise how few we know. Our knowledge is patchy: we know a lot about vertebrate animals and flowering plants, but not much about bacteria, fungi or worms. We know a lot about species living in temperate lands, but little about those living in the tropics, where 75% of all species probably live. The total number of living species may well exceed 10 million, and if we include extinct species the figure is increased by a factor of 100. A good classification system is needed to keep track of all this variety. The science of classification is called taxonomy. Principles of Taxonomy Many different classification systems have been devised, but the one biologists use is based on the work of the Swede Carolus Linnaeus in the mid-18th century. Linnaeus introduced three important innovations. He devised a hierarchical structure for classification. In a hierarchy organisms with similar characteristics are grouped together, and these groups are contained within larger composite groups. There is no overlap between groups, and a species can only appear once. These two diagrams represent hierarchical classifications, and both forms are used in biology. He gave each rank in the hierarchy a standard name. There are seven ranks or levels in the biologists’ classification: (Some modern classifications also include a higher rank called the domain, as we shall see.) So you need to remember KPCOFGS. He introduced the binomial nomenclature for naming organisms unambiguously. This simply consists of the first two ranks: the generic name (with a capital letter) and the specific name (with a small letter), and he used Latin names rather than different local-language names. The binomial names are italicised when printed (or underlined if hand-written) and after a first mention, the generic name can be abbreviated to the first letter e.g. Panthera leo (lion) and P.tigris (tiger). For most purposes the binomial name is enough to identify an organism, but a full 7-rank lineage can be given to avoid confusion. Linnaeus’s universal standard system replaced non-standard common and local names, and is still universally used today. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 4 What is a Species? For such a fundamental and apparently simple concept, the species is surprisingly hard to define. Here are four different definitions, each focussing on a different aspect of the “species”: 1. Morphology definition: members of the same species have similar characteristics. These characteristics could include their appearance or morphology (e.g. body shape, number of legs, leaf shape, etc.); the structure of their cells (e.g. composition of organelles, ribosomes, cell walls); their biochemistry (e.g. particular metabolic pathways or storage molecules). This is the most obvious definition, and is still useful, but it can be misleading for determining a phylogeny. It can be difficult to distinguish between homologous structures (which look similar because they arose from a common ancestor, e.g. the pentadactyl limb); and analogous structures (which look similar because they arose independently to do a similar job, e.g. a wing). 2. Ecological definition: members of the same species have the same ecological niche. An organism’s niche is its role in the ecosystem: where it lives, how it feeds, what conditions it needs to survive, who it competes with, how it reproduces and so on. Members of the same species must have the same niche, since that is what they are adapted to. 3. Reproduction definition: members of the same species can breed together in their natural environment to produce fertile offspring but cannot breed with members of other species. This is the most useful definition, as it can be tested fairly easily, and applies directly to the process of speciation itself (p17), but it too has its limitations. For one thing, this definition doesn’t apply to the millions of asexually-reproducing organisms, nor to extinct species. And even for sexually-reproducing species, two organisms that would not normally breed in the wild (perhaps because they live in different parts of the world) may be able to interbreed in the artificial environment of a zoo, a garden or a lab. This is particularly true of plants, which can quite easily be hybridised. Even in the wild, some closely-related species can interbreed, such as a horse and donkey to produce a mule, but the offspring is usually sterile, so is not a fertile organism. 4. Evolutionary definition: members of the same species share a unique common ancestor with each other but not with members of any other species. This is the most modern definition of a species and is the basis of phylogenetics – placing species in their correct evolutionary family tree. This can only be done by analysing the DNA sequences of different species to see how closely related they really are (see below). It can still be difficult to deduce relationships accurate since some genes can be transferred from one species to another by horizontal gene transfer. Biologists will no doubt continue to debate this species problem, but that doesn’t stop us using the species as a useful basic unit of classification. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 5 Phylogenetics We now know that all life on Earth is related, and all species have arisen through evolution. So the aim of taxonomists today is to develop phylogenies; family trees representing true evolutionary relationships, rather than just convenient groupings. Phylogenies are represented by phylogenetic trees, just like family trees. Branching points on phylogenetic trees can be interpreted in two ways: Going forward in time from the past, they represent speciation events, when one species splits in two (see p17). Going backward in time from the present, they represent the most recent common ancestor (MRCA) of all the species after the branch. In the tree shown here, species A and B are closely related because they have a recent common ancestor (at point Y), while they are more distantly related to species C because their common ancestor with C lived further in the past (at point X). This diagram (from the Ancestor’s Tale) shows the phylogeny of some mammals. The numbers are the times in millions of years (My) between branches: HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 6 Sequencing DNA Phylogenies and true ancestry can only be determined by comparing