Midterm 2 Flashcards
Who came up with the idea of biodiversity classification? What did they invent?
Carl Von Linnaeus - invented binomial nomenclature = classical taxonomy system
What did Linnaeus believe about organisms? Suggested?
Believed in immutability of species = suggested world’s biodiversity originated east Turkey where Noah’s ark landed
Why use binomial nomenclature and not common names? 5 reasons
1- consistency
2- clear communication between languages
3- some species have no common name
4- clear distinction between species and subspecies
5- evolutionary (phylogenetic) interpretation
What is taxonomy?
The science and system of classifying organism
What is taxon (or plural Taxa)?
A single level in the taxonomic classification system
What is systematics?
Science and system of organization and classifying Taxa and understanding the evolution of traits based on their phylogenetic relations
What are the 2 methods of systematics?
1- phenetic
2- phylogenetic
Explain phenetic as a method of systematics
Species are grouped according to their overall similarities
Explain phylogenetic as a method of systematics
Species are classified according to how they shared a common ancestor
Identify the 2 methods and 3 schools of systematics and which ones are linked
(Method) phenetic –> (school) numerical taxonomy
(Method) phylogenetic –>
(school) cladistics = phylogenetic systematics
(school) evolutionary taxonomy = evolutionary systematics
What does scientific nomenclature and taxonomy reflect?
Phylogenetic relationships = all members of a tax on should share a single common ancestor
How can we figure out phylogenetic relationships if we can’t go back in time?
We use evolutionary principles to compare traits among Taxa
What is phylogenetic systematics?
Philosophy and methodology for the reconstruction of ancestor - descendant relationships amongst a set of Taxa
What are the 4 basic tenets of phylogenetic systematics?
1- characters
2- history of changes
3- distribution of characters
4- monophyletic groups
What is the first basic tenets of phylogenetic systematics?
Characters used to reconstruct a phylogeny are modifications of pre-existing characters
What is the second basic tenets of phylogenetic systematics?
History of changes in characters reflect the ancetsor-descendant relationships of organisms so bearing the characters
What is the third basic tenets of phylogenetic systematics?
Distribution of characters among a set of Taxa is used to identify monophyletic groups
What is the fourth basic tenets of phylogenetic systematics?
Monophyletic groups are identified by shared derived traits. All other Taxa outside the monophyletic group possess the ancestral trait
What is cladistics?
Relationships are determined by the presence of synapomorphies = shared/derived characters
What are the 2 ways characters can occur?
1- plesiomorphic = primitive or original state
2- apomorphic = derived state
What is the monophyletic group?
Defined by synapomorphies (contains hypothetical common ancestor and all of its descendants)
What is paraphyletic group?
Group containing a hypothetical common ancestor and some (but not all) of its descendants
What is the polyphyletic group?
Taxa not including their hypothetical common ancestor
How does phylogenetic classification relate to cladistics?
It groups species based on their most recent common ancestor
How does phylogenetic classification relate to cladistics work? And what is it called?
species split during evolution = forms 2 descendant species = cladistic classification groups them together
Called sister species
Who and when came up with the idea of phylogenetic classification relating to cladistics?
Ridley in 1996
What is a phylogenetic tree a hypothesis of?
Evolutionary relationships between species
What is the problem of a phylogenetic tree as a hypothesis and why is this?
Can’t know true pattern of ancestor-descendent relationships as we can’t travel back in time = only generate most probably with data given
The characters used to reconstruct a phylogeny come from? (3)
1- fossil record
2- morphological traits of living of museum species
3- genetic sequences
What is used to distinguish monophyletic groups/traits?
Shared derived traits
What is another name for monophyletic groups?
Clades
What is homology?
Similarity in character due to a common ancestry evolving from the same ancestral state
What is the important note about homology?
Homologous characters can appear very different
What is analogy?
similarity in a character due to evolutionary convergence = not shared ancestor
What is important to note about analogy and convergence?
Evolutionary convergence that affects analogy where the convergence is phenotypic is usually the result of NS
In the example of bat wings and bird wings explain homology?
Forelimbs = homology as both are inherited from a common ancestor with forelimbs
In the example of bat wings and bird wings explain analogy?
