20181010200408ctenophores__1_1 x20181010200413chimera_theory_of_mesozoan_evolution1 20181010200338invert_exam_2_take_home_fall_20181 20181010200352problem_of_the_pda1 20181010200358the_search_for_the_urbilaterian_ancestor1 x
This is not really an “essay” but if you take a look at the Invertebrate Zoology Take home exam you’ll see the instructions. Just to note: (problem of the PDA + the search for the urbilaterian ancestor are for question 1) (question 2 is based on the ctenophores) (question 3 is based on the reading Chimera theory of Mesozoan evolution) I’m not sure how many pages this may take so I wrote 3 pages because its all mini questions. Answers should be from the reading and not from google which is emphasized in the instructions, also should be cited
Ctenophores: Structure, Development and Affinities:
From:
Shape and Size of Ctenophores:
The name Ctenophora was coined by Eschscholtz in 1829 for a group of marine plankton animals commonly known as “Comb jellies” or “Sea walnuts”. Ctenophora refers to the locomotory comb-like plates on the body (Gr. Kestos – comb, phoros – bearing). About 80 species have been described. Some are abundant enough to be ecologically important
Shape:
Different members have variable shapes. A typical one like Pleurobrachia is somewhat spherical.
Size:
Moderate, usual range few millimeters to 20 cms.
Symmetry:
Biradial. Structures are tetramerously arranged in a radial fashion around the oral-aboral axis.
Colour:
Usually transparent, tentacles and combplates are tinged with white, orange or purple.
Structure of Ctenophores:
The spherical body can be divided into two hemispheres. The mouth lies at one end or oral pole and a sense organ at the opposite end or aboral pole.
(i) Combplates:
Eight equally spaced rows of paddle plates arranged on the sides of the body and are used in swimming. The comb rows are composed of a series of short ciliary plates or ctenes. The cilia are strong and propel the animal slowly through the water.
(ii) Tentacles:
Two in number, found nearer to the aboral end on opposite sides of the body. They are extremely long, solid and retractile. Tentacles emerge from deep ciliated epidermal blind pouch or tentacular sheath. Tentacle bears short lateral branches or pinnae. Nematocysts are absent, but tentacles possess peculiar adhesive cells called lasso cells or colloblasts which help in food capture.
Sense Organs of Ctenophores:
Apical sensory organ is a deep seated statocyst at aboral pole. It is lined by tall, ciliated epithelial cells. Statocyst contain statolith and balancers. It is covered by a roof like a dome or bell, formed of fused cilia. The sensory organ serves as an organ of equilibrium.
Body Wall of Ctenophores:
Composed of an outer epidermis and an inner gastrodermis separated by a thick gelatinous mesogloea. The epidermis is syncytial and contains many gland cells, sensory cells and pigment granules. Mesogloea contains amoebocytes, connective tissue fibres muscle fibres and some nerve cells.
Digestive System of Ctenophores:
Mouth slit-like situated in the centre of the lower end. It leads into a long tubular pharynx lined with epidermis. The pharynx opens into a small but wide stomach. It gives out a system of five gastrovascular canals which extend throughout jelly in a definite arrangement. The stomach and gastrovascular canals are lined with gastrodermis. Two anal canals open to the outside near the aboral sense organ, each by an anal pore.
Ctenophores feed on small planktonic organisms and are voracious Food is captured by trapping in colloblast. Digestion is extracellular in pharynx and intracellular in gastrovascular canals.
Respiratory and Excretory System of Ctenophores:
There are no respiratory structures. Gaseous exchange takes place through general body surface.
Excretory System:
No definite excretory organs. Cell rosettes consisting of a double circlet of ciliated gastrodermal cells, surround openings leading from the gastrovascular canals to the mesogloea. They may be excretory or osmoregulatory.
Nervous System of Ctenophores:
There is no localized control centre. The epidermal nerve plexus is concentrated in a ring around the mouth, and at the base of the comb rows, where it forms the radial nerves. The nerves are not true nerves, but the condensation of the nerve net. The nervous system controls muscular movements and determines the. activity of cilia on the combrows.
The aboral sense organ is a statocyst or balance organ useful in maintaining normal orientation.
Reproductive System and Development of Ctenophores:
All are hermaphrodites. Reproduction is sexual only and asexual reproduction is totally absent. Gonads develop from endoderm in the form of bands in the meridional canals of the gastrovascular system.
Development:
Generally fertilization is external. Cleavage is total, determinate and unique in ctenophores called disymmetrical. Usually free swimming characteristic cydippid larva occurs which undergoes gradual metamorphosis. Some ctenophores exhibit a strange phenomenon called dissogeny in which both the larva and adult reproduce sexually. There is no alternation of generation.
Ctenophores have great powers of regeneration. Lost or wounded parts, even the statocyst, are replaced or repaired by regeneration.
Affinities of Ctenophores:
Many zoologists still keep ctenophores as Acnidaria, a subphylum of Colenterata.
The affinities of these animals can be studied under following heads:
1. Affinities with Cnidaria
2. Affinities with Platyhelminthes.
1. Affinities with Cnidaria:
Ctenophores resemble Cnidaria in:
1. Having a strong biradial symmetry and an oral-aboral axis.
2. Diploblastic body.
3. Medusa like body with a gelatinous mesenchymal mesogloea.
4. Absence of coelom.
5. Similar but more advanced endodermal gastrovascular cavity.
6. Diffused epidermal nerve plexus.
7. Presence of statocyst.
8. Absence of nephridia.
9. Absence of respiratory organs.
10. Endodermal gonads.
On the basis of above affinities with cnidaria, many zoologists treat them as a class of phylum Coelenterata.
