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OCN 201 Biology Lecture 6

Marine Animals

Illustration : Ernst Haeckel

I. The Invertebrates

The Animal Family Tree

Bilateria

Radiata

Ancestral Protist

Round Worms

Mollusks

Segmented Worms

Arthropods

Vertebrates

Echinoderms

Cnidarians

Ctenophores

Sponges

Flatworms

PlacozoaNo symmetry

Segmented Worms

Arthropods

Vertebrates

The Genome of the Ctenophore

Mnemiopsis leidyi and Its Implications

for Cell Type Evolution

Joseph F. Ryan, Kevin Pang, Christine E. Schnitzler, Anh-Dao Nguyen, R. Travis Moreland, David K. Simmons, Bernard J. Koch, Warren R. Francis, Paul Havlak, NISC Comparative Sequencing Program, Stephen A. Smith, Nicholas H. Putnam, Steven H. D. Haddock, Casey W. Dunn, Tyra G. Wolfsberg, James C. Mullikin, Mark Q. Martindale, Andreas D. Baxevanis*

Introduction: An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. The phylogenetic relationship of ctenophores (comb jellies) to other animals has been a source of long-standing debate. Until recently, it was thought that Porif-era (sponges) was the earliest diverging animal lineage, but recent reports have instead suggested Ctenophora as the earliest diverging animal lineage. Because ctenophores share some of the same complex cell types with bilaterians (such as neural and mesodermal cells), the phylogenetic position of ctenophores affects how we think about the early evolution of these cell types.

Methods: We have sequenced, annotated, and analyzed the 150-megabase genome of the cteno-phore Mnemiopsis leidyi. We have performed detailed phylogenetic analyses on these new data using both sequence matrices and information on gene content. We conducted extensive genomic inventories on signaling pathway components and genes known to be critical to neural and meso-dermal cell types, among others.

Results: Our phylogenetic analyses suggest that ctenophores are the sister group to the rest of the extant animals. We fi nd that the sets of neural components present in the genomes of Mnemiopsis and the sponge Amphimedon queenslandica are quite similar, suggesting that sponges have the necessary genetic machinery for a functioning nervous system but may have lost these cell types. We also fi nd that, although Mnemiopsis has most of the genes coding for structural components of mesodermal cells, they lack many of the genes involved in bilaterian mesodermal specifi cation and, therefore, may have independently evolved these cell types.

Discussion: These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells. This evolutionary framework, along with the comprehensive genomic resources made available through this study, will yield myriad discoveries about our most distant animal relatives, many of which will shed light not only on the biology of these extant organisms but also on the evolutionary history of all animal species, including our own.

FIGURES IN THE FULL ARTICLE

Fig. 1. M. leidyi life history and anatomy.

Fig. 2. Previously proposed relationships of the fi ve deep clades of animals.

Fig. 3. Tree produced by maximum-likelihood analysis of the EST set.

Fig. 4. Tree produced by maximum-likelihood analysis of gene content.

Fig. 5. The origin of postsynaptic genes.

Fig. 6. Inventory of myogenic components in M. leidyi.

SUPPLEMENTARY MATERIALS

Materials and MethodsFigs. S1 to S10Tables S1 to S31References

The phylogenetic position of the ctenophore

Mnemiopsis leidyi and its implications regarding

the origin of mesodermal cell types. (A) Adult M. leidyi. (B) Summary of the relationships of the fi ve main branches of animals and the outgroup Choano-fl agellata. (C) Inventory of myogenic specifi cation genes in Mnemiopsis. Components present in the Mnemiopsis genome are in blue, and names are underlined. Absent components are in red. The lack of many of these factors in Mnemiopsis indicates that ctenophore mesodermal cell types are specifi ed differ-ently than in bilaterians, suggesting that they perhaps evolved independently in these two lineages.

