BIOL 321 Flashcards
where does the vast majority of primary production occur
upper 50m
depth of sunlight
200m
waters oxygen carrying capacity
2.5% of air by volume
oxygen movement in water
300,000X slower than in air
Reynolds number
Re
intertial : viscous forces
low Re
highly viscous
small fish in water
all movement requires propulsion (no gliding)
Linnaeus taxonomic classification scheme
Kingdom Phylum Class Order Family Genus Species
Taxon
any named group of organisms that is sufficiently distinct to be assigned to a category
Monophyletic
a group derived from a single common ancestor that contains all descendants of that ancestor
paraphyletic
group derived from a single common ancestor that does not contain all descendants of that ancestor
paraphyletic example
Invertebrates, reptiles
percent of described species that belong to phylum Chordata
5%
Largest extinction in history
P - T extinction, 250mya
95% of species-level diversity lost
Binomic species name
Generic name specific name
italicized on computer, underlined by hand
Abbreviating species name
Generic name can be abbreviated (A. species) after being spelled out once, only if there is not another genera that starts with the same letter
Species name with researcher who described it
sometimes first name is put after the species name, not underlined/italicized
Balanus amphitrite Darwin
unless described by Linnaeus then species name is followed by L.
may also be followed by date
Euphausia superba, Dana 1858
When a species is reclassified
descriptors name is placed in brackets Ilyanassa obsoleta (Say)
proposed replacement to Linnaean system
PhyloCode
rankless
domains
3 - higher than kingdoms
bacteria
archaea
eukarya
kingdoms
6 Eubacteria (bacteria) Archaebacteria (Archae) Fungi (Eukarya) Protista (Eukarya) Planti (Eukarya) Animalia (Eukarya)
Eukaryote
cells contain nuclear and membranes around organelles
convergence
independent evolution of similar features in species of different lineages
features resemble each other that are not from an LCA
Analogous features
convergence
Plesiomorphic
primitive, ancestral, original trait
ESTs
expressed sequence tags
Ecdysozoa
molting animals
2 protostome clades
Ecdysozoa
Lophotrochozoa
Homologous features
ancestral
Apomorphic
derived, advanced trait
A novel evolutionary trait that is unique to a particular species and all its descendants and which can be used as a defining character
direction of evolutionary change
polarity
evolving towards ancestral or derived character?
classic taxonomy
Evolutionary Systematics
Evolutionary Systematics weighting
characters with more phylogenetic information are given more weight
how Evolutionary Systematics are constructed
homologous characters used to deduce general relationships
resemblance taken in to account before completed
Evolutionary Systematics and paraphyletic groups
not troubled by
i.e. groups like Reptilia are ok in classic taxonomy
Evolutionary Systematics downfalls
slow
requires experience
lacks objectivity and standardized methodology
Phylogenetic Systematics
Cladistics
how Cladistics are constructed
only with synapomorphies
Cladistics and paraphyletic groups
NOT ok
all taxa must contain all descendants of an ancestor
Cladistic benefits
standardized methods and procedures
accommodates molecular data
does not require experience like Evolutionary Systematics
Synapomorphy
shared character derived from common ancestor in which it originated
evolutionary novelties
How to construct Cladistics with molecular data
start at same spot along code
compare 1 bp at a time
if b.p.’s are same = no phylogenetically useful info
1 bp difference = 1 evolutionary event
Problems with molecular data in Cladistics
deletions/insertions - sequences have to be re-aligned
LBA
long branches attract
- rapidly evolving gene sequences produce longer branches that tend to group closely together
- a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related
- enough changes have occurred that lineages look similar
When b.p. changes are believed to have occurred too many times, erasing signs of molecular evolution
Saturated sequence
two-branched
biramous
as in crustacean appendages
subtidal
live below tidal line
rarely exposed to air
planktonic
mobile w/ negligible locomotion
subject to currents
drift
deposit feeder
ingest sediment, digest organic material as sediment moves through digestive tract
single branched
uniramous
insect appendages exclusively uniramous
ectosymbiont
live near or on body of other participant
both symbionts benefit
mutualism
one symbiont benefits while the other is neither benefited nor harmed
commensalism
term for symbiont that benefits in commensalism
commensal
Saturation