(a) Affinities with Hydrozoa:
Ctenophores show following resemblances with Hydrozoa:
1. General body surface corresponds to exumbrellar surface of a medusa.
2. Stomodaeum corresponds to subumbrellar surface of medusa.
3. Simple gastrovascular cavity.
4. Thick, gelatinous mesogloea.
5. Two opposite tentacles in sheath.
(b) Affinities with Anthozoa:
1. Ciliated ectoderm of Anthozoa is forerunner of combplate.
2. A well-developed stomodaeum.
3. Endodermal gonads.
4. Release of gametes through mouth.
5. Biradial symmetry.
6. Gut in embryos four lobed.
7. Cellular mesogloea.
Differences from Cnidaria:
1. Presence of combplates.
2. No tentacles around mouth.
3. Presence of colloblasts.
4. An aboral sense organ.
5. Mesenchymal muscles.
6. Definite organization of digestive system.
7. Presence of anal pores.
8. Determinate cleavage.
9. Absence of a planula larva.
10. Presence of cydippid larva.
11. Complete absence of polymorphism.
12. Absence of alternation of generation and asexual reproduction.
2. Affinities with Platyhelminthes:
Two ctenophores viz. Coeloplana and Ctenoplana exhibit following resemblances with polyclad turbellarians.
1. Dorsollventrally flattened body.
2. Crawling mode of locomotion.
3. Ciliated epidermis.
4. Lobed gastrovascular cavity.
BioSystems 73 (2004) 73–83
A “chimera” theory on the origin of dicyemid mesozoans:
evolution driven by frequent lateral gene transfer
from host to parasite
Tomoko Noto∗, Hiroshi Endoh
Department of Biology, Faculty of Science, Kanazawa University, Kanazawa 920-1192, Japan
Received 13 February 2003; received in revised form 8 August 2003; accepted 2 September 2003
Abstract
The phylogenetic status of the enigmatic dicyemid mesozoans is still uncertain. Are they primitive multicellular organisms or
degenerate triploblastic animals? Presently, the latter view is accepted. A phylogenetic analysis of 18S rDNA sequences placed
dicyemids within the animal clade, and this was supported by the discovery of a Hox-type gene with a lophotrochozoan signature
sequence. This molecular information suggests that dicyemid mesozoans evolved from an ancestral animal degenerately. Consid-
ering their extreme simplicity, which is probably due to parasitism, they might have come from an early embryo via a radical trans-
formation, i.e. neoteny. Irrespective of this molecular information, dicyemid mesozoans retain many protistan-like or extremely
primitive features, such as tubular mitochondrial cristae, endocytic ability from the outer surface, and the absence of collagenous
tissue, while they do not share noticeable synapomorphy with animals. In addition, the 5S rRNA phylogeny suggests a somewhat
closer kinship with protozoan ciliates than with animals. If we accept this clear contradiction, dicyemids should be regarded as
a chimera of animals and protistans. Here, we discuss the traditional theory of extreme degeneration via parasitism, and then
propose a new “chimera” theory in which dicyemid mesozoans are exposed to a continual flow of genetic information via eating
host tissues from the outer surface by endocytosis. Consequently, many of their intrinsic genes have been replaced by host-derived
genes through lateral gene transfer (LGT), implying that LGT is a key driving force in the evolution of dicyemid mesozoans.
© 2003 Elsevier Ireland Ltd. All rights reserved.
Keywords:Dicyemid mesozoans; Protistans; Triploblastic animals; Lateral gene transfer; Parasitism; Chimera
1. Introduction
The dicyemid mesozoans, obligate endosymbionts
found in the renal system of benthic cephalopods,
are one of the simplest multicellular organisms (re-
viewed by Furuya and Tsuneki, 2003). They consist
of one long axial cell surrounded by a single layer
of 20–40 multiciliated somatic cells. The axial cell
∗ Corresponding author. Tel.:+81-76-264-6099;
fax: +81-76-264-6099.
E-mail address:tnoto@sgkit.ge.kanazawa-u.ac.jp (T. Noto).
contains a large polyploid nucleus and intracellular
stem cells, called axoblasts (Fig. 1). Dicyemids lack
distinguishable organs, except for a gonad-like struc-
ture that appears during one stage of their life cycle.
According to Nouvel (1948), in the late 18th cen-
tury, Filippo Calvolini of Italy found small worm-like
organisms—dicyemid mesozoans—in octopuses. In
1849, Kölliker named them dicyemids, because they
produce two types of embryos in their life cycle. In
1876, Van Beneden called them Mesozoa, to express
his belief that the group occupied an evolutionarily
intermediate position between the Protozoa and the
0303-2647/$ – see front matter © 2003 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.biosystems.2003.09.002
74 T. Noto, H. Endoh / BioSystems 73 (2004) 73–83
Fig. 1. Dicyemid mesozoans. Light micrograph of nematogen adult
(left) and the diagram of the identical adult (right). AB, axoblast
(agamete); AC, axial cell; AN, axial cell nucleus; C, calotte; DE,
developing embryo; PC, peripheral cell. Bar represents 10�m.
Metazoa. Some investigators have maintained his
position (Beneden, 1882; Hartmann, 1925; Hyman,
1940; Dodson, 1956; Lapan and Morowitz, 1974).
Conversely, some have proposed that mesozoans have
undergone secondary simplification from a worm-like
animal as a result of extreme parasitism (Nouvel,
1947; McConnaughey, 1951; Stunkard, 1954). Con-
sequently, it has long been controversial whether the
dicyemids are truly primitive multicellular organ-
isms or secondarily degenerated metazoans. Recent
molecular evidence has added to the debate between
these two views, and the second view tends to be fa-
vored (Katayama et al., 1995; Kobayashi et al., 1999;
Pawlowski et al., 1996). In contrast, information on
biological traits shows a drastically different aspect of
dicyemids. There are no definitive characters support-
ing a close kinship of dicyemids with animals, while
many show an affiliation with protistans. This situa-
tion renders the phylogenetic position of dicyemids
enigmatic. This paper highlights the contradiction be-
tween molecular information and biological traits in
the phylogenetic position of dicyemid mesozoans. We
propose a new theory that resolves this contradiction
rationally, leading to the conclusion that dicyemid
mesozoans are a chimera organism of animals and
protistans.
2. Background
Molecular sequence data are increasingly used to
analyze phylogenetic relationships among eukaryotes.
