BIOL10010 Summary Notes PDF

BIOL10010 - SUMMARY NOTES 1.1: Understand the historical context that has led to our current understanding of evolution and classification of species. Early Thoughts on Classification: - Aristotle (384–322 BCE): One of the first to attempt a systematic classification of living organisms. He categorised animals based on their physical characteristics and habitats. - Carl Linnaeus (1707–1778): Developed the binomial nomenclature system, which is still in use today. His work, Systema Naturae, laid the foundation for modern taxonomy by grouping organisms based on shared physical traits. Pre-Darwinian Evolutionary Ideas: - Jean-Baptiste Lamarck (1744–1829): Proposed an early theory of evolution, suggesting that organisms could pass on traits acquired during their lifetime to their offspring (Lamarckism). This idea was later refuted but was significant in the history of evolutionary thought. Darwin and Natural Selection: - Charles Darwin (1809–1882): Published On the Origin of Species in 1859, introducing the theory of natural selection. Darwin proposed that species evolve over time due to the differential survival and reproduction of individuals with favourable traits. - Alfred Russel Wallace (1823–1913): Independently conceived the theory of evolution by natural selection. His work prompted Darwin to publish his own findings. The Modern Synthesis: - Early 20th Century: The modern synthesis integrates Darwinian evolution with Mendelian genetics. Key figures include: ○ Ronald Fisher, J.B.S. Haldane, and Sewall Wright: Developed the mathematical framework for population genetics. ○ Theodosius Dobzhansky: Published Genetics and the Origin of Species, which helped bridge the gap between genetics and evolution. ○ Ernst Mayr: Emphasised the importance of geographic isolation in the formation of new species. ○ George Gaylord Simpson: Applied evolutionary theory to the fossil record, emphasising the role of natural selection in shaping evolutionary history. Molecular Biology and Genetics: - James Watson and Francis Crick (1953): Discovered the structure of DNA, which provided a molecular basis for inheritance and variation. - Molecular Phylogenetics: The use of DNA sequences to reconstruct evolutionary relationships has revolutionised classification, leading to more accurate phylogenetic trees. Recent Developments: - Genomics: The sequencing of entire genomes has provided insights into the genetic basis of evolution and the relationships between species. - Evo-Devo (Evolutionary Developmental Biology): This field studies how changes in developmental processes contribute to evolutionary changes, offering explanations for the diversity of life forms. Impact on Classification: - Cladistics: Focuses on the branching patterns of evolution, classifying organisms based on common ancestry and evolutionary relationships rather than just physical similarities. - Three-Domain System: Proposed by Carl Woese, it divides life into three domains (Bacteria, Archaea, and Eukarya) based on genetic and molecular evidence. 1.2: Identify the three pillars of Darwin’s theory of Evolution: that species are not immutable, that species have diverged from common ancestors, and that natural selection shapes divergence. Darwin’s theory of evolution is founded on three key pillars: 1. Species Are Not Immutable: Darwin argued that species are not fixed and unchanging (immutable). Instead, they undergo gradual changes over time. This was a revolutionary idea because it challenged the prevailing belief in the static nature of species. Darwin observed variations within species and how these variations could be inherited by subsequent generations, leading to gradual change. 2. Common Descent: Darwin proposed that all species have diverged from common ancestors. This concept of common descent means that species that are similar share a more recent common ancestor, while species that are less similar share a more distant common ancestor. The branching pattern of descent resembles a tree, often referred to as the "Tree of Life." This idea implies that the diversity of life we see today has arisen from a single or a few original forms through a long process of divergence and speciation. 3. Natural Selection: Natural selection is the mechanism that Darwin proposed for how evolution occurs. It is based on the following observations: - Variation: Individuals within a species exhibit variations in traits. - Inheritance: Some of these variations are heritable and can be passed onto offspring. - Differential Survival and Reproduction: Because of limited resources, not all individuals survive and reproduce. Those with traits that are better suited to their environment are more likely to survive and reproduce. Over time, favourable traits become more common in the population, leading to adaptation and, ultimately, the evolution of new species. Natural selection acts on existing variation within a population, shaping the traits that increase an organism's fitness in its environment. These three pillars—species change over time, species share common ancestors, and natural selection drives the evolutionary process—form the foundation of Darwin’s theory of evolution, explaining the diversity and complexity of life on Earth. 1.3: Describe the features of a phylogeny. A phylogeny, also known as a phylogenetic tree, is a diagram that represents the evolutionary relationships among various biological species or entities based upon similarities and differences in their physical and/or genetic characteristics. Here are the key features of a phylogeny: 1. Root: The root of the tree represents the most recent common ancestor of all the entities in the phylogeny. It is the starting point of the tree and signifies the point at which the ancestral lineage splits into two or more descendant lineages. 2. Branches: Branches are lines that connect nodes, representing the evolutionary path from one ancestor to its descendants. The length of a branch can indicate the amount of evolutionary change or the time elapsed. 3. Nodes: Nodes are points where branches split. There are two types of nodes: - Internal Nodes: Represent common ancestors shared by the descendant lineages that diverge from that point. - Terminal Nodes (or Tips/Leaves): Represent the current species or entities being studied. These are the endpoints of the tree. 4. Clades: A clade, also known as a monophyletic group, includes a common ancestor and all of its descendants. Clades represent a single branch on the tree of life, highlighting groups that share a common evolutionary history. 5. Sister Groups: Sister groups are pairs of clades that emerge from the same node. They are each other's closest relatives, sharing an immediate common ancestor not shared by any other group. 6. Outgroup: An outgroup is a species or group of species that is used as a point of reference. It is outside the group of interest (the ingroup) but is related enough to provide a point of comparison for determining the ancestral and derived traits of the ingroup. 7. Polytomy: A polytomy is a node from which more than two branches emerge. This can indicate an unresolved pattern of divergence, where it is unclear how the descendants are related to each other, or it can represent a rapid radiation of multiple lineages from a common ancestor. 8. Branch Lengths; Branch lengths can represent different things depending on the tree: - Ultrametric Trees: Branch lengths are proportional to time. - Phylograms: Branch lengths are proportional to the amount of evolutionary change. 9. Labels and Annotations - Terminal nodes are often labelled with the names of the species or entities. - Internal nodes may be labelled with hypothetical ancestors or specific traits that define the divergence at that point. - Trees can also include annotations such as bootstrap values, which provide a measure of confidence in the inferred relationships. 2.1: Mutation creates variation that may be heritable. What is a Mutation? A mutation is a change in the DNA sequence of an organism. Mutations can occur in various ways, such as through errors during DNA replication, exposure to certain chemicals or radiation, or through viral infections. These changes can affect a single nucleotide (point mutations), larger sections of DNA (insertions, deletions, or duplications). Types of Mutations: 1. Point Mutations: Changes in a single nucleotide. - Silent Mutations: Do not change the amino acid sequence of a protein. - Missense Mutations: Change one amino acid in the protein, potentially altering its function. - Nonsense Mutations: Introduce a premature stop codon, leading to a truncated and usually nonfunctional protein. 2. Insertions and Deletions: Addition or loss of nucleotide sequences, which can result in frameshift mutations that alter the reading frame of a gene. 3. Duplication: A segment of DNA is copied and inserted into the genome, potentially leading to gene redundancy. 4. Inversions and Translocations: Segments of DNA are reversed or moved to new locations, potentially disrupting gene function. How Mutations Create Variation: Mutations introduce new genetic variations within a population. These variations can affect an organism's traits (phenotype) in different ways: - Neutral Mutations: Have no effect on the organism's fitness. - Beneficial Mutations: Provide some advantage to the organism, increasing its fitness. - Harmful Mutations: Decrease an organism's fitness, potentially leading to reduced survival or reproduction. Heritability of Mutations: For a mutation to contribute to evolution, it must be heritable. Heritable mutations occur in the germ cells (sperm and eggs) and can be passed on to the next generation. Mutations in somatic cells (body cells) are not inherited by offspring. Role of Mutations in Evolution: Mutations are the primary source of genetic variation, which is essential for the process of evolution. This variation provides the raw material upon which natural selection acts. Here’s how: 1. Genetic Diversity: Mutations increase the genetic diversity within a population, leading to a range of different traits. 2. Natural Selection: Different environmental pressures can favour certain mutations. Organisms with beneficial mutations are more likely to survive and reproduce, passing those mutations to their offspring. 3. Adaptation: Over time, the accumulation of beneficial mutations can lead to adaptations, where populations become better suited to their environments. 4. Speciation: The accumulation of genetic differences can eventually lead to the formation of new species, particularly if populations become isolated and undergo different selective pressures. 2.2: Genetic Drift is the random sampling of alleles across generations and is more influential in small populations. What is Genetic Drift? Genetic drift is a mechanism of evolution that refers to random changes in the frequency of alleles (different forms of a gene) within a population from one generation to the next. Unlike natural selection, which is driven by differential survival and reproduction based on traits, genetic drift occurs due to chance events. How Genetic Drift Works: In each generation, some individuals may, by chance, leave behind more offspring than others. These random events can cause certain alleles to become more common or completely disappear from the population, irrespective of their impact on survival or reproduction. Key Features of Genetic Drift 1. Random Sampling: Allele frequencies change purely by chance rather than by selective pressures. 2. Founder Effect: When a small group of individuals breaks off from a larger population to form a new population, the new population's genetic makeup may not be representative of the original population. This can lead to a high frequency of certain alleles and a loss of genetic diversity. 