<<

Marine I. The

OCN 201 Lecture 7 Illustration :

Arthropods Segmented Worms The

Family Tree Mollusks

Echinoderms 40 animal phyla Round Worms Cnidarians 32 phyla are multicellular invertebrates

Ctenophores No Ancestral

)]

that

that

27

” ”

RESEARCH ARTICLE ArthropodsM. leidyi EST Set RESEARCH ARTICLE “ Segmented

SUMMARY Set “ Worms

Vertebrates SpizellomycesM. leidyi punctatus Batrachochytrium dendrobatidis Cryptococcus neoformans READ THE FULL ARTICLE ONLINE Saccharomyces cerevisiae

The Genome of the Ctenophore http://dx.doi.org/10.1126/science.1242592Phycomyces blakesleeanus )] methods. To understand the

Rhizopus orizae 28 Outgroup et al Citeramoredetaileddescriptionofthe this article asAmoebidium J. F. Ryan parasiticum., leidyi and Its Implications Science 342, 1242592 (2013).Sphaeroforma arctica DOI: 10.1126/science.1242592Capsaspora_owczarzaki Monosiga ovata Salpingoeca rosettamodel as implemented in RAxML ( for Type 72 Monosiga brevicollisG

Pleurobrachia pileus We found no support in any of these analyses Mnemiopsis leidyi

shown oral side down. are about

ment of Ctenophora as to all other

Maximum-likelihood analyses support the place-

of Placozoa, , and Bilateria (Tr,Cn,Bi).

Cnidaria and Bilateria (Cn,Bi) and for a broad support for a sister relationship between

Joseph F. Ryan, Kevin Pang, Christine E. Schnitzler, Anh-Dao Nguyen, R. Travis Moreland, animals (Tr,) (Table 1 and fig. S1). We recovered Placozoa being the sister lineage to the rest of

for (Cn,Ct), Diploblastica (Bi,), or

atotalof16analyses(Table1).

od and matrix. This multifactorial strategy yielded

outgroups (table S11) in each combination of meth-

ogy, we included four different sets of nonmetazoan effect of outgroup selection on our ingroup topol-

Mertensiid sp in PhyloBayes ( and Bayesian [with the CAT model as implemented

GTR+

matrices by using maximum-likelihood [with the

animals, 64.9% missing data). We analyzed both

nldsprilgnmcdata genomic partial includes from many taxa (58

mals, 19.6% missing data) and an

includes only data from complete (13 ani-

and fraction of missing data: a

matrices that differ in breadth of sampling

of sequence evolution. We assessed two data

sampling used in previous phylogenomic analyses

has allowed us to improve on the ctenophore The availability of the complete genome of David K. Simmons, Bernard J. Koch, Warren R. Francis, Paul Havlak, FIGURES IN THE FULLPhylogenetic PositionARTICLE of Leucetta chagosensis raphanus 88

NISC Comparative Sequencing Program, Stephen A. Smith, Nicholas H. Putnam, Porifera Fig. 1.M. leidyi M. leidyi history and .

Steven H. D. Haddock, Casey W. Dunn, Tyra G. Wolfsberg, James C. Mullikin, 77 Oscarella lobularis

Tr

Po

Ct Cn Bi Oopsacas minuta Mark Q. Martindale, Andreas D. Baxevanis* Fig. 2. Previously98 proposed relationshipsCarteriospongia foliascens

of the fi ve deep97 of animals. queenslandica www.sciencemag.org

Suberites domuncula (Bi,) Fig. 3. Tree produced96 by maximum-likelihoodLubomirskia baicalensis

Ephydatia muelleri)Ctenophoraas Introduction: An understanding of ctenophore biology is critical for reconstructing events that The label at the

analysis of the EST set. B genome is low to 96 m. See the supplementary materials fo adhaerens occurred early in animal evolution. The phylogenetic relationship of ctenophores (comb jellies) to m Placozoa

other animals has been a source of long-standing debate. Until recently, it was thought that Porif- Fig. 4. Tree produced by maximum-likelihoodCyanea capillata

