Evolution Notes

Evolution Introduction

  • Evolution: Change over a period of time.
  • Modern organisms descended from ancient organisms.
  • Species change over time, adapting to their environment.
  • Study of evolution provides insights into:
    • Nature of life
    • Origins of life
    • Diversity of living beings
    • Similarities and differences in structure and function

Origin of Life: Theories

  • Theories are uncertain.
  • Major theories:
    1. Special Creation:
      • Supported by most religions and civilizations.
      • Life was created by a supernatural power at a particular time.
      • Theological approach focuses on the reason behind creation.
      • Scientific theories concentrate on how beings came into existence. There is no intellectual conflict between scientific and theological theories.
    2. Spontaneous Creation:
      • Life arose from non-living matter.
      • Popular theory, coexisted with special creation.
      • Aristotle believed life arose from pre-existing parents and spontaneous generation due to natural forces.
      • Disproved by scientific advancements.
      • Redi (1688): Observed that worms in decaying flesh were fly larvae, supported biogenesis (life from pre-existing life).
      • Spallanzani (1765): Vegetables didn't support growth after heat treatment and sealing.
      • Louis Pasteur: Disapproved spontaneous creation with experiments.
    3. Cosmozoan:
      • Life on earth has an extraterrestrial origin.
      • Arrhenius (1908): Cosmozoan or panspermia theory.
      • Assumed advanced civilizations on other planets infected Earth.
    4. Biochemical Evolution:
      • Life arose as per chemical and physical laws.
      • Oparin (1923): Simple compounds (nitrides, oxides, ammonia, methane) formed complex organic compounds under electric charges and UV rays.
      • Accumulation in oceans resulted in primeval soup.
      • Miller-Urey experiment (1953):
        • Stanley Miller (graduate student of Harold Urey) designed an apparatus to simulate early Earth conditions.
        • Included a spark chamber with electrodes, a flask for boiling, and a condenser.
        • Used methane, ammonia, hydrogen, and water.
        • Exposed to electric discharges, followed by condensation and boiling for 18 days.
        • Identified 15 amino acids, organic acids, ribose sugar, and adenine.

Theories of Evolution

Lamarck's Theory of Evolution

  • Jean Baptiste Lamarck: French naturalist.
  • Theory based on inheritance of acquired characteristics.
  • Use and disuse of abilities led to organisms gaining or losing abilities.
  • Examples:
    • Blacksmith's strong biceps muscles.
    • Snakes' elongated body and loss of limbs due to creeping.
    • Flat fishes' eyes migrating to the upper side.
    • Giraffe's lengthening neck due to reaching high leaves.
  • Importance on the animal's needs to form organs for adaptation.
  • Discredited because use or disuse doesn't transfer abilities to the next generation.
  • August Weismann's experiments: Cut off tails of rats for 80 generations, but tailless offspring were never born.

Theory of Natural Selection

  • Charles Darwin:

    • H.M.S. Beagle voyage in June 1831.
    • Observed differences in species on different islands in the Galapagos.
    • Observed completely different species exclusive to some islands.
    • Provided logical insight into how and why evolution occurred.

  • Natural selection:

    • Differences in organisms' abilities to survive and reproduce based on inheritable traits.
    • Thomas Malthus: More offspring are produced than can survive due to limited resources.
    • Survival depends on hereditary factors.
    • Individuals with favorable traits survive and reproduce.
    • Individuals with less favorable traits are eliminated.
    • Gradual change in the population, accumulating favorable variations over time.

  • Wallace and Darwin:

    • Wallace wrote to Darwin about his ideas on natural selection.
    • Darwin published his ideas.
    • Darwin and Wallace agreed to publish simultaneous papers.
    • Darwin's book, The Origin of Species, was an immediate sensation.