reduced appearance of sequence divergence that results from reverse mutations, homoplasies (convergence) and other multiple changes occurring at single sites along two lineages
symbiont that lives within the body of the other participant
endosymbiont
Parasitism
depend on host for life
obligate
may or may not improve hosts activities
Ancestral state
the character state exhibited by the ancestor from which current members of a clade have evolved
Apomorphy
any derived or specialized character
Autapomorphy
a derived character possessed by only one descendant of an ancestor, and thus of no use in discerning relationships among other descendants
Clade
a group of organisms that includes the most recent common ancestor of all its members and all descendants of that ancestor
every valid clade forms a “monophyletic” group
Cladogenesis
the splitting of a single lineage into two or more distinct lineages
Cladogram
pictorial representation of branching sequences that are characterized by particular changes in key morphological or molecular characteristics
Derived state
an altered state; modified from ancestral condition
apomorphic state
Homology
characters that have the same evolutionary origin from a common ancestor, often coded for by the same gene
Homology is the basis for
all decisions about evolutionary relationships
homoplasy
independent acquisition of similar characteristics from different ancestors
Monophyletic taxon
a group of species that evolved from a single ancestor and includes all descendants of that ancestor
Every valid clade
must form a monophyletic taxon
Node
a branching point on a cladogram
outgroup
a group of taxa outside the group being studied
outgroups are used to
‘root’ the tree and imply the direction of evolutionary change (polarity)
paraphyletic group
group of species sharing an immediate ancestor but not including all descendants of that ancestor
parsimony
a principle stating that, in the absence of other evidence, one should always accept the least complex scenario
pleisiomorphy
ancestral/primitive character
polarity
direction of evolutionary change
polyphyletic grouping
incorrect grouping containing species that descended from two or more different ancestors
members do not all share the same immediate ancestor
When a gene sequence loses its phylogenetic signal due to numerous base-pair substitutions
saturation
sister groups
two groups descended from the same immediate ancestor
synapomorphy
derived character that is shared by the LCA and two or more descendants
homologous characters that define clades
taxon
any named group of organisms
Invertebrate lifestyles
sessile
sedentary
motile
invertebrate habitats
majority marine - most hospitable
freshwater - more challenging
terrestrial - most challenging
challenges with freshwater habitat
maintaining osmotic pressure
water is often ephemeral
wider temperature fluctuations
challenges with terrestrial habitat
avoiding desiccation
retaining water
excreting toxic byproducts (urine)
types of benthic habitats (marine or fresh)
epifaunal
infernal
interstitial
feeding methods in invertebrates
suspension feeding detritivores deposite feeders herbivores carnivores
Metazoan pie chart
invertebrates are 95% of Metazoans
Invertebrate pie chart
beetles >1/4
flies, bees/wasps, butterflies, other insects, chelicerates, crustacea, molluscs, vertebrates (~1/16), other
arthropods = ~7/8
pelagic habitats (marine or fresh)
planktonic
Grazing carnivores
exploit sessile organisms
Predators
feed on actively motile prey (as opposed to grazing)
scavengers
feed on dead organisms (carnivory)
types of deposit feeders
selective
non-selective
why is phylogeny important
essential for asking questions about evolution (must know polarity)
cladogram
diagram of a phylogenetic hypothesis
nested sets of sister clades
branch point
node
multicellularity evolved
from unicellularity multiple times uniquely (at least 7)
Animal multicellularity requires
cell adhesion
cell specialization and interdependence
embryonic differentiation
Importance of cell adhesion
all cells come from single founder cell (fertil. egg)
to become multicell. they must attach together
Why cell adhesion is not enough
some unicellular organisms attach together as well
Importance of cell specialization
KEY to multicell. "Division of labour" *Intercellular signaling VIP* organization otherwise chaos
Importance of embryonic differentiation
allows cells to become specialized and recruited to form functional body plan
also tells about evolution
Tissues
large aggregates of same type of cell
Metazoan tissue types
epithelial connective nervous muscle gametogenic
Epithelial tissue
likely most important
primary interface w/ outside environ.
