Bio 2 Exam 1

phylogeny

the evolutionary history and relationship of an organism or group of organisms

phylogenetic tree

is a diagram used to reflect evolutionary relationships among organisms or groups of organisms (they are hypothesis because we will fully know their extent)

branch point

the point where a split occurs, and represents where a single lineage evolved into a distinct new one due to the environment.

The 3 types of phylogenetic trees

Y- Branching, Box, and Circular

Parsimony

means that events occurred in the simplest, most obvious way (with the fewest changes)

Clade

a most recent common ancestor (MRCA) and all of its descendants

MRCA

Most Recent Common Ancestor

Sister Taxa

two species or clades that are each other’s closest relatives on a given tree

Homology

shared traits that came from a common ancestor due to the similarities

Practice Question (Parismony) - Which tree below is most parsimonious (has the maximum parsimony)?

Tree #1

Practice Question (MRCA) - Which node shows the MRCA of gorilla and human?

C

According to this tree, the closest relatives (sister taxa) of gorillas are

Humans + chimpanzees + bonobos

Practice Question (Sister Taxa) - On the phylogeny below, the sister taxon of             SARS 5 + 6 + 7 is SARS

8

Practice Question (Sister Taxon) - On the phylogeny below, the sister taxon of             SARS 5 is SARS

6 + 7 + 8

Practice Question (MRCA) - On the phylogeny below, which node (A-F) shows the MRCA of SARS 5 and SARS 7?

E

Practice Question (MRCA) - On the phylogeny below, which node (A-F) shows the MRCA of SARS 2 and SARS 5?

C

Practice Question (MRCA) - Which letter (A-E) shows the MRCA of platypus and elephant?

D

Ancestral Trait

old trait that came before

Derived Trait

new trait that came after

Ancestral vs. Derived traits are

relative

Practice Question (Traits) - For (modern) humans and Neanderthals, knuckle walking is _____, and bipedal walking is ____.

Ancestral ; Derived

Practice Question (Traits) - For marsupials, live birth is a(n) ___ trait and a pouch is a(n) ___ trait.

Ancestral ; Derived

Practice Question (Traits) - For the platypus lineage (branch), hair is a(n) ___ trait and an amniote egg is a(n) ___ trait.

Derived ; Ancestral

Practice Question (Traits) - Four limbs are ____ for Tetrapods and ____ for Reptiles.

Derived ; Ancestral

Practice Question (Traits) - Vertebrae are ____ for Tetrapods and _____ for Vertebrates.

Ancestral ; Derived

Synapomorphy

a shared, derived trait

3 questions to determine them

1) Homology? are they shared

2) Derived ? is it a new trait

3) Unique ? are the traits unique to the organism or group

Practice Question (Synapomorphies) - Synapomorphies of mammals most clearly include

Milk and mammary glands

Homoplasy

shared character not inherited from a common ancestor

Practice Question (Shared Traits) - A bottlenose dolphin  can recognize itself in         a mirror.  Self-recognition is a  ______ for great apes, and a ______ for dolphins & great apes.

Homology ; Homoplasy

Practice Question (shared traits) - A skeleton and  four limbs is a ____ for animals and a ____ for brush-footed

Homoplasy ; Homology

Practice Question (Shared Traits) - An clear, unambiguous synapomorphy of tetrapods is

4 bony limbs

Outgroup

closely related taxon with ancestral traits

A useful outgroup for building the entire tree      of mammals    + reptiles would be

Salamander

Assume this tree is complete.  Compared to the chimp + bonobo clade, its sister human clade has been

(B) and (C)

According to this tree of African apes

Homo erectus and H. sapiens could have met in Africa

Polytomy

A node on a phylogeny where more than two lineages descend from a single ancestor

According to this tree, a clear synapomorphy of reptiles is

Molting

Monophyletic

when a group includes a most recent common ancestor and ALL of it’s descendants

Paraphyletic

when a group includes a most recent common ancestor and some of its descendants

Polyphyletic

groups that share traits however they have a different most recent common ancestor

Parasitic Plants (those in blackshow) are show to be what type of group ?

Polyphyletic

According to the phylogeny below, Australopithecus is ____phyletic and Homo is ____phyletic.

Para ; Mono

Beetles that are not herbivorous are

Monophyletic

Beetles that feed on flowering plants are

Polyphyletic

Beetles that feed on cone-bearing plants are

Paraphyletic

HIV is

Polyphyletic

The phylogeny of the SARS virus below suggests that the original host of SARS was most likely

Bat

On the phylogeny below, the clade of   SARS 2, 3, and 4 most clearly

is not resolved

Phylogram

a type of phylogenetic tree where the branch lengths signify evolutionary change

Big Bang

theory on how the universe expanded from a single point of high density and temperature

Supernovas

they are early stars made from dust and gas

Practice Question (Life’s Origins) - In general, the evolution of new types of plants is associated with ____ in O2 concentration and ____ in CO2 concentration

Rise ; Fall

Practice Question (Life’s Origins) - The evolution of giant insects is associated with ____ in O2 concentration and ____ in CO2 concentration

Rise ; Fall

Big 3 Metapatterns

Genetic Information

Membrane

Metabolism (Chemical Reaction)

Genes First Hypothesis

States that life began from self replicating RNA.

Metabolism First Hypothesis

States that life began from chemical reactions placing them before genetic material

Lipids first hypothesis

States life began from self-assembling structures.

