Phylogenetic Tree: Understanding Evolutionary Relationships

Homo Luzonensis

• Newly discovered ancient human species from the Philippines
• Adds a branch to the human evolutionary tree
• Fossils found in Callao Cave, Luzon, echoing the discovery of Homo floresiensis in 2004
• Researchers found 13 bones from at least three individuals dating back 67,000 years
• Remains suggest the individuals were short, like Homo floresiensis
• Some scientists question creating a new species based on limited material
• Others suggest the Luzon finds could be a Homo floresiensis variant
• Island isolation can cause odd evolutionary changes
• Accepting as a new species is reasonable until more finds are available

Human Evolution

• Recent discoveries shift the human evolution timeline from a simple tree to a thicket
• Ancient human species survived to within the last 100,000 years
• Significant overlap may have existed between our ancestors and these ancient species
• Southeast Asia was once home to numerous human species
• Homo erectus migrated to China and Indonesia
• Denisovans may have reached Papua New Guinea's vicinity
• H. floresiensis existence questions early humans' seafaring ability due to the deep channel isolating Flores
• The presence of H. luzonensis in the Philippines strengthens this notion, as Luzon was never attached to mainland Asia

Meeting Homo Luzonensis

• The cave where H. luzonensis was found was initially explored in 2003
• Exploration was abandoned until the Flores discovery
• Researchers returned in 2007 after ancient humans were proven to have reached seemingly inaccessible islands
• A nearly complete human foot bone was found in a 67,000-year-old animal bone layer
• Further excavations revealed more human material including adult finger and toe bones, teeth, and a child's femur
• The teeth are notably small, suggesting a small body size
• Remains show modern and ancient aspects
• Teeth resemble modern humans, while hands and feet resemble australopithecines
• The find raises questions about the relationship between humans on Flores and Luzon
• As to whether they are closely related or separate species that both experienced island dwarfism
• Some suggest the primitive features indicate a pre-Homo dispersal out of Africa
• Claiming that H. erectus and H. luzonensis are the last survivors of that early wave
• Others believe they are descendants of Homo erectus, subject to island dwarfing
• More ancient human remains on Luzon and other Southeast Asian islands are required

Introduction to Evolutionary Relationships

• All life on Earth originated from a common ancestor
• Genes reflect shared ancestry
• DNA sequences in genes acquired slight changes as species differentiated through evolutionary time
• Changes accumulate over time
• Species that diverged long ago have more DNA differences
• Scientists use this variation as a molecular clock to help estimate divergence times
• The longer two species have been separate, the more distantly related they are
• Scientists collect information to make evolutionary connections
• Darwin proposed that life's evolutionary history forms a branching tree
• Phylogeny describes the evolutionary relationships between groups of organisms being compared

Evidence for Tracing Evolutionary Relationships

• Morphologic evidence (form and function)
• Genetic evidence
• Similar structures can be either homologous or analogous
• Homologous structures are similar due to inheritance from a common ancestor
• Analogous structures are similar because they evolved to do the same job in unrelated organisms
• Bones in a whale's front flipper are homologous to bones in the human arm (not analogous)
• Wings of a butterfly and a bird are analogous (not homologous)
• Wings of a bird and a bat are both homologous and analogous
• Scientists must determine which type of similarity exhibits to decipher the phylogeny

Cladistics

• Molecular systematics, using information at the molecular level, has grown with DNA technology
• DNA is made of four bases: adenine (A), cytosine (C), guanine (G), and thymine (T)
• Genes are distinct DNA locations
• The base sequence in a gene determines the order of amino acids in a protein
• The amino acid sequence acts as the blueprint for protein assembly
• Closely related organisms should have similar or even identical amino acid sequences in shared genes
• The more similar the sequence, the more similar the function, thus suggesting closer evolutionary ties
• "Molecular phylogeny" compares sequence data
• Ranks organisms' relatedness based on DNA differences

Cladistics Systems

• Cladistics organizes traits
• Sorts organisms into clades where each clade has organisms descended from a single ancestor
• Cladogram displays the relationships between clades
• Beetles branched off first, then wasps, bees, and ants, and finally flies branched off butterflies and moths

Cladogram Definition

• A cladogram is the graphical representation of the hypothetical phylogenetic relationship between groups of organisms
• Used to determine evolutionary relationships
• Derived from Greek words "clados" (branch) and "gramma" (characters)
• A diagram shows a pattern of characters among organisms

Feature of Cladograms

• Trees show statements of relationship and do not indicate ancestors or descendants
• Branch lengths do not indicate the number of evolutionary changes
• Cladograms are generated by analyzing morphological characters and DNA/ RNA sequencing data
• Computational phylogenetics is also used with existing characters
• Preparation assumption for phylogenetic trees
• All consist of lines that branch off from other lines representing hypothetical ancestors of different organisme

Parts of a Cladogram

• Clade/ Ingroup : Are groups of organisms or genes that include the most recen common ancestor of all its members and descendants
• Taxon/ Outgroup: The most distantly related group of animals that isn't necessarily a clade and functions as a point of reference
• Branches: the line that connects all other part of the cladogram, with the length representing the extent of the relationship

Key Components of a Cladogram

• Root: Initial common ancestor of all organisms in the cladogram
• Node: Represents a hypothetical ancestor that gives rise to two or more daughter taxa
• Nodes: The bifurcating branch point of divergence in all cladograms
• Indicate where a group of organisms divides or separates into further groups

Building Cladograms

• Based on morphological traits or molecular data (DNA, RNA, or protein)
• Two main approaches
• Using morphological/ structural characters
• Using molecular characters

