Need to Know

Macroevolution

evolution at a scale larger than speciation above the species level depicted in a tree-like diagram

Phylogeny

the hypothesized evolutionary relationships of a group of species, represented as a phylogenetic tree

ALL organisms are related by

descent from a common ancestor.

There is a bifurcating (branching) pattern to evolution

as in speciation events where a single lineage splits into two or more distinct lineages.

Change in characteristics occurs

in lineages over time

Evolution is not a

progressive ladder it is a rooted, branching tree

A taxonomic unit at any level is called a

taxon

What are the 8 levels of classification in order of biggest to smallest

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Humans and apes

share a common ancestor

Linnaeus came up with

a hierarchical classification system that goes from the most inclusive taxa to the least inclusive/most specific taxa

There are three Domains (that was not known until 70’s)

Bacteria, Archaea, Eukarya

What is this part of a phylogenic tree known as

Sister Taxa

What does the blue box represent

The unique ancestor of C

What does the green box represent

The common ancestor of B and C

What does the yellow box represent

The common ancestor of A, B, and C

Each species or unit being mapped on the phylogeny is a

taxon

Sister groups or sister taxa share

their most common ancestor

Each lineage has

ancestors that are unique to that line

Each phylogeny has/represents a

time line

The branches of a tree can be

rotated or swiveled around branch points without changing relationships

In phylogeny square or V trees

equal the same thing just different representations

Basal Taxon (Outgroup)

refers to a lineage that diverges early in the history of a group and lies on a branch that is close to the common ancestor of the group.

A clade or a monophyletic group is

a grouping that includes a common ancestor and all the descendents (living and extinct) of that ancestor

Clades can be nested in

larger clades

The oldest taxa is

the basal taxon that diverged first from the common ancestor. (Closest to the root of the tree)

Paraphyletic Group/Clade

a grouping that includes a common ancestor but not all of its descendants.

Polyphyletic Group/Clade

Grouping of species with different common ancestors

To infer phylogenies, systematists gather information about

structures, protein/DNA sequences… of living organisms and fossils

Organisms with more similarities are likely to be

more closely related than organisms with different structures or sequences

Homologies are

phenotypic and genetic similarities due to shared ancestry

Homologous Structures

Anatomical features in different species that share a common ancestry, reflecting evolutionary relationships.

Analogous Structures

Anatomical features in different species that serve similar functions but do not share a common ancestry, resulting from convergent evolution.

Contrast between Homologous and Analogous Structures

The contrast between homologous and analogous structures lies in their origins; homologous structures arise from a common ancestor and reflect evolutionary relationships, while analogous structures evolve independently to perform similar functions without sharing a common ancestry.

Convergent Evolution

The process by which unrelated species evolve similar traits or adaptations in response to similar environmental challenges, leading to analogous structures.

A phylogenetic tree represents a

hypothesis about evolutionary relationships

Phylogenetic trees show

patterns of descent, not phenotypic similarity

Phylogenetic trees do not always indicate

when species evolved or how much change occurred in a lineage

Do NOT assume that

a taxon evolved from the taxon next to it – sister taxa share a common ancestor, which was neither one of the descendent taxa

Divergent Evolution

the process in which two or more related species become more dissimilar over time, often due to different environments or selective pressures.

Homologous Structures are created by

Divergent Evolution

Vestigial Structures

A feature in an organism that is a historical remnant of a structure that served a function in the ancestor of the organism

Analogous structures are created by

Convergent Evolution

Shared Ancestral Character

A character that originated in an ancestor of the clade and are not useful for deducing relationships withing the clade (i.e. Backbone)

Shared Derived Trait

An evolutionary novelty unique to a particular clade which are useful in determining relationships/ building phylogenies (i.e. Legs)

An outgroup is used to

Distinguish between shared ancestral and derived characters

A trait can be both

Ancestral and Derived

We use a character matrix to

construct the simplest phylogeny with the fewest evolutionary steps (principle of parsimony)

Traits shared by many were

derived early and those shared by few evolved later

A derived trait is one that

Differs from its form in the ancestor of a lineage

The amniotes —reptiles, birds, and mammals—are distinguished from amphibians by their

Water-sealing amniotic membranes that protects the embryo from drying out

Phylogeny

is the evolutionary history of a species or a group of species

Why Study Phylogeny?

Classification: depict accurate patterns of relatedness for

organizing the diversity of life on Earth

• Forensics: assess DNA evidence in court cases to inform

situations, e.g. where someone has committed a crime or

where the father of a child is unknown.

• Identifying the origin of pathogens: to learn more about a

new pathogen outbreak and which species it is related to

• Conservation: to inform conservation policy about species

to prevent them from becoming extinct.

• Bioinformatics & computing: Computer algorithms involved

in analyzing molecular data and finding optimal

phylogenetic trees. Merging of Computer Science & Biology

binomial nomenclature

a system for naming species using two Latin names, the genus and species.

