Classification & Diversity of Life

Characteristics of Life

• Organisms respond to diverse stimuli, e.g., plants bending toward light.

• All organisms use a source of energy for metabolic activities.

• All organisms reproduce to increase their numbers.

• All organisms are made of cells.

• Organisms are highly organized structures consisting of one or more cells.

Diversity of Life

• Diversity of Life happened as a result of evolution or adaptive radiation.

• Adaptive radiation is an evolutionary pattern where a single species rapidly diversifies into different kinds of closely related species to adapt to specific environmental changes.

Origin of Life

• Chemical evolution was the first step, with complex organic molecules forming from simpler inorganic molecules through chemical reactions in the oceans.

• Biological evolution led to the formation of life and complex organisms.

Domains of Life

• Living things have evolved into three large clusters called "domains":

  • Bacteria

  • Archaea

  • Eukaryota (or Eukarya)

• Eukaryota is Eukaryotic.

• Order of appearance:

  • Bacteria evolved first.

  • Gave rise to Archaea.

  • Eukaryota evolved recently.

Domains of Life - Details

• Bacteria

  • Prokaryotes with cell wall containing peptidoglycan.

  • Wide variety of lifestyles, including many that can produce their food.

• Archaea

  • Prokaryotes but with no peptidoglycan and with similarities to Eukaryotes in genome organization.

  • Usually live in extreme conditions, e.g., high salt concentrations, high temperatures.

  • Bacteria and Archaea are Prokaryotic

• Eukaryota (or Eukarya)

  • Eukarya is Eukaryotic.

Domains and Kingdoms Over Time

• Three Domains:

  • Bacteria

  • Archaea

  • Eukarya

• Six Kingdoms:

  • Bacteria

  • Archaea

  • Protists

  • Plants

  • Fungi

  • Animals

How Diversity of Life is Identified

• Systematics: The study of the diversity of organisms and the relationship between them.

• Systematics considers:

  • Taxonomy: The science of naming organisms and grouping them into logical categories.

  • Phylogeny: The science that explores the evolutionary relationships among organisms.

Taxonomy

• Taxonomy is the scientific study of naming, identifying, and classifying groups of biological organisms based on shared characteristics.

• The current taxonomic system has EIGHT levels in its hierarchy.

• Taxonomic hierarchy is arranging organisms into successive levels of biological classification, either decreasing or increasing order from kingdom to species and vice versa.

• Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank.

Taxonomic Hierarchy

• Domain is the highest (most general) rank.

• Taxonomic ranks from general to specific:

  • Domain

  • Kingdom

  • Phylum

  • Class

  • Order

  • Family

  • Genus

  • Species

Development of Taxonomy

• Introduced by Carolus Linnaeus.

• He developed the system based on physical and structural similarities.

• Used binomial system of nomenclature to classify organisms.

• In this system, each species is assigned a unique two-part name: Genus & Species.

  • Genus: A group of closely related organisms ranks below family and includes more than one species.

  • Species: A closely related group of organisms, which comprise similar characteristics.

Rules: Binomial Nomenclature

• Equus is the genus name for Horses and their close relatives.

  • Equus burchellii, the Zebra

  • Equus africanus, the Donkey

• Binomial names are either italicized or underlined.

• The first letter of the genus is capitalized; the specific species is NOT capitalized.

Phylogeny

• Phylogeny is the study of evolutionary relationships among different groups of organisms.

• Phylogeny is based on derived characteristics:

  • Fossils

  • Comparative anatomy studies

  • Life cycle information

  • Biochemical and molecular studies

Fossil Record

• A fossil is the preserved remains of a dead organism from millions of years ago in sediments, such as sand and mud

• Fossils are found in rocks, and can take many forms

  • Body Fossils: The preserved physical remains of an organism, such as bones, teeth, shells, or leaves.

  • Trace Fossils: Indirect evidence of an organism's activity, like footprints, burrows, or nests.

  • Chemical Fossils: Molecular traces of life, like organic molecules that remain after the organism has decomposed.

Comparative Anatomy

• Comparative anatomy is the study of similarities and differences in the anatomy of different species.

• The hands of several different animals.

• They all have the same basic pattern of bones.

• They inherited this pattern from a common ancestor.

• However, their forelimbs now have different functions.

Life Cycle Information

• Life cycles show how animals grow and reproduce. For example,

• Butterfly starts as an egg, then becomes a caterpillar, pupa (chrysalis), and finally an adult butterfly.

• Frogs begin as eggs, turn into tadpoles, and grow into adult frogs.

• These stages help animals adapt and survive in different environments.