3. Bottleneck Effect: A sudden reduction in population size due to a catastrophic event (e.g., natural disasters, disease outbreaks) can result in a loss of genetic variation. The surviving population may have different allele frequencies than the original population, simply due to the random survival of individuals. 4. Fixation and Loss of Alleles: Over time, genetic drift can lead to the fixation of certain alleles (where an allele's frequency reaches 100%) and the loss of others (frequency reaches 0%). Influence of Population Size: Genetic drift has a more significant impact on small populations than on large ones for several reasons: 1. Reduced Genetic Variation: Small populations have less genetic variation to begin with, so random changes in allele frequencies can have a more pronounced effect. 2. Greater Fluctuations: In small populations, the random sampling of alleles can lead to larger fluctuations in allele frequencies from one generation to the next. 3. Faster Fixation or Loss: Alleles can become fixed or lost more quickly in small populations due to the higher impact of random events on the overall gene pool. Example of Genetic Drift: Imagine a small population of 10 rabbits with two alleles for fur colour: A (brown) and a (white). If, by chance, more brown rabbits reproduce than white ones in a particular generation, the frequency of the A allele will increase. If this happens over several generations, the white allele (a) might disappear entirely, not because it was less advantageous, but purely due to random chance. Long-Term Effects of Genetic Drift: - Reduced Genetic Diversity: Over time, genetic drift can reduce genetic diversity within a population, making it more vulnerable to environmental changes and diseases. - Population Divergence: In isolated populations, genetic drift can lead to divergence in allele frequencies, potentially contributing to the formation of new species (speciation). In summary, genetic drift is a stochastic process that can significantly influence the genetic makeup of populations, especially small ones. It operates through random sampling of alleles, leading to changes in allele frequencies that are not necessarily related to the adaptive value of the traits they encode. 2.3: Natural selection is a microevolutionary process that shapes the phenotypes of organisms to match their environment. What is Natural Selection? Natural selection is a process where individuals with certain heritable traits tend to survive and reproduce more successfully than others because those traits are better suited to their environment. Over time, this differential reproductive success leads to changes in the frequency of those traits in the population. How Natural Selection Works: 1. Variation: There must be variation in traits within a population. These variations are often due to genetic differences. 2. Inheritance: Traits must be heritable, meaning they can be passed down from parents to offspring. 3. Differential Survival and Reproduction: Individuals with traits that provide a survival or reproductive advantage are more likely to survive and reproduce. These advantageous traits become more common in the population over generations. Types of Natural Selection: 1. Stabilising Selection: Favours the average phenotype and selects against extreme variations. This type of selection reduces variation and tends to keep the population stable over time. - Example: Human birth weight, where low or high weights have higher mortality rates. 2. Directional Selection: Favours one extreme phenotype over others, causing a shift in the population’s trait distribution. - Example: The increase in antibiotic-resistant bacteria due to the use of antibiotics. 3. Disruptive Selection: Favours individuals at both extremes of the phenotypic range over intermediate phenotypes. This can lead to a bimodal distribution of traits and potentially contribute to speciation. - Example: Darwin’s finches, where beak sizes that are either very small or very large are favoured due to differing food sources. Natural selection shapes phenotypes through the following processes: 1. Adaptation: Traits that enhance an organism’s fitness (ability to survive and reproduce) in a particular environment become more common. Adaptations can be structural (e.g., the thick fur of Arctic animals), behavioural (e.g., migratory patterns in birds), or physiological (e.g., the ability of some plants to tolerate high salt concentrations). 2. Co-evolution: When two or more species exert selective pressures on each other, leading to adaptations in response to each other. This is common in predator-prey relationships, host-parasite interactions, and mutualistic relationships. - Example: The evolution of long proboscises in pollinators like moths to match the deep tubes of certain flowers. 3. Sexual Selection: A form of natural selection where individuals with certain traits are more likely to attract mates and reproduce. This can lead to pronounced differences between males and females (sexual dimorphism). - Example: The elaborate plumage of male peacocks, which attracts females. Microevolutionary Changes: Natural selection operates on the level of populations and causes microevolutionary changes, which are small-scale changes in allele frequencies within a population over a few generations. These changes can eventually lead to larger evolutionary patterns (macroevolution) over longer time scales, potentially resulting in the emergence of new species. Summary: Natural selection is a fundamental microevolutionary process that drives the adaptation of organisms to their environments. It operates through variation, inheritance, and differential reproductive success, leading to changes in the frequency of advantageous traits in a population. This process results in the development of phenotypes that are well-suited to specific environmental conditions, promoting survival and reproduction. 2.4: Non-random mating can, in some circumstances, alter allele frequency over generations. What is Non-Random Mating? Non-random mating occurs when individuals do not choose their mates randomly from the population. Instead, they select mates based on specific traits, behaviours, or other factors, which can influence which alleles are passed on to the next generation. Types of Non-Random Mating: Assortative Mating: Individuals prefer mates that are similar to themselves in certain traits. - Positive Assortative Mating: Mating with individuals that are similar (e.g., size, colour, behaviour). - Negative Assortative Mating: Mating with individuals that are different (e.g., opposite traits). Inbreeding: Mating between closely related individuals, leading to an increase in homozygosity and a decrease in heterozygosity within the population. - Example: Self-fertilisation in plants, or mating within a small isolated population. Outbreeding (or Outcrossing): Mating between unrelated or less closely related individuals, leading to an increase in genetic diversity and heterozygosity. Sexual Selection: A form of non-random mating where individuals choose mates based on traits that are perceived as desirable, often related to fitness and reproductive success. - Example: Female birds selecting males with bright plumage or elaborate courtship displays. Effects on Allele Frequencies: Non-random mating influences allele frequencies in various ways: Assortative Mating: - Positive Assortative Mating: Can increase the frequency of homozygous genotypes and reduce the frequency of heterozygous genotypes. This can lead to a reduction in genetic diversity within the population. - Negative Assortative Mating: Can increase the frequency of heterozygous genotypes, potentially maintaining or even increasing genetic diversity. Inbreeding: - Increases homozygosity, which can lead to inbreeding depression—a reduction in fitness due to the increased likelihood of expressing deleterious recessive alleles. - Can result in a change in allele frequencies if certain alleles become more common due to their presence in the limited gene pool. Outbreeding: - Increases heterozygosity and genetic diversity, which can enhance the population's ability to adapt to environmental changes. - Can introduce new alleles into the population, altering allele frequencies. Sexual Selection: - Can lead to changes in allele frequencies if certain traits that are favoured by mates become more common. This can result in sexual dimorphism, where males and females exhibit different traits. - Traits that are favoured by sexual selection may become exaggerated over generations. Example of Non-Random Mating Impact: Consider a population of flowers where some individuals have red petals (RR or Rr) and others have white petals (rr). If bees prefer red petals and these flowers are more likely to be pollinated, individuals with the R allele will have higher reproductive success. Over generations, the frequency of the R allele may increase in the population due to this non-random mating preference. 2.5: Gene flow describes the spread of genetic variation across geographical areas due to migration, hybridization or gamete dispersal. What is Gene Flow? Gene flow, also known as gene migration, is the movement of genetic material within and between populations. This process results in the spread of genetic variation across different geographical areas. Gene flow can occur through the migration of individuals, hybridization between populations, or dispersal of gametes. Mechanisms of Gene Flow: Migration - Description: Movement of individuals from one population to another where they interbreed, introducing new alleles into the population. - Example: Birds migrating between islands and breeding with local populations, introducing new genetic traits. Hybridization - Description: Interbreeding between individuals from different species or genetically distinct populations, resulting in hybrid offspring that carry genetic material from both parent populations. - Example: Hybrid plants resulting from the cross-pollination of different species, combining genetic material from both parents. Gamete Dispersal - Description: Movement of gametes (e.g., pollen, seeds, or sperm) across different populations, facilitating gene flow without the physical movement of individuals. - Example: Pollen being carried by wind or insects from one plant population to another, resulting in cross-pollination and genetic mixing. Effects of Gene Flow: Increase Genetic Variation - Gene flow introduces new alleles into a population, enhancing genetic diversity and potentially increasing the population's ability to adapt to changing environments. Reduce Genetic Differences Between Populations - Continuous gene flow between populations can homogenise allele frequencies, reducing genetic differentiation and making populations more similar genetically. Prevent Speciation - By maintaining genetic similarity between populations, gene flow can inhibit the divergence of populations and thus the formation of new species. Introduce Beneficial or Deleterious Alleles: Gene flow can introduce alleles that improve or decrease fitness, depending on environmental conditions and selective pressures. Examples of Gene Flow Animal Migration: Wildebeests in Africa migrate between regions, and their interbreeding with local populations introduces new genetic diversity. Human Migration: Historical and contemporary human migrations have led to gene flow between different ethnic groups, contributing to the genetic diversity of modern human populations. Plant Dispersal: Seeds carried by animals, wind, or water can germinate and grow in new areas, introducing new genetic material to local plant populations. 