Wings = analogy as both wings evolved from different ancestors that didn’t have wings
When is homology and analogy not easy to tell apart? And why?
When phenotype is similar
Due to shared ancestry (homo) or convergence (Ana)
What is the first solution in telling apart homology and analogy?
Use traits that are very likely to be selectively neutral = no advantage or disadvantage
What is the second solution in telling apart homology and analogy?
Use many many selectively neutral traits as unlikely all influenced by selection the same way = DNA
Who created the Caminalcules?
Joseph H. Camin
What are Caminalcules?
Imaginary animals used for exercises for the principles and problems associated with classification and cladistic relationships (sequence of character change)
What are the 4 things to describe Caminalcules?
1- “evolutionary” derived
2- a degree of “genetic” similarity
3- monophyletic group
4- no preconceptions as to taxonomic significance
How is an organism’s evolutionary history documented?
In its genome
How does molecular systematics help to document an organism’s evolutionary history through it’s genome?
Uses DNA to get relatedness
How many bases of DNA has scientists discovered and in what?
110 Billion sequences of DNA in 1000’s of species
How does 2 species help to document an organism’s evolutionary history through it’s genome? (2)
More recently branched from common ancestor the more similar the 2 species are in DNA sequences
Longer the 2 species have separated the more diverged their DNA are
What can neutral variation do?
Neutral variation among DNA sequences can be used to get a molecular clock
What do phylogenies allow us to evaluate?
Evaluate the hypothesis about the origins of biodiversity
What does eukaryote mean?
Tue nucleus
When did eukaryotes first appear?
Fossil record shows 1.5-2.1 BYA
What is a eukaryote?
Membrane bound nucleus and organelles
How did cells change from prokaryotes to eukaryotes?
Prokaryotes = simple strand of DNA inside cell Eukaryotes = mitochondria, nucleus with DNA bond inside
What was the 2 major changes needed for prokaryotes to evolve into eukaryotes?
1- internal membrane and organelles known as endomembrane system
2- multicellularity = 1st eukaryotes were unicellular and many still are
What are the 5 internal membranes and organelles in the endomembrane system as one of the major changes needed for prok->euk?
1- smooth and rough ER 2- Golgi apparatus 3- vesicles 4- nuclear envelope 5- plasma membrane = interact with endomembrane organelles
What hypothesis is connected to the internal membranes and organelles as a major change from pro->euk?
Infolding hypothesis = endomembrane system resulted from infolding and pinching off of the plasm membrane
Explain how the plasm membrane pitches off and what does it form in the infolding hypothesis
Cell membrane dips inwards
Cell membrane closes around the inwards dip
The now closed dip is pinched off to floats off into cell = called a vesicle
What hypothesis is connected to the multicellularity as a major change from pro->euk?
Colony hypothesis = suggest multicellularity began when single-called organisms started to form colonies
Explain the 5 steps as to how colony hypothesis worked
1- unicellular flagellated protist 2- multiple flagellates make aggregate 3- unspecialized flagellate cells form hollow sphere 4- specialized reproductive cells form 5- cells begin to fold in to make tissue
What are the 4 steps that determined colonial green algae range of independence?
1- single-called and independent
2- individuals in colonies break apart and live independent
3- some individuals no longer independent
4- most not independent
In the 4 steps that determined colonial green algae range of independence and are the types of algae associate with each step?
1- single-called = Chlamydomonas
2- break apart = Gonium, Pandoria, Eudorina
3- no longer = Pleodorina
4- not indep = Volvox
What can a colony provide?
Protection
What 2 organelles are thought to have different origins than those of the infolding hypothesis?
Mitochondria and chloroplast
Where is it believe that mitochondria and chloroplast evolved from? What is this hypothesis called?
Descendants of free-living prokaryotes = endosymbiotic hypothesis
How does endosymbiotic hypothesis work?
Larger cells engulf smaller cells
Smaller cells live symbiotically within larger rather than being digested
Who found evidence of the endosymbiotic hypothesis?
Dr Margulis
What are the 4 basic idea that Dr Margulis discover for the endosymbiotic hypothesis?