READ THE FULL ARTICLE ONLINEhttp://dx.doi.org/10.1126/science.1242592

Cite this article as J. F. Ryan et al., Science 342, 1242592 (2013). DOI: 10.1126/science.1242592

n

u

c

l

e

u

s

A B C

Ctenophora

Choanoflagellata

Placozoa

Porifera

Bilateria

Cnidaria

Wnt/Wg

BMPs/dpp

Shh/hh

FGF

NK2

Mef2

NK3

Lbx

NK4

Snail

Eomes

Gli

Noggin

Six1/4

Slp

Twist

GATA

Eya

MyoG

Myf5

Mrf4

MyoD

The list of author affi liations is available in the full article online.*Corresponding author. E-mail: [email protected]

RESEARCH ARTICLE SUMMARY

13 DECEMBER 2013 VOL 342 SCIENCE www.sciencemag.org 1336

Published by AAAS

(Science, Dec 2013)

0.2

Cryptococcus neoformans

Podocoryna carnea

Ptychodera flava

Symsagittifera roscoffensis

Carteriospongia foliascens

Oscarella lobularis

Amoebidium parasiticum

Petromyzon marinus

Strongylocentrotus purpuratus

Halocynthia roretzi

Pleurobrachia pileus

Helobdella robusta

Ephydatia muelleri

Lottia gigantea

Montastraea faveolata

Monosiga ovata

Lubomirskia baicalensis

Crassostrea virginica

Salpingoeca rosetta

Leucetta chagosensis

Sphaeroforma arctica

Boophilus microplus

Drosophila melanogaster

Saccharomyces cerevisiae

Capsaspora_owczarzaki

Aiptasia pallida

Porites astreoides

Terebratalia transversa

Daphnia pulex

Oopsacas minuta

Monosiga brevicollis

Saccoglossus kowalevskii

Cyanea capillata

Anemonia viridis

Amphimedon queenslandica

Hydra magnipapillata

Asterina pectinifera

Clytia hemisphaerica

Acropora palmataAcropora millepora

Euprymna scolopes

Nematostella vectensis

Capitella telata

Phycomyces blakesleeanusRhizopus orizae

Xiphinema index

Batrachochytrium dendrobatidis

Mertensiid sp

Convolutriloba longifissura

Sycon raphanus

Gallus gallus

Nemertoderma westbladi

Spizellomyces punctatus

Oscarella carmela

Anoplodactylus eroticus

Isodiametra pulchra

Mnemiopsis leidyi

Euperipatoides kanangrensis

Schmidtea mediterranea

Hydractinia echinata

Xenoturbella bocki

Suberites domuncula

Metridium senile

Branchiostoma floridae

Echinoderes horni

Ciona intestinalis

Cerebratulus lacteus

Trichoplax adhaerens

Paraplanocera oligoglena

Meara stichopi

Outgroup

Ctenophora

Porifera

Cnidaria

Bilateria

Placozoa

82

9845

44

83

99 99

8843

94

95

93

8485

44

96

96

72

88

77

9897

96

= 100 bootstrapsupport

Fig. 3. Tree produced by maximum-likelihood analysis of the EST Set. The tree was produced from a matrix consisting of 242 genes and 104,840 aminoacid characters. Circles on nodes indicate 100% bootstrap support. Support placing ctenophores as sister to the rest of Metazoa is 96% of 100 bootstrapreplicates.

13 DECEMBER 2013 VOL 342 SCIENCE www.sciencemag.org1242592-4

RESEARCH ARTICLE

asdeterm

ined

bybaa.pl

(25),was

98.2%.In

94.8%

ofcases,asingleEST

mappedcompletely

toasinglescaffold.T

hese

numberssuggestthat

theassemblyis

both

completeandaccurately

assembled.

Characteris

ticsof

theM.leidyiG

enom

e

The

M.leidyigenom

eisam

ongthesm

allest7%

ofgenomes

whencomparedwith

thosecataloged

intheAnimalGenom

eSize

Database(26)

andis

denselypacked

with

gene

sequences.Itencodes

16,548

predictedprotein-coding

loci,w

hich

make

up58%

ofthegenome,andweconservativelyas-

sign

44%ofthesegene

predictions

intohomology

groups

with

non-ctenophores.The

averagelength

ofan

unspliced

M.leidyitranscriptis5

.8kb.Eight

percento

fpredictedgenesareem

bedded

within

othergenes.T

hisn

umberofnestedintro

nicgenes

ishigh

comparedtoothergenom

es(tableS2

),but

may

beinflatedow

ingtoasubsetof

thesebeing

alternativelyexpressedexons.The

levelofrepeti-

tivesequence

intheM.leidyig

enom

eislow

tomoderate,ascomparedtootherm

etazoans

(tables

S3andS4

);thishasmadeitpossibletoproducea

high-qualitygenomeassemblybasedon

paired-

endandmate-pairsequencing

alone.Additional

characteristicsof

this

genomearepresentedin

tables

S5to

S10.