2.6: Recombination and independent assortment can create novel combinations of alleles at different loci. What is Recombination? Recombination is a process during meiosis where genetic material is exchanged between homologous chromosomes. This exchange occurs during prophase I of meiosis through a mechanism called crossing over, which results in chromosomes that contain a mix of alleles from both parent chromosomes. What is Independent Assortment? Independent assortment is a principle of genetics discovered by Gregor Mendel, stating that alleles of different genes are distributed independently of one another during the formation of gametes. This occurs because homologous chromosome pairs align randomly along the metaphase plate during meiosis I, leading to the random distribution of maternal and paternal chromosomes to the gametes. Mechanism of Recombination: 1. Crossing Over: During prophase I of meiosis, homologous chromosomes pair up and exchange segments of their genetic material. This creates new combinations of alleles on each chromosome. - Example: If a chromosome has alleles A and B on one chromatid and a and b on the homologous chromatid, crossing over can result in chromatids with combinations such as A and b, or a and B. 2. Chiasmata Formation: The points where chromosomes cross over and exchange genetic material are called chiasmata. Multiple chiasmata can form along the length of homologous chromosomes, increasing the number of possible allele combinations. Mechanism of Independent Assortment: 1. Random Alignment: During metaphase I of meiosis, homologous chromosome pairs align randomly along the metaphase plate. Each pair's orientation is independent of the orientation of other pairs. - Example: For a diploid organism with two pairs of chromosomes, the possible combinations of chromosomes in the gametes are AB, Ab, aB, and ab, assuming A and a are alleles on one chromosome pair and B and b are alleles on another pair. 2. Segregation into Gametes: The random alignment leads to the random segregation of maternal and paternal chromosomes into gametes, producing a variety of genetic combinations. Importance in Genetic Diversity: Recombination and independent assortment are crucial mechanisms for generating genetic diversity within populations. - Increased Variation: Novel combinations of alleles can result in new traits that may be beneficial, neutral, or deleterious. This variation is essential for natural selection. - Adaptation: Populations with genetic diversity are better equipped to adapt to changing environments, as they are more likely to have traits that are survival advantages. - Disease Resistance: Genetic diversity can enhance the overall health and resilience of a population by reducing the likelihood that all individuals will be susceptible to the same diseases. - Speciation: Over long periods, the accumulation of genetic differences through recombination and independent assortment can lead to the divergence of populations and the formation of new species. 3.1: Understand the significance of genetic dominance and be able to calculate Mendelian ratios using ‘Punnett squares’. Dominant alleles are those that mask the effect of another allele when both are present in an organism. They are usually represented by a capital letter (e.g., A). Recessive alleles are those that are masked by a dominant allele and only show their effect if both alleles are recessive. They are represented by a lowercase letter (e.g., a). Genotype: The genetic makeup of an organism; the combination of alleles (e.g., AA, Aa, aa). Phenotype: The physical expression of the genotype (e.g., having a dominant trait like brown eyes vs. a recessive trait like blue eyes). Example 1: Monohybrid Cross: Consider a trait controlled by a single gene with two alleles: A (dominant) and a (recessive). Parents' Genotype: Aa (heterozygous for both) A a A AA Aa a Aa aa → Genotype Ratio: 1 AA : 2 Aa : 1 aa → Phenotype Ratio: 3 dominant (AA and Aa) : 1 recessive (aa) Example 2: Dihybrid Cross. Consider two traits, each controlled by a different gene with two alleles. Assume: Trait 1: A (dominant) and a (recessive) Trait 2: B (dominant) and b (recessive) Parents' Genotype: AaBb x AaBb AB Ab aB ab AB AABB AABb AaBB AaBb Ab AABb AAbb AaBb Aabb aB AaBB AaBb aaBB aaBb ab AaBb Aabb aaBb aabb → Genotype Ratio: 1 AABB : 2 AABb : 1 AAbb : 2 AaBB : 4 AaBb : 2 Aabb : 1 aaBB : 2 aaBb : 1 aabb → Phenotype Ratio: 9 dominant for both traits (A_B_) : 3 dominant for A and recessive for b (A_bb) : 3 recessive for A and dominant for B (aaB_) : 1 recessive for both (aabb) Calculating Mendelian Ratios 1. Determine the genotypes of the parents. 2. Set up the Punnett square based on the parents' genotypes. 3. Fill in the Punnett square to find all possible genotypes of the offspring. 4. Count the occurrences of each genotype to determine the genotype ratio. 5. Determine the phenotype for each genotype and count the occurrences to determine the phenotype ratio. Practice Q: In pea plants, tall (T) is dominant over short (t), and yellow seeds (Y) are dominant over green seeds (y). Cross two plants that are heterozygous for both traits (TtYy x TtYy). Genotypes of Parents: TtYy x TtYy TY Ty tY ty TY TTYY TTYy TtYY TtYy Ty TTYy TTyy TtYy Ttyy tY TtYY TtYy ttYY ttYy ty TtYy Ttyy ttYy ttyy → Genotype Ratio: 1 TTYY : 2 TTYy : 1 TTyy : 2 TtYY : 4 TtYy : 2 Ttyy : 1 ttYY : 2 ttYy : 1 ttyy → Phenotype Ratio: 9 tall yellow : 3 tall green : 3 short yellow : 1 short green 3.2: Understand that the Hardy-Weinberg theorem provides the expected relationship between alleles, genotypes and phenotypes in diploid populations The Hardy-Weinberg theorem is a fundamental principle in population genetics that provides a mathematical model for predicting the genetic variation of a population at equilibrium. It describes the expected relationship between alleles, genotypes, and phenotypes in diploid populations under specific conditions. Conditions for Hardy-Weinberg Equilibrium: The Hardy-Weinberg equilibrium assumes that a population is not evolving and that the following conditions are met: 1. No Mutation: No new alleles are introduced into the gene pool. 2. Random Mating: All individuals have an equal chance of mating with each other, without any preference for specific genotypes. 3. No Natural Selection: All genotypes have equal chances of survival and reproduction. 4. Large Population Size: The population is large enough to prevent random genetic drift. 5. No Gene Flow: No migration occurs in or out of the population. Allele and Genotype Frequencies: In a diploid organism, each individual carries two alleles for each gene, one from each parent. Let’s denote: p: The frequency of the dominant allele (A) q: The frequency of the recessive allele (a) Since there are only two alleles, the sum of their frequencies is 1: p + q = 1 Hardy-Weinberg Equation: The Hardy-Weinberg equation relates allele frequencies to genotype 2 2 frequencies in a population: 𝑝 + 2𝑝𝑞 + 𝑞 = 1 Where: - p² : The frequency of homozygous dominant genotype (AA) - 2pq : The frequency of heterozygous genotype (Aa) - q² : The frequency of homozygous recessive genotype (aa) Understanding the Theorem: - Allele Frequencies: If you know the frequency of one allele, you can calculate the other: - q=1-p - p=1-q Genotype Frequencies: Using the Hardy-Weinberg equation, you can calculate the expected frequencies of each genotype in the population: - Frequency of AA = p² - Frequency of Aa = 2pq - Frequency of aa = q² Phenotype Frequencies: For traits where one allele is dominant over the other, the phenotypic frequencies can be derived from the genotype frequencies: - Frequency of dominant phenotype (AA or Aa) = p² + 2pq - Frequency of recessive phenotype (aa) = q² Example Calculation: Suppose we have a population where the frequency of the recessive allele (a) is 0.3 (q = 0.3). We can calculate the frequencies of the dominant allele (A), the genotypes, and the phenotypes. Calculate p: p = 1 − q = 1 − 0.3 = 0.7p = 1 - q = 1 - 0.3 = 0.7 Calculate genotype frequencies: - Frequency of AA = p² - (0.7)² = 0.49 - Frequency of Aa = 2pq = 2(0.7)(0.3) = 0.42 - Frequency of aa = q² = (0.3)² = 0.09 Calculate phenotype frequencies: Assuming A is completely dominant over a: - Frequency of dominant phenotype (AA or Aa) = p² + 2pq = 0.49 + 0.42 = 0.91 - Frequency of recessive phenotype (aa) = q² = 0.09 The Hardy-Weinberg theorem serves as a null hypothesis for studying genetic changes in populations. By comparing observed genetic data with expected frequencies under Hardy-Weinberg equilibrium, scientists can identify factors like natural selection, genetic drift, mutation, non-random mating, and gene flow that may be influencing the population. Understanding and applying the Hardy-Weinberg theorem allows researchers to: - Predict and understand the genetic structure of populations. - Study evolutionary processes and how they affect genetic variation. - Monitor changes in allele frequencies over time to identify evolutionary pressures. 3.3: Understand how deviations from Hardy-Weinberg expectations can reveal microevolutionary change. Factors Causing Deviations from Hardy-Weinberg Equilibrium Mutation: Changes in DNA sequence that introduce new alleles into a population. - Impact: Increases genetic variation. If mutation rates are significant, they can alter allele frequencies and cause deviations from Hardy-Weinberg expectations. Non-Random Mating: Individuals select mates based on certain traits, leading to assortative mating or inbreeding. - Impact: Increases homozygosity and reduces heterozygosity. This can shift genotype frequencies without changing allele frequencies, deviating from Hardy-Weinberg equilibrium. Natural Selection: Differential survival and reproduction of individuals based on their genetic traits. - Impact: Alters allele frequencies by increasing the frequency of advantageous alleles and decreasing the frequency of disadvantageous alleles, causing deviations from equilibrium. Genetic Drift: Random changes in allele frequencies, especially in small populations. - Impact: Can lead to significant fluctuations in allele frequencies over time, causing deviations from Hardy-Weinberg equilibrium due to the random nature of the changes. Gene Flow (Migration): Movement of individuals and their alleles between populations. - Impact: Introduces new alleles into a population or alters the frequencies of existing alleles, leading to deviations from equilibrium as the population's genetic structure changes. Detecting and Interpreting Deviations: Chi-Square Test - Usage: A statistical method to compare observed genotype frequencies with expected frequencies under Hardy-Weinberg equilibrium. - Interpretation: A significant chi-square value indicates that the population is not in Hardy-Weinberg equilibrium, suggesting the presence of evolutionary forces. Observed vs. Expected Frequencies - Method: Calculate the expected genotype frequencies using the Hardy-Weinberg equation and compare them to observed frequencies. - Interpretation: Discrepancies between observed and expected frequencies can point to specific factors (e.g., excess homozygosity suggesting inbreeding). Examples of Microevolutionary Changes: Industrial Melanism in Peppered Moths - Scenario: Before the industrial revolution, light-coloured moths were more common. During the industrial revolution, dark-coloured moths became more common due to pollution darkening tree bark. - Impact: Natural selection favoured the dark-coloured moths in polluted areas, altering allele frequencies and demonstrating microevolution. Sickle Cell Anaemia and Malaria - Scenario: The sickle cell allele (HbS) provides a survival advantage against malaria in heterozygous individuals (HbA/HbS) but causes sickle cell anaemia in homozygous individuals (HbS/HbS). - Impact: In regions where malaria is prevalent, the frequency of the HbS allele is higher than expected under Hardy-Weinberg equilibrium due to natural selection favouring the heterozygous genotype. Founder Effect - Scenario: A small group of individuals colonise a new area, carrying a subset of the genetic variation from the original population. - Impact: Genetic drift in the small founder population can lead to significant deviations from Hardy-Weinberg equilibrium and rapid changes in allele frequencies. 