1- double membrane
2- morphology of chloroplast
3- morphology of mitochondria
4- dividing schedules
Explain double membrane as 1 of the 4 supports that Dr Margulis discovered about the endosymbiotic hypothesis
As the mitochondria and chloroplast were engulf by a cell they developed a double membrane
Explain morphology of chloroplast as 2 of the 4 supports that Dr Margulis discovered about the endosymbiotic hypothesis
The morphology of chloroplast is similar to Cyanobacteria
Explain morphology of mitochondria as 3 of the 4 supports that Dr Margulis discovered about the endosymbiotic hypothesis
Morphology of mitochondria is similar to aerobic bacteria (an alpha-proteobacterium)
Explain dividing schedules as 4 of the 4 supports that Dr Margulis discovered about the endosymbiotic hypothesis
Mitochondria and chloroplast divide on a different schedule than rest of cell - and divide through binary fission like prokaryotes
What did the 1980’s bring around?
Technology to sequence DNA
What did the technology of sequence DNA in the 1980’s allow? (2)
- Showed mitochondria and chloroplast have own unique DNA which is similar to certain bacteria
- Our nuclear DNA similar to Archea means engulfing cell was Archea
How is mitochondria DNA inherited? What can I be used for?
Inherited from only mother = used to trace maternal lineages
What is the oldest evidence on mtDNA?
Otzi = iceman frozen for 5300 yrs = samples resulted in oldest complete human mtDNA
What is sterile inflammation?
Occurs when damaged cells release mitochondria and immune system mistakes mitochondria as invading bacteria
There are 3 hypothesis as to explain the evolution of eukaryotes from prokaryotes, what is the first one? What does this show?
All eukaryotes have or had (remnants) of mitochondria but not all have chloroplast
Endosymbiosis of aerobic bacteria happened very early on
There are 3 hypothesis as to explain the evolution of eukaryotes from prokaryotes, what is the second one? Where is this shown?
Mitochondria can be reduced or lost = in the supergroup Excavata we can see this
What is the name of the organism that shows lost mitochondria? What are the remnants called?
Diplomonads - remnants called mitosomes
What is the name of the organism that shows reduced mitochondria? What are the semi-functioning mitochondria called?
Parabasalids - semi-functioning called hydrogensomes
There are 3 hypothesis as to explain the evolution of eukaryotes from prokaryotes, what is the third one? What does this mean?
Plastid evolution
Plastid=chloroplast
Explain plastid evolution
Members of Archeaplastida have plastids consistent with primary endosymbiosis of Cyanobacteria to become chloroplasts
What does Archeaplastida mean?
Archea = ancient Plastida = plastid
What are the 4 organisms included in Archeaplastida?
1- red algae
2- chlorophyta gr. algae
3- charophyta gr. algae
4- land plants
What is secondary endosymbiosis?
When single-called ancestors of red and green algae that had plastids were engulfed by other cells
What does secondary endosymbiosis result in?
Plastids with more than 2 membranes
What engulfed the red aglae ancestor?
All chromalveolata
What a re the 2 subgroups of chromalveolata that engulfed red algae ancestor?
1- Alveolates
2- Stramenopiles
What are the 3 organism under the subgroup Alveolates as a chromalveolata? State whether lost or remnants of plastids
Dinoflagellates
Apicomplexans - remnants of plastids
Ciliates - lost plastids
What are the 4 organism under the subgroup Stramenopiles as a chromalveolata? State whether lost or remnants of plastids
Brown algae
Golden algae
Diatoms
Water molds - lost plastids
How many ways were great algae engulfed?
2
What was the first way in which green algae ancestors were engulfed?
Euglenozoans - no other Excavata has evidence of plastids
What was the second way in which green algae ancestors were engulfed?
Chlorarachniophytes (type of cercozoan) - no other Khizaria has evidence of plastids but remnants of original symbiont cell
What are protists?
Everything expect fungi, plants and animals
What can protist be?
Paraphyletic = descendant of same ancestor Polyphyletic = derived from many ancestors
What defines a protists?
Partly by structural level (unicellular eukaryotes) and partly exclusion from definition if plants/animals/fungi
What kind of group are the protists?
Ranges from single-called microscopic members, simple multicellular forms and complex giants (seaweed)
How many groups of protists are there?
6
What are the 6 groups of protists?