the DNA sequence of different species, since it is only DNA that is actually passed down from generation to generation. DNA can be extracted from the cells of living organisms and the sequence of bases read using sequencing machines. These sequencing machines use a kind of chromatography called gel electrophoresis that separates DNA fragments by length so that their base sequence can be read off the gel (more in unit 10). The entire genomes of thousands of species have now been sequenced, allowing more detailed phylogenies to be deduced. By 2016, the genomes of some 1,000 eukaryotic species and 10,000 prokaryotic species had been published. There are a number of projects to organise the sequencing of different groups of life on Earth. For example the Global Genome Initiative aims to sequence at least one species from every one of the 9,500 known animal and plant families. Using DNA Sequences for Classification By comparing the DNA sequences from two different living species we can determine their relatedness. The more similar the two sequences the more closely related the species are. This is because over long periods of evolutionary time DNA slowly accumulates random mutations. Closely-related living species have similar DNA sequences because they have a recent common ancestor so their DNA has only had a short time to accumulate different mutations. More distantly related species have more different sequences because their common ancestor lived longer ago so their DNA has had more time to accumulate different mutations. Because the DNA mutations happen at a steady and predictable rate, the number of differences in DNA sequences can be used as a molecular clock to estimate the time since the last common ancestor. For example, the gene for the protein cytochrome C mutates at an average rate of 1 base every 4 million years, so if two living species have 3 bases differences in their genes for cytochrome C, they must have diverged about 12 million years ago. Various genes are commonly used to compare species: The gene for the blood protein haemoglobin is found in all animals. The gene for the respiratory enzyme cytochrome C is found in all eukaryotes. The gene for the small subunit ribosomal RNA molecule (16S rRNA) is found in all known organisms. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 7 This 16S rRNA molecule is ideal for classification studies because it and accumulates mutations only very slowly (since its role is so fundamental), so its sequence can be compared over long periods of time. The 16S rRNA gene is only about 1500 bases long, small enough to be sequenced easily using early, crude sequencing techniques but also large enough to retain organism-specific information. Bioinformatics These genome sequences represent vast amounts of data. Bioinformatics is a new branch of biology concerned with storing, analysing, using and making sense of all that biological data. The sheer quantity of data is so large that the field has required the development of powerful new computers; novel mathematical algorithms for searching and analysing the databases; and statistical analysis techniques. All new DNA sequences are deposited in the international database GenBank, which is maintained by the US National Centre for Biotechnology Information (NCBI). Anyone can access and search GenBank, and NCBI provides numerous tools for searching and analysing sequence data. Some of the goals of bioinformatics are: to assemble large complete genome sequences from the sequences of the short fragments used in sequencing machines. to compare the DNA sequences of different species, in order to draw phylogenetic trees and deduce evolutionary history. to find genes within a sequence of DNA, by comparison with known genes. to predict the amino acid sequence of proteins from their gene sequence and so predict the protein’s structure and even function. to develop interesting and informative new ways of visualising all this complex data. to design new drugs and enzyme inhibitors DNA and human classification Comparison of DNA sequences have led to a new phylogeny for humans. It used to be thought that humans were separate from all other apes, but we now know that humans are closely related to chimpanzees, and indeed some taxonomists think that humans should be reclassified as the "third chimpanzee": HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 8 Classifying Life on Earth Many different systems have been tried to classify life on Earth as this chart shows: 1735 Linnaeus 1866 Haeckel 1938 Copeland 1969 Whittaker 1990 Woese 2 kingdoms 3 kingdoms 4 kingdoms 5 kingdoms 3 domains Monera Prokaryota Protoctista Protoctista Protista Fungi Fungi Plantae Plantae Animalia Animalia Protista Vegetabile Plantae Plantae Animale Animalia Animalia Bacteria Bacteria Archaebacteria Archaea Eucarya From Greek times until the 19th century, living things have been divided into just two groups: animals (if they moved) and vegetables (if they didn’t). The great German biologist Haeckel first introduced a kingdom of microbes (called Protista), and in the 20th century the division between prokaryotes and eukaryotes was finally recognised. In the 1960s the American biologist Whittaker introduced a 5 kingdom system, which has proved to be influential and is still the system most used in biology education. Five Kingdoms The five kingdoms are: prokaryotae (or monera), protoctista (or protista), fungi, plantae and animalia. This table summarises the main features of each kingdom, and the diagram on the next page shows a few of the main phyla. The three “higher” kingdoms are defined mainly by their niches: absorption for fungi, production for plants and consumption for animals. The protoctista kingdom is not well defined, and simply contains all the eukaryotes that aren’t animals, plants or fungi. Kingdom Prokaryotae Kingdom Protoctista Kingdom Fungi Kingdom Plantae Kingdom Animalia prokaryotic eukaryotic eukaryotic eukaryotic eukaryotic Complexity unicellular or colonial unicellular or multicellular mostly multicellular multicellular with differentiation multicellular with extensive differentiation Cell wall peptidoglycan varied chitin cellulose none Nutrition very varied varied absorption photosynthesis ingestion Life Cycle asexual varied haploid dominant alternating diploid-haploid diploid dominant Characteristic Cell type HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 HGS Biology A-level notes page 9 NCM/2/16 A Level Biology Unit 5 page 10 Three Domains In the 1970s the American microbiologist Carl Woese realised that there was enormous diversity within the prokaryote kingdom and proposed that it be split in two. Furthermore the differences between the two groups of prokaryotes were even bigger than the differences between the prokaryotes and the eukaryotes. Woese therefore proposed that all life should be divided into three domains: The Archaea (or ancient life); the Bacteria (or true bacteria) and the Eukarya (or eukaryotes). In the simplest version of the three domain classification (shown above), the domains Archaea and Bacteria contain one kingdom each, while the domain Eukarya contains the four eukaryotic kingdoms. However, DNA studies are showing that few of the traditional kingdoms are phylogenetically correct, so biologists are moving to a more accurate phylogenetic tree like this: The principle differences between the three domains are summarised in this table: Bacteria Archaea Eukarya nucleus and organelles none none present Ribosomes 70S 70S 80S introns no sometimes frequent formyl-methionine methionine methionine yes no no 10 polypeptides 5 polypeptides 12 polypeptides circular without histones circular with histones linear with histones peptidoglycan proteinaceous S-layer cellulose/chitin D-glycerol, ester link L-glycerol, ether link D-glycerol, ester link initiator amino acid sensitive to antibiotics RNA polymerase DNA cell wall membrane phospholipids HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 11 The Archaea The initial classification of the Archea as a separate domain was based on the sequences of the 16S rRNA gene, which was very different from both eukaryotes and bacteria. Further study has shown that the Archaea share some features with bacteria (they’re both prokaryotes and have 70S ribosomes) and some features with the Eukarya (they use the same enzymes for transcription and translation). But some features are unique to the Archaea domain. For example the Archaea have a unique phospholipid in their cell membranes: Many of the Archaea are extremophiles i.e. they live in extreme environments. They include: Thermophiles Cells that live in environments hotter than 60°C, such as hot springs and deep-sea thermal vents. The current record for the hottest growth temperature is 122°C, for Methanopyrus kandleri. Psychrophiles Cells that live in environments colder than -15°C, such as permafrost and polar ice. Halophiles Cells that live in environments with a salt concentration higher than 15% (compared to 3% in seawater), such as the Dead Sea in Israel and the Great Salt Lake in Utah. Acidophiles and Alkaliphiles Cells that live in environments with pH<3 or pH>9 respectively. Barophiles Cells that live in environments under high pressure, such as deep oceans with pressures exceeding 300 atmospheres. Xerophiles Cells that live in very dry environments, such as arid desert soils and rocks. The Archea play an important role in both the carbon and nitrogen cycles. The nitrogen fixing bacteria and the nitrifying bacteria are Archeans. The methanogens use a unique respiration that reduces carbon dioxide to methane using hydrogen gas. CO2 + 4H2 → CH4 + 2H2O These methanogens are obligate anaerobes, poisoned by traces of oxygen. They are found in swamps, marshes, and the intestines of mammals, and are responsible for creating natural gas and the methane gas that is currently contributing to the greenhouse effect. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 12 Evolution and Natural Selection We have seen that there are millions of different species currently living on our planet. Each species is different and has found a unique way of living; of solving the problems of surviving and reproducing successfully. Where did all this diversity come from? 17th Century Most people believed in Creationism, which considered that all life was created just as it is now. This was not based on any evidence, but was instead a belief. 18th Century Naturalists began systematic classification systems and noticed that groups of living things had similar characteristics and appeared to be related. So their classifications looked a bit like family trees. European naturalists travelled more widely and discovered more fossils, which clearly showed that living things had changed over time, so were not always the same. Extinctions were also observed (e.g. dodo), so species were not fixed. Selective breeding was widely practised and it was realised that species (like crops, working dogs, racing pigeons) could be changed dramatically by selection. 19th Century Lamark (1809) proposed a hypothesis that living things changed by inheriting acquired characteristics. e.g. giraffes stretched their necks to reach food, and their offspring inherited stretched necks. This is now known to be wrong, since many experiments (and experience) have shown that acquired characteristics are not inherited. Nevertheless Lamark's theory was one of the first to admit that species changed, and to try to explain the change. Charles Darwin (1859) published "On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life", which proposed the idea of natural selection, a far better explanation for the changes in species. “Origin” has since been recognised as one of the most important books ever written. A very similar theory was also proposed by Alfred Wallace, and Darwin and Wallace agreed to publish at the same time. 20th Century Mendel’s work on genetics was rediscovered and combined with Darwin’s theory to form modern Darwinism. Many new techniques, like fossil dating, DNA sequencing, molecular biology, microbiology and mathematical modelling, gradually formed an extensive and overwhelming body of experimental evidence for Darwinism. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 13 Darwin's Theory of Evolution by Natural Selection Darwin observed that most organisms have far more offspring than survive to maturity – most organisms die young from predation, disease and competition, so that populations are usually fairly constant in size. Darwin realised that the organisms that die young were not random, but were selected by their characteristics. He concluded that individuals that were better adapted to their environment compete better than the others, survive longer and reproduce more, so passing on more of their successful genes to the next generation. Darwin explained the giraffe's long neck as follows: 1. In a population of horse-like animals there would be random genetic variation in neck length. 