4.1: Distinguish between prezygotic isolation and postzygotic isolation, and list the reproductive barriers can lead to speciation Speciation is the process by which populations evolve to become distinct species. Reproductive isolation, which prevents gene flow between populations, is crucial for speciation. Reproductive barriers can be classified into two main categories: prezygotic and postzygotic isolation. Prezygotic Isolation: Prezygotic isolation prevents fertilisation and the formation of a zygote. This type of isolation includes various mechanisms that occur before mating or fertilisation. Temporal Isolation: Different species breed at different times (seasons, times of day, or years). - Example: Two species of frogs may inhabit the same area but one breeds in early spring while the other breeds in late summer. Habitat Isolation: Species live in the same region but occupy different habitats, so they rarely encounter each other. - Example: Two species of snakes might live in the same geographic area, but one prefers aquatic environments while the other prefers terrestrial environments. Behavioural Isolation: Differences in mating behaviours prevent species from recognizing each other as potential mates. - Example: Different species of birds have distinct courtship rituals, such as unique songs or dances. Mechanical Isolation: Physical differences in reproductive organs prevent successful mating. - Example: Flowers of different species may have structures that require specific pollinators, preventing cross-pollination. Gametic Isolation: Even if mating occurs, the gametes (sperm and egg) of different species are incompatible and cannot fuse to form a zygote. - Example: In sea urchins, species-specific proteins on the surface of the eggs and sperm prevent fertilisation by different species. Postzygotic Isolation: Postzygotic isolation occurs after fertilisation and affects the viability or fertility of the resulting hybrid offspring. This type of isolation includes mechanisms that reduce the survival and reproductive success of hybrids. Hybrid Inviability: Hybrids fail to develop properly and do not reach reproductive age. - Example: Crosses between different species of salamanders result in embryos that fail to develop fully and die early in development. Hybrid Sterility: Hybrids are sterile and cannot produce offspring. - Example: Mules, which are hybrids between horses and donkeys, are typically sterile and cannot reproduce. Hybrid Breakdown: Hybrids are viable and fertile, but their offspring (the second generation) are inviable or sterile. - Example: Some species of cultivated rice can produce fertile hybrids, but when these hybrids breed, the next generation shows reduced fertility or inviability. Reproductive Barriers Leading to Speciation: The accumulation of reproductive barriers can lead to speciation, which can occur through various mechanisms: Allopatric Speciation: Occurs when populations are geographically separated, leading to genetic divergence and the evolution of reproductive barriers. - Example: The formation of a mountain range can separate populations of a species, leading to allopatric speciation. Sympatric Speciation: Occurs within a single geographic area when reproductive barriers arise without geographic separation. - Example: Polyploidy in plants, where a sudden doubling of chromosome number creates reproductive isolation. Parapatric Speciation: Occurs when populations are adjacent to each other and there is limited gene flow between them, leading to divergence and speciation. - Example: Grass species that grow on mine tailings with heavy metal tolerance can speciate from nearby populations that do not tolerate heavy metals. Peripatric Speciation: A form of allopatric speciation where a small population becomes isolated at the edge of a larger population. - Example: Island species often evolve through peripatric speciation when a small group colonises a new island. 4.2: Recognise hybridisation between different species can occasionally occur, resulting in gene flow and exchange of alleles. Hybridization between different species can sometimes occur, leading to gene flow and the exchange of alleles. This process can have significant evolutionary implications, contributing to genetic diversity and potentially facilitating adaptation. - Hybridization is the interbreeding between individuals from different species or genetically distinct populations. When hybridization occurs, it can result in the formation of hybrids, which can carry alleles from both parent species. - Gene Flow through hybridization introduces genetic material from one species into the gene pool of another, potentially influencing the genetic makeup and evolutionary trajectory of the recipient species. Conditions Favouring Hybridization - Overlap in Geographic Range: Species must come into contact in the same area. - Similar Breeding Times: Overlapping breeding seasons increase the likelihood of hybridization. - Compatible Reproductive Structures: Physical compatibility of reproductive organs facilitates mating. - Behavioural Similarities: Similar mating behaviours can reduce prezygotic barriers. Effects of Hybridization: Increased Genetic Diversity: - Hybridization can introduce new alleles into a population, increasing genetic diversity and providing material for natural selection to act upon. - Example: Hybrid plants often exhibit increased vigour and resistance to diseases, a phenomenon known as hybrid vigour or heterosis. Adaptive Introgression: - Beneficial alleles from one species can introgress (become incorporated) into another species, enhancing adaptation to specific environments. - Example: Certain populations of wild mice have acquired pesticide resistance alleles through hybridization with domestic mice. Creation of New Species: - In some cases, hybrids can become reproductively isolated from both parent species and evolve into a new species (hybrid speciation). - Example: Helianthus anomalus, a sunflower species, originated from hybridization between Helianthus annuus and Helianthus petiolaris. Genetic Swamping: - Extensive hybridization can lead to genetic swamping, where the genetic identity of one species is diluted or replaced by another species. - Example: Invasive species can hybridise with native species, leading to a loss of genetic integrity in the native species. Examples of Hybridization: - Plants: Many plants hybridise easily, and hybridization has been a significant factor in the evolution of numerous plant species. Example: Wheat is a result of multiple hybridization events between different grass species. - Animals: While less common than in plants, animal hybridization does occur and can have important ecological and evolutionary consequences. Example: The coywolf, a hybrid of coyotes, wolves, and domestic dogs, exhibits traits from all three species and has adapted to various environments. - Birds: Hybridization is relatively common among birds, especially in areas where ranges overlap. Example: The European goldfinch and the canary can hybridise, producing fertile offspring. 4.3: Identify that balancing selection maintains genetic diversity in a population by keeping alleles at frequencies higher than expected by chance. Balancing selection is a type of natural selection that maintains genetic diversity in a population by keeping multiple alleles at higher frequencies than would be expected by chance alone. Unlike directional selection, which favours one allele over others, balancing selection promotes the persistence of genetic variation within a population. Mechanisms of Balancing Selection: Heterozygote Advantage (Overdominance): Heterozygous individuals (those with two different alleles) have a higher fitness than either of the homozygous forms (those with two identical alleles). - Example: The sickle cell allele (HbS) provides resistance to malaria when present in the heterozygous state (HbA/HbS). Individuals with one sickle cell allele and one normal allele have a survival advantage in malaria-endemic regions compared to those with two normal alleles (HbA/HbA) or two sickle cell alleles (HbS/HbS). Frequency-Dependent Selection: The fitness of an allele depends on its frequency in the population. Often, rare alleles have a selective advantage precisely because they are rare. - Example: In a population of predators and prey, if a particular prey phenotype becomes too common, predators may more easily recognize and capture individuals with that phenotype. As a result, rare phenotypes have a survival advantage, maintaining genetic diversity. Environmental Heterogeneity: Different alleles confer advantages in different environments or under different conditions, leading to the maintenance of multiple alleles in a population. - Example: In a geographically diverse environment, plants may have different alleles that confer advantages in different microhabitats, such as wet versus dry areas. These environmental differences help maintain multiple alleles within the overall population. Examples of Balancing Selection: Human Leukocyte Antigen (HLA) Genes: HLA genes are involved in immune system function, and their diversity allows for better recognition of a wide range of pathogens. - Mechanism: Heterozygote advantage and frequency-dependent selection both contribute to maintaining high levels of HLA diversity. Individuals with a diverse set of HLA alleles can recognize and respond to a broader array of pathogens. Self-Incompatibility in Plants: Many flowering plants have mechanisms to prevent self-fertilisation, promoting cross-pollination and genetic diversity. - Mechanism: Self-incompatibility alleles are maintained at high frequencies because they ensure that plants mate with genetically different individuals, enhancing genetic diversity and reducing the risk of inbreeding. MHC Genes in Vertebrates: Major Histocompatibility Complex (MHC) genes play a crucial role in immune system function by presenting pathogen-derived peptides to immune cells. - Mechanism: Balancing selection acts on MHC genes through heterozygote advantage and frequency-dependent selection, maintaining a high level of genetic diversity to effectively combat a wide range of pathogens. Balancing selection is vital for maintaining genetic diversity within populations, which in turn enhances adaptability and resilience to changing environments and emerging threats. By preserving multiple alleles, populations are better equipped to respond to environmental pressures, pathogens, and other selective forces, contributing to long-term survival. 