BIO-214: #5 Phylogenetics & Taxonomy

What is phelogeny?

• The evolutionary history & relationship of an organism/group of organisms

• Describes the organism’s relationships

  • From which organisms it may have evolved

  • Which species it is most closely related

• Provides information on shared ancestry, NOT on how organisms are similar/different

What is a phelogenetic tree used for?

• Shows the evolutionary pathways & connects among organisms

• Diagram used to reflect evolutionary relationships among organisms/group of organisms

• Map of evolutionary history

What does it mean for a phelogenetic tree to be “rooted” or “unrooted”?

• Rooted: There is a single ancestral lineage to which all organisms represented in the diagram relate

• Unrooted: do not show a common ancestor, but show relationships among species

What is a branch point in a phelogenetic tree?

Node on the phelogenetic tree where a single lineage splits into distinct new ones

What is a basal taxon on a phelogenetic tree?

Branch on a phylogenetic tree that has not diverged significantly/remains unbranched from the root ancestor

What are sister taxa?

two line lineages that diver from the same branch point

What is a polytomy?

A branch with more than two lineages & serves to illustrate where scientists have not definitely determined all of the relationships

Does the rotation at branch points change tine information on the phelogenetic tree?

• No

• Each taxon’s evolution from the branch point was independently of each other

What is the field of systemics?

• Field that scientists use to organize & classify organisms based on evolutionary relationships

• Use data from:

  1. Fossils

  2. Studying the body part structures

  3. Molecules an organism uses

  4. DNA analysis

What are the misconceptions/limitations of the phylogenetic tree?

1. People make assumptions that more closely related organisms look more alike

   • False: if two closely related lineages evolved under significantly varied habitats, then the two groups will appear differently

2. Branches do not account for the length of time, only evolutionary ordered

   1. A branch length does not mean more time has passed or not

What is a clade?

Shows the relationships between taxa, but are not formal relationships (only shows related species) because they share the same common ancestor

What is taxonomy?

Science of classifying organisms

What is a hierachical system?

Organization from larger to smaller, more specific categories

1. Who was Carl Linnaeus?

2. What model did he use?

3. How did scientists divide organisms after the common beginning of all life?

1. Inventor of the taxonomic classification system (Linnaean system)

   • Swedish botanist, zoologist, & physician

2. Used a hierarchical model

   • Starts off at the point of origin

   • Groups become more specific until 1 branch ends as a single species

3. Divided into three large categories (domains)

   1. Bacteria

   2. Archaea

   3. Eukarya

What is the order of the hierachical classification?

Domain → Kingdom → phylum → class → order → family → genus → species

What is a taxon?

• The name at each level in the taxonomic classification system

  • Phylum:Chordata

  • Class: Mamalia

  • Order: Carnivora

  • Family: Canidae

  • Genus: Canis

  • Species: Lupis

What is the bionomical nomenclature?

• System of two-part scientific names for an organism

• Genus capitalized, species italized

• Canis lupus → C. lupis

What are subspecies?

• Members of the same species that are capable of mating and reproducing viable offspring

• Separated due to geographic or behavioral isolation, or other factors

What two types of evidence are used for phylogentic evolutionary investigations?

1. Morphologic (form & function)

2. Genetic

What are homologous structures?

• Structures that overlap morphologically (in form) & genetically

• Stem from developmental similarities that are based on evolution/embryonic origin

• Ex: bones in bat & bird wings

  • Grouping of bones, not just a single bone

  • More complex the feature, the more likely any kind of overlap is due to a common evolutionary past

What are analogous structures?

• Similar environmental pressures & natural selection produce similar adaptations in organisms from different evolutionary lineages

• Insects & bats

  • Both use wings to fly, but the wing structure & embryonic origin is different.

1. What is molecular systematics?

2. What are the limitations of molecular systematics?

• technique that uses molecular evidence to identify phylogenetic relationships

• Limitations

  1. Mutations might cause mishaps when reading DNA sequences

  2. distantly related organisms may randomly share a high percentage of bases in the same locations → They SEEM to be closely related, but are not

What are cladistics?

• System that sorts organisms with homologous traits into clades

• groups of organisms that descended from a single ancestor

What are the 3 types of clades?

1. Monophyletic group

2. Paraphyletic

3. Polyphyletic

What is a monophyletic group?

• group of organisms that evolved from a common ancestor

• Must stem from a single point on the tree

What is a paraphyletic group?

Some, but not all of the descendants originated from a common ancestral species

What is a polyphyletic group?

Clade that includes distantly related species, but does not include their most recent common ancestor

1. What does the phrase “descent with modification” mean?

2. What pattern is seen in the phylogentic tree of life?

• Organisms evolve from common ancestors and then diversify

  • related organisms have many of the same characteristics & genetic codes, changes occur

• Pattern

  1. A change occurs in an organism’s genetic makeup → leads to a new trait that becomes prevalent in the group

  2. Many organisms descend from this point & have this trait

  3. New variations continue to arise

     • Some are adaptive & persistent, leading to new traits

  4. With new traits, a new branch point is determined (go back to step 1 & repeat)

What is a shared ancestral character?

