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116 Cards in this Set

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C
Group A is sister taxon to Group I

True or False
False

group I no longer exists: its genetic lineage is now divided between taxa B and C

So Group A is sister taxon to Groups B and C
List the sister taxon (or taxa) for:

a) B
b) G and H
c) E, F, G, and H
d) E
a) C
b) E, F
c) D
d) F
a) Which taxon or taxa share characters 6 and 7?

b) Which taxon or taxa share characters 6 and 5?

c) Which of the numbered features is present in taxon E?

d) Which of the numbered features is present in taxon H?
a) E, F, G, H

b) D

c) 6,7,9

d) 6,7
a) How many evolutionary steps were needed for Tree 2?

b) How many evolutionary steps were needed for Tree 3?
a) 2

b) 2
a) List the number of changes found for each tree

b) Which tree is most likely to represent the pathway of evolution according to the Principle of Parsimony?

c) How did you decide which tree was most parsimonious?
b) Tree 1

c) Set outgroup to be arbitrarily zero. Then look at how many evolutionary steps to change into a non-zero number for each character state. The most parsimonious totaled to be the least number of steps.
a) Ingroup is L,M,N. Fill in Tree 3, there's only 1 correct construction. Find the total number of changes for each tree.

b) Which character(s) could be used to identify members of group L,M,N?

c) Which character provides no useful information about the relationships among taxa L.M.N?

d) Most likely sister group to taxon L?

e) Ancestral state for character 1?

f) Which state(s) are derived for character 1?
a) Tree 3 (from left to right): XMLN

b) 1,4,6

c) 2,3,5

d) M

e) 1

f) 0, 2
Why would character(s) on a data matrix not be considered phylogenetically informative?
No variation--no change

One taxon different, all others same--only 1 evolutionary step
If the wolf-like morphology occurs in the animals that share it because this body form produces a very efficient predator, the morphology is an example of _____________ evolution.
Convergent

-two dissimilar species come to look like each other
Is a group containing grass, bees, and Formica a monophyletic group? Explain
No

one of the descendants of the most recent common ancestor of this group (Myrmica) has been left out.
Assuming the tree is correct, does the term "prokaryote" describe a monophyletic group?

Note: Prokaryote = Bacteria & Archaea
No

A monoplyletic group is a group that contains ALL descendants of a single recent common ancestor
In which of the trees do prokaryotic taxa form a monophyletic group?
Tress 1 & 2
Use clues obtained from the names of organisms, and from your general knowledge, to match the scientific names at left below with the correct description at right

Hints:
Holger Jannasch was a microbiologist who explored deep ocean habitats.
The Greek root "halos" refers to sea or salt.
The Latin root "lactis" means milk.
Is the organism whose fundamental metabolism is shown in Figure 4 aerobic or anaerobic?
Aerobic
The curve for Escherichia coli is in red. What do you notice about its optimum temperature in relation to where it occurs in nature?
Its optimum temperature (30-40 C) is also the same as the normal human body temperature. E. Coli is commonly found in the intestines.
What problems do you foresee if a laterally transferred gene were used in a phylogenetic analysis?
Introduced genes are highly variable

Genetic material is able to be transferred amongst many organisms, even those who are extremely distant

Lots of polytomies
How might a cell protect itself from foreign DNA in light of transformations, conjugations, and transductions?
The cell can produce its own foreign body fighters like interferons or have its host's phagocytes help, or become unfavored by natural selection so that the genes can be lost
When might invasion with novel DNA from other organisms in the same habitat provide an advantage to the new host?
Increase favor of natural selection, like antibiotic resistance, ability to tolerate new things, etc.
Explain in your own words, why molecular sequence techniques revolutionize environmental microbiology.
You can make a list of many different organisms from any location in the world because all organisms have the ss-RNA gene. It makes it easier to draw a tree and figure out extinctions, branches, MRCA. Information like this would be useful to figure out new ideas, plans, drugs, etc.
A cladogram is a hypothesis about evolutionary relationships. Explain how hypotheses about evolutionary relationships can be tested.
It can be tested with more evidence from fossils, dispersal and geological events, DNA, and comparing sister taxa. It'll either help accept or refute the hypothesis and make better cladograms.
Taxon
a group of organisms at an unspecified level of classification scheme