Biochemical and Molecular Studies

• For years, it was assumed that humans were most closely related to chimpanzees.

• By analyzing DNA sequences, researchers find that humans and chimpanzees share about 98% of their DNA with non-functional genes and remaining 2% provides the major differences between them.

Phylogenetic Tree or Phylogram

• Phylogenetic tree is a diagram known as Phylogram that shows relationships among different groups of organisms.

• All the branches in a phylogram represent any evolutionary distance between different groups.

• The length of the branches indicates the differences between the DNA.

Cladistics: Cladogram and Clade

• Cladistics is a method to evaluate the degree of relatedness among organisms within a species based on shared characters and similarity of species derived from ONE Ancestor.

• Cladistics involves diagram known as Cladogram.

• Each Cladogram Contains several Clades.

• A clade is a group of organisms that consists of a common ancestor and descendent species with shared Characteristics or Traits.

Cladistics based on Molecular Data

• The length of the branches indicates the differences between the DNA.

• DNA also shows that humans and chimpanzees diverged from a common ancestor species that lived between 8 and 6 million years ago.

• Derived shared trait (Tail Loss)

• Unique Trait, Bipedal

Difference between Cladistics and Phylogeny

• Cladistics is often used to trace a very common ancestor of one species and study their characteristics. Phylogenetics is the study of the relationships and evolutionary history between groups of organisms.

• All the branches in a cladogram are of equal length as they do not represent any evolutionary distance. All the branches in a phylogram represent any evolutionary distance between different groups.

Macroevolution vs. Microevolution

Macroevolution

• Complete different species

• Large changes

• Longer period of time

Microevolution

• Within species

• Small changes

• Only a few generations

Microevolution and Macroevolution - Detailed

• Microevolution

  • Involves minor differences in genes between populations of the same species.

  • Happens on a smaller scale from generation to generation.

  • Involves only small changes to DNA, such as point mutations, producing only small changes to phenotype (green to brown color).

• Macroevolution

  • Large scale, major biological changes occur over millions of years.

  • Involves the origin of new species from a common ancestor or from one species into two different species.

  • Involves the extinction of species.

  • Involves evolution of new features such as formation of backbone, wings etc.

How Evolution Occurs

• Evolution happens due to FOUR basic ways:

  • Mutation

  • Gene Flow (Migration)

  • Genetic Drift

  • Natural Selection

Mutation and Gene Flow

• Mutation

  • Mutations are changes in the base sequence of DNA.

  • Mutations are the source of new genes/alleles, thus increase diversity.

  • For example, Some “green genes” randomly mutated to “brown genes” so more brown color beetles are seen in the population than they were before the mutation.

• Gene Flow (Migration)

  • The migration is the movement of individuals into and out of populations, resulting genes(alleles) either being added or removed from a population.

  • Migration shuffles genes between populations; thus prevent speciation and diversity

  • For example, brown beetles to join green beetle population and make gene for brown coloration more frequent.

Genetic Drift

• Genetic drift involves a significant change in gene frequency that is NOT a result of natural selection.

• Genetic drift results from random or chance events for example i.e., from a natural disaster or from indiscriminate human hunting.

• Genetic drift occurs when the population size is limited or small

• Decrease in Diversity (Especially in Small Populations)

• For example, green beetles were killed when someone stepped on, so by random chance more brown beetles reproduced.

Natural Selection

• Natural selection is nature’s way of "choosing" which traits are best for survival, and those traits become more common in the group.

• Natural selection can both increase and decrease genetic diversity, depending on the specific conditions and the environment.

• Natural selection is not random and occurs in response to environmental changes leads to Adaptation.

• Selected naturally, for example-

  • Green beetles are easier for the birds to spot and eat, So brown beetles escaped predation.

  • So, Brown beetles survived to reproduce and over time more brown beetles selected and survived.

The Theory of Natural Selection

• In 1858, Charles Darwin suggested the theory of natural selection as a mechanism for evolution.

• Darwin surveyed the south seas (mainly South America and the Galapagos Islands) to collect plants and animals.

• On the Galapagos Islands, Darwin observed different types of species that lived no where else in the world.

• These observations led Darwin to write a book named “Origin of Species by Means of Natural Selection”

Types of Natural Selection

• Stabilizing Selection: decrease diversity

  • genetic diversity decreases as the population stabilizes on a particular trait

• Directional Selection: decrease diversity

  • Changes in weather, climate, or food availability lead to directional selection and select individuals who can survive the extreme changes

• Disruptive Selection: increase diversity

  • genetic diversity is more as a wide range of the population is selected.