1- Excavata 2- Chromalveolata 3- Rhizaria 4- Archaeplastida 5- Amoebozoa 6- Opisthokonts
Group 1 Excavata of protists - What are the 3 features to know?
1- hallow (excavated) ventral feeding grove
2- all single-called
3- modified or lost mitochondria
What is a type of Group 1 Excavata of protists?
Giardia - causes “beaver fever”
What are the 3 different types of mitochondria in Group 1 Excavata of protists?
1- Diplomonad = remnants/non-functional called mitosomes
2- Parabasalids = semi-functional called hydrogensomes
3- Euglenozoans = single/oversized called kinetoplast
What is special about the Euglenozoans as a type of mitochondria from Group 1 Excavata of protists? (2)
- Are mixotrophic = use autotrophy and heterotrophy
- Acquire plastids from secondary endosymbiosis of gr. Algae ancestor
Group 2 Chromalveolata of protists - what are its 2 subgroups?
1- Alveolates
2- Stramenopiles
Explain Alveolates as Group 2 Chromalveolata of protists - 2 features
1- membrane-bound alveoli (vesicles) located in layer under plasma membrane
2- most single-called
Explain how Alveolates of Group 2 Chromalveolata of protists got their plastids
Acquired via secondary endosymbiosis of a red algae ancestor = Like all chromalveolata
What are the 3 types of Alveolates and state if they still have plastids - Group 2 Chromalveolata of protists
1- Dinoflagellates = still has them
2- Apicomplexans = remnants of plastids
3- Ciliates = lost plastids
What is notable about Dinoflagellates as a types of Alveolates of Group 2 Chromalveolata of protists?
Zooxanthellae = symbiotic relationships with reef = building coral and can cause red tide
What is notable about Apicomplexans as a types of Alveolates of Group 2 Chromalveolata of protists?
Plasmodium causes malaria
What is notable about Ciliates as a types of Alveolates of Group 2 Chromalveolata of protists?
Ruminant Mammals house microscopic organism in their rumen = most common protozoan here
Explain Stramenopiles as Group 2 Chromalveolata of protists - 1 feature
Have 2 flagella = one smooth and one hairy
Explain how Stramenopiles of Group 2 Chromalveolata of protists got their plastids
Acquired plastids via secondary endosymbiosis of red algae ancestor like all chromalveolata
What are the 4 types of Stramenopiles and state if they still have plastids - Group 2 Chromalveolata of protists
1- Diatoms = still has them
2- Golden algae = still has them
3- Brown algae = still has them
4- Water molds = lost their plastids
What is notable about the 4 types of Stramenopiles of Group 2 Chromalveolata of protists?
1- Diatoms = Silica shells give glassy appearance
2- Golden algae = cause taste and odor events
3- Brown algae = foundations of productive marine ecosystem
4- Water molds = Irish potato famine
Group 3 Rhizaria of protists - 2 features
1- all unicellular
2- use pseudopod for movement
What are the 3 types and state if they still have plastids - Group 3 Rhizaria of protists
1- Radiolarians = no chloroplasts
2- Forams = no chloroplast
3- Cercozoans = some have plastids from secondary endosymbiosis of gr algae (chloractinophytes = mixotrophic) = recent event as remnants of engulfed cell present
Group 4 Archaeplastids of protists - 2 features
1- all photoautotrophs
2- share common ancestor and acquired plastids from first endosymbiosis of Cyanobacteria
What are the 4 types from Group 4 Archaeplastids of protists that acquire their protists from by first endosymbiosis?
1- red algae
2- chlorophyte green algae
3- charophyte green algae
4- plants
Group 5 Ameobozoa of protists - 2 features
1- unicellular
2- use pseudopod for movement
What are 3 examples of Group 5 Ameobozoa of protists?
Slime mold
Gymnamoebas
Entamoebas
Group 6 Opisthokonts of protists - 1 feature
posterior flagellum at some point in life cycle
What are 4 examples of Group 6 Opisthokonts of protists?
Nucleariids
Fungi
Choanoflagellates
Animals
What was the first way slime molds went to multicellularity?
Cell multiplication = mitosis
What was the second way in which slime molds went to multicellularity?
Cell aggregation = cellular slime molds
What is a type of cell aggregation for slime molds? What are they?