Tr

Po

Ct Cn

Bi Clytia hemisphaerica

SCIENCE

ctenophore . [Photo credit for (A): courtesy of Bruno Vellutini] 200 (Science 2013) analysisLater development of of gene content. magnipapillata era (sponges) was the earliest diverging animal lineage, but recent reports have instead suggested transcript is 5.8 kb. Eight 96 Podocoryna carnea Cnidaria

Ctenophora as the earliest diverging animal lineage. Because ctenophores share some of the same M. leidyi

Fig. 5. The origin) of postsynaptic .Hydractinia echinata (Tr,)

complex cell types with bilaterians (such as neural and mesodermal cells), the phylogenetic position M Nematostella vectensis 82 Anemonia viridis Fig. 6. Inventoryto of myogenic components

of ctenophores affects how we think about the early evolution of these cell types. )One-

J

M. leidyi Aiptasia pallida)Ctenophoraassistergrouptothe

in M. leidyiD .

Metridium senile D )Diploblasticahypothesis.Weseeno

Methods: We have sequenced, annotated, and analyzed the 150-megabase genome of the cteno- Acropora palmata F

Ct

Po

Tr Cn Bi Acropora millepora phore Mnemiopsis leidyi. We have performed detailed phylogenetic analyses on these new data SUPPLEMENTARY(about 10 cm MATERIALS Porites astreoides

using both sequence matrices and information on gene content. We conducted extensive genomic Montastraea faveolata )Coelenteratahypothesis.(

inventories on signaling pathway components and genes known to be critical to neural and meso- Materials and Methods bockiA Figs. S1 to S1045 Nemertoderma westbladi

M. leidyi Meara stichopi

tables S5 to S10.

characteristics of this genome are presented in

end and mate-pair sequencing alone. Additional

high-quality genome assembly based on paired-

S3 and S4); this has made it possible to produce a

dermal cell types, among others. moderate, as compared to other metazoans (tables

tive sequence in the

alternatively expressed exons. The level of repeti- A), (E), and (F) and very little support for (B) (see

may be inflated owing to a subset of these being

is high compared to other genomes (table S2), but

other genes. This number of nested intronic genes

percent of predicted genes are embedded within of an unspliced 98 groups with non-ctenophores. The average length )Gastrulastage.( Isodiametra pulchra

Tables S1 to S31I Results: Our phylogenetic analyses suggest that ctenophores are the sister group to the rest of the Symsagittifera roscoffensis

References Convolutriloba longifissura

)Adult

Po

Ct

Tr Cn

extant animals. We fi nd that the sets of neural components present in the genomes of Mnemiopsis Bi Saccoglossus kowalevskii A and the are quite similar, suggesting that sponges have the ( Ptychodera flava Strongylocentrotus purpuratus

necessary genetic machinery for a functioning but may have lost these cell types. Asterina pectinifera

)andis 44 26 Branchiostoma floridae We also fi nd that, although Mnemiopsis has most of the genes coding for structural components of 13 DECEMBER 2013 VOL 342 )Aboralviewofcydippidstage.( 83 Petromyzon marinus mesodermal cells, they lack many of the genes involved in bilaterian mesodermal specifi cation and, C Gallus gallus = 100 bootstrap BilateriaGenome therefore, may have independently evolved these cell types. intestinalis support Halocynthia roretzi

The phylogenetic position of the ctenophore ), was 98.2%. In

Po

Tr

Cn Ct 43 Bi Echinoderes horni Discussion: These results present a newly supported view of early animal evolution that accounts Mnemiopsis leidyi)Earlycleavagestages.( and88 its implications regarding Xiphinema index H 94

for major losses and/or gains of sophisticated cell types, including and muscle cells. This the origin of mesodermal cell types.Euperipatoides (A) Adult kanangrensis to 0.2 99 Anoplodactylus eroticus M. leidyi

M. leidyi. (B) SummaryE of the99 relationships of the fi ve evolutionary framework, along with the comprehensive genomic resources made available through Boophilus microplus main branches of animals and the outgroup Choano-Daphnia pulex this study, will yield myriad discoveries about our most distant animal relatives, many of which will 93 )PoriferaassistergrouptotherestofMetazoa.(

fl a g e l l a t a . ( C) Inventory of myogenic specifi cation C Drosophila melanogaster

