Phylogenetic Tree: Key Terms

Phylogenetic Tree Terminology

• A node signifies a common ancestor on a phylogenetic tree.
• A branch represents an evolutionary lineage on a phylogenetic tree.
• Sister groups are two lineages sharing a recent common ancestor.
• A polytomy is a node where more than two branches emerge, indicating an unresolved divergence pattern.
• A derived trait evolved in a lineage and distinguishes its members.
• An ancestral trait is shared by all members of a clade and was present in their common ancestor.
• A synapomorphy is a shared derived trait unique to a monophyletic group.
• A monophyletic group includes a common ancestor and all its descendants.
• A paraphyletic group includes a common ancestor and some, but not all, of its descendants.
• A polyphyletic group does not include the common ancestor of all members of the taxon.
• Homoplasy is trait similarity due to reasons other than common ancestry, such as convergent evolution.
• Parsimony favors the simplest explanation, selecting phylogenetic trees with fewer evolutionary changes.
• Convergent evolution is the independent evolution of similar traits in different lineages.
• Adaptive radiation involves rapid diversification into many species, each adapted to a unique ecological niche.

Using Phylogenetic Trees

• Phylogenetic trees are used to visualize evolutionary relationships through branching patterns and nodes.
• Closer groups on a phylogenetic tree mean a closer relationship.

Data Matrices in Phylogenetics

• Data matrices organize character states like trait presence/absence or DNA sequences for different taxa.
• The matrices are utilized in phylogenetic analysis to construct trees and infer shared, derived traits revealing evolutionary relationships.

Principle of Parsimony

• Parsimony provides a logical and objective method for choosing among various phylogenetic trees.
• Choosing the tree that minimizes evolutionary changes improves the likelihood of reflecting evolutionary history.

Fossil Record: Strengths

• Fossils give direct insight into past life, dating of evolutionary events and revealing extinct lineages.
• Fossils also showcase transitional forms.

Fossil Record: Limitations

• The fossil record is incomplete because not all organisms fossilize.
• Fossilization is environmentally biased.
• Obtaining DNA from fossils is usually difficult, and gaps in the record can hinder reconstruction of evolutionary transitions.

Earth's History

• Origins of life were marked by the evolution of prokaryotes and eukaryotes
• The Cambrian explosion then diversified life
• Mass extinctions and rises of groups like mammals also left their mark

Adaptive Radiations

• Adaptive radiation leads to a lineage diversifying into numerous species that are each adapted to a specific ecological niche.
• Examples of adaptive radiation includes Darwin’s finches of the Galapagos Islands, Hawaiian silverswords and mammalian diversification after the dinosaurs.

Cambrian Explosion

• Animal life rapidly diversified in the Cambrian, and also resulted in many major phyla.
• This occurred due to increased oxygen levels, the evolution of Hox genes, the origin of eyes, increased ocean calcium, and predator-prey dynamics.

Hox Genes

• Hox genes are regulatory genes that are crucial for body plan development in animals
• They are highly conserved among animal phyla and determine the arrangement of body segments.
• Hox gene changes are considered to have greatly spurred animal body plan diversification during the Cambrian explosion.

Extinctions

• Background extinctions are normal, they occur at a low rate, and are due to competition, disease, and environmental changes.
• Mass extinctions involve large-scale losses over a short time, which impacts a significant percentage of species caused by events such as asteroid impacts and volcanic eruptions.

Bacteria and Archaea: Prokaryotes

• Bacteria and archaea lack nuclei and membrane-bound organelles.
• Most Bacteria and archaea are unicellular, use DNA as genetic material and use ribosomes for protein synthesis.
• Most have cell walls and plasma membranes and reproduce through binary fission.

Differences in Structure of Bacteria and Archea

• Bacterial cell membranes typically consist of phospholipid bilayers that have fatty acids connected by ester bonds.
• Archaeal cell membranes often use lipid monolayers.
• The archaeal lipids also have ether linkages and branched isoprenoid chains
• Bacteria include peptidoglycan, but Archaea lack peptidoglycan and instead have polysaccharides and proteins.