  • Darwin's views on evolution:

    “Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

Observed Cases of Natural Selection

  1. Insect Resistance to Insecticides:
    • Some insects resistant to insecticides survive and flourish.
    • Result of genetic variability in the population.
    • Beneficial genetic makeup survives.
  2. Bacterial Resistance to Antibiotics:
    • Some bacteria have antibiotic resistance genes in their plasmid.
    • Survive in the presence of antibiotics.
    • Bacteria transfer the plasmid to other bacteria by transformation.
  3. Increased Frequency of Sickle Cell Anemia in Africans:
    • Hemoglobin (Hb) transports oxygen.
    • Discovery of hemoglobin S (HbS) by Linus Pauling.
    • Vernon Ingram identified abnormality in the amino acid sequence of the β-globin chain (β6Glu→Val).
    • Normal concave cells become sickled.
    • β6Glu→Valβ6Glu→Val
  • Sickle cell anemia:
    • Produced due to mutation in the beta chain of hemoglobin.
    • Sickle shape obstructs blood flow, causing blood blockage in capillaries and extreme pain.
    • The gene for the beta chain of hemoglobin in normal RBCs codes for glutamic acid, which is hydrophilic.
    • Mutation changes the codon on the mRNA to code for valine instead of glutamic acid. Valine is hydrophobic.
    • The abnormal haemoglobin of SCD: HbS
    • Presence of hydrophobic valine in the beta chain acts as a hydrophobic pocket to which the other hydrophobic residues (phenylalanine and leucine) in the beta chain bind.
    • At low oxygen pressure, deoxy-HbS polymerises and gets organised in long polymer fibres that deform, stiffen, and weaken the red blood cell
    • Recessively inherited, follows Mendelian pattern.
    • Normal cell phenotype is dominant.
    • Heterozygous individuals show sickled phenotype under low oxygen conditions.
    • Sickle cell eventually bursts and dies. Sickling of cells reduces the oxygen carrying capacity of RBCs.
    • Sickle cell and resistance to malaria:
      • Reduced oxygen carrying capacity gives protection against malaria.
      • Malaria pathogen completes early life cycle in RBCs, requires oxygen.
      • Heterozygous and homozygous recessive individuals are protected from malaria.
      • Natural selection evident in the distribution of sickle cell trait in malaria-prone areas.
      • Suggests evolution used sickle cell trait as protection against malaria.
  • Loophole in Darwin's theory:
    • Couldn't explain inheritance of traits.
    • Couldn't explain vestigial organs.
    • Couldn't explain overspecialization of structures (antlers, tusks).

Importance of Population Genetics

  • Natural selection is understood by observing changes in a population.
  • Evolution results from change in gene frequencies within a population.
  • Important to describe events that change gene frequencies.
  • Biologists didn't understand genetic details of natural selection until transmission genetics (early 1900s).
  • Rediscovery of Gregor Mendel's publications paved the way for the development of population genetics in the 1930s and 1940s.
  • Modern Synthesis: Principles of evolution integrated with modern genetics.
  • Biologists study mechanistic aspects of evolution and broad evolutionary patterns.

Evidence for Evolution

  1. Fossil Evidence:
    • Preserved remains of ancient organisms.
    • Found in sap, mineral replacement, ice, or traces (footprints, molds).
    • Demonstrate intermediate forms, showing evolution.
  2. Embryonic Evidence:
    • Embryonic stages of various organisms share similar features.
    • Duck and chick embryos both have webbed feet.
    • Chick embryo loses webbed feet later since it's not needed.
  3. Genetic Evidence:
    • DNA sequences in a gene family are usually different.
    • Multiple copies of a gene allow selection of mutations that provide advantages.
    • Useful mutated gene is selected for in succeeding generations.
    • If the mutated gene is a total loss (pseudogene), the functional copy is still there to carry out its role.
    • The presence of pseudogenes is evidence of evolution in the gene.
    • Globin gene family in vertebrates is a good example.
    • Found in hemoglobin and myoglobin.
    • Globin genes arose from a single common ancestral gene.
    • Each hemoglobin molecule is a tetramer containing two identical α-globin subunits, two identical β-globin subunits, and four heme pigments.
    • Differential gene expression during development has physiological significance.
      • A characteristic organization is realized while studying the globin genes from various organisms like mammal or fish, each of them contains three exons and two introns.
      • Globin like polypeptides such as plant leghemoglobin and the muscle protein myoglobin, reveals the presence of four exons and three introns.
      • A pathway for evolution of globin genes:
        • It is thought that the modern globin gene has evolved from an ancestral form as the result of fusion between two of the globin exons.
        • A primitive globin gene has one exon.
        • Duplication of the globin gene followed by a mutation that produced two different genes α and β gene
        • A process of genetic rearrangement caused genes (α and β) to separate
        • Further events of mutation generating the globin gene that exists today. The human α and β genes are present on chromosome 16 and 11.