)PlacozoaassistergrouptotherestofMetazoa.( life history and anatomy. shed light not only on the biology of these extant organisms but also on the evolutionary history of genes in Mnemiopsis. Components present in the E Schmidtea mediterranea

all animal , including our own. Mnemiopsis genome are in blue, and names are Paraplanocera oligoglena genome is among the smallest 7%

Po

Tr

Ct Cn 95 Bi Capitella telata underlined. Absent components are in red. The lack of Helobdella robusta many of these factors84 in Mnemiopsis indicatesCerebratulus that lacteus

M. leidyi 85 )Close-upviewofcombrows.( Terebratalia transversa

ctenophore B mesodermal44 cell types are specifi ed differ-

Euprymna scolopes M. leidyi ently than in bilaterians, suggesting that they Lottiaperhaps(Cn,Ct) gigantea (Ct,Bi) (Po,) (Ct,)

evolved independently in these two lineages. Crassostrea virginica

sign 44% of these gene predictions into

up 58% of the genome, and we conservatively as-

16,548 predicted -coding loci, which make

densely packed with gene sequences. It encodes AB C D E F

in the Animal Genome Size Database (

of genomes when compared with those cataloged

The

Characteristics of the

assembled.

the assembly is both complete and accurately

to a single scaffold. These numbers suggest that

94.8% of cases, a single EST mapped completely

as determined by baa.pl25 (

Table 1). Ct, Ctenophora; Po, Porifera; Tr, Placozoa; Cn, Cnidaria; Bi, Bilateria.

support in any of our analyses for the hypotheses in (

rest of Metazoa. (

sister to Bilateria. (

bottom of each pane corresponds to the header of Table 1. (

Fig. 2. Previously proposed of relationships the five deep clades of animals.

celled fertilized embryo. (

long). (

Fig. 1. 1242592-2 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 amino A B Cnidaria C FGF acid characters. Circles on nodes indicate 100% bootstrap support. SupportBMPs/dppplacing ctenophores as sister to the rest of Metazoa is 96% of 100 bootstrap RESEARCH ARTICLE replicates. Shh/hh Bilateria NK2 1242592-4 13 DECEMBER 2013 VOL 342 SCIENCE www.sciencemag.org Wnt/Wg Noggin s Placozoa u GATA le c Twist u Eomes n Lbx Porifera MyoG Mef2 Slp NK3 Snail Mrf4 Ctenophora Eya Six1/4 Myf5 MyoD Choanoflagellata ArthropodsGli NK4 Segmented Worms The list of author affi liations is available in the full article online. Vertebrates The*Corresponding author. Animal E-mail: [email protected] 1336 13 DECEMBER 2013 VOL 342 SCIENCE www.sciencemag.org Published by AAAS Tree Mollusks

Echinoderms Round Worms

Cnidarians Text

Bilateria

)]

that

that

27

M. leidyi

EST Set

Genome Set

M. leidyi

)] methods. To understand the

28

ramoredetaileddescriptionofthe

model as implemented in RAxML (

G

We found no support in any of these analyses

embryo shown oral side down. Embryos are about

ment of Ctenophora as sister group to all other

Maximum-likelihood analyses support the place-

of Placozoa, Cnidaria, and Bilateria (Tr,Cn,Bi).

Cnidaria and Bilateria (Cn,Bi) and for a clade

broad support for a sister relationship between

animals (Tr,) (Table 1 and fig. S1). We recovered

Placozoa being the sister lineage to the rest of

for Coelenterata (Cn,Ct), Diploblastica (Bi,), or

atotalof16analyses(Table1).

od and matrix. This multifactorial strategy yielded

outgroups (table S11) in each combination of meth-

ogy, we included four different sets of nonmetazoan

effect of outgroup selection on our ingroup topol-

in PhyloBayes (

and Bayesian [with the CAT model as implemented

GTR+

matrices by using maximum-likelihood [with the

animals, 64.9% missing data). We analyzed both

nldsprilgnmcdata genomic partial includes from many taxa (58

mals, 19.6% missing data) and an

includes only data from complete genomes (13 ani-

and fraction of missing data: a

matrices that differ in breadth of taxon sampling

of gene sequence evolution. We assessed two data

sampling used in previous phylogenomic analyses

has allowed us to improve on the ctenophore

The availability of the complete genome of Phylogenetic Position of

M. leidyi Radiata

Tr

Po

Ct Cn

Ctenophores Bi www.sciencemag.org

(Bi,) Flatworms

)Ctenophoraas

The label at the

B

genome is low to

m. See the supplementary materials fo

m

Tr

Po

Ct

Cn

Bi

SCIENCE

ctenophore body plan. [Photo credit for (A): courtesy of Bruno Vellutini]