2. Animals with long necks were slightly better adapted as they could reach more leaves, and so were better-nourished. These longer-necked animals lived longer, through more breeding seasons, and so had more offspring. 3. The shorter-necked animals would be more likely to lose the competition for food, so would be poorly nourished and would probably die young from predation or disease. They would have few, if any, offspring. 4. So in the next generation there were more long-neck alleles than short-neck alleles in the population. If this continued over very many generations, then in time the frequency of long-neck alleles would increase and so the average neck length would increase. [Today it is thought more likely that the selection was for long legs to run away from predators faster, and if you have long legs you need a long neck to be able to drink. But the process of selection is just the same.] Darwin wasn't the first to suggest evolution of species, but he was the first to suggest a plausible mechanism for the evolution - natural selection, and to provide a wealth of evidence for it. Darwin used the analogy of selective breeding (or artificial selection) to explain natural selection. In selective breeding, desirable characteristics are chosen by humans, and only those individuals with the best characteristics are used for breeding. In this way species can be changed over a period of time. All domesticated species of animal and plant have been selectively bred like this, often for thousands of years, so that most of the animals and plants we are most familiar with are not really natural and are nothing like their wild relatives (if any exist). The analogy between artificial and natural selection is a very good one, but there is one important difference - Humans have a goal in mind; nature does not. Summary of Natural Selection 1. There is genetic variation in characteristics within a population 2. Individuals with characteristics that make them less well adapted to their environment will die young from predation, disease or competition, so they will not pass on their alleles. 3. Individuals with characteristics that make them well adapted to their environment will live longer and reproduce, passing on their alleles to their offspring. 4. The allele frequency will change in each generation. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 14 Natural Selection and Adaptation The result of Natural Selection is that organisms who survive are well-adapted to their ecological niche. A species’ niche means its role in its particular habitat. This role might include its position in the food chain (producer, herbivore, predator, parasite); its use of resources (e.g. to build nests); its method of reproduction (e.g. coloured flowers to attract insects); its contribution to matter cycles (e.g. nitrogen fixing, decomposer); etc. Successful organisms have features (called adaptations or adaptive traits) that make them good at surviving in their niche, because natural selection has selected for these traits, so these traits help the organism to survive and reproduce. These adaptive traits can take different forms: Anatomical adaptations. For example a cactus plant has tiny spine-shaped leaves, large roots and a swollen stem to allow it to survive in a dry habitat. Physiological adaptations. For example the thermophilic archaea have special proteins and membrane lipids that are stable at high temperatures and do not denature like normal proteins. Behavioural adaptations. For example the mating behaviour of many birds (including singing, dancing and nest-building) help them to find a mate and so reproduce successfully. All these adaptations arose by means of natural selection. Note that you can’t say that an individual organism adapts to its surroundings in the way that a human might adapt to a new job. The process of biological adaptation (developing adaptive traits like wings) applies to whole populations and takes place gradually over long, evolutionary timescales of hundreds of thousands of years. An organism can be adapted to its niche, or have an adaptation, but it can’t become adapted, and certainly not in its lifetime. Adaptive traits give the appearance of design, but this is misleading and in fact close examination often reveal design flaws. For example the vertebrate eye is an anatomical adaptation that has the appearance of being designed, but the retina is actually rather poor, with an unnecessary blind spot. The explanation for this poor design is that the eye was created by evolution from simpler structures, not designed from scratch. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 15 Examples of Natural Selection We’ll look at some examples of natural selection in action. In fact most things you’ll study in the biology course (like protein structure, lung anatomy, the nitrogen cycle, disease, anything) are examples of natural selection. It has been said that nothing in biology makes sense, except in the light of evolution. Bacterial resistance to antibiotics. We learnt in Unit 2 how antibiotics kill bacteria, but now some antibiotics no longer work because the bacteria are resistant to them. This resistance is a good example of natural selection. Sometimes, at random, mutations occur when bacterial DNA is replicated. These mutations may have any effect (and most will be fatal), but just occasionally a mutation occurs that makes that bacterium resistant to an antibiotic. For example the mutation might modify an enzyme so that it can bind and hydrolyse penicillin – it is a penicillinase enzyme. So this cell is now resistant to penicillin. What happens next? Imagine the mutation happened in a bacterial cell living in your gut. The mutated cell will reproduce by binary fission and pass on its resistance gene to its offspring, forming a new strain of bacteria in your gut. If there is no antibiotic present in your gut (most likely) this mutated strain may well die out due to competition with all the other bacteria, and the mutation will be lost again. However, if you are taking penicillin, then penicillin will be present in the bacteria's