Species, a phylum, any other group of organism

New taxa result from the splitting of a common ancestral taxon into descendants

Taxa can rotate around the node
Tree
a diagram depicting a pattern of lineage splitting – aka evolutionary tree

Branching pattern on a tree represents ancestor descendant relationships

To construct a tree, need evidence and to determine parsimony (least number of steps)

Ancestral character states and outgroup comparisons – needed in order to determine the most likely tree

When constructing trees must eliminate useless data – aaag or aaaa

Recognize that trees able to freely rotate, need morphology to characterize tree (subjective- behavioral data, DNA – molecular data)
Cladogram
tree depicts only the sequence of splitting events

Each cladogram is a hypothesis about evolutionary relationships among taxa
Phylogram
the length of each branch in a tree intended to be proportional to the amount of evolution that has occurred after the lineage splitting event
Sister Taxa
form by lineage splitting
extant
living species
MRCA
most recent common ancestor – all cladograms have one -
Characters
features or traits of organisms – can be morphological, molecular, and behavioral

Indicating a character means that it originated there and passed to all descendants of lineages from that point on

Map characters one at a time
Principle of Parsimony
biologist accept the most likely tree as the one with the least/ simplest steps that explains all the evidence
Ingroup
taxa of interest that are derived from a MRCA
Outgroup Method
based on the assumptions that the character state shared between the ingroup and the outgroup is ancestral
Derived Trait
character states that evolve beyond the MRCA and are novel for the ingroup taxa
Why is knowing Ancestral Traits helpful?
Knowledge of the ancestral states is useful because it tells which of the character states was present before in the ingroup before it actually evolved within the group and which evolved before the ingroup formed.
Polarity
can determine by knowing which character state is ancestral and which is derived
Reversal of State
way in which the character state starts at 0 changes to 1 and returns back to 0, causes extra steps – typically unparsimonious . when a character evolves independently evolves twice
Why are morphological, molecular and behavioral characters are all useful for phylogenetic data?
need some variation such that they come in different character states
need to be derived from a common ancestral form – homology (common ancestry)
homologous characters
present in organisms because they were inherited from a common ancestor

example – mammals share hair, mammary glands, four chambered heart
If 2 structures look the same but did NOT come from a common ancestor must have evolved ___
independently

Example: fish fin and dolphin fin – though appear similar evolved independently because don’t not have the same funtion. Dolphins are part of the mammalia family and classified under mammary glands etc.
Homoplasious/ analogous
two structures with the same morphology but the morphology was not inherited from a common ancestor
Convergent
if the structures were shaped by NATURAL SELECTION for the same function (one way to form homoplasious structures

EX: Dolphins and fish fins
Traditional Classification
italicized and binomial

genus then species (often descriptive)

Kinky prostitutes can offer feel good sex (kingdom, phyla, class, order, family, genus, species) – point of hierarchy is to indicate different degrees of relationship
Cladistics
construction of cladograms

critical that each part of the cladogram represents a monophyletic group (group contains all the descendants of a single common ancestor)
Polytomy
undefined branching pattern
How many trees possible when there are 4 taxa with 1 outgroup?
3
Paraphyletic
MRCA but not all descendants
Polyphyletic
NO MRCA – least informative
Congruent
when characters support the hypothesized tree
3 domains of life
Bacteria, eukarya, and archaea
Eukarya
house genetic info within a membrane bound nucleus, large organisms
Prokaryotes
archaea and bacteria – the overwhelming majority of organisms