Phylog

enetic

Positio

nof

M.leidyi

TheavailabilityofthecompletegenomeofM.leidyi

hasallowed

usto

improveon

thectenophore

samplingused

inprevious

phylogenom

icanalyses

ofgene

sequence

evolution.Weassessed

twodata

matrices

thatdiffer

inbreadthof

taxonsampling

andfractionofmissing

data:a

“Genom

eSet”that

includesonlydatafro

mcompletegenomes(13ani-

mals,19.6%

missing

data)and

an“EST

Set”that

includespartialgenomicdatafrom

manytaxa

(58

animals,64.9%

missing

data).Weanalyzed

both

matrices

byusingmaximum

-likelihood[with

the

GTR+Gmodelasimplem

entedinRAxM

L(27)]

andBayesian[with

theCATmodelasimplem

ented

inPh

yloB

ayes

(28)]m

ethods.T

ounderstand

the

effectofoutgroup

selectionon

ouringroup

topol-

ogy,weincluded

fourdifferentsetsofnonm

etazoan

outgroups(tableS11)ineach

combinationofmeth-

odandmatrix

.Thismultifactorialstrategy

yielded

atotalof1

6analyses

(Table1).

Wefoundno

supportinanyof

theseanalyses

forCoelenterata(Cn,Ct),

Diploblastica(Bi,),or

Placozoa

beingthesister

lineage

totherest

ofanim

als(Tr,)

(Table1andfig

.S1).W

erecovered

broadsupportforasister

relationshipbetween

CnidariaandBilateria(Cn,Bi)andforaclade

ofPlacozoa,C

nidaria,andBilateria(Tr,C

n,Bi).

Maxim

um-likelihoodanalyses

supportthe

place-

mentof

Ctenophoraas

sister

groupto

allother

Bi

Cn

(Cn,

Ct)

(Ct,B

i)(P

o,)

(Ct,)

(Tr,)

(Bi,)

Ct

Tr Po

Bi

Ct

Cn

Tr Po

Bi

Cn

Tr Ct

Po

Bi

Cn

Tr Po

Ct

Bi

Cn

Ct

Po

Tr

Bi

Cn

Ct

Po

Tr

AB

CD

EF

Fig.

2.Previously

prop

osed

relation

shipsof

thefive

deep

clad

esof

anim

als.Thelabelatthe

botto

mofeach

pane

correspondstotheheaderofTable1.(A)Coelenteratahypothesis.(B)Ctenophoraas

sistertoBilateria.(C)

Poriferaassistergroup

totherestofMetazoa.(D)Ctenophoraassistergroup

tothe

restofMetazoa.(E)Placozoa

assistergroup

totherestofMetazoa.(F)Diploblastica

hypothesis.Weseeno

supportinanyof

oura

nalysesforthe

hypotheses

in(A),(E),and(F)a

ndverylittle

supportfor

(B)(see

Table1).Ct,Ctenophora;Po,Porifera;Tr,Placozoa;Cn,Cnidaria;B

i,Bilateria.

Fig.

1.M.leidyilife

historyandanatom

y.(A)A

dultM.leid

yi(about10

cmlong).(B)Close-upvie

wofcombrows.(C)Aboralvie

wofcydippidstage.(D)O

ne-

celledfertilized

embryo.(EtoH)Earlycleavagestages.(I)Gastrulastage.(JtoM)

LaterdevelopmentofM

.leid

yiem

bryo

shownoralsidedown

.Embryosareabout

200mm

.See

thesupplementarymaterialsfora

moredetaileddescriptionofthe

ctenophorebody

plan.[Photocreditfor(A):courtesyofBrunoVellutini]

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Bilateria

Radiata

Ancestral Protist

Round Worms

Mollusks

Segmented Worms

Arthropods

Vertebrates

Echinoderms

Cnidarians

Ctenophores

Sponges

Flatworms

PlacozoaNo symmetry

Text

asdeterm

ined

bybaa.pl

(25),was

98.2%.In

94.8%

ofcases,asingleEST

mappedcompletely

toasinglescaffold.T

hese

numberssuggestthat

theassemblyis

both


assembled.