200

Later development of

transcript is 5.8 kb. Eight

M. leidyi

)

(Tr,)

M

to

)One-

J

M. leidyi

)Ctenophoraassistergrouptothe

D

D

)Diploblasticahypothesis.Weseeno

F

Ct

Po

Tr

Cn

Bi

(about 10 cm )Coelenteratahypothesis.(

A No symmetry

M. leidyi

tables S5 to S10.

characteristics of this genome are presented in

end and mate-pair sequencing alone. Additional

high-quality genome assembly based on paired-

S3 and S4); this has made it possible to produce a

moderate, as compared to other metazoans (tables

tive sequence in the

alternatively expressed exons. The level of repeti- A), (E), and (F) and very little support for (B) (see

may be inflated owing to a subset of these being

is high compared to other genomes (table S2), but

other genes. This number of nested intronic genes

percent of predicted genes are embedded within

of an unspliced

groups with non-ctenophores. The average length )Gastrulastage.(

I Placozoa

)Adult

Po

Ct

Tr

Cn

Bi A

Sponges(

)andis 26

13 DECEMBER 2013 VOL 342

)Aboralviewofcydippidstage.(

C

Genome

), was 98.2%. In

Po

Tr

Cn Ct

Bi Ancestral

)Earlycleavagestages.(

H to

ctenophores M. leidyi

E

)PoriferaassistergrouptotherestofMetazoa.(

C

)PlacozoaassistergrouptotherestofMetazoa.(

life history and anatomy.

E

genome is among the smallest 7%

Po

Tr

Ct Cn

Bi Protist

M. leidyi

)Close-upviewofcombrows.(

B

M. leidyi

(Cn,Ct) (Ct,Bi) (Po,) (Ct,)

sign 44% of these gene predictions into homology

up 58% of the genome, and we conservatively as-

16,548 predicted protein-coding loci, which make

densely packed with gene sequences. It encodes AB C D E F

in the Animal Genome Size Database (

of genomes when compared with those cataloged

The

Characteristics of the

assembled.

the assembly is both complete and accurately

to a single scaffold. These numbers suggest that

94.8% of cases, a single EST mapped completely

as determined by baa.pl25 (

Table 1). Ct, Ctenophora; Po, Porifera; Tr, Placozoa; Cn, Cnidaria; Bi, Bilateria.

support in any of our analyses for the hypotheses in (

rest of Metazoa. (

sister to Bilateria. (

bottom of each pane corresponds to the header of Table 1. (

Fig. 2. Previously proposed of relationships the five deep clades of animals.

celled fertilized embryo. (

long). (

Fig. 1.

1242592-2 RESEARCH ARTICLE Phyla • Placozoa • Porifera (sponges) • Cnidarians (jellyfish, corals, hydroids) • Ctenophores (comb jellies) • Flat Worms • Round Worms • Molluscs (clams, snails, squid, octopi) • Segmented Worms • (, crabs, ) • Echinoderms ( stars, brittle stars)

Placozoa

• Simplest animal? • Lacks symmetry • Only four cell types • No tissues or organs • Found on surfaces • Probably feeds on surface and • Can fold itself to create a digestive pocket Porifera (sponges)

• “” may be or silica spicules, or entirely of the protein • Benthic -- intertidal to abyssal, all latitudes • Suspension Feeders (feeding on , bacteria. A few exceptions) • Large range of cell types, lack of types • Source of many bioactive compounds