Prokaryotes are non-monophyletic missing eukarya thus it is paraphyletic
Body Forms
Coccus – sphere

Bacillus – rod shapped

Helical – spiral/ twisted

Some have flagellum - not a homologous trait between the two groups, if seen will be singular post anterior
Phospholipid membrane
surrounded by cell wall
Asexual reproduction
binary fission, either disperse or form multicellular colonies where some cells have specialized functions
Energy
To gather energy – captured by light (phototrophy) or taken by chemical reactions (chemotrophy)

Captured energy must be converted into ATP using an electron source

Electron donors – inorganic substances (H2S and ammonia NH4) or organic substances (lactate or CH4 methane)
Lithotrophs
use inorganic electron donors
Organotrophs
use organic electron donors
Carbon Source
atmosphere CO2 or from organic compounds

Autotrophs carbon source is from inorganic carbons

Heterotrophs – carbon source taken from sugar (glucose)

Other growth requirements – S, P, M, N
Vertical Transmission
When the cell divides, chromosome copied so each daughter cell is genetically identical to the original cell.

Passing of genes from haploid parents to daughter or ancestor to descendant
Plasmids
small circular DNA, accessory genes – not essential for the normal cell function allow to be pathogen etc.
Housekeeping genes
the large circular chromosomes required for critical function
Lateral gene transfer
plasmids able to be genetically transferred among microorganisms – among distantly related forms
transformation
DNA fragments from cells are moved into intact cells, fragments incorporated into the genome by CROSSING OVER (recombination), portion of the hosts DNA replaced with new sequence from outside cell. If can transform = “competent”
conjugation
: form of mating. Can occur between distantly related cells. A Pilus (tube) forms between cells (sex tube). Plasmid in donor cell replicates and passes through the sex tube to the other cell, pilus then breaks
Transduction
use viral phage particles, can move genetic material over large evolutionary distances – cause death to the cell
Problems with Lateral Gene Transfer
causes very messy and complex evolutionary history harder to phylogentically analyze

Can analyze RNA/DNA using genetic analysis – use PCR to replicate the sequence – align and determine relationships
LAST UNIVERSAL COMMON ANCESTOR – LUCA
MRCA for all life (3 domains: bacteria, eukarya, archaea)
Characters specific (synampomorphies) to Archaea:
Occasional plasmids

methanogens

No photosynthesis via chlorophyll

Polymerase 2

No operons

Linear
Synampomorphies for bacteria
NONE all shared with either archaea or eukarya
Synapmorphies for eukarya
No nitrogen fixation,

rare plasmids,

membrane bound lipids,

mitosis,

RNA polymerase I, II,III,

ribosome size 80s,

no operons,

nucleotides usually linear
LUCA synapomorphies:
DNA with ACTG

3 letter codon

lipoprotein membrane
How to determine if a gene is ancestral
Compare base pair sequence for a particular gene, if related organisms then expect genes to have similar transmissions

If gene inherited from a common ancestor then expect it to be shared widely/ distributed among descendants

All genes inherited from a single common ancestor should produce same tree – if transferred gene then have very different trees

Low number of GC = unstable = more likely for LGT
2 ways unique proteins arise in a genome
LGT

Mutation
Most likely to transfer by LGT
pathogens then antibiotic synthesis then energy metabolism
mutualistic interactions of archaea and bacteria
Symbiotic interactions – long term associations between 2 organisms

mutualism +/+

predation/ parasitism +/-

bacteria = both mutualism and
predation

archaeons never parasitic only +/+

extreme forms of multulasim in eukaryotes – cyanobacteria --> chloroplasts; alpha-proteobacteria --> mitochondria

bacteria example – fix nitrogen for plants – legumes and rhizods – rhizobium bacteria in soil invade root tissue and attach to plant in form of nodules. Inside nodules able to fix nitrogen use nitrogenases (enzyme). Inside nodule appear RED due to leghemoglobin