A phylogenetic analysis of 5S rRNA data suggested
that dicyemids are more closely related to protozoan
ciliates than to multicellular animals (Ohama et al.,
1984). Halanych (1991)argued that the 5S rRNA
molecule is too small to contain phylogenetic informa-
tion sufficient for appropriate reconstruction of evolu-
tionary relationships, although his tree also indicated a
close relationship between mesozoans and protozoan
ciliates. By contrast, 18S rDNA analyses placed the
mesozoans as triploblastic animals (Katayama et al.,
1995; Pawlowski et al., 1996). However, 18S rDNA
phylogenies are sometimes misleading (Loomis and
Smith, 1990) and may be inadequate to elucidate
relationships among groups more than 500 million
years old (Rodorigo et al., 1994). In practice, rRNA-
and protein-coding gene-based phylogenies can con-
tradict each other drastically, as in theTrypanosoma
(Alvarez et al., 1996; Germot and Philippe, 1991) and
amitochondrial protozoa like microsporidia (Keeling
et al., 2000) andEntamoeba(Hasegawa et al., 1993).
The validity of molecular sequence data for deduc-
ing phylogenetic relationships depends on selecting
macromolecules that are ubiquitous, have a highly
conserved primary structure, and are functionally
conserved during evolution (Müller, 1995).
Since the sequences used to construct phy-
logenies of the dicyemid mesozoans so far are
RNA-coding genes, a phylogeny based on represen-
tative protein-coding genes is needed to provide more
robust data. Microtubules are structures that are char-
acteristic of eukaryotic cells; they are associated with
cell movement via major cytoskeleton components,
axonemes, and the 9+ 0 basal body/centriole, sug-
gesting that their evolution may have paralleled that of
eukaryotes (Edlind et al., 1996). �-Tubulin sequences
from a wide variety of eukaryotic species have been
reported (Burns, 1991) and used for phylogenetic
analyses (Edlind et al., 1996). In order to elucidate
T. Noto, H. Endoh / BioSystems 73 (2004) 73–83 75
the phylogenetic relationship between the dicyemids
and other eukaryotes, we cloned and sequenced four
�-tubulin genes from two dicyemid species as a
representative protein-coding gene. In our�-tubulin
phylogeny, dicyemid mesozoans were again placed
within higher invertebrates, rather than near lower
ones, such as platyhelminths, different from the 18S
rDNA analysis (Appendix A). In both trees from 18S
rDNA and �-tubulin genes, however, the exact posi-
tion of the dicyemid mesozoans within animals was
not supported by reliable bootstrap values because of
the poor resolutions. These analyses only indicate that
the dicyemid mesozoans are involved in the triploblas-
tic animals, but not in fungi and protists. Most of
the molecular information, including the presence of
a Hox-type gene discussed below, strongly suggests
that dicyemid mesozoans are triploblastic animals.
Is this conclusion fully convincing? We suspect that
there is still something wrong with it.
3. Theoretical consideration of the status of
dicyemid mesozoans
3.1. Are dicyemids triploblastic animals?
Since Whitman (1883)regarded the simplicity of
the mesozoans as not at all primitive, but the result of
extreme parasitic degeneration, several investigators,
such asStunkard (1954), have strongly maintained this
viewpoint. In the last decade, two lines of evidence
suggesting that dicyemids evolved degenerately from
animals have accumulated. The 18S rDNA phylogeny
suggested that dicyemids were triploblastic animals
(Katayama et al., 1995; Pawlowski et al., 1996). Re-
cently, the presence of a Hox-type gene,DoxC, was
reported in the dicyemid mesozoanDicyema orien-
tale (Kobayashi et al., 1999). The analysis of the
homeodomain sequence indicated that it has the high-
est homology with a member of the ‘middle’ group
of Hox genes, supporting the 18S rDNA phylogeny.
In addition, the so-called ‘spiralian peptide’ motif
was confirmed, so the authors advocated the affinity
of dicyemids with lophotrochozoans, which consist
of brachiopods, annelids, nemertines, platyhelminths,
and mollusks including cephalopods, which are the
hosts of the dicyemid mesozoans (Aguinaldo et al.,
1997; Adoutte et al., 1999). The �-tubulin gene phy-
logeny presented here leads to a similar conclusion,
although the resolution of animals was low (Appendix
A). Based on this molecular information, there are
grounds for classifying dicyemids as triploblastic
animals. It is possible that extreme degeneration oc-
curred to an unimaginable extent via parasitism. This
interpretation requires an explanation of such extreme
simplicity; dicyemid adults consist of some 30 cells,
which are derived from an axoblast or fertilized egg
involving at most 5–9 cell divisions. These cells never
divide again during the organism’s life (Furuya et al.,
1992, 1994). Considering this, one is compelled to
postulate that dicyemids evolved by neoteny from an
early embryo at the level of a morula. Recent studies
in developmental biology have accumulated much
knowledge on the body plan and many genes involved
in morphogenesis have been identified (e.g. reviewed
by Prince, 2002). The loss of some such genes might
have been responsible for the extreme degeneration.
This approach might elucidate whether the simplic-
ity of dicyemids is really derived from an ancestral
animal by parasitic degeneration. Simultaneously, it
might be possible to clarify experimentally how the
primitive or protistan-like traits were generated or
reverted, accompanying the simplification in body
construction.
3.2. Why are there so many primitive or
protistan-like features?
The extremely simple dicyemid mesozoans lack a
nervous system and gut. For this reason,Cavalier-
Smith (1993)once placed the phylum Mesozoa in the
kingdom Protozoa; this recommendation must show
foresight. Now he still gives the Mesozoa the rank of a
distinct subkingdom (Cavalier-Smith, 1998). We agree
with his proposal, since dicyemids maintain many
protistan-like features, and have radical simplification.
No articles comprehensively describe the primitive
or protistan-like features. Therefore, we summarize
these features and discuss them in some detail.
Noting that dicyemid mesozoans had protozoan
features,Hartmann (1907)coined the term Moru-
loidea for them. Since then, the following evidence
of their primitiveness has been noted. They have (1)
a double-stranded ciliary necklace, (2) tubular cristae
in their mitochondria, (3) endocytic ability from the
outer surface, (4) an absence of collagen in the extra-
76 T. Noto, H. Endoh / BioSystems 73 (2004) 73–83
cellular matrix (ECM), (5) cell-to-cell junctions, and
(6) distinct phases of asexual (nematogen) and sexual
(rhombogen) reproduction.