line internal compartments - determines what goes in and out
Epithelia components
Apical surface flagella (not always) Intercellular junctions micro-villi (not always) basal surface nuclei basal lamina (not always) apico-basal polarity
Apical surface
apical membrane of a polarized cell is the surface of the plasma membrane that faces lumen or outside environment
intercellular junction
adherons
contact between cells
enable communication
reduce stress on cell
basal lamina
layer of extracellular matrix secreted by epithelial cells, on which the epithelium sits
point of attachment
permeability barrier
cell polarity
spatial differences in the shape, structure, and function of cells
apical-basal polarity
a specialised apical membrane facing the outside of the body or lumen of internal cavities, and a specialised basolateral membrane localised at the opposite side, away from the lumen
Importance of apical-basal polarity
secrete different materials
have different structures (e.g. flagella)
connective tissue
collagen cells not connected in extracellular matrix 'wander around' structural integrity (e.g. blood, bone)
Nervous tissue
specialized to transmit information
neurons have high density and diversity
allow message transmission throughout organism
how nervous tissue works
change in potential through the ion channels is carried down the length of the neuron
muscle tissue
specialized for shortening
important for animal movement
how muscle tissue works
actin and myosin slide relative to each other
Major groups of metazoans
Porifera Cnidaria Ctenophora Placozoa Bilateria
Porifera and Placozoa shared characteristic
no nerves
no muscles
Metazoan phylogeny hypotheses
- Porifera, (Placozoa, Cnidaria, (Bilateria, Ctenophora))
2. Ctenophora, (Porifera, (Placozoa, (Bilateria, Cnidaria)))
Problem with metazoan hypothesis 1
It has a trichotomy
trichotomy
3 sister groups following 1 node
perfectly/fully resolved phylogenies only have 2 sister groups
problem with metazoan hypothesis 2
just controversial new data (molecular)
Porifera habitat
marine and freshwater
Porifera lifestyle
sessile adults
suspension feeders - mostly bacteria, some plankton
aquiferous system
interconnected system of water canals
unique to sponges
do sponges have tissues
yes
what tissues do sponges have
nerve/muscle - no
connective tissue - yes
epithelial tissue - yes
name of sponge epithelial tissue
protoepithelia
Protoepithelial tissue
less differentiated than other metazoans
Sponge interior compartment
spongocoel
atrium
empty space
sponge species
8000
98% marine
non-self recognition
alloincompatibility
as in sponges
flagellated cells lining spongeocoel
choanocytes
‘funnel cells’
collar cells
form choanoderm
collar cell functions
generate curent to maintain circulation in/through sponge
capture food particles
capture sperm
choanoderm
interior sponge tissue - facing spongocoel
collar of collar cells
apical flagellum surrounded by microvilli
middle sponge layer
mesohyl
wandering cells in mesohyl
archaeocytes
Mesohyl
gelatinous
non-living
acellular but containing live cells
Archaeocyte features
amorphous amoeboid wander in mesohyl - cytoplasmic streaming essential functions develop into specialized cells
Archaeocyte functions
digest food particles from choanocytes store digested food role in non-self recognition may produce flagellated sperm and egg role in waste elimination
Sponge Support Elements
spicules
fibers
Spicule structure
siliceous
calcareous
fiber structure
spongin (collagen-like)
secrete spongin fibers
spongocytes
secrete spicules
sclerocytes
spongocytes and sclerocytes come from what types of cells
archeaocytes
sponge water entry
ostium
porocyte
sponge water exit
osculum
support element functions
maintain sponge shape
discourage predation
systematics (systematics)
dormant sponge structure
gemmule
gemmule features
dormant structure
certain times of yr
mostly freshwater, especially temperate latitudes
resistant to desiccation, freezing, anoxia
withstand unfavourable conditions
asexual reproduction - multiple clones
formation of gemmule
archaeocytes phagocytize other cells to accumulate nutrients - cluster together w/i sponge - surrounding cells secrete thick protective covering capsule - parent sponge dies - gemmules released in to water - enter metabolic arrest - survive - break open and release cells in favourable conditions
Vernalization
many gemmules must spend several months at low T before capable of hatching