Characteris

ticsof

theM.leidyiG

enom

e

The

M.leidyigenom

eisam

ongthesm

allest7%

ofgenomes

whencomparedwith

thosecataloged

intheAnimalGenom

eSize

Database(26)

andis

denselypacked

with

gene

sequences.Itencodes

16,548


loci,w

hich

make

up58%


sign

44%ofthesegene

predictions

intohomology

groups

with

non-ctenophores.The

averagelength

ofan

unspliced


.8kb.Eight

percento


bedded

within

othergenes.T

hisn

umberofnestedintro

nicgenes

ishigh


es(tableS2

),but

may

beinflatedow

ingtoasubsetof

thesebeing


levelofrepeti-

tivesequence

intheM.leidyig

enom

eislow


etazoans

(tables

S3andS4



paired-


alone.Additional

characteristicsof

this


tables

S5to

S10.

Phylog

enetic

Positio

nof

M.leidyi


hasallowed

usto

improveon

thectenophore

samplingused

inprevious

phylogenom

icanalyses

ofgene

sequence


twodata

matrices

thatdiffer

inbreadthof

taxonsampling


data:a

“Genom

eSet”that

includesonlydatafro


mals,19.6%

missing

data)and

an“EST

Set”that


manytaxa

(58

animals,64.9%

missing

data).Weanalyzed

both

matrices

byusingmaximum

-likelihood[with

the

GTR+Gmodelasimplem

entedinRAxM

L(27)]

andBayesian[with

theCATmodelasimplem

ented

inPh

yloB

ayes

(28)]m

ethods.T

ounderstand

the

effectofoutgroup

selectionon

ouringroup

topol-

ogy,weincluded


etazoan


combinationofmeth-

odandmatrix


yielded

atotalof1

6analyses

(Table1).

Wefoundno

supportinanyof

theseanalyses



Placozoa

beingthesister

lineage

totherest

ofanim

als(Tr,)

(Table1andfig

.S1).W

erecovered


relationshipbetween


ofPlacozoa,C


n,Bi).

Maxim


supportthe

place-

mentof

Ctenophoraas

sister

groupto

allother

Bi

Cn

(Cn,

Ct)

(Ct,B

i)(P

o,)

(Ct,)

(Tr,)

(Bi,)

Ct

Tr Po

Bi

Ct

Cn

Tr Po

Bi

Cn

Tr Ct

Po

Bi

Cn

Tr Po

Ct

Bi

Cn

Ct

Po

Tr

Bi

Cn

Ct

Po

Tr

AB

CD

EF

Fig.

2.Previously

prop

osed

relation

shipsof

thefive

deep

clad

esof

anim

als.Thelabelatthe

botto

mofeach

pane





tothe


assistergroup


hypothesis.Weseeno

supportinanyof

oura

nalysesforthe

hypotheses

in(A),(E),and(F)a

ndverylittle

supportfor

(B)(see


i,Bilateria.

Fig.

1.M.leidyilife

historyandanatom

y.(A)A

dultM.leid

yi(about10




ne-

celledfertilized


LaterdevelopmentofM

.leid

yiem

bryo

shownoralsidedown

.Embryosareabout

200mm

.See



ctenophorebody


13DEC

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ICLE

ctenophores

• Placozoa

• Porifera (sponges)

• Cnidarians (jellyfish, corals, hydroids)

• Ctenophores (comb jellies)

• Flat Worms

• Round Worms

• Molluscs (clams, snails, squid, octopi)

• Segmented Worms

• Arthropods (copepods, crabs, shrimp)

• Echinoderms (sea stars, brittle stars)

Invertebrate Phyla

Placozoa

• Simplest animal?