  • Evolution of Life

    • First life developed about 3.8 billion years ago.
    • Water vapor, nitrogen, methane, and ammonia used for food and energy.
    • Metabolic reactions catalyzed by metals like iron and magnesium.
    • Photosynthetic organisms emerged around 3.5 billion years ago.
    • Oxygen released into the atmosphere.
    • Life forms appeared utilizing oxygen.
    • Oxygen has to bind to a carrier and not supposed to react with that carrier. After binding it has to be transported to cells.
    • Chlorophyll evolved earlier for photosynthesis, a porphyrin ring containing magnesium.
    • Heme: A porphyrin ring containing iron.
    • Hemoglobin: Heme bound to globin molecule.
    • Hemoglobin binds to oxygen in the lungs and gives blood its red color.

  • Myoglobin is a single polypeptide chain while vertebrate hemoglobins are tetrameric.

    • Both are oxygen binding proteins.
    • Leghemoglobin is also bind to oxygen, but found exclusively in root nodules of legume plants like soyabean.
    • Phylogenetic tree showing the evolutionary history of globin protein

  • Porphyrins:

    • We need to understand how a small change in a molecule has led to the diverse functions. For this we need to examine molecules such as haemoglobin, myoglobin, haemocyanin, leghaemoglobin and chlorophyll. All of them are modified porphyrins.
    • Accommodate different metal atoms at their centers.
    • Very stable due to conjugation (alternating single and double bonds).
    • Nature utilizes properties of porphyrin ring for multiple functions.

  • Haemoglobin

    • All of us know it is the oxygen carrying molecule of blood.
    • O2O_2 is only marginally soluble (< 0.0001 M) in blood plasma at physiological pH. Therefore evolution has favored the development of mechanisms for better oxygen transport molecule.
    • We have about 150 g of the protein which is known as haemoglobin (Hb) per liter of the blood
    • Effective oxygen carrier, O2O_2 concentration in the bloodstream reaches 0.01 M.
    • The same concentration as air.
    • Hb-O<em>2{O<em>2} complex transfers O</em>2{O</em>2} molecules to myoglobin (Mb) in tissues, which transports oxygen through muscle.
    • For a single Hb molecule binds with four oxygen molecules.
    • An Fe(II) atom is present at the centre of each heme. Four of the six coordination sites around this atom are occupied by nitrogen atoms from a planar porphyrin ring.
    • The fifth coordination site is occupied by a nitrogen atom from a histidine side chain on one of the amino acids in the protein. The last coordination site is available to bind an O2{O_2} molecule.
    • The distance between the iron atoms of adjacent hemes in hemoglobin is very large: between 250 and 370 nm

  • The act of binding an O<em>2{O<em>2} molecule at one of the four hemes in hemoglobin leads to a significant increase in the affinity for O</em>2{O</em>2} binding at the other hemes.Thus, a cooperative interaction occurs that makes Hb an excellent carrier for oxygen.

  • Myoglobin molecule

    • Similar structure to Hb, with heme group buried inside.
    • Prevents hemes from coming too close together.
      • Proteins need to bind O2{O_2} reversibly; Fe(II) heme can't do this alone.
      • When there is no globin to protect the heme, it reacts with oxygen to form an oxidized Fe(III) atom instead of an Fe(II)-O2{O_2} complex.
      • Mb (4 haeme group) has a greater affinity towards oxygen than Hb(single haeme group). This difference is related to its different role: whereas hemoglobin transports oxygen, myoglobin's function is to store oxygen.

The protein part requirements for both the molecules Mb and Hb has been discussed below:

  • Being large Hb can’t enter muscle tissue.
  • Further to prevent from clotting, blood has to move.
  • Hence Hb is not an ideal structure for delivering oxygen in muscle tissues and its storing.
  • Since myoglobin is a storage protein, its affinity towards oxygen should not differ with its concentration.
  • Hence evolution has favored a similar molecule, a monomeric protein which is more compact.
  • Thus the life systems have utilized the heme group for two different functions (i) for transporting oxygen and (ii) for storing oxygen. This has achieved by combining the heme group with different proteins ie the globin part.