cells in outer sponge layer
Pinacocytes
Pinacocyte features
flattened contractile cells
form pinacoderm layer
line incurrent canals
Pinacocyte contraction
major/minor sponge shape change
regulate flow by changing incurrent opening size
levels of sponge construction
basic –> complex
asconoid, syconoid, leuconoid
Increased sponge complexity achieved by
increasing invagination of choanocyte layer away from spongocoel
increased flagellated surface area
Majority of sponge types (complexity)
leuconoid
sponge Classes
Calcarea
Demospongiae
Hexactinellida
Homoscleromorpha
How sponge Classes are defined
chemical composition
support element morphology
Class Calcarea characteristics
CaCO3 spicules only class to include all 3 complexities only class w/ extant asconoids
Class Demospongiae characteristics
largest class ≥80% of all species mostly leuconoid spicules/fibers = spongin and/or silica, some chitin NO CaCO3 only class w/ freshwater species
Family Cladorhizidae
Demospongiae carnivorous most lack ostia, oscula, choanocytes engulf prey in epithelial cell and new filaments may have symbiotic bacteria
Class Hexactinellida features
“Glass Sponges”
syconoid or leuconoid
entire sponge is syncytial
interconnected 6-ray spicules of Si and Chitin
Syncytial
multinucleate mass
not separated in to cells
Type of reproduction in sponges
asexual- fragmentation or gemmules/buds
sexual- sperm and eggs
Gamete producer in sponges
many species are hermaphroditic so individuals produce both gametes
Sponge sexual reproduction
choanocyte- sperm capture- dedifferentiate to amoeboid form- move sperm to mesohyl- egg fertilized in mesohyl
Phylum Placozoa defining characteristics
small, multicellular, amorphous, mobile
no body cavity, digestive system, nervous system
2 layers of ciliated epithelium sandwiching multinucleate contractile cells
cells in a Placozoa
~1000 per layer
~3000
Phylum Placozoa species
only 1 described, poorly understood
Trichoplax adherents
molecular work suggests ~10 unknown
Placozoa size
~2mm in lab
much smaller in field
Placozoa genome
smallest of any known animal
98 million b.p.’s
Placozoa habitat
unknown
Placozoa cells
no basal lamina
ventral layer = columnar cells w/ flagella
glandular cells secrete digestive enzyme for extracellular digestion
upper layer contains ‘shiny spheres’ for defense
dissagregated cells can reform fn animal
regenerate pieces that are cut off
Placozoa reproduction
asexual - budding, fragmentation
binary fission
possibly sexual
Placozoa mitochondrial genome
largest known
43,079 b.p.’s
more closely related to unicellular organisms?
basal group or secondary loss?
Choanoflagellate
unicellular heterotrophs collared, flagellated look like individual choanocytes but also form colonies possibly evolved in to sponges?
Sponge asexual reproduction
fragmentation
gemmules
sponge fragmentation
bit of sponge body separates, piece of somatic tissue grows in to new organism
sponge sex
mostly hermaphroditic (not simultaneously), can switch sex in next spawning season
sponge sperm
differentiate from choanocytes or archaeocytes
broadcast spawn in to surrounding sea water through osculum
sponge eggs
differentiate from archaeocytes in mesohyl
sponge larvae
released from osculum
flagellated, swimming
allows for dispersal
looks like an olive with short little hairs at end
diapause
period of suspended development, especially during unfavorable environmental conditions (e.g. gemmule)
Cladorhizidae spicules
hook-shaped spicules on tendrils
act like velcro, hook on to exoskeleton of prey
new species of deep ocean carnivorous sponge
Chondrocladia
‘harp sponge’
Late Jurassic time
145 MYA
sponges in Jurassic
siliceous sponge reef belt (hexactinellida), 7000km, anywhere on planet, between NA/Baltica and Gondwana, extinct at end of Jurassic
how do sponges persist as sessile organisms
- secondary metabolites
- intracellular bacterial symbionts synthesizing secondary metabolites
secondary metabolites
defence
may be: unpalatable, toxic, antibacterial
BC sponges
Hexactinellid reefs formed by 3 species of glass sponge (not same species as from Jurassic)
discovered in 2005
unique to BC, nowhere else
sponge internal communication
allow ions into membrane - potential difference - message propagated through whole body - can create whole body response to external disturbance
how can a sponge propagate a message through its whole body
one cell at a time
open and close.. neighbour opens and close.. neighbour..