• Lacks symmetry

• Only four cell types

• No tissues or organs

• Found on surfaces

• Probably feeds on surface algae and bacteria

• Can fold itself to create a digestive pocket

• “Skeleton” may be calcareous or silica spicules, or entirely of the protein collagen

• Benthic -- intertidal to abyssal, all latitudes

• Suspension Feeders (strain plankton, bacteria. A few exceptions)

• Large range of cell types, lack of tissue types

• Source of many bioactive compounds

Porifera(sponges)

Diversity in size & shape,Many growth forms

MBARI

Sponge SkeletonsGlass sponge

( Venus’ Flower Basket)

Natural SpongeCalcareous Sponge

collagen

Sponge Anatomy

choanocyte


Bilateria

Radiata

Ancestral Protist

Round Worms

Mollusks

Segmented Worms

Arthropods

Vertebrates

Echinoderms

Cnidarians

Ctenophores

Sponges

Flatworms

Placozoa

Ctenophores(comb jellies)



• Earliest branching metazoan phylum?

• All are marine

• Pelagic from 0 to >3000 m (few benthic creepers)

• Have eight rows of cilia (comb rows)

• Carnivorous

• Use tentacles with sticky colloblasts

• Some directly ingest prey (Beroe)

asdeterm

ined

bybaa.pl

(25),was

98.2%.In

94.8%

ofcases,asingleEST

mappedcompletely

toasinglescaffold.T

hese

numberssuggestthat

theassemblyis

both


assembled.

Characteris

ticsof

theM.leidyiG

enom

e

The

M.leidyigenom

eisam

ongthesm

allest7%

ofgenomes

whencomparedwith

thosecataloged

intheAnimalGenom

eSize

Database(26)

andis

denselypacked

with

gene

sequences.Itencodes

16,548


loci,w

hich

make

up58%


sign

44%ofthesegene

predictions

intohomology

groups

with

non-ctenophores.The

averagelength

ofan

unspliced


.8kb.Eight

percento


bedded

within

othergenes.T

hisn

umberofnestedintro

nicgenes

ishigh


es(tableS2

),but

may

beinflatedow

ingtoasubsetof

thesebeing


levelofrepeti-

tivesequence

intheM.leidyig

enom

eislow


etazoans

(tables

S3andS4



paired-


alone.Additional

characteristicsof

this


tables

S5to

S10.

Phylog

enetic

Positio

nof

M.leidyi


hasallowed

usto

improveon

thectenophore

samplingused

inprevious

phylogenom

icanalyses

ofgene

sequence


twodata

matrices

thatdiffer

inbreadthof

taxonsampling


data:a

“Genom

eSet”that

includesonlydatafro


mals,19.6%

missing

data)and

an“EST

Set”that


manytaxa

(58

animals,64.9%

missing

data).Weanalyzed

both

matrices

byusingmaximum

-likelihood[with

the

GTR+Gmodelasimplem

entedinRAxM

L(27)]

andBayesian[with

theCATmodelasimplem

ented

inPh

yloB

ayes

(28)]m

ethods.T

ounderstand

the

effectofoutgroup

selectionon

ouringroup

topol-

ogy,weincluded


etazoan


combinationofmeth-

odandmatrix


yielded

atotalof1

6analyses

(Table1).

Wefoundno

supportinanyof

theseanalyses



Placozoa

beingthesister

lineage

totherest

ofanim

als(Tr,)

(Table1andfig

.S1).W

erecovered


relationshipbetween


ofPlacozoa,C


n,Bi).

Maxim


supportthe

place-

mentof

Ctenophoraas

sister

groupto

allother

Bi

Cn

(Cn,

Ct)

(Ct,B

i)(P

o,)

(Ct,)

(Tr,)

(Bi,)

Ct

Tr Po

Bi

Ct

Cn

Tr Po

Bi

Cn

Tr Ct

Po

Bi

Cn

Tr Po

Ct

Bi

Cn

Ct

Po

Tr

Bi

Cn

Ct

Po

Tr

AB

CD

EF

Fig.

2.Previously

prop

osed

relation

shipsof

thefive

deep

clad

esof

anim

als.Thelabelatthe

botto

mofeach

pane





tothe


assistergroup


hypothesis.Weseeno

supportinanyof

oura

nalysesforthe

hypotheses

in(A),(E),and(F)a

ndverylittle

supportfor

(B)(see


i,Bilateria.

Fig.