5.1: Compare the mechanisms of inter-sexual and intra-sexual selection to explain their roles in the evolution of sexually dimorphic traits. Inter-sexual Selection (Mate Choice): Occurs when individuals of one sex (typically females) select mates based on certain traits. The traits favoured are often indicators of good genes, health, or the ability to provide resources. - Examples: Bright plumage in male peacocks, elaborate courtship dances in birds. Intra-sexual Selection (Mate Competition): Occurs when individuals of one sex (typically males) compete among themselves for access to mates. This competition can involve direct physical contests, displays of strength, or other forms of rivalry. - Examples: Antlers in male deer, large body size in male gorillas, tusks in walruses. Roles of Inter-sexual Selection: - Drives the evolution of traits that are attractive to the opposite sex. - These traits often have no direct survival benefit and may even be costly to the individual (e.g., bright colours making them more visible to predators). - Sexual dimorphism results from females consistently selecting mates with certain traits, leading to exaggerated features in males over generations. Roles of Intra-sexual Selection: - Drives the evolution of traits that enhance the ability of an individual to outcompete others of the same sex. - These traits often confer a survival advantage in the context of competition but may also be costly in terms of energy or risk of injury. - Sexual dimorphism arises because males that are more successful in competition tend to pass on their genes, leading to the evolution of larger, stronger, or more aggressive males. Interaction Between the Two - In many species, both inter-sexual and intra-sexual selection act simultaneously. - For example, a male peacock's tail is favoured by inter-sexual selection, but his ability to display it effectively can also involve intra-sexual competition. - Similarly, in species where males compete for territory (intra-sexual selection), the winners may then be chosen by females based on their territorial success (inter-sexual selection). Evolutionary Outcomes: Sexual Dimorphism: The combined effects of inter- and intra-sexual selection often lead to pronounced differences between males and females of a species. - Peacocks and Peahens: Males have large, colourful tails (inter-sexual selection) and compete to display them most effectively (intra-sexual selection). - Lions: Males have manes, which may help in combat with other males (intra-sexual selection) and also signal health and vigour to females (inter-sexual selection). 5.2: Describe the mechanisms driving coevolution, including the red queen hypothesis. Coevolution: Coevolution refers to the process by which two or more species influence each other's evolution over time. This reciprocal evolutionary change is driven by interactions such as predation, parasitism, competition, and mutualism. Key Mechanisms Driving Coevolution: Mutualism: Occurs when two species benefit from their interaction, leading to reciprocal evolutionary changes that enhance this relationship. - Example: The relationship between flowering plants and their pollinators (e.g., bees). Flowers may evolve traits like specific colours or scents to attract particular pollinators, while pollinators may evolve traits that allow them to extract nectar more efficiently. Antagonism: This involves interactions where one species benefits at the expense of the other, such as in predator-prey or host-parasite relationships. - Example: In a predator-prey relationship, as prey species evolve better defence mechanisms (e.g., camouflage or speed), predators may evolve better hunting strategies (e.g., improved senses or speed). Competitive Coevolution: Occurs when species compete for the same resources. The evolutionary arms race between competing species leads to adaptations that help them outcompete their rivals. - Example: Different plant species may evolve different root structures or flowering times to minimise competition for nutrients or pollinators. The Red Queen Hypothesis: The Red Queen Hypothesis is named after a character in Lewis Carroll's Through the Looking-Glass who states, "It takes all the running you can do, to keep in the same place." - In evolutionary biology, this hypothesis suggests that species must continuously adapt and evolve not just for reproductive advantage but simply to survive while pitted against ever-evolving opposing organisms. Application in Coevolution: In a coevolutionary context, the Red Queen Hypothesis implies that species are in a constant evolutionary arms race. For instance, as prey species evolve better defences, predators must evolve more effective means of overcoming those defences just to maintain their current level of success. - This hypothesis is particularly relevant in host-parasite relationships. As hosts evolve better immune responses, parasites evolve new ways to evade or suppress these defences, leading to a continuous cycle of adaptation. Examples of Coevolutionary Relationships: - Host-Parasite Coevolution: Example: The relationship between humans and the influenza virus. As the human immune system evolves to recognize and fight off the virus, the virus evolves new mutations to evade the immune response, leading to the need for annual flu vaccines. - Plant-Herbivore Coevolution: Example: Some plants produce toxins to deter herbivores. In response, some herbivores evolve resistance to these toxins, which may lead plants to evolve even stronger defences. Outcomes of Coevolution - Reciprocal Adaptation: Both species in a coevolutionary relationship may develop adaptations that enhance their interaction—either as mutual partners or as antagonists. - Increased Specialisation: Coevolution can lead to increased specialisation, where species become highly adapted to each other. This can result in mutual dependence (as in many pollinator-plant relationships) or highly specific parasitic relationships. 5.2: Recognize adaptations and counter-adaptations within coevolving interactions. Adaptations and Counter-Adaptations in Coevolving Interactions: In coevolving relationships, species often develop adaptations in response to each other, leading to a dynamic cycle of adaptation and counter-adaptation. This evolutionary "arms race" results in a series of escalating changes in both species. Predator-Prey Interactions: Adaptation: Prey Camouflage: Many prey species evolve camouflage to blend into their environment, making it harder for predators to detect them. Example: The peppered moth, which evolved darker coloration during the Industrial Revolution to match soot-covered trees, making it less visible to predators. Counter-Adaptation: Predator Improved Vision: In response, some predators may develop sharper vision or better pattern recognition to detect camouflaged prey. Example: Some birds of prey, like hawks, have evolved exceptional visual acuity to spot camouflaged or hidden prey from a distance. Host-Parasite Interactions Adaptation: - Host Immune Response: Hosts often evolve stronger immune systems or specific defences to resist or eliminate parasites. - Example: The evolution of the human immune system to recognize and fight off different strains of viruses and bacteria. Counter-Adaptation: - Parasite Immune Evasion: Parasites may evolve mechanisms to evade or suppress the host’s immune system, such as antigenic variation. - Example: The malaria parasite (Plasmodium) can change the proteins on its surface to avoid detection by the host’s immune system. Plant-Herbivore Interactions: Adaptation: - Plant Chemical Defences: Many plants produce toxic chemicals to deter herbivores Example: Milkweed plants produce cardenolides, which are toxic to most insects. Counter-Adaptation: - Herbivore Detoxification: Some herbivores evolve mechanisms to detoxify or tolerate the chemicals produced by plants. - Example: The monarch butterfly caterpillar has evolved the ability to consume milkweed despite its toxicity, and even uses the toxins to make itself poisonous to predators. Mutualistic Interactions: Adaptation: Pollinator Specialisation: Certain pollinators evolve specific traits that allow them to access nectar from flowers with particular shapes or sizes. - Example: The long proboscis of the hawk moth, which is adapted to extract nectar from deep, tubular flowers. Counter-Adaptation: Plant Flower Morphology: In response, plants may evolve flowers that match the morphology of their preferred pollinators, ensuring efficient pollination. - Example: Some orchids have evolved flowers that resemble the shape of female insects, attracting male insects that attempt to mate with the flower, thus ensuring pollination. Competitive Interactions: Adaptation: Resource Partitioning: Competing species may evolve to exploit different resources or niches to reduce direct competition. - Example: Different bird species might evolve different beak shapes to exploit different types of food, such as seeds, insects, or nectar. Counter-Adaptation: Niche Expansion: In response, a competing species might expand its niche or develop new foraging strategies to access a broader range of resources. - Example: Some finches in the Galápagos Islands have evolved to exploit various food sources, leading to a diversity of beak shapes within the same population. Evolutionary Arms Race - Coevolution often results in an evolutionary arms race, where adaptations in one species drive counter-adaptations in the other, leading to continuous cycles of evolutionary change. 5.3: Interpret and explain examples of coevolution between mutualistically and antagonistically interacting species. Coevolution can be observed in both mutualistic (where both species benefit) and antagonistic (where one species benefits at the expense of the other) interactions. Below are some examples illustrating how coevolution shapes these relationships. Mutualistic Coevolution - Example 1: Pollinators and Flowering Plants - Interaction: Many flowering plants and their pollinators (e.g., bees, butterflies, hummingbirds) engage in mutualistic relationships, where the plant provides nectar as a food source, and the pollinator facilitates the plant's reproduction by transferring pollen from one flower to another. Coevolutionary Adaptations: - Flower Adaptations: Flowers may evolve specific shapes, colours, and scents that attract their preferred pollinators. For instance, some flowers have evolved tube-like structures that are only accessible to pollinators with long proboscises. - Pollinator Adaptations: Pollinators, in turn, may evolve physical traits like long proboscises to access nectar deep within flowers, or specific behaviours that enhance their efficiency in pollinating these plants. Example: The relationship between the yucca plant and the yucca moth is a classic example. The moth not only pollinates the yucca plant but also lays its eggs in the plant's flowers. The moth larvae feed on some of the developing seeds, but enough seeds remain to propagate the plant, ensuring mutual benefit. Example 2: Mycorrhizal Fungi and Plants - Interaction: Mycorrhizal fungi form symbiotic associations with the roots of many plants, enhancing the plant’s nutrient uptake (especially phosphorus) while receiving carbohydrates produced by the plant through photosynthesis. Coevolutionary Adaptations: - Plant Adaptations: Plants may evolve root structures that are more conducive to fungal colonisation, maximising nutrient exchange. - Fungal Adaptations: Fungi may evolve more efficient mechanisms to extract nutrients from the soil and transfer them to the plant, enhancing the mutualistic relationship. - Example: Over millions of years, many plant species have become so dependent on mycorrhizal fungi that they cannot survive without them, demonstrating a deep coevolutionary relationship. Antagonistic Coevolution - Example 1: Predator-Prey Dynamics - Interaction: In predator-prey relationships, predators and prey are in a constant evolutionary arms race. Prey species evolve defences to avoid being eaten, while predators