• A characteristic that is found in the ancestor of a group

• All the organisms in the taxon or clade have that trait

What is a shared derived character?

• Characteristic on a phylogenetic tree that only a certain clade of organisms share

• Only some of the organisms have the characteristic

• The characteristic derived at some point but DOES NOT include all the ancestors in the tree

What is maximum parsimony?

Applying the simplest, most obvious way with the least number of steps

1. Who created the first phylogenetic tree?

2. What features did this tree have?

1. Charles Darwin

   • His phylogenetic tree served as a prototype for subsequent studies\

2. Features

   1. Single trunk: represents a common ancestor

   2. Branches: represents the divergence of species from this ancestor

What were some limitations to the Classic Model/Darwinian Phylogenetic Tree?

1. Assumes that species evolve clonally

   • asexual reproduction

     • species produce offspring themselves

     • Reality: eukaryotes reproduce sexually

   • Random mutations are the only cause of genetic variety

     • Laws of Mendelian genetics explain that mutations within a species causes genetic variety

2. Did not consider the concept of genes transferring between unrelated species

1. What is Horizontal Gene Transfer (HGT)/Lateral Gene Transfer?

2. How does HGT affect the classical tree model?

3. In which organisms is HGT more prevalent?

1. Transfer of genes between unrelated species

   • May play a major role in evolution

   • introduces genetic material from one species to another by mechanisms other than the vertical transmission from parents to offspring → influences phenotypes

2. Complicates the simple tree model

3. More prevalent in prokaryotes

   • HGT & mutations are sources of genetic variation

1. What do genome fusion theories propose?

2. How is it tied to the endosymbotic theory?

• Genome fusion led to the evolution of the first eukaryotic cells via the endosymbiosis of prokaryotic species

• Endosymbiotic theory

  • One prokaryotic species was taken inside another species’ cytoplasm → fusion of two prokaryotic genomes

  • Species may have been from Archaea and Bacteria

Why are the evolutionary orgins of nuclear & mitochondrial DNA different?

• Mitochondrial DNA

  • derived from the bacteria’s circular genomes that ancient prokaryotic cells engulfed

  • smallest chromosome

  • only inherited from the maternal side

• Nuclear DNA/ eukaryotic nucleus

  • Prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome

    • No evidence of a nucleolus or nuclear pore tho

1. What is the nucleus-first hypothesis?

2. What is the mitochondria-first hypothesis?

3. What is the eukaryote-first hypothesis?

1. Nucleus-first hypothesis

   • nucleus evolved in prokaryotes first → fusion of the new eukaryote with bacteria that became the mitochondria

2. Mitochondria-first hypothesis

   • mitochondria were first established in a prokaryotic host → acquired a nucleus (by fusion or other mechanisms) to become the first eukaryotic cell

3. Eukaryote-first

   • prokaryotes actually evolved from eukaryotes by losing genes & complexity (sounds sus)

PROKARYOTIC mechanisms, mode of transmission, & examples?

1. Mechanism 1: Transformation

   • Mode of Transmission: Bacteria uptake naked DNA

   • Ex: many prokaryotes

2. Mechanism 2: Transduction

   • Mode of Transmission: a virus transfers the genes

   • Ex: Bacteria

3. Mechanism 3: Conjugation

   • Mode of Transmission: A hollow tube, or pilus, transfers genes between organisms

   • Ex: many prokaryotes

4. Mechanism 4: Gene Transfer Agents

   • Mode of Transmission: transfer random genomic segments from one prokaryotic species to another

   • Ex: purple non-sulfur bacteria

   • Most likely derived from bacteriophage DNA in

How did scientists find the first Gene Transfer Agents (GTAs)?

• GTS were derived from bacteriophage DNA inserted into a prokayote that lost the ability to produce new bacteriophages

• GTAs carry random DNA pieces from one organism to another

• GTAs & viruses are effecient HGT (horizontal gene transfer) vehicles with a major impact on prokaryotic evolution

EUKARYOTIC mechanism, mode of transmission, & examples?

1. Mechanism 1: From Food organisms

   • Mode of Transmission: transfer of fungal genes by HGT

   • Ex: aphid

     • Aphids make carotenoids on their own

2. Mechanism 2: Jumping genes 🙂

   1. Mode of Transmission: transposons/jumping genes

   2. Ex: rice & millet plants

3. Mechanism 3: Epiphytes/Parasites

   • Mode of Transmission: unknown

   • Ex: Yew tree fungi

     • fungi species feed on yew trees

4. Mechanism 4: Viral infections

How does HGT affect the classic “tree of life” model?

• Eukaryotes evolved from a pool of many species that were sharing genes by HGT mechanisms

• Web/network, rather than a tree with a single origin

What is the “web of life” model?

• Phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution

• Similar to the ficus tree model (multiple trunks represent multiple evolutionary origins)

What is the “ring of life” model?

• Phylogenetic tree model where all three domains of life evolved froma pool primitive prokaryotes

• Takes into consideration HGT AND genomic fusion into account