Using Morphological/Structural Characters

• Three steps to build a cladogram:
  • Step One "The Table"
  • Step Two "The Venn Diagram"
  • Step Three "The Cladogram"

Step One "The Table"

• Create a "characteristics chart" that analyzes which characteristics each species has
• Fill in "x" for yes (trait present) and "o" for no (trait absent)
• Count the number of "yes" entries for each characteristic, revealing shared ancestral characteristics
• Traits with fewer "yes" entries are shared derived characters developed later

“The Venn Diagram"

• A step to help learn to build cladograms
• Draw a multi-circular Venn diagram using as many circles as there are characters
• Start with the central character that is shared by all the taxa the outer circle
• Write species that have only that set of characters inside each section.
• Write the outgroup which do not share any trait on the outside of the Venn Diagram to serve as the comparison

"The Cladogram"

• Turn Venn Diagram into cladogram by writing the traits on the main line, and species on the branches
• On the cladogram you put all the characters and the species in the correct evolutionary history

Tree of Life: Three Domain System

• Organisms are related in a branching pattern called "the tree of life"
• "Tree thinking" is invaluable in deciphering the divergence of organisms, living and defunct, as it helps to unknot the branching evolutionary relationships
• Tree explains the passage of time and the ancestors of all those living things

Three Domain System

• A classification system developed by Carl Woese in 1990
• Classifies biological organisms
• Genetic sequencing allows a new analysis of the relationship between organism
• Groups organisms based on differences in Ribosomal RNA (rRNA) structure
• Organisms are classified into three domains and six kingdoms
• Cells originate form a common ancestor cell termed the last universal common ancestor (LUCA)
• LUCA evolved into the domains Archaea, Bacteria, and Eukarya

Archaea

• Domain contains single celled organism
• Includes genes that are like both bacteria and eukaryotes
• They are prokaryotic organisms and do not have a membrane-bound
• They lack internal cell organelles and similar in size and shape to Bacteria
• Differ from bacteria in cell wall composition and differ from both bacteria and eukaryotes in membrane

Three Main Domains

• Crenarchaeota that includes hyperthermophiles and thermoacidophiles
• Euryarchaeota that includes methanogens that require an oxygen-free environment
• Korarchaeota is where only few species that live in places such as hot springs are found

Bacteria Domain

• Organisms are feared because some are pathogenic
• Essential to life with some providing the human microbiota.
• Perform essential function to digest and absorb nutrients for nutrients from food in which prevent pathogenic microbes from colonizing where the aid activating is

Bacteria Group

• Grouped into five main categories
• Proteobacteria is bacterium that covers the largest group of bacteria and includes Vibrio
• Cyanobacteria are bacteria that are capable of green algae because of their color
• Firmicutes are positive bacteria includes Mycoplasms
• Chlamydiae are parasitic bacteria to include pneumonia
• Spirochetes are bacteria containing example to Lyme and syphilis

Eukarya Domain

• Includes eukaryotes and organisms for fungi and plants
• Contains that bacteria cells that typically resists to include antibiotics organisms
• Plants and animals that is includes algae and mammals

Phylogenetic Tree

• Hypothetical visual representation connecting the relationships between different organisms that leads common ancestors to descendants over evolutionary time.

Building Phylogenetic Trees

• Compare DNA sequences instead of physical traits
• Closely related species have a common ancestor, that split and evolved
• The more change in DNA, the more distant relatives they are.
• Steps: Align, compare and identify the sequences with the least amount of difference
• Draw the first group that reflect closest relatives and complete the other sequence
• Remember that tree are to show intent with closely related or due to different environmental conditions

Taxonomy

• An early taxonomist was Greek philosopher Aristotle who organized five hundred types of animal
• By the sixteenth century, explorers had discovered so many new species to continue to be based on what people could see
• Carolus Linnaeus who distinguished plants by their sexual parts and introduced the binomial name for a species

3.4 Taxonomy

• Linnaean System of Classification – The Swedish botanist Carolus Linnaeus developed system to try to classify all living things
• System of classification is the way of classifying organisms and how they have similar
• Includes kingdom, phylum, class, order, family, genus and species
• The first letter is always capitalized while the specific is not and can be in bold letters
• Has different examples for each English meaning
• Note: The linnaean method is artificial where it classifies organisms based on morphological similarities and evolutionary relationships

Recombinant DNA Technology

• Humans have selected plants and animals for desired traits
• Traits sought after and produced involve processes such as breeding practice
• Inserting and expressing molecular biology in the genetic engineering process involves the use to modify traits in the target organism
• Recombinant may involve new introduction and an enhancement by increasing expression or disrupting inhibition

General Outline of Recombinant DNA technology

• Involves cutting by restriction entymes like endonucleases, that cut DNA molecules at sticky ends
• Selection used in propagating is bacteria and Yeast
• Ligation of DNA strands permanently seals the DNA
• Transfer of plasma is transferred through shock treatments
• Selections process screens the process through antibiotic gene
• Sequencing gene to find out primary structure of protein

Methods of plasmid insertion to the target organism

• Biolistic: a "gene gun" is used to fire DNA-coated pellets on plant tissues
• Plasmid insertion by heat shock: used to transfer plasma into a bacterial host, where cells acquire new traits
• Electroporation: process were pores expanded through a electric shock known as electroporation for insertion to a host cell
• Selections marker are present in solutions which the cell can then grow and propagate into colonies
• Transformed cells: genes also produce colored in certain inserted
• Confirm presence through amplify DNA large copies

Explore how to construct a Venn diagram to illustrate evolutionary relationships between animal species. Learn how 'tree thinking' helps understand phylogenetic trees, and the critical role of the outgroup. Discover Carl Woese's contribution and the importance of genetic sequencing in modern biological classification.