Mycetozoa (slime molds or fungus animals) - neither fungi nor animals but are protists
If slime molds have any resemblance to fungi what is it? And in which way?
Analogous and not homologous = convergent role in decomposition of leaf litter and organic debris
How do slime molds move and feed? What is this similar to?
Via Pseudopodia (like an amoeba)
Though slime molds feed and move like an amoeba, what are they actually closer to and why?
Relatively close to fungi and animals due to comparisons of proteins sequences
Cellular slime molds like Dictyostelida straddle the line between what?
Individuality and multicellularity
What is the feeding stage of Dictyostelida?
Individual or solitary cells
What happens to Dictyostelida when there is a lack of food? What is this called? What happens to the cells?
Cells form aggregate (“slug”) that functions as one unit
Called pseudoplasmodium
Cells retain identity
What do aggregates of Dictyostelida form?
Aggregates of amoebas form fruiting bodies that produce spores in sexual reproduction
What is the 6 stages to the asexual reproduction of a Dictyostelida?
1- solitary cell = feeding stage 2- aggregated amoebas 3- migrating colony 4- fruiting bodies 5- spores 6- emerging amoeba
What is the 3 stages to the asexual reproduction of a Dictyostelida?
1- amoebas through the process of meiosis
2- aggregated amoebas
3- zygote through the process of syngamy
What is cyclic AMP?
cAMP is adenosine monophosphate with phosphate bonded internally to form cyclic molecule
What is cAMP generated from?
From ATP by the enzyme adencylcyclase
What does cAMP function as in slime molds?
Acrasin
What are the 4 classifications of Animalia or Metazoa?
1- cell number
2- body symmetry
3- developmental pattern
4- evolutionary relationships
What are the 2 subgroups of the classification of cell number for Metazoa?
1- unicellular
2- multicellular
What are the 3 subgroups of the classification of body symmetry for Metazoa?
1- asymmetrical
2- radial symmetry
3- bilateral symmetry
What is the first subgroup of the classification of developmental pattern for Metazoa and all its relative groups (5)?
Germ layers:
1- Diploblastic
2- triploblastic
- acoelomate, pseudocoelomate, eucoelomate
What is the second subgroup of the classification of developmental pattern for Metazoa and all its relative groups (2)?
Cleavage patten:
1- radial
2- spiral
On the animal phylogenetic tree that is based on morphological, fossil, and genetic evidence, what are the 9 groups to known and their respected animals?
Porifera = sponge Cnidaria = cnidarians Echinodermata = echinoderms Chordata = chordates Mollusca = mollusks Annelida = annelids Platyhelminthes = flatworms Nematoda = roundworms Arthropoda = arthropods
Evolutionary relationships as a classification for metazoa is based on what?
18 small ribosomal RNA
What are the 6 major features of animal development?
1- symmetry 2- number of germ layers 3- types of body cavity 4- protostome vs deuterostome 5- segmentation (metamerism) 6- 2-way vs 1-way digestive track
Explain symmetry as a major feature of animal development and how many types
The number of ways you can divide an animal
Asymmetrical, radial, bilateral
Explain asymmetrical as a type symmetry as a major feature of animal development. Name the animal/phylum associated with it
Can’t not divide the animal in 2 mirror images
Sponges (Porifera)
Explain bilateral as a type of symmetry as a major feature of animal development. What is it associated with with?
One 1 mirror image and one way
Due to cephalization = concentration of neurons and sensors at one end = head
Explain radial as a type of symmetry as a major feature of animal development. What animal/phylum?
More than 1 mirror imagine
Cnidarians (Cnidaria)
What is Pentaradial symmetry? What animal/phylum does this happen to?
5 ways to divide
Echinoderms (Echinodermata)
Explain number of germ layers as a major feature of animal development and how many types
2 = diploblastic and triploblastic
During embryogenesis:
Diploblastic develop 2 layers = ectoderm and endoderm
Triploblastic develop 3 layers = ectoderm, endoderm, and mesoderm between the 2
How many germ layers do sponges (Porifera) have?