The discipline of systematics

Classifies organisms and determines their evolutionary relationships, and represented in a phylogeny

Linnaean taxonomy and systematics can

differ from each other

Anatomical homologies are sometimes

not visible in adult organisms, only in the embryonic state

Horizontal Gene Transfer

The movement of genes from one genome to another

Vertical Gene Transfer

The movement of genes from parent to offspring

Horizontal Gene Transfer occurs by

exchange of transposable elements and plasmids, viral infection, and fusion of organisms

Disparities between gene trees can be explained by

Horizontal Gene Transfer

Horizontal Gene Transfer has played a key role in

The evolution of both prokaryotes and eukaryotes

Which way do you read a geologic record table

Right to Left

Cambrian Explosion

A significant event in Earth's history marked by a rapid diversification of life forms in the fossil record, occurring approximately 541 million years ago. (Oldest of the three events)

Permian Extinction

The mass extinction event that occurred around 252 million years ago, leading to the loss of approximately 90% of marine species and 70% of terrestrial vertebrates, marking the end of the Paleozoic Era. (Second oldest of the three events)

KT Extinction

The mass extinction event that occurred around 66 million years ago, resulting in the extinction of approximately 75% of species, including the dinosaurs, marking the end of the Mesozoic Era. (Youngest of the three events)

What are the four steps of the Hypothesis if the formation of simple cells (Abiogenesis)

The four steps of the hypothesis for the formation of simple cells include the synthesis of organic molecules, the formation of polymers, the development of self-replicating molecules, and the encapsulation of these molecules within membranes to form protocells.

RNA was most likely the

first genetic material

The tree of life is not

a branching tree it’s more of a tangled web

Lateral gene transfe

is sideways between different lineages

Antibiotic resistance is due to

horizontal gene transfer and you can pick up resistant strains in hospitals

Any bacteria or virus that has infected you can

change your genome

8% of the human genome came from

viral infection

Inserting corrected genes into humans

CRISPER

We have gone through

5 ME and we are living through the 6th ME now

Precambrian Eon

1-Life originated (expand soon) (precursors of prokaryotes by 3.5 bya)

2-Prokarytotes gave rise to oxygen revolution 2.7 bya

3-1st eukaryotic cell came into existence 1.8 bya

Paleozoic era

Old Life

Mesozoic era

Mid Life

Cenozoic

Current Life

Organic molecules may have formed in certain types of

clay minerals (the clay facilitated reactions in helping materials stick together)

Miller and Urey and others generated

generated amino acids and RNA bases using heat and electrical spark (modeling volcanic heat and lightning) under early Earth conditions in the lab

What do you need for a protocell?

Fats and water (lipid drop) You form a compartment if you mix lipids with water

Life began the moment that

genetic molecules began to replicate and evolve by natural selection

Life began in a

self-catalyzing RNA world

The existence of ribozymes

(RNA that can serve as an enzyme) (before proteins existed) may have been the first genetic material

By natural selection, cells with DNA

had to have formed as DNA is a more long-term stable molecule

The first organisms were

single celled prokaryotes (Earths sole inhabitants for 1.5 Billion Years)

Stromatolites

The oldest fossils (3.5 Billion Years Ago)

Most atmospheric Oxygen (O2) is of

Biological Origin

The O2 revolution marks a change in Earth’s atmosphere due to

Photosynthetic prokaryotes (Not Plants)

Banded Iron Formations are

evidence in change in atmosphere

The endosymbiont theory proses that

Mitochondria and plastids (Chloroplasts) were formally small prokaryotes living within larger host cells as prey or internal parasite

What caused the second increase of oxygen

Plants

Oxygen is very reactive (TOXIC)

It can even damage our cells and DNA by creating unstable free radicals, antioxidants protect us (Oxygen may be why aging might be inevitable)

In the oxygen revolution there was

selection for primarily aerobic bacteria and cell respiration

Way more energy is produced through

aerobic respiration compared to anaerobic respiration.

What came first Mitochondria or Chloroplast

Mitochondria

All eukaryotic cells have

Mitochondria but not chloroplasts

Which eukaryotes have plastids

Plants and algae

Three steps of Serial Endosymbiosis

Large cell establishes membranes and inner compartments (invagination of membrane making a double membranous nucleus)

Larger cell then engulfs a small prokaryote (aerobic bacterium, photosynthetic bacterium)

Those prokaryotes then become organelles withing the larger cell leading to the formation of mitochondria and chloroplast

Why is serial endosymbiosis a theory

There is a lot of evidence for this: Scientists have demonstrated endosymbiosis in the lab and both organelles have their own circular DNA that looks like bacterial DNA. The inner membrane of organelles looks like those of bacteria. They divide like bacteria. They even have ribosomes that look like bacterial ribosomes (as well as sensitivity to antibiotics)