Types of Natural Selection - Details

• Stabilizing Selection: Culls extreme variations, narrows the width of distribution.

• Directional Selection: Favors one extreme, shifts distribution left/right.

• Disruptive Selection: Favors both extremes, creates bimodal distribution.

Natural vs. Artificial Selection

• Natural selection is any selection process that occurs as a result of an organism's ability to adapt to its surroundings. Natural selection affects the entire population of a species. Results in increase in biodiversity

• Artificial selection is selective breeding that is imposed by an external entity, usually humans, in order to enhance the frequency of desirable features. Artificial selection only affects the selected individuals. Results in decrease in biodiversity as it decrease genetic diversity

How New Species Originate

• Speciation is the evolutionary process by which new biological species arise due to natural selection and mutation

• There are two main mechanisms of speciation:

  • Geographic isolation (due to migration, natural barrier to movement)

  • Adaptation (adaptations are responsible for making the species more genetically diverse)

  • Polyploidy (due to abnormal cell division in meiosis): Polyploidy leads to additional sets of chromosomes(3n, 4n ) instead of diploid

Geographic Isolation

• A few individuals migrate to an island and establish a population faraway from their original home.

• Several barriers, such as the uplifting of mountains, rerouting of rivers, or the formation of deserts can subdivide a population in an area.

• Occurs when several individuals from a population die out and others become separated.

Speciation by Polyploidy

• Polyploidy is a condition in which a normally diploid cell $(2n)$$$(2n)$$ or organism acquires one or more additional sets of chromosomes $(3n, 4n)$$$(3n, 4n)$$

• Polyploids are common among plants, as well as among certain groups of fish

  • Examples- Cotton (52 Chromosomes, 4n) and goldfish (200 Chromosomes, 4n)

• How does polyploidy occur?

  • Polyploidy may occur due to abnormal cell division during Meiosis or Mitosis

Types or Patterns of Evolution

• Evolution over time can follow several different patterns:

  • Extinction

  • Adaptive radiation

  • Divergent Evolution

  • Convergent Evolution

  • Parallel Evolution

  • Co-evolution

Extinction

• Extinction is a typical pattern in evolution in which groups of organisms die out.

• Extinction is a natural phenomenon predicted by Darwin in his theory of evolution.

• A species goes extinct if it cannot adapt to environmental changes.

• Over the history of the Earth, over 99% of all the species that have ever lived have gone extinct.

Adaptive Radiation

• Adaptive Radiation is an evolutionary pattern that happens over a short period of time in which a species diversifies rapidly into different kinds of closely related species to adapt to specific environmental changes.

  • Examples:

    • Darwin's finches of the Galapagos

    • Honeycreeper birds

    • Cichlid fish of lakes Malawi

Divergent Evolution

• Divergent evolution involves species with a common ancestor that change to become increasingly different over time

  • Example:

    • Dog species came from ancestor, wolf

    • Zebra, Donkey and Horse (Ancestor-Pliohippus)

Convergent Evolution

• Convergent evolution involves unrelated species (different ancestor) that develop similar characteristics over time (have analogous structure).

  • Examples:

    • Spines in desert plants

    • Wings in bats, dragonflies, and swallows

    • Body shape of whales, sharks, and tuna

    • Fins of Sharks, Ichthyosaurs and Dolphins

Parallel Evolution

• Parallel evolution happens when two closely related species independently develop similar traits because they face similar challenges in their environments.

• Parallel evolution is likely to occur in species that are closely related in evolutionary terms, though it's not necessary for them to have a recent or direct common ancestor.

  • Examples:

    • North American cactus and the African euphorbia developed similar adaptations, which are their thick stems and sharp quills to survive the hot, arid climates, but have different families.

    • Tasmanian Wolf (Australia) and Timber Wolf (North America). They both animals have similar body shape and hunting behavior), even though they are different species

Co-evolution

• Coevolution (the prefix co- means evolves together) refers to the process by which two or more species or entities influence each other's evolutionary development over time through the process of natural selection.

  • Examples:

    • Predator-Prey Relationships: Predators and prey often evolve in tandem. For instance, a predator may evolve faster running speeds, while the prey evolves better camouflage or quicker reflexes.

    • Pollination: Flowers and pollinators (like bees or birds) evolve together. Flowers may develop traits like specific colors or scents to attract particular pollinators, while pollinators evolve traits that make them more effective at transferring pollen.

• Many birds feed on butterflies, but they tend to avoid some kinds that taste bad such as Monarch

• To avoid being eaten by birds, some butterflies evolved to look more like the Monarch and this creates problems for birds, which gets trouble spotting the differences between the two