Phylogenetic Trees: Common Ancestry and

Divergence1B1: Organisms share many conserved core processes and features that evolved and are

widely distributed among organisms today. 1B2: Phylogenetic tress and cladograms are graphical representations (models) of evolutionary

history that can be tested.2D2: Homeostatic mechanisms reflect both common ancestry and divergence due to

adaptations in different environments

Shared Characteristics of Life

• Three main domains:• Bacteria – prokaryotic – single celled, no nucleus • Archaea – prokaryotic – single celled, no nucleus – closer relation to

eukaryotes – determined by looking at the rRNA (ribosomal RNA)• Eukaryotes – contain a nucleus and other membrane bound organelles

• All three domains share:• Same type of genetic material: DNA and or RNA• Central Dogma: DNAmRNAchain of amino acids (aka protein)• Metabolic pathways: ATP is the energy coinage for all three domains

• Cellular Respiration: Glycolysis, Kreb Cycle, Oxidative Phosphorylation (aka Electron Transport Chain)

Shared Characteristics of Eukaryotes• Endomembranes:• Nucleus: contains the genetic material (DNA)• Endoplasmic Reticulum: transports proteins to Golgi Complex• Golgi Complex: packages, sorts, transports proteins

• Organelles:• Mitochondria• Ribosomes• Chloroplast (only in plant cells)

• Linear Chromosomes

Phylogeny

• The evolutionary history of a species or group of species• To construct a phylogeny biologists use systematics

• A discipline focused on classifying organisms and determining their evolutionary relationships

• Systematists use data ranging from fossils, molecules (proteins), and genes (DNA, mDNA, rRNA) to infer evolutionary relationships• Info is used to construct a tree of life• Tree continues to be refined as additions information becomes available• Phylogenetic Tree: a branching diagram that shows the evolutionary

history of a group of organisms; represents a hypothesis

Terminology of a Phylogenetic Tree• Branch point: represents the divergence of two evolutionary lineages from a

common ancestor• Taxon (plural, taxa): think of it as describing the species level on a phylogenetic

tree• Sister taxa: group of organisms that share an immediate common ancestor and

hence are each other’s closest relatives• Rooted: brand point represents the last common ancestor of all the taxa in the

three• Polytomy: branch point from which more than two descendant group emerge;

indicates the evolutionary relationships among the descendant taxa are not yet clear• Clade: is a group of organisms that consists of a common ancestor and all its

lineal descendants

How to read a phylogenetic tree

What We Can and Cannot Learn from Phylogenetic Trees• Sequence of branching in a tree does not indicate actual ages of the

particular species• No assumptions should be made about when particular species

evolved or how much genetic change occurred in each evolutionary lineage• Cannot assume a taxon on a phylogenetic tree evolved from the taxon

next to it we can only infer sister taxa shared a common ancestor

Morphological and Molecular Homologies• Similarities due to shared ancestry are called

homologies• Two main types: •Morphological homology – similar structures due to a

common ancestor• Genetic homology – similar DNA sequences due to a

common ancestor

Partner Share

•Will the morphological homologies match the genetic homologies? In other words – if there is a structural change will there be a genetic change and vice versa? • If the morphological homology and genetic homology do not match then which one is more reliable when constructing a phylogenetic tree?

Sorting Homology from Analogy

•Morphological divergences between related species can be great and their genetic divergences small (or vice versa)• Analogy – similarity due to convergent evolution • Convergent evolution – occurs when similar environmental

pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages• Ex: Bat wing is analogous, not homologous, to a bird’s wing

• Both organisms evolved wings; however, they came from different common ancestors

Pair Share

•Explain the difference between homology and analogy. Explain why distinguishing between the two is critical when constructing an Phylogenetic Tree

Shared characters are used to construct phylogenetic trees• In constructing a tree the first step is to distinguish

homologous features from analogous features • Second biologist place species into groups of clades• Clade: an ancestor species and all of its descendants• Monophyletic – consists of an ancestral species and ALL of its

descendants• Paraphyletic – consists of an ancestral species and SOME of its

descendants • Polyphyletic – consists of taxa with more than one ancestral

species

Shared Ancestral and Shared Derived Characters• Shared ancestral character – characteristic that is

shared by ALL the ancestors in the taxon including the shared common ancestor• Shared derived character – characteristic that is not

shared by the common ancestor but appeared later in the evolutionary sequence

Inferring Phylogenies Using Derived Characters• Outgroup: a species from and evolutionary lineage that is known to

have diverged before the lineage being studied• Ingroup: a group of species whose evolutionary relationship we seek

to determine• By comparing members of the ingroup to each other and to the

outgroup, we can determine which were derived at the various branch points

Let’s Practice

With the person sitting next to you use the data table to construct a phylogenetic tree

2D2: Homeostatic mechanisms reflect both common ancestry and divergence due to adaptations in different environments

• Homeostatic mechanisms:• Osmoregulation: process by which organisms control solute concentrations

and balance water gain and loss• For physiological systems to function properly, the relative concentrations of water and

solutes must be kept within fairly narrow limits• Ions such as sodium and calcium must be maintained at concentrations that permit

normal activity of muscles, neurons, and other body cells• Excretion: breakdown of nitrogenous molecules releases ammonia, a very

toxic compound, the process of eliminating the nitrogenous waste • Thermoregulation• Digestive Mechanisms• Circulatory