Differences in DNA and Gene Expression of Bacteria and Archea

• Bacteria include simple RNA polymerases, unlike Archaea that have more complex and eukaryote-like RNA polymerases.
• Eukaryotes share similar gene expression with Archaea.

Abundance and Habitats of Bacteria and Archea

• Bacteria and archaea are incredibly abundant and live in diverse environments, including soil, water, air, inside other organisms, and extreme conditions.

Extremophiles

• These are organisms that can thrive in extreme environments like hot springs, high pH or specific pressures.
• Enzymes that these organism produce are used in industrial and medical applications.

Medical Significance of Bacteria and Archea

• Bacteria are pathogenic or benifical
• Archea are not typically pathogens

Koch's Postulates

• These are a set of criteria required to establish a causal relationship between a microbe and a disease.
• These postulates are a requirement in establishing a microbe as the specific etiological agent of a disease,

Germ Theory

• Microorganisms cause diseases

Endospores

• Bacillus and Clostridium are capable of producing highly resistant endospores, and they are medically significant due to their resilience against elimination.
• This leads to persistence of infections like anthrax and tetanus.

Antibiotics

• Bacteria are becoming more resistant to antibiotics over time

Biofilms

• Communities of microorganisms attached to surfaces and surrounded by extracellular polymeric substances (EPS)
• They are commonly resistant to antibiotics and disinfectants.

Bioremediation

• This technique is implemented with microorganisms to clean up pollutants.
• It allows microbes to break down toxic substances into harmless products.

Enrichment Culture

• It grows a specific type of desired microorganism within a sample through optimal conditions for growth

Metagenomics

• This is the study of collective genetic material in a microbial community from environmental samples.
• It involves studying microbial diversity, novel genes, and microbial roles.

Microbial Phylogeny

• Microbial phylogeny is based on rRNA gene sequences, other gene sequences, and phenotypic character states.

Challenges in Microbial Phylogeny

• Microbial phylogeny is challenged by horizontal gene transfer, difficulty culturing microbes, rapid mutation rates, and complications in defining microbial species.

Horizontal Gene Transfer

• Genetic material can be transferred between different species
• It can occur through transformation, transduction, or conjugation

Plasmid

• Plasmids are smaller and circular DNA structures that can allow for antibiotic resistance

Bacterial and Archaeal Shapes and Sizes

• They are small, and vary from nanometers to micrometers
• Common shapes: Cocci (spherical), Bacilli (rod-shaped), Spirilla (spiral), Vibrios (comma-shaped)

Gram-Postive vs Gram-Negative Bacteria

• Gram-positive: Stains purple due to Thick peptidoglycan layer.
• Gram-negative: Stains pink due to thin peptidoglycan layer, and outer membrane with lipopolysaccharide (LPS).

Energy and Carbon Acquisition

• Phototrophs: Obtain its energy from light
• Chemotrophs obtain energy from chemical compounds
• Autotrophs obtain carbon from inorganic sources (e.g., CO2)
• Heterotrophs obtain carbon from organic sources

Cellular Respiration

• ATP is produced by oxidizing organic molecules.
• Aerobic respiration uses oxygen, while anaerobic respiration use other substances as final electron acceptors.
• ATP synthase is powered by the proton gradient resulting from the electron transport chain.

Fermentation

• Fermentation occurs without oxygen to make ATP
• NAD+ is subsequently regenerated through lactic acid and alcohol fermentation.

Photophorylation

• Light energy powers ATP production through the use of a light energy induced proton gradient

Methagens vs Methanotrophs

• Methanogens: Archaea that produce methane as a metabolic byproduct.
• Methanotrophs: Bacteria that consume methane.

Oxygen Revolution

• Cyanobacteria, which perform oxygenic photosynthesis, dramatically increased oxygen in the atmosphere

Nitrogen Cycle

• Microbes assist with converting forms of atmospheric Nitrogen

Microbial diversity

• Bacteria and archaea are phylogenetically very diverse, though the text declines to elaborate further

Protists - Are They a Paraphyletic or Polyphyletic Group?