evolve strategies to overcome these defences. Coevolutionary Adaptations: - Prey Adaptations: Prey may develop physical defences (e.g., spines, shells), chemical defences (e.g., toxins), or behavioural strategies (e.g., herding, camouflage). - Predator Adaptations: Predators may evolve enhanced senses, speed, or specialised hunting techniques to counteract prey defences. - Example: The evolutionary relationship between cheetahs and gazelles showcases this coevolution. Gazelles have evolved incredible speed and agility to evade predators, while cheetahs have evolved to be one of the fastest land animals to catch swift prey. Example 2: Host-Parasite Relationships - Interaction: In host-parasite relationships, the parasite benefits at the expense of the host. This interaction drives the host to evolve defences, while the parasite evolves strategies to bypass those defences. Coevolutionary Adaptations: - Host Adaptations: Hosts may develop immune responses, physical barriers, or behaviours that reduce parasite transmission or impact. - Parasite Adaptations: Parasites may evolve mechanisms to evade the host’s immune system, increase their reproductive rate, or manipulate the host’s behaviour to enhance transmission. - Example: The relationship between humans and the malaria parasite (Plasmodium) is a well-known example. The human immune system has evolved to recognize and fight the parasite, but the parasite has countered by evolving rapid antigenic variation, making it difficult for the immune system to detect and eliminate it. Summary of Coevolutionary Outcomes: - Mutualistic Interactions: Coevolution in mutualistic relationships often leads to increased specialisation and interdependence between species. Both partners adapt to enhance the benefits they receive from the relationship, which can lead to highly specialised interactions. - Antagonistic Interactions: In antagonistic relationships, coevolution drives an ongoing evolutionary arms race, with each species developing adaptations and counter-adaptations in response to the other. This dynamic can result in rapid evolutionary changes and increased specialisation in defence and offence mechanisms. 6.1: Character change in molecular phylogenies can occur in a clock like fashion and that enables us to put time stamps on evolutionary events. Molecular phylogenies are diagrams or "trees" that represent the evolutionary relationships between different species or genes, typically DNA, RNA, or protein sequences. Character Change: refers to mutations or alterations in the nucleotide or amino acid sequences over time. These changes accumulate as species diverge from a common ancestor. The Molecular Clock Hypothesis: The molecular clock is a concept that suggests genetic mutations accumulate at a relatively constant rate over time. - Clock-like Fashion: If the rate of molecular change (e.g., mutation rate) is relatively constant, then the number of changes (or differences) between two sequences can be used to estimate the time since they diverged from a common ancestor. - This rate of change acts like a "clock," providing a method to put time stamps on evolutionary events. Application of the Molecular Clock: - Calibrating the Clock: The molecular clock needs to be calibrated with known data, such as fossil records or geological events, which provide a timeline for certain evolutionary divergences. Once calibrated, this clock can be applied to other lineages to estimate the timing of evolutionary events. - Estimating Divergence Times: By comparing the number of genetic differences between species and applying the molecular clock, scientists can estimate when two species last shared a common ancestor. - For example, the molecular clock has been used to estimate the divergence times between humans and our closest relatives, the chimpanzees, as well as to date the origin of major evolutionary events like the appearance of vertebrates or flowering plants. Constant Rate Assumption: The molecular clock assumes a constant rate of molecular change over time, which may not always hold true across all lineages or genes. Some genes or organisms may evolve faster or slower due to various factors such as natural selection, genetic drift, or changes in population size. Rate Variation: Different genes or regions of the genome may evolve at different rates. For instance, non-coding regions might accumulate mutations more rapidly than coding regions due to less selective pressure. - Techniques like relaxed molecular clocks account for these variations by allowing the rate of molecular change to vary across different branches of the phylogenetic tree. Case Study: HIV Evolution: The molecular clock has been applied to study the evolution of the HIV virus, allowing researchers to estimate when the virus first entered the human population. By analysing the genetic sequences of HIV samples from different times, scientists can track how the virus has evolved and spread, helping to date the origin of the pandemic. Implications for Evolutionary Biology: - Dating Speciation Events: The ability to put time stamps on evolutionary events helps in understanding the timing and sequence of speciation events, migration patterns, and the origins of various traits. - Understanding Evolutionary Rates: The molecular clock provides insights into the rates of evolution across different lineages and can highlight periods of rapid evolution. 6.2: Appraise molecular genetic basis of natural selection in microevolutionary case studies. Microevolution refers to evolutionary changes within a population or species over a relatively short period. These changes often result from natural selection acting on genetic variation. By examining the molecular genetic basis of natural selection in specific case studies, we can understand how genetic changes lead to adaptation and evolution. Case Study: Antibiotic Resistance in Bacteria: Antibiotic resistance is a well-known example of microevolution, where bacterial populations evolve to survive in the presence of antibiotics. Molecular Basis: - Genetic Mutations: Antibiotic resistance often arises due to mutations in bacterial DNA that confer survival advantages under antibiotic pressure. For instance, mutations in the gene coding for the bacterial ribosome can prevent antibiotics like streptomycin from binding effectively, allowing the bacteria to survive. - Horizontal Gene Transfer: Bacteria can also acquire resistance genes from other bacteria through horizontal gene transfer (HGT). For example, the bla gene encodes beta-lactamase, an enzyme that deactivates penicillin, and can be transferred between bacteria via plasmids. Natural Selection: - Selective Pressure: In the presence of antibiotics, bacteria with resistance genes have a survival advantage and reproduce more successfully than non-resistant strains. Over time, the frequency of resistant bacteria increases in the population. Outcome: - Rapid Evolution: This process leads to the rapid evolution of antibiotic-resistant strains, making some infections harder to treat and demonstrating how natural selection operates on genetic variations at the molecular level. Case Study: Lactase Persistence in Humans: Lactase persistence, the ability to digest lactose into adulthood, is a trait that has evolved in certain human populations, particularly those with a history of dairy farming. Molecular Basis: - Genetic Variation: The persistence of lactase production is associated with mutations in the regulatory region of the LCT gene, which encodes lactase, the enzyme that breaks down lactose. - A specific SNP (single nucleotide polymorphism), such as -13910 C>T, in the regulatory region enhances the expression of the LCT gene in adults. Natural Selection: - Selective Advantage: In populations where dairy farming was prevalent, individuals with lactase persistence could digest lactose and obtain nutritional benefits from milk, giving them a survival and reproductive advantage. - This selective advantage led to an increase in the frequency of the lactase persistence allele in these populations over time. Outcome: Geographic Distribution: Lactase persistence is common in populations of European and some African ancestries, reflecting the history of dairy farming and natural selection acting on the LCT gene. Case Study: Sickle Cell Anaemia and Malaria Resistance: The sickle cell trait, caused by a mutation in the haemoglobin gene (HBB), is an example of a genetic adaptation to malaria in regions where the disease is endemic. Genetic Mutation: The sickle cell mutation results from a single nucleotide change in the HBB gene, leading to the production of abnormal haemoglobin (HbS). When two copies of the mutation are inherited, it causes sickle cell disease. However, individuals with one copy of the mutation (heterozygotes) have a mix of normal haemoglobin (HbA) and sickle haemoglobin (HbS). Natural Selection: - Selective Advantage: Heterozygous individuals with the sickle cell trait (HbAS) have a survival advantage in malaria-endemic regions because the presence of HbS in their red blood cells provides some protection against the malaria parasite Plasmodium falciparum. - As a result, the frequency of the HbS allele is maintained at higher levels in these populations despite the detrimental effects of sickle cell disease in homozygotes. Outcome: - Balanced Polymorphism: The persistence of the sickle cell allele in malaria-endemic regions is an example of balanced polymorphism, where natural selection maintains multiple alleles in a population due to the heterozygote advantage. Case Study: Beak Size in Darwin's Finches: Darwin’s finches in the Galápagos Islands exhibit variation in beak size and shape, which has evolved in response to the availability of different food sources. Molecular Basis: - Genetic Regulation: Variation in beak size among finch species is partly due to differences in the expression of the BMP4 and Calmodulin genes, which regulate beak development. - Higher levels of BMP4 expression are associated with broader, stronger beaks suitable for cracking large seeds, while Calmodulin influences the length of the beak. Natural Selection: - Selective Pressure: During periods of drought, when only large seeds are available, finches with larger, stronger beaks have a survival advantage because they can access food, leading to an increase in beak size in the population. - Conversely, when smaller seeds are abundant, finches with smaller beaks may be favoured. Outcome: - Adaptive Radiation: This process has led to adaptive radiation, where different finch species have evolved to occupy various ecological niches, each with beak shapes and sizes adapted to their specific feeding habits. 