environment, and these mutated cells are now at a selective advantage: the antibiotic kills all the normal bacterial cells, leaving only the mutant cells alive. These cells can then reproduce rapidly without competition and will colonise the whole environment. The mutant cells have been selected by the environment and so the frequency of the resistance allele in the population will increase. Remember that the original mutation is a random event, not caused by the presence of the antibiotic, but the spread of the allele is due to selection by an antibiotic-rich environment. There are now so many strains of antibiotic-resistant bacteria that it is getting more difficult to treat disease. One of the most famous is MRSA (methicillin-resistant Staphylococcus aureus), a bacterium responsible for a variety of diseases from staphylococcal food poisoning to toxic shock syndrome, and now resistant to penicillin, methicillin and vancomycin. These bacteria are effectively untreatable at present. The best solution is to minimise the use of antibiotics so that the resistant strain has no selective advantage, and may die out. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 16 Lactose tolerance in humans. Some people are lactose intolerant, and feel ill (including diarrhoea and vomiting) when they drink milk. In fact globally most human adults are lactose intolerant and this is the normal condition: lactose tolerance in adults is a mutation. All infant mammals make lactase to digest lactose in their mother’s milk, and they all stop producing lactase after they are weaned (its production is switched off at about age four in most humans). Around 10,000 years ago humans gradually changed from being mainly hunter-gatherers to being mainly farmers, and for the first time animal milk was available as a food source. Humans who, through a chance mutation, could drink milk without feeling ill were at an advantage, as they could supplement their normal diet with milk in harsh times (and farming was very unreliable in the early days). By natural selection they survived and their genes spread in their populations. As a result, in human societies that adopted pastoral (animal) farming (such as most Europeans, northern Indians and some Africans), people are generally lactose tolerant today, while the rest (most Asians, Africans, native Americans and Australians) remain lactose intolerant as adults. HIV resistance in humans. The AIDS virus HIV first arose in human populations in the 1930s in West Africa, where it spread from primates through the practice of killing and eating “bush meat”. Since then it has gradually spread around the world. Why is HIV so fatal to humans, but has so little effect on chimps? It turns out that chimps are resistant because they have a protein (called CCL3) that stops HIV entering and infecting white blood cells. Humans have this protein too, and it seems that the more copies of the gene for CCL3 you have, the more resistant you are to HIV. Chimps have on average 11 copies of the CCL3 gene, African humans have on average 6 copies, and non-African humans have on average 2 copies. In Africa people who, by chance, have many copies are favoured and will reproduce, while those with few copies die young without reproducing. So natural selection in humans explains the frequency of the CCL3 gene. A thousand years in the future, if we have not developed a medical cure for HIV, the whole human population will probably have evolved to possess around 11 copies of CCL3. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 17 Speciation – The Origin of New Species We’ve seen how species can change through natural selection, but how does this change lead to new species? The simple answer is that new species are formed when an existing species splits into two separate groups. Remember the definition of a species: members of the same species can breed together to produce fertile offspring but cannot breed with members of other species. So for the two groups to become two different species they must be reproductively isolated, so that there is no mixing of genes between them If members of the two groups can still interbreed If interbreeding between the two groups is then there will be gene flow between them and they somehow prevented, then there is no gene flow and will not be reproductively isolated. They will remain the two groups are reproductively isolated. They members of the same species. could become different species. There are many ways that reproductive isolation can come about, but they are grouped into two methods: allopatric speciation and sympatric speciation. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 18 Allopatric Speciation Allopatric speciation happens when two populations of the same species become geographically separated (allopatric literally means “different fatherland”). This is by far the most common kind of speciation. 1. Start with an interbreeding population of one species. 2. The population becomes divided by a physical barrier such as water, mountains, desert, or just a large distance. This can happen in various ways: When some of the population migrates or is dispersed to a new area, such as an isolated island or the other side of a mountain or large river. The dispersal must be over an unusually large distance so that it is not repeated and the new group remains isolated. Land birds, insect and plant seeds can be carried unusually large distances in a storm and small animals can unintentionally “raft” across oceans on fallen trees. Isolated islands like Madagascar, Hawaii and the Galapagos were colonised this way. When the geography changes catastrophically e.g. an earthquake could create an impassable rift; the lava flow from a volcano could create an impassable barrier, rising sea level could create islands; or falling sea level could isolate lakes. When the geography changes gradually e.g. erosion could create a deep valley like the Grand Canyon; plate tectonic movements cause whole continents to move apart (which explains why similar species are found in South America and Africa). The isolated population could be as small as a few seeds or a single pregnant female. The populations must be reproductively isolated, so that there is no gene flow between the groups. 