1.M.leidyilife

historyandanatom

y.(A)A

dultM.leid

yi(about10




ne-

celledfertilized


LaterdevelopmentofM

.leid

yiem

bryo

shownoralsidedown

.Embryosareabout

200mm

.See



ctenophorebody


13DEC

EMBE

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13VO

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RESE

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ICLE

lobate

cestid

beroe cydippid

Ctenophores

• Named for the stinging cells (cnidocytes)

• Radial symmetry

• Two forms: polyps and medusae (some have alternation of generations)

• Asexual and Sexual Reproduction

Cnidarians(anemones, corals, jellyfish)

• Radial symmetry

• Simple Digestive system (blind sac)

• No circulatory, respiratory or excretory systems

• carnivores/detritovores

• Primitive nerve networks

Polyp Medusa

Cnidocytes

• Prey capture

• Turf wars

• Defense

Cnidocytes

toxins

Class Hydrozoa: hydroids and hydromedusaeClass Anthozoa: Sea anenomes, corals, sea pensClass Cubozoa: sea wasps and box jelliesClass Scyphozoa: jellyfish (big jellies)

Jellyfish


Bilateria

Radiata

Ancestral Protist

Round Worms

Mollusks

Segmented Worms

Arthropods

Vertebrates

Echinoderms

Cnidarians

Ctenophores

Sponges

Flatworms

Placozoa

• Turbellarian flatworms are marine, benthic

• Infauna from intertidal to deep sea

• Carnivorous or herbivorous

• Move by cilia or undulations

• Mouth but no anus

• Cephalization

Flatworms(Platyhelminthes)

• Flow-through digestive system!

• Found all over (terrestrial, freshwater, marine)

• VERY abundant free-living in benthic infauna

• Many other types are parasitic

• Many are deposit feeders, detritivores

Roundworms(Nematodes)


Bilateria

Radiata

Ancestral Protist

Round Worms

Mollusks

Segmented Worms

Arthropods

Vertebrates

Echinoderms

Cnidarians

Ctenophores

Sponges

Flatworms

Placozoa

MAJOR CLASSES

• Bivalvia (Clams, oysters, mussels)

• Gastropoda (snails, nudibranchs)

• Cephalopoda (squid, octupus, nautilus)

Molluscs

• Many burrowing and boring

• Others attach to rocky surfaces

• Suspension feeding or selective deposit feeding

Bivalves Burrowing

boring

• Many with shells (snails, whelks, etc.) some types without shells (e.g. nudibranchs)

• Some planktonic forms (e.g. pteropods)

• Herbivores and carnivores, deposit and suspension feeders

• Have a radula (a toothed scraper)

Gastropods

• Well developed brains and eyes

• Many have ink sacs

• Only one type still has external shell (Chambered nautilus)

• Carnivores; Have a radula and beak for tearing food

• Many can rapidly change colors (camouflage, communication)

Cephalopods

Molluscs


Bilateria

Radiata

Ancestral Protist

Round Worms

Mollusks

Segmented Worms

Arthropods

Vertebrates

Echinoderms

Cnidarians

Ctenophores

Sponges

Flatworms

Placozoa

• Major Class: the Polychaetes

• Mostly benthic, a few planktonic

- predatory epifauna

- tube-dwelling infauna (deposit/suspension feeders)

Segmented Worms(Annelids)

well developed central nervous

system

PolychaetesFood capture & Gas Exchange

tube dwelling

Christmas tree worm

Arthropoda(jointed foot)

• Exoskeleton (protection, leverage)

• Striated Muscle (quick, powerful)

• Herbivores, carnivores, omnivores

• External Skeleton requires molting

Arthropoda: CrustaceaMalacostraca

amphipodsisopodsostracods

mysids

decapod

branchiopods

copepods

Arthropoda

• Vast majority of marine arthropods are crustaceans

• Exceptions: marine insects, cheliceriformes (e.g., horseshoe crabs, pycnogonids)

halobates

horseshoe crabs

Arthropods


Bilateria

Radiata

Ancestral Protist

Round Worms

Mollusks

Segmented Worms

Arthropods

Vertebrates

Echinoderms

Cnidarians

Ctenophores

Sponges

Flatworms

Placozoa

• Echino derm = spiny skin

• Most are suspension or deposit feeders, sea stars also predatory

• From intertidal to abyssal depths, nearly all are benthic

• Have tube feet

• Bilaterally symmetric as larvae, adults pentaradially symmetric

Echinoderms

Sea Stars

Brittle Stars

Sea Cucumbers

Sea Urchins

Crinoids

Echinoderms

Echinoderms

Questions?

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