Diversity in size & shape, Many growth forms

MBARI Sponge Glass sponge ( Venus’ Flower Basket) Natural Sponge

collagen

Sponge Anatomy

Arthropods Segmented Worms The Animal Vertebrates

Family Tree Mollusks

Echinoderms Round Worms

Cnidarians

Bilateria

Ctenophores Radiata Flatworms

Placozoa Sponges Ancestral Protist

Ctenophores (comb jellies) Ctenophores (comb jellies) • All are marine • Pelagic from 0 to >3000 m (few benthic

creepers)

)]

that

that

27

” ”

Have eight rows of cilia (comb rows) M. leidyi EST Set

• “

Genome Set “

• Carnivorous M. leidyi

)] methods. To understand the 28 Use with sticky colloblasts ramoredetaileddescriptionofthe

• model as implemented in RAxML (

G

We found no support in any of these analyses

embryo shown oral side down. Embryos are about

ment of Ctenophora as sister group to all other

Maximum-likelihood analyses support the place-

of Placozoa, Cnidaria, and Bilateria (Tr,Cn,Bi).

Cnidaria and Bilateria (Cn,Bi) and for a clade

broad support for a sister relationship between

animals (Tr,) (Table 1 and fig. S1). We recovered

Placozoa being the sister lineage to the rest of

for Coelenterata (Cn,Ct), Diploblastica (Bi,), or

atotalof16analyses(Table1).

od and matrix. This multifactorial strategy yielded

outgroups (table S11) in each combination of meth-

ogy, we included four different sets of nonmetazoan

effect of outgroup selection on our ingroup topol-

in PhyloBayes (

and Bayesian [with the CAT model as implemented

GTR+

matrices by using maximum-likelihood [with the

animals, 64.9% missing data). We analyzed both

nldsprilgnmcdata genomic partial includes from many taxa (58

mals, 19.6% missing data) and an

includes only data from complete genomes (13 ani-

and fraction of missing data: a

matrices that differ in breadth of taxon sampling

of gene sequence evolution. We assessed two data

sampling used in previous phylogenomic analyses

has allowed us to improve on the ctenophore The availability of the complete genome of

• Some directly ingest prey () Phylogenetic Position of

M. leidyi

Tr

Po

Ct

Cn

Bi www.sciencemag.org

• Can be invasive (e.g., ) (Bi,)

)Ctenophoraas

The label at the

B

genome is low to

m. See the supplementary materials fo

m

Tr

Po

Ct

Cn

Bi

SCIENCE

ctenophore body plan. [Photo credit for (A): courtesy of Bruno Vellutini]

200

Later development of

transcript is 5.8 kb. Eight

M. leidyi

)

(Tr,)

M

to

)One-

J

M. leidyi

)Ctenophoraassistergrouptothe

D

D

)Diploblasticahypothesis.Weseeno

F

Ct

Po

Tr

Cn

Bi

(about 10 cm )Coelenteratahypothesis.(

lobate A

M. leidyi

tables S5 to S10.

characteristics of this genome are presented in

end and mate-pair sequencing alone. Additional

high-quality genome assembly based on paired-

S3 and S4); this has made it possible to produce a

moderate, as compared to other metazoans (tables

tive sequence in the

alternatively expressed exons. The level of repeti- A), (E), and (F) and very little support for (B) (see

may be inflated owing to a subset of these being

is high compared to other genomes (table S2), but

other genes. This number of nested intronic genes

percent of predicted genes are embedded within

of an unspliced

groups with non-ctenophores. The average length

)Gastrulastage.(

I

)Adult

Po

Ct

Tr

Cn

Bi

A

(

)andis 26

13 DECEMBER 2013 VOL 342

)Aboralviewofcydippidstage.(

C

Genome

), was 98.2%. In

Po

Tr

Cn

Ct

Bi

)Earlycleavagestages.(

H

to

M. leidyi

E

)PoriferaassistergrouptotherestofMetazoa.(

C

)PlacozoaassistergrouptotherestofMetazoa.(

life history and anatomy.