Freeze-fracture analysis identifies the ciliary neck-
lace, a structural array of integral membrane proteins
that has been valuable as a genetically fixed mem-
brane character for addressing phylogenetic questions
(Bardele, 1981). The pattern of protein arrangement
in protists is remarkably varied, whereas inverte-
brates, including the Porifera and Cnidaria, have a
consistent pattern. Animals are characterized by a
triple-stranded necklace, while dicyemid mesozoans
share a double-stranded necklace structure with pro-
tistan ciliates and opalinids (Bardele et al., 1986).
Generally, animals lack the ability to take in food
or particulate materials via their outer surface. In con-
trast, the dicyemids can take in particulate material,
such as ferritin (Ridley, 1968) or host spermatozoa
(Nouvel, 1933), from the surface of their peripheral
cells by phagocytosis. This characteristic is strikingly
different from that of animals. If degeneration in fact
occurred, the degenerated ancestor would have had to
regain the ability to endocytose material from the outer
cell surface, concomitant with the loss of the diges-
tive tract. However, no embryos in animals retain the
endocytic ability even in the stage of gastrula.
The shape of mitochondrial cristae is a diagnos-
tic character for taxa, although it is not necessarily
crucial; there are a few instances in which the shape
of the cristae alternates within the life cycle, as in
Trypanosoma bruceiand certain platyhelminths. An-
imals, fungi, and plants generally have mitochondria
with plate-like cristae, whereas protistans have either
tubular or discoidal cristae (Gray et al., 1998). In di-
cyemids, the cristae are tubular, like those of most
protistans, throughout their life cycle, unlike most an-
imals (Ridley, 1968, 1969).
The synapomorphy that is considered crucial to the
affiliation of mesozoans to animals is the presence
of collagenous connective tissue, but not multicellu-
larity (Willmer, 1990; Cavalier-Smith, 1993, 1998).
So far, electron microscopic observation has yet
to identify an extracellular matrix (ECM), such as
collagen-like structures, in dicyemids (Furuya et al.,
1997). Recently, the dicyemid mesozoanKantharella
antarcticawas observed by electron microscopy using
fibronectin, laminin, and type IV collagen antibod-
ies to investigate the ECM (Czaker, 2000). All three
ECM components were located intracellularly, but
not intercellularly, unlike the typical ECM. Indeed,
fibronectin- and laminin-like molecules have also
been confirmed in protistans such as kinetoplastid
Leishmania(Del Cacho et al., 1996) and apicom-
plexan Eimeria (Lopez-Bernad et al., 1996). These
observations strongly suggest that this intracellular
distribution of ECM components is primitive. The
absence of ECM in dicyemids might be responsi-
ble for body organization, which does not reach the
tissue level typical of animals (Furuya et al., 1997).
The only similar case in animals is the turbellarian
group Acoela, which lacks an intercellular matrix
(Rieger, 1985). Consequently, a relationship between
dicyemids and acoelomates must be considered.
With reference to this problem, cell junctions
such as gap junctions (cytoplasmic connections) and
adherens-like junctions have been confirmed in di-
cyemids, but typical septate junctions are absent
(Furuya et al., 1997). The gap junction is thought
to function in cell-to-cell communication and the
exchange of molecules between neighboring cells.
Although lower animals, such as placozoans and
sponges, lack gap junctions, a similar channel system
is believed to develop. Even in protistans, such junc-
tions are observed when cell-to-cell union occurs.
For example, in order to synchronize the conjuga-
tion process and ciliary movement between pairing
partners, a cytoplasmic connection is formed during
conjugation in ciliates in which a multicellular state
is transiently established. The adherens junction has
also been discovered in the multicellular structure of
non-metazoan cellular slime molds, coupled with a
�-catenin homologue (Grimson et al., 2000). Further-
more, it is well known that multicellularity occurred
independently many times in the course of evolution,
even in protistans (Willmer, 1990; Bonner, 1997).
These discoveries outside the animal kingdom show
that the potential for cell junction formation had
already developed in protistans. Accordingly, inter-
cellular junctions are not necessarily crucial to solve
phylogenetic relationships.
Finally, dicyemids have distinct phases of asexual
and sexual reproduction. In the nematogen phase,
larvae develop asexually from a diploid axoblast,
whereas in the rhombogen phase, larvae are pro-
duced from a fertilized egg. The former appears
protistan-like, although regenerative reproduction is
T. Noto, H. Endoh / BioSystems 73 (2004) 73–83 77
observed in some animals. This feature is too dif-
ferent from that in triploblastic animals to imagine
how dicyemids acquired the alteration of asexual and
sexual reproduction.
4. The chimera theory can solve the
discrepancy
As mentioned above, dicyemids maintain many
protistan-like or extremely primitive features and
lack noticeable morphological characters that are
shared with animals; however, most of the molecular
information obtained so far strongly suggests that
dicyemids are true animals. How should this discrep-
ancy be interpreted? Here, we present a new theory
to resolve this discrepancy. It may be reasonable
to regard dicyemids as a chimera of protistans and
animals, in which dicyemids acquired many genes
from their host via lateral gene transfer (LGT). Sev-
eral lines of evidence have recently shown that LGT
via phagocytosis occurs with higher than expected
frequency (Doolittle, 1998; Schubbert et al., 1997,
1998; Bushman, 2002). For example, theTetrahymena
genome project (http://www.tigr.org/tdb/tgi/ttgi/) has
determined that approximately 80 genes out of 3500
sequences determined so far came from bacteria, in
spite of their free-living mode. Dicyemids are re-
stricted to a renal appendage in cephalopods, where
they absolutely depend on their host for all nutrients.