6.3: An appreciation that genetic analysis can help us understand demographic process that shape population structures. Genetic Markers and Population Structure: Genetic Markers: These are specific sequences of DNA that can be used to study genetic variation within and between populations. Common genetic markers include microsatellites, single nucleotide polymorphisms (SNPs), and mitochondrial DNA (mtDNA). Population Structure: The distribution of genetic variation across a population can reveal its structure, such as the presence of subpopulations, levels of inbreeding, and patterns of genetic differentiation. Demographic Processes Inferred from Genetic Data: Migration and Gene Flow: - Gene Flow: Gene flow refers to the transfer of genetic material between populations through migration. Genetic analysis can help detect the extent of gene flow and identify the sources and destinations of migrating individuals. - Case Study: Human Migration Patterns: Analysis of genetic variation in human populations, such as the distribution of certain SNPs, has provided insights into historical migration patterns, including the out-of-Africa migration of modern humans and the subsequent colonisation of other continents. - Impact on Population Structure: Gene flow can reduce genetic differences between populations, leading to increased genetic homogeneity. Conversely, restricted gene flow can lead to greater genetic differentiation and the development of distinct subpopulations. Population Bottlenecks and Founder Effects: - Bottlenecks: A population bottleneck occurs when a population's size is drastically reduced, leading to a loss of genetic diversity. Genetic analysis can identify signatures of bottlenecks, such as reduced heterozygosity and loss of rare alleles. - Founder Effects: When a small group of individuals colonise a new area, the genetic diversity of the new population is limited to that of the founders. This can lead to a population that is genetically distinct from the original population. - Case Study: Cheetah Bottleneck: Genetic analysis of cheetahs has revealed extremely low genetic diversity, a result of a historical population bottleneck. This lack of diversity has implications for the species' vulnerability to disease and environmental changes. - Impact on Population Structure: Bottlenecks and founder effects can lead to significant changes in population structure, often resulting in populations with lower genetic diversity and increased susceptibility to genetic drift. Population Expansion and Contraction: - Population Expansion: When a population expands, genetic diversity can increase as new mutations arise and spread. Genetic analysis can detect signs of recent expansion, such as an excess of rare alleles and specific patterns in the distribution of genetic variation. - Population Contraction: Contraction, or a decrease in population size, can lead to a reduction in genetic diversity and an increase in genetic drift. Genetic analysis can identify contractions by detecting a decrease in genetic diversity and an increase in inbreeding. - Case Study: Post-Ice Age Expansion: Genetic evidence from various species shows patterns of population expansion following the last Ice Age, as species recolonized areas that had been uninhabitable during glacial periods. - Impact on Population Structure: Expansion can lead to increased genetic diversity and the formation of new subpopulations, while contraction can reduce genetic diversity and increase genetic differentiation between populations. Inbreeding and Genetic Drift: - Inbreeding: Inbreeding occurs when individuals within a population mate with close relatives, leading to an increase in homozygosity and the potential expression of deleterious alleles. Genetic analysis can detect inbreeding by examining levels of heterozygosity and identifying regions of the genome with low genetic diversity. - Genetic Drift: Genetic drift is the random fluctuation of allele frequencies in a population, particularly in small populations. Genetic drift can lead to the fixation of alleles and a reduction in genetic diversity. - Case Study: Island Populations: Island populations, which are often small and isolated, are particularly susceptible to genetic drift and inbreeding. Genetic analysis of island species has shown high levels of genetic differentiation and reduced genetic diversity compared to mainland populations. - Impact on Population Structure: Inbreeding can lead to an increase in genetic homogeneity within populations, while genetic drift can lead to divergence between populations, contributing to the formation of distinct population structures. Tools and Methods for Genetic Analysis: - Population Genetics Software: Tools like STRUCTURE, ADMIXTURE, and FST calculations are used to analyse genetic data and infer population structure, admixture, and levels of genetic differentiation. - Phylogeography: Phylogeography combines genetic data with geographical information to study the historical processes that have shaped the distribution of genetic variation within species. - Coalescent Theory: Coalescent theory is a mathematical framework used to trace the ancestry of gene copies back to a common ancestor, helping to infer demographic history and population dynamics. Implications for Conservation and Management: - Conservation Genetics: Understanding the genetic structure of populations is crucial for conservation efforts. Populations with low genetic diversity may be at risk of inbreeding depression and may have reduced adaptive potential, making them more vulnerable to environmental changes. - Management of Endangered Species: Genetic analysis can inform the management of endangered species by identifying genetically distinct populations that require separate conservation strategies or by guiding the design of breeding programs to maintain genetic diversity. TOPIC 2: PHYSIOLOGY 7.1: Define and contrast anaerobic and aerobic respiration. Anaerobic Respiration: - Definition: Anaerobic respiration is a type of respiration that occurs in the absence of oxygen. During this process, cells break down glucose (or other molecules) to produce energy without using oxygen. - Process: In anaerobic respiration, glucose is only partially broken down. This results in the production of lactic acid in animals (lactic acid fermentation) or ethanol and carbon dioxide in plants and some microorganisms (alcoholic fermentation). - Energy Yield: Anaerobic respiration produces less energy (only 2 ATP molecules per glucose molecule) compared to aerobic respiration. - Location: It typically occurs in the cytoplasm of cells. - By-products: The by-products of anaerobic respiration are lactic acid or ethanol and carbon dioxide, depending on the organism. Aerobic Respiration: - Definition: Aerobic respiration is a type of respiration that occurs in the presence of oxygen. This process involves the complete breakdown of glucose into carbon dioxide and water, producing energy. - Process: Aerobic respiration includes glycolysis, the Krebs cycle, and the electron transport chain, leading to the complete oxidation of glucose. - Energy Yield: It produces a high amount of energy, yielding about 36-38 ATP molecules per glucose molecule. - Location: Aerobic respiration takes place in the mitochondria of cells. - By-products: The by-products are carbon dioxide and water. Key Contrasts: - Oxygen Requirement: Anaerobic respiration occurs without oxygen, while aerobic respiration requires oxygen. - Energy Efficiency: Aerobic respiration is more efficient, producing significantly more ATP than anaerobic respiration. - End Products: The end products differ, with anaerobic respiration producing lactic acid or ethanol, while aerobic respiration produces carbon dioxide and water. - Location in the Cell: Anaerobic respiration happens in the cytoplasm, whereas aerobic respiration occurs in the mitochondria. 7.1: Explain why gas exchange is important and what features of gas exchange surfaces increase the rates of diffusion. Importance of Gas Exchange: Gas exchange is a crucial biological process in which organisms exchange gases with their environment, particularly oxygen (O₂) and carbon dioxide (CO₂). It is vital for several reasons: 1. Oxygen Supply for Respiration: Oxygen is essential for aerobic respiration, a process by which cells produce energy (ATP). Without an adequate supply of oxygen, cells cannot generate the energy needed for survival and function. 2. Removal of Carbon Dioxide: Carbon dioxide is a by-product of cellular respiration. If it accumulates in the body, it can lower the pH of blood and tissues, leading to harmful conditions such as acidosis. Gas exchange ensures the removal of CO₂, maintaining the body's pH balance. 3. Maintaining Homeostasis: Efficient gas exchange helps maintain homeostasis by regulating the levels of gases in the blood, ensuring that cells receive enough oxygen while removing excess CO₂. Features of Gas Exchange Surfaces that Increase Diffusion Rates: 1. Large Surface Area: Gas exchange surfaces, such as alveoli in the lungs or gill filaments in fish, have a large surface area relative to the volume of the organism. This allows more gas molecules to diffuse across the surface simultaneously, increasing the rate of gas exchange. 2. Thin Membranes: Gas exchange surfaces are typically only one or a few cells thick, creating a short diffusion distance. This thinness allows gases to quickly diffuse across the surface, speeding up the exchange process. 3. Moist Surfaces: The presence of moisture on gas exchange surfaces facilitates the diffusion of gases. Gases like oxygen must dissolve in water before they can diffuse across cell membranes, so a moist surface ensures efficient diffusion. 4. Rich Blood Supply (Vascularization): Gas exchange surfaces are well-supplied with blood vessels (capillaries) in animals. This ensures that oxygen is rapidly transported away from the exchange surface and carbon dioxide is brought to it, maintaining a steep concentration gradient, which is essential for efficient diffusion. 5. Ventilation Mechanisms: In animals, mechanisms such as breathing or water flow over gills help maintain a high concentration of oxygen and a low concentration of carbon dioxide at the gas exchange surface. This steep concentration gradient drives faster diffusion. 6. Permeability to Gases: The membranes at the gas exchange surfaces are highly permeable to gases, allowing oxygen and carbon dioxide to easily diffuse across them. 7.2: Describe the main structure used by plants and fungi for gaseous exchange. The main structures used by plants and fungi for gaseous exchange are specialised to facilitate the exchange of gases like oxygen (O₂) and carbon dioxide (CO₂) with their environment. Gaseous Exchange in Plants: Stomata: - Location: Stomata are small openings typically found on the underside of leaves, though they can also be present on stems and other green parts of the plant. - Structure: Each stoma (singular of stomata) is surrounded by two guard cells that control its opening and closing. - Function: Stomata allow gases like oxygen and carbon dioxide to diffuse in and out of the leaf. During photosynthesis, carbon dioxide enters the leaf through the stomata, and oxygen, a by-product of photosynthesis, exits through them. Stomata also facilitates the release of water vapour in a process called transpiration. Lenticels: - Location: Lenticels are small, spongy openings found on the bark of woody stems and roots. - Structure: Lenticels appear as slightly raised areas on the surface of the plant and have a loose arrangement of cells, creating air spaces for gas exchange. - Function: Lenticels allow the exchange of gases between the internal tissues of the stem or root and the external environment, enabling respiration even in parts of the plant covered by bark. Spongy Mesophyll: - Location: Located within the leaf, particularly in the lower part of the leaf beneath the palisade mesophyll. - Structure: The spongy mesophyll consists of loosely arranged cells with large air spaces between them. - Function: These air spaces allow gases like oxygen and carbon dioxide to diffuse throughout the leaf, aiding in both photosynthesis and respiration. Gaseous Exchange in Fungi: Hyphae: - Location: Hyphae are the long, thread-like structures that make up the body of a fungus, collectively forming the mycelium. - Structure: Hyphae have a large surface area relative to their volume, which facilitates efficient gas exchange. - Function: The thin walls of hyphae allow gases like oxygen to diffuse into the cells for respiration and carbon dioxide to diffuse out. Fungi typically rely on diffusion for gas exchange, as they lack specialised structures like stomata. Pores (in Fungal Fruiting Bodies): - Location: In some fungi, especially those with fruiting bodies like mushrooms, pores or openings in the structure (e.g., in the gills or the cap) can assist with gas exchange. - Function: These pores allow the exchange of gases between the fruiting body and the environment, ensuring that the cells within receive enough oxygen for respiration. In both plants and fungi, these structures are adapted to maximise the efficiency of gaseous exchange, enabling them to maintain their metabolic processes such as photosynthesis, respiration, and growth. 