No - they lack tissues
Explain body cavity as a major feature of animal development (called/how many types)
Called Coelom = body cavity that is not a gut - separates guts from body muscles and internal organs suspended within coelom
3 types: acoelomate, eucoelomate, and pseudocoelomate
Explain eucoelomate as a type of body cavity as a major feature of animal development
“True” coelom = is fluid-filled cavity completely surrounded by mesoderm-derived tissue
Explain acoelomate as a type of body cavity as a major feature of animal development, layers and what animal/phylum
Lacks body cavity
Layers = ectoderm, mesoderm, endoderm, and digestive cavity (one inside the other)
Flatworms (Platyhelminthes)
Explain eucoelomate as a type of body cavity as a major feature of animal development, layers and what animal/phylum
True cavity
Layers = ectoderm, mesoderm, coelom forms within mesoderm as 2 “semicircles”, endoderm
Annelids (Annelida), mollusks (Mollusca), arthropods (Arthpoda), echinoderms (Echinodermata), chordates (Chordata)
Explain pseudoelomate as a type of body cavity as a major feature of animal development, layers and what animal/phylum
Has body cavity but sandwiched between mesoderm and endoderm = it’s a mistake
Layers: ectoderm, mesoderm, pseudoelom, endoderm
Roundworms (Nematoda)
Explain the 4 difference of protostome vs deuterostome as a major feature of animal development
1- cleavage patterns
2- determinate vs indeterminate development
3- coelom formation
4- origin of mouth and anus
Explain cleavage pattern as a difference in protostome vs deuterostome as a major feature of animal development
Protostomes has spiral cleavage pattern = 8 cell stage of development, upper 4 cells sit offset on top of lower 4
Deuterostomes has radial cleavage pattern = 8 cell stage of development, upper 4 cells sit directly above lower 4
Explain determinate vs indeterminate as a difference in protostome vs deuterostome as a major feature of animal development
Cell fate in protostomes is determined early = determinate cleavage
Cell fate in deuterostomes is flexible = indeterminate cleavage
Explain coelom formation as a difference in protostome vs deuterostome as a major feature of animal development
Protostomes = schizocoely = part of mesoderm separates to form coelom Deuterostomes = enterocoely = mesoderm pinches off to form the coelom
Explain origin of mouth and anus as a difference in protostome vs deuterostome as a major feature of animal development
Protostomes = blastopore becomes mouth and anus develops later Deuterostomes = blastopore becomes anus and mouth develops later
Explain segmentation as a major feature of animal development and type
How the animal body is split up due to organ and body specialization
Metamerism = many repeating segments
What 3 animals/phylums show segmentation as a major feature of animal development? Explain
Earthworms/annelids (Annelida) - metamerism in body
Arthropods (Arthropoda) - metamerism in trunk
Chordates (Chordata) - metamerism in vertebral column and Amphioxus (lancet)
Explain 2-way vs 1-way digestive tract as a major feature of animal development
2-way = food in and wages out though same opening = mouth but no anus = "incomplete" digestive tract 1-way = food travels in one direction = has both mouth and anus = "complete" digestive tract
Explain the 2 points of coloniality vs multicellularity in metazoa
- cell specialization = transport of nutrients and communication between cells
- advanced characters at the morphological and biochemical levels
Explain Choanoflagellates findings?
No fossils record - some marine species secrete delicate loricae (outer coverings made of interwoven silica bars)
Explain Choanoflagellates colony?
Few are colonial for part of life cycle = show limited cell differentiation and integration into a unit
What does the Choanoflagellates colonies show us?
Best living examples of what ancestors of all metazoans may have look like
Explain Choanoflagellates anatomy (3)
Proterospongia = has a number cells embedded in jelly-like matrix = privatize level of cell differentiation
Flagellated cells with collar structures = move colony through water
Amoeboid cell = on inside divide into new cells = growth
What are the 3 metazoa cell junctions?
1- Occluding
2- Desmosomes
3- Gap junctions
Explain Occluding as a cell junction of metazoa
Seals off intercellular spaces from environment
What are the 2 types of Occluding cell junctions for metazoa?
1- septate junctions = in all invertebrates
2- tight junctions = in vertebrates, tunicates and some arthropods
Explain Desmosomes as a type of cell junction fro metazoa
Adhesion
Explain gap junctions as a type of cell junction fro metazoa
Chemical and electrical communications = only in Hydrozoa and bilateria