They have endocytic ability mentioned above and
the uptake of host spermatozoa has been observed
repeatedly. Furthermore, the calotte (the most ante-
rior cells) cilia are stiffer, shorter, thicker and more
closely set than those of other peripheral cells, and
occasionally penetrate the epithelial cells of the renal
appendages, resulting in erosion of the tissue (Ridley,
1968). Therefore, they are exposed to a continual
flow of genetic information from the host via their
food (fragments of the host tissue and spermatozoa).
This situation increased the chance of the dicyemid
germline genome taking in host DNA. The obser-
vation that two�-tubulin genes fromDicyemodeca
contained a short intron at precisely the same site
as in the host gene may reflect such gene flow from
the host (Appendix A). This assumption reason-
ably interprets the inconsistent facts; the presence of
lophotrochozoan-like genes, such as Hox-type genes,
and many protistan-like features. A certain laterally
transferred gene from the host may have driven multi-
cellularization of an ancestral unicellular dicyemid to
some extent, and this would have led to multiciliation
and polyploidization of somatic nuclei accompanied
by DNA rearrangement (Noto et al., 2003), as seen
in ciliates. Nevertheless, the intrinsic nature of the
putative protistan ancestor might have remained un-
changed, resulting in the creation of a ‘chimera.’ In
this sense, dicyemids are truly the ‘Mesozoa,’ mak-
ing this term even more appropriate. Frequent LGT
might be an important driving force in the evolu-
tion of dicyemids in particular and in host–parasite
relationships in general. This viewpoint will be in-
dispensable for clarifying the origin of dicyemid
mesozoans.
5. Perspective
To date, only a few genes in dicyemids have been
analyzed. If a genome project in dicyemid were car-
ried out, or many more genes were analyzed, we ex-
pect there to be two major classes of genes identi-
fied: animal-like genes and protistan-like genes. At
present, the 5S rRNA gene is the only gene that does
not show the affiliation of dicyemids to animals. If our
theory is true, it may be a vestige derived from its an-
cestor. The discovery of additional genes of this type
would lend support to our theory. Now we must await
the accumulation of such information on the genes of
dicyemids.
With reference to this theory, quite recently, fre-
quent LGTs were systematically analyzed in protis-
tan diplomonads (Andersson et al., 2003). The authors
suggest that LGT is a likely source accounting for
anomalous phylogeny patterns which are observed in
different genes. If LGT events are assumed to be fre-
quent in a certain species, an estimation of molecular
phylogeny should be cautiously made.
Finally, the collection of completely sequenced
mitochondrial genomes has been expanding rapidly
(Gray et al., 1998). Generally, mitochondrial DNA
(mtDNA) in animals is roughly equal in size, gene
content, and genome organization; it ranges from 14
to 20 kb in size and is circular. In contrast, protistan
mtDNA is very different from animal mtDNA in that
it is extraordinarily diverse in size, form, and gene
http://www.tigr.org/tdb/tgi/ttgi/
78 T. Noto, H. Endoh / BioSystems 73 (2004) 73–83
content. No knowledge of dicyemid mtDNA is yet
available, except for the presence of minicircle DNAs
encoding cytochrome oxidase I, II, and III (Watanabe
et al., 1999). These minicircles all have relatively
long non-coding regions. Extrapolating the size of
the entire genome based on the ratio of the known
coding and non-coding sequences, dicyemids appear
to have mtDNA larger than that of animals. This is
inconsistent with the general tendency for parasites
to downsize their mt genome as an adaptation to
parasitism (Gray et al., 1999; Saccone et al., 2000).
Indeed, dicyemids seem to maintain a small num-
ber of high-molecular weight mitochondrial genes in
germ cells, separately from the minicircles (H. Awata,
personal communication). The entire mitochondrial
genome of dicyemids must be analyzed in detail to
determine their phylogenetic relationship.
Acknowledgements
We thank R. Kofuji, T. Hanyuda and K. Ishida,
for construction of phylogenetic trees, and H. Awata
for a kind supply of her unpublished results, and S.
Sakurai, Y. Sasayama and T.G. Doak for encourage-
ment to accomplish this work. We are also grateful
to A. Sawabe, Y. Sasayama, and K. Yamamoto for
sampling and maintenance of the host materials. This
work was partially supported by Sasakawa Scientific
Research grant.
Fig. 2. Map of the�-tubulin genes from dicyemids and the host octopus. BTov1 (1635 bp) was obtained from the hostO. vulgaris.
BTdv1 (1220 bp) and�BTdv2 (1217 bp) or BTda1 (1310 bp) and BTda2 (1327 bp) were obtained fromDicyemasp. orD. antinocephalum,
respectively. Horizontal lines represent a putative protein-coding region and introns located in the identical sites are shown as triangles in
the same colors. Numbers in the triangles and round brackets denote the intron number and their length in base pair, respectively. Crosses
in �BTdv2 represent nonsense mutation.
Appendix A. Phylogenetic analysis of dicyemids
from �-tubulin gene sequences
A.1. Characterization ofβ-tubulin genes from two
dicyemid species
Four different�-tubulin sequences were character-
ized. Two�-tubulin sequences were obtained fromDi-
cyemasp. (BTdv1 and�BTdv2) and the other two se-
quences fromDicyemodeca antinocephalum(BTda1
and BTda2). Additionally, a�-tubulin gene was cloned
from the hostOctopus vulgaris(BTov1). No indels
were observed except one pseudogene (�BTdv2) de-
scribed below. One intron in the two sequences from
Dicyema sp. and four introns in the two sequences
from D. antinocephalumwere identified (Fig. 2). They
are all short in length, ranging from 20 to 35 bp. The
site of the first intron was identical among the four
sequences. On the other hand, octopus�-tubulin gene
carries one long intron the site of which coincides with
the third intron ofD. antinocephalumsequences. One
gene fromDicyemasp. (�BTdv2) is thought to be a
pseudogene because of three nonsense mutations in
the middle regions and two deletions in the 3′ region
of the ORF, leading to frameshift mutation. Accord-
ingly, the other three sequences were used for the fol-
lowing phylogenetic analysis. No signature sequence
shared between dicyemids and animals was detected.