7.2: Explain other features of plants and fungi that assist with the process. Additional Features in Plants: Thin Leaves: - Feature: Many plants have leaves that are thin and flat, with a large surface area relative to their volume. - Function: This structure minimises the distance that gases need to diffuse, making it easier for carbon dioxide to reach photosynthetic cells and for oxygen to exit the leaf. Air Spaces in Leaf Tissue: - Feature: The spongy mesophyll in leaves contains large intercellular air spaces. - Function: These air spaces allow for the free movement of gases within the leaf, facilitating the distribution of carbon dioxide to photosynthesizing cells and the removal of oxygen produced during photosynthesis. Cuticle: - Feature: The cuticle is a waxy layer that covers the epidermis of leaves and stems. - Function: While primarily serving to reduce water loss, the cuticle is usually thin or absent near stomata, ensuring that gas exchange is not hindered while still protecting the plant from dehydration. Active Transport in Guard Cells: - Feature: Guard cells surrounding stomata can actively pump ions in and out to control their opening and closing. - Function: By regulating the opening of stomata, plants can optimise gas exchange according to environmental conditions, such as reducing water loss during drought or maximising CO₂ intake during daylight for photosynthesis. Root Hairs: - Feature: Root hairs are tiny extensions of root epidermal cells. - Function: Although primarily involved in water and nutrient absorption, root hairs increase the surface area of roots, which can also facilitate the absorption of oxygen from the soil for root respiration. Additional Features in Fungi: Large Surface Area of Mycelium: - Feature: The mycelium, composed of a network of hyphae, often spreads extensively within the substrate (e.g., soil, decaying matter). - Function: This large surface area relative to volume maximises exposure to oxygen and allows efficient gas exchange across the entire mycelium, supporting aerobic respiration. Thin Hyphal Walls: - Feature: The walls of hyphae are generally thin and permeable. - Function: This structure allows gases to diffuse easily into and out of the hyphae, facilitating respiration throughout the fungal body. High Permeability of Hyphal Cell Walls: - Feature: The cell walls of fungal hyphae are highly permeable to gases. - Function: This permeability ensures that oxygen can readily diffuse into the cells and carbon dioxide can diffuse out, supporting the metabolic needs of the fungus. Fruiting Body Structure: - Feature: The structure of fungal fruiting bodies, such as mushrooms, often includes gills, pores, or other features that create large surface areas. - Function: These structures allow for efficient gas exchange during the production of spores, which is a metabolically active process requiring significant oxygen. Saprophytic Lifestyle: - Feature: Many fungi are saprophytes, meaning they live on dead or decaying organic matter, which is often rich in oxygen. - Function: This lifestyle ensures that fungi have access to the oxygen they need for respiration, as decaying matter has plenty of air spaces where gases can be exchanged. 7.3: Describe the main structures of the gas exchange systems of animals. 1. Lungs (Mammals, Birds, Reptiles, and Amphibians): - Structure: Lungs are the primary gas exchange organs in most terrestrial vertebrates, including mammals, birds, reptiles, and amphibians. They are typically composed of multiple lobes and are located within the thoracic cavity. Alveoli (Mammals): - Structure: Mammalian lungs contain tiny air sacs called alveoli. Alveoli are spherical structures with extremely thin walls made up of a single layer of epithelial cells. - Function: Alveoli provide a large surface area for gas exchange. Oxygen diffuses from the alveoli into the surrounding capillaries, while carbon dioxide diffuses from the blood into the alveoli to be exhaled. Parabronchi (Birds): - Structure: In birds, lungs contain structures called parabronchi, which are tiny air tubes that allow for a continuous flow of air. - Function: Parabronchi enables a highly efficient gas exchange process. As air flows in one direction through the lungs, blood flows in the opposite direction, maintaining a strong concentration gradient for gas exchange (called cross-current exchange). Pulmonary Capillaries: - Structure: Surrounding the alveoli (in mammals) or parabronchi (in birds) are dense networks of capillaries. - Function: These capillaries allow for close contact between blood and the gas exchange surface, facilitating rapid diffusion of gases. 2. Gills (Fish and Aquatic Invertebrates): - Structure: Gills are the primary respiratory organs in most aquatic animals, including fish and some invertebrates like crustaceans and mollusks. Gills are often located on either side of the head and are composed of gill arches, gill filaments, and lamellae. Gill Filaments: - Structure: Each gill arch supports multiple gill filaments, which are long, thin structures that extend outward into the water. - Function: Gill filaments increase the surface area available for gas exchange. Lamellae: - Structure: Gill filaments are covered with lamellae, which are thin, plate-like structures that contain capillaries. - Function: Lamellae provide an even greater surface area for gas exchange and allow for efficient diffusion of oxygen from the water into the blood and carbon dioxide from the blood into the water. Countercurrent Exchange System: - Structure: Blood flows through the lamellae in the opposite direction to the flow of water. - Function: This countercurrent exchange system maintains a strong concentration gradient for oxygen and carbon dioxide, maximising the efficiency of gas exchange. 3. Tracheal System (Insects): - Structure: Insects have a unique gas exchange system called the tracheal system, which consists of a network of tubes called tracheae and smaller tubes called tracheoles. Spiracles: - Structure: Spiracles are small openings on the body surface of an insect that lead to the tracheal system. - Function: Spiracles allow air to enter and exit the tracheal system. They can open and close to regulate gas exchange and minimise water loss. Tracheae and Tracheoles: - Structure: Tracheae are larger tubes that branch into finer tubes called tracheoles, which extend throughout the insect's body. - Function: Tracheoles deliver oxygen directly to the insect's tissues and cells, and carbon dioxide diffuses back out through the same network. This direct delivery system bypasses the need for a circulatory system to transport gases. 4. Skin (Some Amphibians and Earthworms): - Structure: In some animals, particularly amphibians like frogs and some annelids like earthworms, the skin is an important gas exchange organ. Moist Surface: - Structure: The skin of these animals is kept moist by mucus or environmental water. - Function: A moist surface is essential for the diffusion of gases, as oxygen and carbon dioxide must dissolve in water to diffuse across cell membranes. Rich Capillary Network: - Structure: Just beneath the skin, there is a dense network of capillaries. - Function: The close proximity of blood vessels to the surface allows for efficient gas exchange directly through the skin. 5. Book Lungs (Arachnids, such as Spiders and Scorpions): - Structure: Book lungs are respiratory organs found in arachnids. They consist of stacked, leaf-like structures called lamellae contained within an internal chamber. Lamellae: - Structure: The lamellae are thin, plate-like structures arranged in parallel, similar to the pages of a book. - Function: Air enters the chamber through a small opening (spiracle) and diffuses across the lamellae, where gas exchange occurs between the air and the blood within the lamellae. 7.3: Compare and contrast different gas exchange structures that exist in animals that extract gases from water versus air. Gas exchange structures in animals have evolved to optimise the extraction of gases from either water or air, depending on their environment. While both types of structures serve the same fundamental purpose—facilitating the exchange of oxygen (O₂) and carbon dioxide (CO₂)—their designs are adapted to the specific properties of water or air as the medium for gas exchange. Below is a comparison and contrast of these structures: Gas Exchange in Water: Gills (Fish and Aquatic Invertebrates): Structure: Gills are often composed of gill arches, gill filaments, and lamellae. They are typically external or located in a cavity that allows water to flow over them. Adaptation to Water: - Countercurrent Exchange: Gills use a countercurrent exchange mechanism, where water flows over the gills in one direction while blood flows in the opposite direction through the lamellae. This maintains a strong concentration gradient for oxygen and carbon dioxide, maximising the efficiency of gas exchange. - Large Surface Area: The numerous lamellae provide a large surface area for gas exchange, which is crucial because water contains much less oxygen than air. - Water Flow: Many aquatic animals actively pump water over their gills or position themselves in currents to ensure a continuous flow of water, providing oxygen. Efficiency: - Gills are highly efficient in extracting oxygen from water, but this efficiency is necessary due to the lower oxygen content in water compared to air. The dense nature of water also supports the structure of gills, allowing them to remain open and functional. Gas Exchange in Air: Lungs, Tracheal Systems, and Skin: Lungs (Mammals, Birds, Reptiles, and Amphibians): - Structure: Lungs are internal structures, composed of a complex network of tubes (bronchi, bronchioles) and air sacs (alveoli in mammals). In birds, the lungs are connected to air sacs, and gas exchange occurs in parabronchi. Adaptation to Air: - High Oxygen Content: Air contains a higher concentration of oxygen compared to water, which allows lungs to extract oxygen without the need for the large surface area in gills. - Ventilation: Lungs are ventilated by the movement of air in and out through breathing, which is less energy-intensive compared to the constant water flow required in gills. - Moist Internal Environment: Even though air is the medium, the alveoli in lungs are moist, which aids in the diffusion of gases across the alveolar membranes. Efficiency: - Lungs are highly efficient at extracting oxygen from air due to the higher oxygen content and the use of a circulatory system to transport gases to and from tissues. Tracheal System (Insects): - Structure: The tracheal system consists of a network of tubes (tracheae) that open to the outside through spiracles and branch into finer tubes (tracheoles) that directly reach body cells. Adaptation to Air: - Direct Delivery: The tracheal system directly delivers oxygen to cells without the need for a circulatory system, making it highly efficient for small-bodied terrestrial animals. - Spiracle Regu

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