Practice Question (Early Earth) - Compared to volcanic vents, snowball Earth would have _____ energy available for chemical synthesis, and organic molecules that formed would be ____ stable.

Less; More

Practice Question (Origins of Life) - "Intelligent design" (creationism) is not a scientific hypothesis because it is not

Testable

LUCA

Last Universal Common Ancestor

Luca Hypothesis

• Non Cell

• Proto - Cell

• Community

• Cell

Practice Question (Origins of Life) - This hypothesis suggests that the LUCA was

a protocell

3 domains of life

Bacteria

Archaea

Eukarya

According to this tree, which are sister taxa?

Archaea and Eukarya

Practice Question (Bio Classification) - What Plant is this ?

D

Practice Question ( Virus Size) - A typical virus (e.g. T4 phage) is about ____ times smaller than your fingernail.

100,000

HIV Virus

All Have :

Genome (RNA or DNA)

Capsid (protein)

Some Have :

Envelope (membrane)

Envelope Proteins

Coronavirus

All Have :

Capsid (protein)

Some Have :

Envelope (membrane)

Envelope Proteins

Tobacco mosaic virus

All Have :

Genome (RNA or DNA)

Capsid (Protein)

How did viruses originate

3 possible theories

Virus first - came before cells

Progressive - escape from proto-cells

Regressive - degenerate cells

The Virus world is mostly a version of the _____ hypothesis for the origin of viruses

Progressive

Practice Question (Bacteria) - A synapomorphy of Spirochetes would most likely be

B. Particular DNA Sequences

Gram Positive vs. Gram Negative Bacteria

Gram Positive

• Thick Wall

• 1 membrane

Gram Negative

• Thin wall

• 2 membranes : outer and inner

Practice Question (Bacteria) - Given that the bacterial cell wall is an open mesh of fibers and membranes are selectively permeable, which type of bacteria do you predict would  be more resistant to antibiotics?

Gram Negative

Are viruses alive

evidence that they aren’t :

they are non cellular

they have no metabolism

many crystalline outside of host

evidence that they are :

they have DNA or RNA

they can replicate , mutate , and evolve

Prokaryotes Internal Membranes

Increases surface area for metabolism

The 3 methods of genetic recombination by horizontal gene transfer, in bacteria

Transformation

Conjugation

Transduction

Bacterial Diversity : Shape

Bacteria can come in different forms such as :

Spheres (coccus)

Rods (bacillus)

or Corkscrew (spirillum)

Bacterial Diversity : Size

Bacteria can also come in different sizes : either microscopic , or big enough that they are visible to the naked human eye.

Multicellular Bacteria

• is a single species

• division of labor

• some cells give up reproduction

• examples include Actinobacteria and fruiting bodies of proteobacteria

Biofilms

a type of bacteria that is of mixed species and can be found in many places such as :

• soil & desert crusts

• ocean, shores, streams

• tree trunks and branches

• water pipes

• on and in other organism

Practice Question (Bacteria) - Based on the criteria given, which are multicellular?

Both (B) and (C)

Practice Question (Metabolism) - A soil bacterium that gets its energy and electrons from oxidizing NH4, and its carbon from CO2 would be a:

Chemolithoautotroph

Practice Question (Phylogenetic Trees) - This tree is a ____,      and it shows that      most bacterial & archaeal diversity is known from

Phylogram ; DNA only

Practice Question (Phylogenetic Trees) - In this tree, Bacteria ____ sister to  Archaea + Eukarya , and Archaea are ____.

are ; paraphyletic

Archaea

similar morphology to bacteria , however differ in

• gene expression

• cell structure

• unique membrane phospholipids

• unique crystal protein wall

• unique flagella

Some archaea are thermophiles, a type of extremophile.

meaning they grow best and thrive in very high temperatures , but can in general be found anywhere such as oceans, soil, animal guts and even our skin.

Why are plants and other organisms green ?

They have pigments and when the light hits them , what is reflected back is the color we see (green leaves as an example). All other colors are absorbed.

Absorbtion Spectrum

shows which colors absorb more than others , a low absorption level signifies a higher reflection and therefore a color we can see.

Practice Question (Color Absorption) - The absorption spectrum of the dominant  pigment in this leaf is most likely ?

C

What is the name of this process ?

Photosynthesis

Practice Question (Photosynthesis) - A tree’s wood (mass) comes mostly from

D. CO2

Global Warming & Plan Growth

Global Warming increases photosynthesis but also increases respiration thereby decreasing the growth potential of plants

Practice Question (Plant Growth) - According to the results shown, a tomato plant will grow best at about ____, and will stop growing at about ____.

75°F ; 95° F

Global Warming & Food Security

• CO2 enrichment, but there is a nutrient limitation on photosynthesis

• Plants grow more, but incorporate less nutrients

• Insects grow faster, and are hungrier , eating more plants than usual

• Less nutritious food & more crop losses

Protists

(mostly) microbial eukaryotes

Eukaryotic Cell

main difference between prokaryotes is they have organelles surrounded by membrane

Sex in unicellular eukaryotes

involves

1) mating of + and - genes

2) fertilization

Practice Question (Unicellular Eukaryotes) - What is sex ?

(B) Combining whole genomes

(C) Separating combined genomes

(D) Genetic recombination

Eukaryotic Flagella

• presence is not informative, homoplasious for phylogeny

• morphology can be homologous