It was confirmed that these clones were truly de-
rived from dicyemids by Southern blot analysis using
T. Noto, H. Endoh / BioSystems 73 (2004) 73–83 79
Fig. 3. Southern blot analysis. Each lane contains 1�g of DNA
from Dicyemasp. (Ds) or 5�g of DNA from the hostO. vulgaris
(Ov), which was digested withHindIII. The filters were hybridized
with the radiolabeled BTdv1 probe. A distinct signal is detected
only on dicyemid DNA, but not on the host DNA.
one of the cloned homolog as a probe (Fig. 3). In fact,
contamination of a small amount of the host tissue is
usually unavoidable. However, signals were detected
only on the dicyemid DNA by Southern blot analysis,
but not on the host DNA. Furthermore, the primers
used in this study only amplified a 1.6 kb product from
the host DNA, whereas a 1.2 kb product from the di-
cyemid DNA (data not shown). Both results clearly
indicate that the cloned sequence was derived from
the dicyemid DNA. On the other hand, a small num-
ber of cells of fairly small kinetoplastids,Bodo sp. is
usually identified in culture medium after maintenance
in vitro for 1–2 weeks. The sequence from theBodo
sp. was amplified only after the second PCR and was
placed in a protistan clade, near to kinetoplastids as
expected (Fig. 4). These observations strongly suggest
that there is a fairly small amount of contamination in
our dicyemid DNA preparation to undetectable extent
by Southern blot analysis, if any.
A.2. Phylogenetic analysis of theβ-tubulin sequences
The amino acid sequences of�-tubulins from a total
of 39 eukaryotes were aligned for phylogenetic analy-
sis. As mentioned above, neither the dicyemid nor the
host sequences had deletions or insertions except for
one pseudogene,�BTdv1. Unlike molecules of vary-
ing length, such as rDNA, the consistency of these se-
quences facilitates comparison with others. Based on
378 aligned residues, phylogenies were constructed
using the Neighbor-Joining (NJ) and Maximum Parsi-
mony (MP) methods (Fig. 4). Because both trees are
almost identical, here MP tree was demonstrated with
bootstrap values by MP (left) and NJ (right). When
Trichomonas vaginaliswas used as outgroup, three
major branches with high bootstrap values were gener-
ated in the MP tree: protistan-plant clade as indicated
previously byEdlind et al. (1996), animals, and fungi
including microsporidia as shown byKeeling et al.
(2000). These large assemblages were monophyletic
(bootstrap probability= 73, 97, and 93%, respec-
tively). Fungi formed the sister-group to animals, as
in the rRNA phylogeny (Hasegawa et al., 1993). The
dicyemid mesozoans were positioned within animals,
and outside the protistan-plant clade altogether. Their
close affinity with triploblastic animals was supported
by high bootstrap values, but the bootstrap confidence
level for branchings within animal clade, however, was
lower. The exact phylogenic relationship of dicyemids
and other animals is still not clear. The phylogeny pro-
duced using the ML method was almost identical to
the tree presented here although bootstrap value has
not been calculated (data not shown). According to
our �-tubulin phylogenies, dicyemids group with the
triploblastic animals, being consistent with the rela-
tionships derived from 18S rDNA data.
Appendix B. Materials and methods
B.1. DNA preparation from dicyemids for PCR
Dicyemids were isolated from two different hosts,
O. vulgaris and O. dofleini collected in Notojima is-
land, Ishikawa prefecture, Japan (Noto et al., 2003).
Three different species of dicyemids,Dicyema japon-
icum, D. misakienseand D. acuticephalum, usually
inhabit O. vulgaris, whereasO. dofleiniharbors only
one species,D. antinocephalum(Furuya, 1999). After
isolation and 1 week culture of the dicyemids in Ja-
marin seawater (JSW; Jamarin Laboratory) containing
10% fetal bovine serum (FBS; Sigma) and 7.625%
(w/v) DME/F-12 HAM mixture (Sigma), 10 whole
individuals of dicyemids were washed nine times in
JSW using a micropipette to remove all octopus host
cells, and then digested in 10 mM Tris–HCl, 10 mM
80 T. Noto, H. Endoh / BioSystems 73 (2004) 73–83
Fig. 4. Molecular phylogenetic consensus tree inferred from�-tubulin amino acid sequences by MP. Parsimony analysis was calculated
using the program PROTPARS. Bootstrap resampling was accomplished with the use of the program SEQBOOT (1000 replicates) and
CONSENCE. The topology of NJ tree showed almost the same of MP tree. Numbers at each branch indicate bootstrap percentage greater
than 50%, which was obtained from MP (left) and NJ (right) analysis. The dicyemid mesozoans were placed within the triploblastic
animals supported by high bootstrap values. Accession numbers: AB099885, AB099886, AB099887, AB099888 in dicyemids. AB099884
in the hostO. vulgaris. AB099889 in the kinetoplastidBodo sp.
T. Noto, H. Endoh / BioSystems 73 (2004) 73–83 81
EDTA, 150 mM NaCl, and 0.1% SDS at pH 8.0, con-
taining 100�g/ml proteinase K, at 55◦C for 2 h. Total
DNA was extracted with phenol/chloroform, precipi-
tated in ethanol with 2�l of Pellet Paint Co-Precipitant
(Novagen), and dissolved in 10�l of sterilized water.
The DNA was divided in two aliquots, one of which
was used for every PCR as a template.
B.2. Amplification, cloning, and sequencing of
β-tubulin genes from dicyemids
�-Tubulin genes were isolated by PCR using
B-TU1F (5′-CARTGYGGYAACCARATYGG-3′)
and B-TU2R (5′-TCCATYTCGTCCATRCCYTC-3′)
primers designed to amplify approximately∼1.2 kbp
fragment which account for more than 80% of the
dicyemid �-tubulin gene. A mixture of 25�l of
1× Taq DNA polymerase buffer, 0.2 mM dNTPs,
1 �M of each primer, 5�l of template (sample)
DNA solution, and 0.5 U ofTaq DNA polymerase
(Sawady) was put in a thermal cycler for 35 cy-
cles: each cycle consisted of 60 s at 94◦C, 60 s
at 50◦C, and 60 s at 72◦C. Cloning and sequenc-
ing strategies were described previously (Noto
et al., 2003).