• They are both due to the vast range of endosybiosis and evolutionary histories

Protist Defining Characterisitics

• Protists are are either unicellular or multi, are highly diverse and live in aquatic environments

Protists - impacts of on Human Health and Welfare

• They cause Malaria, Gardaris, and Sleeping sickness

Prosist - Welfare and Roles in Ecosystem

• Used in food production and as filters
• They decompose and live in symbiotic relationships

Obtaining Phylogenetic Data of Eukaryotes

• Includes the use of sequences, structure, fossils, endosymbiosis, and morphological features

Eukaryotic Phylogenetic Trees

• Eukaryotic trees look for monophyletic, paraphyletic, and convergent evolution through endosymbiosis.

Endosymbiotic Theory

• Mitochondria and chloroplasts originated from free-living bacteria that were engulfed by ancestral eukaryotic cells.
• Evidence: Mitochondria and chloroplasts : Circular DNA. : Similar bacterial ribosomes. : Double membranes. : Binary fission. : Phylogenetic analysis of bacterial DNA

Nuclear Envelope Importance and Protist Coverings

• It separates transciption and translation, which allows for more complex regualtion
• Protists have cellulose & silica cell walls, calcium carbonate & silica shells as well as coverings of protein

Significance of Multicellularity

• Results in specialization and increased organisms

Protist Energy and Carbon Acquisition

• Use one of the follow processes: Photoautotrophs, Heterotrophs, Mixotrophs

Protist Movement and Reproduction

• Use flagella cilia, pseudopodia or gliding
• Asexual, Sexual and Alternation of Generations

Alternation of Generations

• Includes both diploid and haploid

Key Eukaryotic Lineages

• Includes the following examples: excavata, SAR Clade, Archaeplastida, & Unikonta

Alternation of Generations Key Features of Land Plants

• The presences of Sporopollenin, Sporangia and male/female structures in plants.

Transition to Land

• Plants transitioned to land through Alternation of Generations, embryos and walled spores

Plant Similarities and Differences to Algae

• The similarities between algea and plants are that they contain a and b chlorophyll, perform eukaryotics functions and possess celluose
• The dissimilarities between algea and plants are that plants have vascular tissue and roots

Phylogenetic Trees and Plant Diversification

• Used as a guide to identify plant transitions

Transitioning to Land

• Land provides more sunlight and abundent CO2 to plantlife

Water Adaptations by Plantlife

• Plants use cuticle, stomata, sporopollenin to help water evaporate

Conducting Water

• Plants moved water using tracheids and early vascular plants

Embyrophyta

• Plants have protected embryos

Plant Life Cycle

• Plants evolved between vascular and non-vascular plants life cycles

Advantages of Pollen and Seeds

• genetic diversity and nutrients

Monocot and Dict Morphology

• One of two cotyledons

Tree Analysis

• determine evolutionary relationships

Fungi

• They decomponse and impact biotechnology

How Fungi Obtain Food

• Fungi obtain food by absorbing the nutrients in their envioronment

Fungi Struture

• Fungi is either unicellular and multicellular

Fungi symbioses

• Fungi exists within Mycorrihizae and Saprophytes

Yeast Forms

• Has two forms, one being filamentous

Coenocytic Hyphae and Surface Area

• Both lacking distinct differences and used to measure surface area

Reproduction of Fungi

• Common through spores but with the use of budding and fragmentation

Conidiia

• Asexual

Animals and Plants

• Fungi are realted

Relationships

• Linked to animals

Phlyogny

• Basal

Genetic trees

• used for more research

Fungal Symbiosis

• They engage in many of them

Degradation and Spore

• Involve the use of lignin,

Gamete Reproduction

• Commonly use spores

Reproduction

• Fungi

Zygasporangium and ascus

• used for meiosis and production

Six Lineage

• Evolved from chntids