3. If the environments (abiotic or biotic) are different in the two places (and they almost certainly will be), then different characteristics will be selected by natural selection and the two populations will evolve differently. Even if the environments are similar, the populations may still change by random genetic drift, especially if the population is small (unit 10). The allele frequencies in the two populations will become different. 4. Much later, if the barrier is now removed and the two populations meet again, they are now so different that they can no longer interbreed. They therefore remain reproductively isolated and are two distinct species. They may both be different from the original species, if it still exists elsewhere. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 19 Sympatric Speciation Sympatric speciation happens when two populations of the same species become reproductively isolated even though they share the same geographical location (sympatric literally means “same fatherland”). It is much rarer than allopatric speciation. How can two groups of the same species in the same place be reproductively isolated? 1. Ecological isolation. Populations can become reproductively isolated if they develop different niches within the same area. A well-described example of this is the fruit fly Rhagoletis pomonella in the United States. The original species lives on hawthorn bushes, but a new population has arisen that feeds on apple trees instead. This new population arose from a mutant fly that was able to digest apples and now the population of “apple flies” has a new niche in apple orchards so are effectively isolated from the “hawthorn flies”. This isolation means the two populations are evolving independently and have already altered their breeding seasons to match the different fruiting seasons of the two plants. They have become two separate species in the same geographical area. 2. Behavioural isolation. Populations can become reproductively isolated if they develop different courtship behaviours. Normally courtship behaviour (such as plumage, dance displays and songs in birds) allows members of the same species to identify themselves and synchronise mating. Mutant birds with a different-coloured plumage will be reproductively isolated from other birds in the same area because they will not attract mates. 3. Temporal isolation. Populations can become reproductively isolated if the timing of their reproductive season changes. Examples include plants that flower at different times, insects that pupate at different times or mammals that come into oestrus at different times. 4. Mechanical isolation. Populations can become reproductively isolated if their anatomy or chemistry changes so that mating is impossible. For example plants can’t interbreed if their flowers are different shapes so the same insects can’t visit them to transfer pollen. As we saw in unit 3, pollen grains are stimulated to germinate on the stigma by particular chemicals that are unique to that species. If the chemicals on a plant stigma change, pollen will not germinate and that plant will be reproductively isolated (though it may be able to self-fertilise). 5. Genetic isolation. Populations can become reproductively isolated if their genes change so that embryos cannot develop, even if mating is possible. The chromosomes of the embryo may not replicate; mitosis may not take place correctly or genes required for embryo development may not be present. Mating does not lead to viable offspring, so the two populations are reproductively isolated. 6. Hybrid sterility. This is a particular example of genetic isolation, where a hybrid is born but is sterile, so can’t itself reproduce. This stops the flow of genes so the two parent groups are still genetically isolated. This is why the states that members of the same species can breed together to produce fertile offspring. A famous example of hybrid sterility is the mule. A mule is the offspring of a male donkey (n=31) and a female horse (n=32). Mules therefore have 63 chromosomes, which can’t form homologous pairs in meiosis, so mules can’t make gametes and are infertile. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 20 Summary of Speciation 1. A population becomes separated into two groups that are reproductively isolated, so that there is no gene flow between the groups. The isolation can be geographical (allopatric) or some other method (sympatric). 2. The two groups’ environments are different, so natural selection favours different characteristics. 3. The allele frequencies in the two groups will change in different ways. 4. Eventually the two populations will be unable to interbreed, so will be different species. Populations of the same species that are currently isolated are called subspecies (or sometimes breeds, varieties or races) and they may in time become distinct species, or they may remain an interbreeding single species. It is meaningless to say that one species is absolutely better than another species, only that it is better adapted to that particular environment. A species may be well-adapted to its environment, but if the environment changes, then the species must evolve or die. In either case the original species will become extinct. Since all environments change eventually, it is the fate of all species to become extinct (including our own). Deep Time and the Origin of Life It takes time to evolve 100 million species and it is now known that the earth is 4,600 million years old. Life (in the form of prokaryotic cells) arose quite quickly, and has existed for around 4,000 million years. These huge spans of time are almost impossible to comprehend, and are often referred to as deep time. This chart illustrates some of the events in the history of the Earth. No one knows how life arose in the first place, but the conditions in the early Earth were very different from now, and experiments have shown that biochemicals like amino acids and nucleotides could be synthesised from inorganic molecules under primordial conditions. We saw in unit 1 how lipid bilayers can form spontaneously, so perhaps that’s how cellular life arose. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 21 Biodiversity Biodiversity simply means the variety of all the life on Earth. The 1992 United Nations Earth Summit in Rio de Janeiro defined biodiversity as "the variability among living organisms from all sources, including, 'inter alia', terrestrial, marine, and other aquatic ecosystems, and the ecological complexes of which they are part: this includes diversity within species, between species and of ecosystems". This definition is adopted by the United Nations Convention on Biological Diversity. There are thus three levels of biodiversity: All three levels of biodiversity are important because all living organisms are inter-related and depend upon each other in numerous ways. All three levels are also linked, for example genetic diversity is necessary to maintain species diversity, and vice versa. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 22 Genetic Diversity The gene pool of a species is defined as all the genes in that species. Members of the same species all have the same genes, but different combinations of alleles. New alleles arise through mutation and existing alleles are recombined by meiosis and random fertilisation during sexual reproduction so that every individual within a species is genetically unique. Genetic diversity of a species is defined as the number of different alleles within a species’ gene pool. We can also talk about the genetic diversity of a particular gene, in which case it is the number of different alleles of that gene in a population. By using modern genome sequencing techniques on a sample of individuals in a population we can actually quantify the genetic diversity. Genetic diversity is important because it is the basis of evolution and survival of a species. A species with a high genetic diversity is likely to have some individuals with the characteristics required to survive a change in the environment, so some members of the species will survive. Low genetic diversity means a species will be unable to cope with environmental changes and so is more likely to become extinct. Genetic diversity is generally higher in large populations and lower in small populations. Genetic Erosion Genetic Erosion refers to the loss of genetic diversity in wild and domesticated species. Genetic diversity is dramatically reduced by selective breeding, since only a small number of alleles are selected. This means that all domesticated farm animals and crops have low genetic diversity and are susceptible to disease and other environmental changes. The issue is considered so serious that the United Nations Food and Agriculture Organization (FAO) has set up a Commission on Genetic Resources for Food and Agriculture to oversee the management of animal genetic resources worldwide. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 23 Species Diversity All the organisms living in a habitat are collectively called its community, and species diversity means the variety of species in a community. Species diversity is useful because it tell us about the complexity, quality and stability of an ecosystem. The simplest measurement is just to count the number of species in the samples - the species richness. However richness alone is not a good measure of diversity because it doesn’t take into account the size of each species population – its abundance. For example a wild meadow and a wheat field might both have 25 species, but in the meadow the species are equally abundant, while in the wheat field 95% of all the plants are the single species of wheat. A good measure of diversity takes into account the species richness and their abundance. One common measure is the Simpson Diversity Index (D): Simpson Diversity Index D N(N 1) n( n 1) where N = total number of individuals (total abundance) n = number of individuals in each species The higher the index, the higher the species diversity. A community where one species is dominant over others has a lower diversity than one where the species are more equitable. For example these two communities each have 100 individuals in 3 species: (a) species A B C total abundance 90 5 5 100 n(n-1) 8010 20 20 D= (100 × 99) = 1.23 8050 8050 (b) species abundance n(n-1) A 34 1122 (100 × 99) B 33 1056 D= = 3.06 3234 C 33 1056 total 100 3234 So (b) is more diverse than (a). A few dominant species tend to decrease the diversity index. Harsh habitats tend to have low species diversity, as only a few species are adapted to the harsh environment. Mild habitats support a high species diversity. The many plant species will lead to high productivity (due to a lot of photosynthesis), which will support a large, complex food web. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 24 Conservation Human activities are reducing biodiversity at all three levels. Ecosystem diversity is reduced by deforestation, mining and building; species diversity is reduced by farming, hunting and habitat destruction; and genetic diversity is reduced by selective breeding and competition with humans. Understanding our impact on biodiversity has led to conservation – the attempt to conserve biodiversity worldwide. Conservation applies to all three levels. The global gene pool is a resource for learning more about life on Earth, and some genes may be able to provide us with useful products for medicine and biotechnology. To maintain the gene pool we need to preserve species diversity and to conserve species diversity we must provide suitable niches for all species by preserving habitat diversity. Conservationists recognise that humans need to exploit the natural world in order to survive. So the aim of conservation today is not to preserve pristine untouched nature, but is the management of our environment to keep the land as a productive resource, but in a sustainable way that maintains biodiversity and will continue to do so in the future for all our descendants. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 25 Justifying Conservation Why is conservation important? There are ethical and economic reasons. Ethical reasons In conservation there are no simple answers and decisions are based on a balance between opposing views, for example: the needs of humans to use and exploit nature for our survival the needs of other animals to live their lives without human interference the needs of humans to enjoy the natural beauty of untouched nature the needs of our descendants to enjoy or use ecosystems as we do the needs of everyone on the planet to avoid catastrophes such as global warming or mass extinctions Economic reasons Conservation is expensive, and, in order to persuade governments and businesses to take an interest, the concept of Ecosystem Services has been devised. The aim of ecosystem services is to teach politicians and other non-scientists some basic ecology and make them more aware of the benefits of the natural world and so hopefully to encourage them to put effort and money into conserving them. Ecosystem services are grouped into four categories: 1. Supporting services. These include the basic functions of all ecosystems, such as nutrient cycling, primary production (photosynthesis), decay and soil formation. These functions underlie everything else. 2. Regulating services. These are also basic functions of all ecosystems, framed so as to emphasise their importance in regulating the natural world. They include the carbon cycle (including its impact on climate change); decay (including sewage treatment to provide clean water); predator-prey interactions (used to control pests and pathogens). 3. Provisioning services. These are all the useful products humans obtain from the natural world, including: food; water; raw materials for building, clothing and industry; minerals (including fossil fuels, metal ores, jewels and raw materials for the chemical industry); medicinal resources (including pharmaceuticals and microbes); genetic resources (i.e. genes that can be used in biotechnology); and energy (including biomass fuels, natural gas, hydro-electric power, etc.). 4. Cultural services. These are the non-material benefits nature provides for people, including recreation (e.g. sports and tourism); education and cultural (e.g. inspiration for literature or art). HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 26 In-Situ Conservation In-situ conservation means conserving whole natural ecosystems and the various species they contain. In practice this means setting up Protected Areas, such as National Parks. In-situ conservation automatically means protecting all three levels of biodiversity – ecosystem, species and genetic. The International Union for the Conservation of Nature (IUCN) oversees the organisation and classification of Protected Areas worldwide. Almost every country in the world has set up Protected Areas to conserve local habitats and their wildlife. There are over 161,000 protected areas in the world with more added daily, representing about 15% of the world's land surface area and 1% of the world's oceans. There are laws forbidding or controlling human activities like building, hunting, farming, mining, industry and other exploitation of Protected Areas, though the specific limitations vary enormously depending of the area. Tourism and education are generally encouraged, though with strict controls. In the UK Protected Areas include: National Parks (NP); Environmentally Sensitive Areas (ESA); Sites of Special Scientific Interest (SSSI); Marine Nature Reserves (MNR); National Nature Reserves (NNR); Local Nature Reserves; Ramsar Wetland Sites (RWS); and World Heritage Sites (WHS). There are 15 National Parks in the UK, and, in contrast to National Parks in other countries, considerable human activity is allowed in National Parks, including farming and towns. The aim is to allow economic development while still protecting the countryside. Advantages of in-situ conservation When a habitat is conserved the whole community is conserved with it, including invertebrates, plants, fungi and microbes. Large numbers of animals and plants can be conserved in-situ, with a correspondingly large genetic diversity. Young animals learn natural skills from families and social groups in their natural environment. Reserves are safe environments to re-introduce animals from captive (ex-situ) breeding programs. Reserves can be popular tourist destinations, which helps to fund them and to educate visitors. Disadvantages of in-situ conservation Many important protected areas are in poor countries, and it can be expensive to maintain and protect a large area. Commercial and political interests (e.g. poachers, loggers, farmers, miners) often compete with conservation interest, and often win. Tourist income can be limited as parks can be expensive to visit. HGS Biology A-level notes NCM/2/16 A Level Biology Unit 5 page 27 Ex-Situ Conservation Ex-situ conservation means conserving species away from their natural habitats. In practice this means collecting specimens in zoos, aquaria, botanical gardens, seed banks and gene banks. Zoos were originally established for entertainment, but now serve the more useful functions of education and conservation. International breeding programs allow endangered species to reproduce safely in captivity and, where possible, released into the wild. Zoos keep electronic studbooks containing genealogical and genetic data on their animals. These studbooks allow the best matings to be arranged between animals held in different zoos, to maximise genetic diversity. Endangered plants may be grown in botanical gardens, and can also be preserved in seed banks, where samples of seeds are dried and preserved cryogenically at -40°C. Large numbers of seeds can be preserved this way for centuries without losing their fertility. The Millennium Seed Bank (MSB), run by the Royal Botanic Gardens, Kew, currently (2015) holds nearly 2 billion seeds from 34,088 wild plant species. Their aim is to conserve the seeds from 75,000 species of plants (25% of known plants) by 2020, including all the UK’s native plants. There is now an attempt to preserve endangered animal species in gene banks, by storing embryos cryogenically. Advantages of ex-situ conservation Animals that endangered in the wild can be protected in zoos. We-managed breeding programs can maintain and even improve genetic diversity. Animals in zoos have a longer life expectancy than in the wild. Since zoos are cheap and easily-accessible, they attract large numbers of visitors, which helps to raise funds and provides an excellent opportunity to educate many people in the importance of conservation work. Disadvantages of ex-situ conservation Only a small number of animals and plants can be conserved ex-situ, with a correspondingly limited genetic diversity. The zoo environment can be small and unnatural for large animals and they do not have the same social interactions. Some of these limitations can be addressed in larger wildlife parks. Young animals do not learn natural skills from observing families and peers in their natural environment. HGS Biology A-level notes NCM/2/16