B.3. Southern blot analysis
For confirmation of the source of�-tubulin gene,
Southern blot analysis using one of clones (BTdv1) as
a probe was carried out as described previously (Noto
et al., 2003).
B.4. Sequence alignment and phylogenetic analysis
Amino acid sequences were inferred from the
PCR product�-tubulin gene sequences, and aligned
with homologs from representative species obtained
from GenBank. Alignments (378 residues) of the
�-tubulin amino acid sequences fromDicyema sp.,
D. antinocephalum, O. vulgaris, and other taxa were
produced using CLUSTAL X (Thompson et al.,
1997). These were then modified by eye to optimize
them. Phylogenetic trees were constructed using the
NJ and MP methods in the programs CLUSTAL X
(Thompson et al., 1997) and PHYLIP version 3.6
(Felsenstein, 2002), respectively. All bootstrap values
(Felsenstein, 1985) were based on 1000 replicates.
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- A “chimera” theory on the origin of dicyemid mesozoans: evolution driven by frequent lateral gene transfer from host to parasite
Introduction
Background
Theoretical consideration of the status of dicyemid mesozoans
Are dicyemids triploblastic animals?
Why are there so many primitive or protistan-like features?
The chimera theory can solve the discrepancy
Perspective
Acknowledgements
Phylogenetic analysis of dicyemids from beta-tubulin gene sequences
Characterization of beta-tubulin genes from two dicyemid species
Phylogenetic analysis of the beta-tubulin sequences
Materials and methods
DNA preparation from dicyemids for PCR
Amplification, cloning, and sequencing of beta-tubulin genes from dicyemids
Southern blot analysis
Sequence alignment and phylogenetic analysis
References
EXAM 2 – TAKE-HOME PORTION
INVERTEBRATE ZOOLOGY
Fall 2018
INSTRUCTIONS:
Worth 75 points.
Do your OWN writing!!!
You may discuss and collaborate with others, but you must turn in your own writing.
Copying and pasting, either from online or published sources, OR straight from another student will be considered PLAGIARISM and will not be tolerated.
Plagiarism of ANY sort will resort in a ZERO for the assignment.
Style and content will be considered for assigning points.
(What this ACTUALLY means is that I’m looking for THOUGHT and reasonable scientific inference from you. There may not be a “right” or “wrong” answer to some of these questions, but show me you are thinking!)
Reference any material you use. You may include your textbook, but do not reference me (the instructor) from lecture or from power-point slides. If it was discussed in class or is mentioned on a slide and you wish to include it, find a primary source to reference.
All papers needed to answer these questions are posted in the CANVAS site for the course. All these papers should be appropriately referenced.
Due: before class TUESDAY, OCTOBER 16th (day of the in-class portion of the exam.
Provide a printed hard copy.
PDA
Read the two papers:
Nelson (2004):
PROBLEMS WITH CHARACTERIZING THE PROTOSTOME-DEUTEROSTOME ANCESTOR
And:
Excerpt from: Gilbert and Barresi: Developmental Biology, Tenth Edition:
The Search
for the Urbilaterian Ancestor
1). Outline, in a paragraph or two the major points of the Nelson article with particular
emphasis on exactly what ARE the problems with characterizing the PDA.
2). What do Gilbert and Barresi mean when they say we’ll need to do “paleontology
without fossils” to answer many questions concerning the PDA?
3). Pick at least 2 genes suggested in the article and explain how they are relvant.
4). Outline why they propose the answer may lie in “larval” forms rather than in adults.
5). What is: Saccorhytus coronaries, and why is it relevant to this discussion? (You are
going to have to research this on your own – PROVIDE A CREDIBLE
REFERENCE)
CTENOPHORES
Read the article:
Ctenophores: Structure, Development and Affinities:
6). Provide a basic description of the Ctenophores, anatomically and ecologically.
7). As regards Protostome vs. Deuterostome, where do the Ctenophora fit?
8). What are the two groups that share some characteristics in common with
Ctenophores?
9). Pick 3 characters, that you believe to be the most significant, from each group that
support potential relationships, and three from each that complicate those
interpretations. Explain why you think those are the most important characters.
10). Finish with a cogent argument (2-3 paragraphs) for what YOU think should be done
phylogenetically with the Ctenophores. (Make your OWN decision DO NOT
just go on the internet and pick something that other people think.)
MESOZOANS
Read the paper:
Noto T. and H. Endoh (2004):
A “chimera” theory on the origin of dicyemid mesozoans: evolution driven by frequent lateral gene transfer from host to parasite.
1). Describe the biology (not evolution) of the MESOZOANS.
2). State the two MAIN opposing hypotheses as to the phylogenetic position of the
MESOZOANS and give the assumptions and supporting evidence for both.
3). Outline and discuss the “new theory” which the authors propose to bridge the
discrepancies of the evolutionary position of the MESOZOANS.
4). Describe the techniques which provide support for their new position.
5). Finish with a cogent argument (1-2 paragraphs) for what YOU think should be done
phylogenetically with the Mesozoans. (Make your OWN decision DO NOT
just go on the internet and pick something that other people think.)
PROBLEMS WITH CHARACTERIZING THE
PROTOSTOME-DEUTEROSTOME ANCESTOR
Society for Developmental Biology
2
00
4
Annual Meeting
Poster Number 2
5
4
Paul A. Nelson
Discovery Institute
Center for Science & Culture
1511 Third Avenue
Suite
8
08
Seattle, WA
9
8101
nelsonpa@alumni.uchicago.edu
Marcus R. Ross
Department of Geosciences
University of Rhode Island
3
1
7
Woodward Hall
9 East Alumni Avenue
Kingston, RI 02881-2019
mross110
6
@postoffice.uri.edu
Abstract
Since Darwin’s time, the origins and relationships of the bilaterian animals have
remained unsolved problems in historical biology (Conway Morris 2000). One of the
central difficulties is characterizing the common ancestor of the protostomes and
deuterostomes. We argue that an unresolved conceptual puzzle has plagued the many
attempts to describe this Urbilaterian, or, in Erwin and Davidson’s (2002)
terminology, the protostome-deuterostome ancestor (PDA). Any organism
sophisticated enough to be a realistic candidate for the PDA, with such characters as
an anterior-posterior axis, gut, and sensory organs, must itself have been constructed
by a developmental process, or by what we term an ontogenetic network (Ross and
Nelson 2002). But the more biologically plausible the PDA becomes, as a functioning
organism within a population of other such organisms, the more it will tend to “pull”
(in its characters) towards one or another of the known bilaterian groups. As this
happens, and the organism loses its descriptive generality, it will cease to be a good
candidate Urbilaterian.