close all cells - stop flow of water in response to environmental disturbance
How Professor George Mackie was able to test membrane potential in sponges
cut up, disagregated cells, they reformed a fleshy clump, put clump on parent sponge, tissue formed around = tumor/graft which an electrode could be attached to
skeleton
solid or fluid system permitting muscles to be stretched back to their original length following a contraction
may be protective, supportive as well
why is a skeleton necessary
muscles can’t do repetitious movement alone
muscles can
shorten/relax
muscles can not
actively extend themselves
how muscles work
antagonize each other
work opposite to each other
e.g. bicep, tricep
aquatic animal skeleton
many use fluid for muscle interaction
why aquatic animals can use liquid skeletons
don’t need extra structure/support like terrestrial organisms (gravity, lack of buoyancy)
hydrostatic skeleton requirements
cavity w/ incompressible fluid
cavity surrounded by flexible outer membrane (deformable)
constant fluid volume
deformable covering or antagonistic muscles
why incompressible fluid is important for a hydrostatic skeleton
to transit pressure changes in all directions
additional hydrostatic skeleton requirement if progressive locomotion is to occur
animal must be able to form temporary attachment to substrate
cnidaria defining characteristic
secretion of complex intracellular organelles called cnidae; planula larvae
Cnidaria habitats
aquatic - marine and freshwater
by far greatest diversity in ocean
Cnidaria marine habitats
benthic and/or pelagic
most cycle between both, some spend whole life in one or other
Cnidaria lifestyle
solitary and/or colonial
sessile/sedentary and/or mobile
predatory (some contain photosynthetic symbionts)
Cnidarian species
> 11,000
>99% marine
cnidaria body plans
medusa polyp some have both as stages some have both at once some are only one stage
Cnidaria major characteristics
true gut (carnivore)
diploblastic
radial symmetry (all life history stages)
nerve net
cnidocytes
alternation of generations (many, not all)
cnidaria tissue layers
epidermis
gastrodermis
diploblastic
cnidaria gelatinous layer
mesoglea
mesoglea
gelatinous
nonliving
may contain living cells from embryonic ectoderm
diploblastic early development
zygote cleavage - 8-cell stage - cleavage - blastula - gastrulation - becomes 2 layers of cells
blastula
hollow ball of cells
gastrulation
invagination
gastrula
2 layers of cells after gastrulation (endoderm and ectoderm)
space between 2 layers of gastrula cells
blastocoel
opening in gastrula
blastopore
Cnidarian blastopore
becomes mouth
cavity inside of gastrula (inside ectoderm)
Archenteron
future gut
why is radial symmetry appropriate for sessile/sedentary organisms
not moving w/ a leading end
sitting still- predators/prey can approach from all sides
Cnidaria epidermis cell types
epitheliomuscle cells nerve cells cnidocytes gland cells interstitial cells
epitheliomuscle cells
in epidermis of cnidarian apical side = bona fide epithelial basal side = muscles w/ actin/myosin sensory cells intra-epithelial neurons
apical surface
facing lumen or external environment
cnidarian sensory cells
neurons in epitheliomuscle cells reach up to apical surface
cnidarian intra-epithelial neurons
neurons in epitheliomuscle cells are embedded in epithelium (in other Metazoans, below epithelium)
basal surface
bottom edge of the cell or tissue adjacent to the basement membrane
Cnidarian nerves are arranged
in a nerve net
appropriate for radial organism transmit stimuli out concentrically to all body parts
choanocyte functions (Porifera)
maintain water flow
capture and ingest particles
capture sperm
transform in to sperm (some species)
why choanocytes must maintain water flow
bring in food particles, gases, remove waste products (uric acid, CO2)
how choanocytes capture particles
caught on sticky mesh between microvilli
choanocyte food digestion
intracellular
often initial digestion then transfer to archeocytes
archaeocyte functions
primarily responsible for food digestion
store nutrients
transform in to gametes
synthesize skeletal elements
pluripotent cells
very capable of differentiating in to different cell types (e.g. archaeocytes)
basic cnidarian body parts
mouth (between tentacles) tentacles GVC body stalk basal disk
cnidocytes
synthesize cnidae (e.g. nematocysts) nettle/stinging thread organelle secreted in cnidoblast discharge explosively variety of functions one of most complex intracellular secretion products known
types of nematocysts
>30 described types many types in one individual main groups 1. glutinants 2. volvent 3. penetrant
glutinant nematocysts
tubule has open end containing adhesive material
volvent nematocysts
threads that wrap around and capture prey
penetrant nematocysts
penetrate through exoskeleton
tubule has open end with neurotoxins
how nematocysts work
Ca+ moves in to capsule increased molality water drawn in to capsule pressure increase pressure discharges capsule capsule turns inside out
nematocyst structure
round, proteinaceous capsule, open at one end hinged operculum cnidocil by opening (trigger) hollow, coiled tube in capsule (thread) may contain barbs
cnidocyte functions
food capture
defense
temporary adhesion to substrate
why barbs don’t poke in to capsule of cnidocyte
they point in
cnidae is turned inside out when ejected
how symbionts avoid stinging from cnidae
secrete mucus that prevents nematocyst from firing
discharged nematocyst
cnidocyte nematocyst capsule barbs thread (tubule) sloughed off - not reusable regenerated from interstitial cells (stem cells)
cnidocyte discharge by
chemical and tactile stimulation
perceived through cnidocil