E

genome is among the smallest 7%

Po

Tr

Ct

Cn

Bi

M. leidyi )Close-upviewofcombrows.(

cestid B

M. leidyi

(Cn,Ct) (Ct,Bi) (Po,) (Ct,)

sign 44% of these gene predictions into homology

up 58% of the genome, and we conservatively as-

16,548 predicted protein-coding loci, which make

densely packed with gene sequences. It encodes AB C D E F

in the Animal Genome Size Database (

of genomes when compared with those cataloged

The

Characteristics of the

assembled.

the assembly is both complete and accurately

to a single scaffold. These numbers suggest that

94.8% of cases, a single EST mapped completely

as determined by baa.pl25 (

Table 1). Ct, Ctenophora; Po, Porifera; Tr, Placozoa; Cn, Cnidaria; Bi, Bilateria.

support in any of our analyses for the hypotheses in (

rest of Metazoa. (

sister to Bilateria. (

bottom of each pane corresponds to the header of Table 1. (

Fig. 2. Previously proposed of relationships the five deep clades of animals.

celled fertilized embryo. (

long). (

Fig. 1. 1242592-2

beroe RESEARCH ARTICLE cydippid Cnidarians (anemones, corals, jellyfish)

• Named for the stinging cells () • Radial symmetry • Two forms: polyps and medusae • Asexual and

• Radial symmetry • Simple Digestive system (blind sac) • No circulatory, respiratory or excretory systems Medusa • /detritovores • Primitive nerve networks Cnidocytes Cnidocytes

• Prey capture • Turf wars • Defense

toxins

Class : hydroids and hydromedusae : Sea anenomes, corals, sea pens Class Cubozoa: sea wasps and box jellies Class : jellyfish (big jellies) Jellyfish and fisheries

Arthropods Segmented Worms The Animal Vertebrates

Family Tree Mollusks

Echinoderms Round Worms

Cnidarians

Bilateria

Ctenophores Radiata Flatworms

Placozoa Sponges Ancestral Protist Flatworms (Platyhelminthes) • Turbellarian flatworms are marine, benthic • Infauna from intertidal to • Carnivorous or herbivorous • Move by cilia or undulations • but no

Roundworms ()

• 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, Arthropods Segmented Worms The Animal Vertebrates

Family Tree Mollusks

Echinoderms Round Worms

Cnidarians

Bilateria

Ctenophores Radiata Flatworms

Placozoa Sponges Ancestral Protist

Molluscs

MAJOR CLASSES • (Clams, oysters, mussels)

(snails, nudibranchs)

• Cephalopoda (squid, octupus, nautilus) Bivalves Burrowing

• Many burrowing and boring boring • Others attach to rocky surfaces • Suspension feeding or selective deposit feeding

Gastropods

• 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)

• Well developed and • Many have ink sacs • Only one type still has external shell (Chambered nautilus) • Carnivores; Use radula and beak for tearing food • Many can rapidly change colors (camouflage, communication)

Arthropods Segmented Worms The Animal Vertebrates

Family Tree Mollusks

Echinoderms Round Worms

Cnidarians

Bilateria

Ctenophores Radiata Flatworms

Placozoa Sponges Ancestral Protist Segmented Worms () • Major Class: the • Mostly benthic, a few planktonic - predatory epifauna

- tube-dwelling infauna (deposit/ suspension feeders) well developed

Polychaetes Food capture & Christmas tree worm

tube dwelling Arthropoda (jointed feet)

(protection, leverage) • Striated Muscle (quick, powerful) • External Skeleton requires molting • Herbivores, carnivores, omnivores

Arthropoda: Crustacea

Malacostraca branchiopods

isopods copepods amphipods

mysids

decapod Arthropoda

• Vast majority of marine arthropods are • Exceptions: marine , chelicerates (e.g., horseshoe crabs, pycnogonids)

horseshoe crabs

halobates

Arthropods Segmented Worms The Animal Vertebrates Family Tree Mollusks

Echinoderms Round Worms

Cnidarians

Bilateria

Radiata Ctenophores Flatworms

Placozoa Sponges Ancestral Protist Echinoderms • Echino derm = spiny skin • Most are suspension or deposit feeders, some grazers (e.g., kelp), sea stars also predatory • From intertidal to abyssal depths, benthic, often have planktonic larvae • Have tube feet • Bilaterally symmetric as larvae, adults pentaradially symmetric

Echinoderms Sea Stars Sea Cucumbers

Sea Urchins Brittle Stars tube feet

Crinoids Echinoderms

Questions?