cyanobacteria example – algae and fungi form LICHENS

thermal vent tube worms – completely depend on internal pockets of chemoautotrophic

bacteria – no light reaches use H2S

bacteria and archaea help in cellulose digestion – TERMITES have protozoa help digest wood
Microbes save the earth
bioremediation uses chemical processes to solve human pollution problems

most are bacteria

ex. Gas storage, oil refining

paper production

fire retarding

by products – carcinogenic

three kinds
-natural attenuation: microbes, substrates and necessary nutrients already present together
-biostimulation – naturally occurring bacteria and archae – but pop artificially enhanced
-bioaugmentation – needed organisms introduced into the environment

methanogenic – archaea, extreme environment, product

methanotophic- metabolize, soil, marshes, reduce methane gas
Microbial eukaryotes
protists (unicellular or colonial eukarya)

very speciallzed organs for

photosynthesis

respire

have genetic info in nucleus
Body Forms of Microbial Eukaryotes
amoeboid – organic shape
- move by extension of the cytoplasm outward – PSEUDOPODIA!

flagellate – have tail
-similar to bacteria


ciliate – short cilia in a row

have cytoskeleton for cell wall

allow to move, adhesion to surfaces
Microbial Eukaryote Reproduction
unicellular (gametes) can fuse to form diplontic bodies – or asexually
Euglena
move: flagellum

photosynthetic evident by color,

MIXOTROPH can also be heterotrophic
Stentor
ciliate

photosynthetic

autotroph – green color
Blepharisima
2 morphs – rod and cannibal double rod , ciliate

HETEROTROPHIC

pink color
Paramecium
heterotrophic
Amoeba
pseudopodia, heterotroph
Chlamydomonas
2 FLAGELLAS! Photosynthetic (green)
Naegleria gruberi
amoeba

move by pseudopodia, over time the amoeba will FLAGELLATE – need more mobility so able to feed – able to SHAPE SHIFT need to adapt to food environment
origins of eukaryotic cell
phagocytis – result of primary and secondary endosymbiosis

primary – bacterium (alpha proteobacteria) engulfed by heterotrophic eukarya

secondary – when the primary eukarya is eaten by another eukarya (with organs)

can determine by number of layers in cell
Strobilus
when sporophylls that bear sporangia are clustered along an axis
Pine life cycle
Megasporangium (nucleus) produce 4 megaspores, 3 degenerate, remaining = egg

Microsporangium – sperm – develop into pollen grain with pollen tube nucleus and 2 sperm buclei
Gymnosperm
3 generations in seed while angiosperm has 2 generations (due to double fertilizaiton) but has 3n endosperm
Aggregate fruits
multiple independent ovaries in a single flower – blackberry
Thallus
body of fungus
Hyphae
filaments make up body of fungi
mycelium
Mass of hyphae
Septa
hyphae may be divided by cross walls – to create individual cells
Unicellular Fungi
yeasts, dimorphic (change between mycelium and yeast form – heat activated like in body temp)
Ascomycota
45,000 species

have tiny sacs

monophyletic

unicellular

filamentous

have septae fungi

internal fruiting body
Basidiomycota
the club fungi

terresterial

filamentous

no flagella

multicellular

long lived dikaryotic stage

tends to be external fruiting body \, 4 nucei exposed

jelly like
aquatic animals have suspension feeding
can be filtered with sieve element, phyranx- mouth with suctions
Intracellular Digestion
– if small can be taken straight into cells – sponges – no GUT CAVITY
Extracellular Digestion
need internal cavity, where enzymes concentrate- sac like, tube etc.

sac guts called one-way or two-way
monoecious
no sex- hermaphrodite – similar to homospory – have both male and female sex cells (they will tend to be the same size)
dieocious
have 2 sexes – male and female – female tend to be larger
Mosaic Cleavage
distribution of mRNA determine fate, if cell LOST early then can NOT be replaced,