It is interesting to see, why there is a requirement of a protein part ie amino acids attached with heme group

  • When molecular oxygen encounters an isolated heme molecule, it rapidly converts the Fe(II) to Fe(III).
  • The oxidized heme binds oxygen very poorly.
  • The oxidation of the heme iron is prevented by the presence of the distal histidine side chain, which prevents the O2{O_2} from forming a linear Fe–O–O bond.
  • The bond between Fe and O2{O_2} is bent, meaning that this bond is not as strong as it might be.
  • Weaker oxygen binding means easier oxygen release.
    Chlorophyll
  • Chlorophyll is the molecule that traps this 'most elusive of all powers' - and is called a photoreceptor.
  • It is found in the chloroplasts of green plants, and is what makes green plants, green.
  • The basic structure of a chlorophyll molecule is a porphyrin ring (similar to haeme) coordinated to a central atom.
  • This is very similar in structure to the heme group found in hemoglobin, except that in heme the central atom is iron, whereas in chlorophyll it is magnesium.
  • Haemocyanin
    • Haemocyanin is another evolved compound from the porphyrin ring.
    • Instead of Fe, haemocyanin has Cu in it.
    • This also serves as an oxygen carrier in some animals.
  • Leghaemoglobin
    • This is the oxygen carrier found in the root nodules of legumes.
    • It is synthesized in a symbiotic interaction with nitrogen fixing bacteria in the root nodules.
    • Similar to haemoglobin it is red in color and carries oxygen for the growing bacteria in the root nodule.
      *
      Here there is structural comparison of hemoglobin, leghemoglobin, myoglobin and beta subunit of hemoglobin:
  1. Form and Function Evidence:
    • The function of a biological structure can be inferred from it shape.
    • The external ear is funnel shaped for focusing sounds from the atmosphere.
    • Vestigial organs: Remains of a structure that was functional in some ancestor but is no longer functional in the organism in question.
    • Humans have a tail bone (the coccyx) but no tail.

Mechanisms Responsible for Evolution

  1. Mutation:
    • Origin of genetic variation.
    • Errors in DNA replication, transcription, and translation.
    • Changes in genetic information, heritable.
    • All mutations are alterations in the nucleotide sequence of DNA.
    • Two categories:
      • Point mutation: Gain, loss, or substitution of a single nucleotide.
      • Chromosomal mutations: Change position or orientation of DNA, or cause duplication or loss.
      • Four types of chromosomal mutations: deletions, duplications, inversions and translocations.
    • Effects of mutation:
      • Scope for evolution.
      • Mutation in somatic cells may benefit the organism immediately.
      • Mutation in germ line cells may have no immediate selective advantage but may cause phenotypic change in offspring.
      • Mutations in germ line cells that get carried to the next generation are often deleterious
  2. Gene Flow:
    • Migration of individuals and movement of gametes between populations.
    • Adds new alleles or changes frequencies of existing alleles.
  3. Genetic Drift:
    • Random changes in allele frequencies in small populations.
    • Population bottlenecks: Disasters reduce population size, leaving a non-representative sample.
    • Founder effect: Few pioneering individuals colonize a new region, unlikely to have all alleles.
  4. Nonrandom Mating:
    • Mating patterns alter genotype frequencies if mates are not chosen at random.

Constraints in Evolution

  • Life forms are constrained by various factors.
  • Growth in cell size constrained by surface area-to-volume ratios.
  • Folding of protein is limited by the bonding capacities of their constituent molecules.
  • Energy transfers that fuel life must operate within the laws of thermodynamics.
  1. Development Process Constraints Evolution:
    • Evolutionary changes cannot start from scratch.
    • Current phenotypes constrained by historical conditions and past selective pressures.
    • New species evolved from existing species by incremental change.
    • Metamorphosis of tadpole to frog prepares aquatic organism for terrestrial existence.
    • Developmental constraints prevent extreme changes.
  2. Trade-offs Constraint Evolution:
    • Adaptations have both fitness costs and benefits.
    • Benefits must exceed costs.
    • Metabolic costs associated with conspicuous features (antlers or horns).
  3. Short-term and Long-term Evolutionary Outcomes Sometimes Differ:
    • Short-term changes in allele frequencies can be observed directly.
    • Long-term patterns influenced by infrequent events or slow processes.
    • Evolutionary processes act differently over time with changing conditions.