SPIRAl
Regulative Cleavage
cell NOT determined by distribution of mRNA but by CHEMICAL GRADIENT , if cell lost then another can compensate for it

RADIAL
Sponges
No true tissue, cells together to form skeletal structure

Body made of channels – special flagellated cells- choanocytes – move H20 and capture food

Large pores – exits for chambers

Radial symmetry

No cephalization

Absent gut
Cnidaria – sea anemones, jellies
Sting bearing

2 body forms
-polyp
-medusa

sexual and asexual reproduction

polyp – asexual – budding or fission - can form clone, if stay together physically then colony

radial symmetry

one way gut

stinging due to nematocyst (hooks)

polyp – anemone

medusa – jellies

yes – cephalization
Mollusca – chitons and bivalves
Shell, mantle, foot, and radula (inside mouth)

Radula – feeding part – scrape algal with mouth to get tissue to eat

Lots of habitats – free living ( squids) or sediments (clams)

Sessile bivalves – suspension feeders

Molluscs example of protostomes

Spiral, mosaic cleavage – blastospore becomes mouth

BLASTOSPORE – TWO MAJOR CLADES –
-Lophotrochozoans – by presence of a trocophore larval stage
-Ecdysozoa – contains animals that grow by molting cuticle

Bilateral – chitons an mollusks

Incomplete chiton gut

Cephalization??
Mollusca – gastropods and cephalopods –snails
Bilateral body

Squid – bilateral

Yes cephalization

Complete 1 way gut

Tentacles
Annelida
Earthworms and leeches

Segmented body – can tell bu outer and inner ring

Each segmented is a repeated body unit – contain both respiratory

Gut NOT segmented – runs from mouth to anus

Terrestrial annelids have a limited range of body types – marine worms very extremely diverse

Protostomes

Spiral mosaic cleavage

Bilateral symmetry

Blind gut

No cephalization

Clitellum - fat band allows for worms to reproduce
Arthropoda - trilobites, chelicerates, myriapoda
Segmented body

External and internal

Curtain of tissue – septum, separates segment

Each segment repeated body

Contains respiratory and reproductive organs

Runs from mouth to anus

Exoskeleton – arthropods have a hardened cuticle – forms a protective covering the body

Evolutionary trend – fusion of segments into discrete body regions – tagmata (singula tagma)

Protostomes – different cleavage – changes spiral cleavage

Blastospore – become the mouth

Cuticle must be molded

Appendages – joints

3 body parts to tagamtized body – cephalon, thorax, pygdium

yes – arthropods cephalized

complete gut
Arthropoda – hexapods
6 legs, attached at joints

hemimetabolous - small increase
What does the barnacle use to extract particles from the water?
Specialized appendages called cirri (modified legs) to comb through the water and trap particles
How do snails, limpets, and chitons stay attached to rocks in the intertidal zone?
It pushes down on the rock surface at the edges and is lifted in the center to create suction. Muscus is also used to increase the suction-cup effect
Are polyps the products of sexual or asexual reproduction, or both? Are new medusae the products of sexual or asexual reproduction? In what stage are gametes produced?
The 1st polyp, from planula, is the product of sexual reproduction, but all later polyps of the same genotype are the result of asexual reproduction

All medusae are the products of asexual reproduction, but they themselves make the gametes (they reproduce sexually)
Is the gut in the sea anemone complete (mouth and anus) or incomplete (mouth only)?
Incomplete

There's a mouth, but no anus

The gut just ends blindly in the middle half of the body
In molluscs, slow-moving animals have open circulatory systems, but rapid swimmers, like the squid, have closed circulatory systems. How can a flying insect with a large demand for oxygen get away with an open circulatory system?
Insects are not using the circulatory system to supply oxygen to all the tissues. They use a separate system, the trachea, to supply oxygen directly to each cell without involving respiratory pigments in the blood. The roles of lungs or gills (oxygen pick-up) and blood (oxygen distribution) are both taken over by the trachea