1. THE PROBLEM
Since Darwin’s time, the origins and relationships of the bilaterian animals have
remained unsolved problems in historical biology (Conway Morris 2000; Valentine
2004). The intractable nature of these problems has been variously explained by
• Few (and equivocal) shared anatomical characters among the phyla – “clearly
identifiable, informative homologs are rare” (Collins and Valentine 2001, 432);
• Missing fossil evidence – “the most striking features of large-scale evolution
are the extremely rapid divergence of lineages near the time of their
origin…what is missing are the many intermediate forms hypothesized by
Darwin” (Carroll 2000, 27); and
• The neo-Darwinian explanatory emphases on allelic variation and speciation –
“the evolution of major complexities in the history of life has had very little to
do with the origin of species” (Miklos 1993, 34; see also Valentine and Erwin
1987, 96-7; Ohno 1996, 8475; Jablonski 2000, 26; and Davidson 2001, 19-20).
The salient event in the bilaterian puzzle is, of course, the Cambrian Explosion: “The
most striking burst of evolutionary creativity in the animal fossil record comes early in
the Phanerozoic, with the Cambrian Explosion of metazoan body plans. This
extraordinary interval…saw the first appearance of all but one of the present-day
skeletonized phyla (along with an array of less familiar forms)” (Jablonski 2000, 22;
Valentine 2004; see also Valentine, Awramik, Signor, and Sadler 1991).
But with the emergence of the research field of “evo-devo” over the past twenty years,
in parallel with the rapid growth of molecular phylogenetics, many workers have tried
new approaches to attacking the long-standing puzzle of the origin of the bilaterians.
“Amazing as it might have seemed only 10 or 15 years ago,” note Peterson et al.
(2000, 1), “the great problem of animal origins has become both the source and object
of experimental inquiry.” It may seem that the puzzle is soon to yield its answer.
We argue, however, that the problem of the origin of the Bilateria is likely to remain
unsolved, at least within the current monophyletic framework, because of two closely-
related difficulties – one conceptual and the other evidential:
2
A Conceptual Difficulty
Any organism sophisticated enough to be a candidate for the common ancestor of the
protostomes and deuterostomes, with such characters as an anterior-posterior (AP)
axis, gut, nervous system, and sensory organs, must itself have been constructed by a
developmental process, or by what can be termed an ontogenetic network (see below).
The more realistic this common ancestor becomes, as a functioning organism within a
population of other such organisms, the more it will tend to “pull” (in its characters,
both developmental and anatomical) towards one or another of the known bilaterian
groups. As this happens, and the organism loses its descriptive generality, it will cease
to be a good candidate Urbilaterian.
An Evidential Difficulty
To derive disparate body plans (sensu Gould) from this common ancestor would
require modifying its early development (Miklos 1993; Arthur 1997; Davidson 2001).
In all known bilaterians, body plan characteristics have their developmental roots in
the earliest stages of ontogeny. Yet the evidence from the model systems of
developmental biology also strongly indicates that Bauplan-disrupting mutations are
inevitably deleterious. Known ontogenetic networks are constrained in their range of
variation. This anomaly has led to proposals of non-uniformitarian temporal
asymmetries in evolutionary processes (e.g., Erwin 1999, Shubin and Marshall 2000).
In short, evolution was different in the past. But different how?
The purpose of this poster is thus two-fold:
1. To encourage reflection about a neglected puzzle of evolutionary theory –
neglected, that is, not in lacking for hypotheses (there are plenty of those), but rather
in a deeper sense. What does it mean, biologically speaking, to be a non-specific
ancestral form? Can we really describe a bilaterian common ancestor that escapes the
constraints we know obtain for the model systems of developmental biology?
2. To ask, Where is the deep variation required by macroevolution? There is a
striking paucity of experimental evidence showing heritable variation in what Wimsatt
and Schank (1988) call the “deeply-entrenched” features of development – i.e., those
processes specifying body plan formation. While the classical neo-Darwinian view of
the conservation of early development has collapsed under the weight of comparative
data, the neo-Darwinian skepticism of macromutations is still amply justified by the
signals returning from current model systems.
3
2. THE DIFFICULTY OF TRYING TO BRING A HYPOTHETICAL
COMMON ANCESTOR INTO FOCUS
The bilaterians we actually know are constructed (in each new generation) by an
ontogenetic network that commences with the fertilized egg. Although it may seem
paradoxical to say so, this ‘if-you’re-an-animal-you-develop’ requirement goes for
hypothetical bilaterians as well, including the postulated common ancestor of the
protostomes and deuterostomes. And therein lies the difficulty.
“Trying to imagine the morphological attributes of ancestral stem-group bilaterians,”
note Peterson et al., “is something of a project for the ‘X-files’” (Peterson et al. 2000,
11). Nevertheless, X-file scripts can be written, and hypothetical common ancestors
can (and indeed need to) be specified. Based on a survey of genetic regulatory
homologies across the bilaterian phyla, Erwin and Davidson (2002, 3029) give their
approximation of the protostome-deuterostome ancestor (PDA) as follows:
“It had an AP axis, a two-ended gut, mesodermal layers and a central and
peripheral nervous system with sensory cell types.”
Now it is likely that even if this hypothetical metazoan were very small – on the scale
of C. elegans, perhaps – it possessed no fewer than several hundred cells in its adult
phenotype, of several distinct cell types (digestive, nervous & sensory, cuticular, germ
line, and so forth). And if it were a developing organism, these differentiated cell
states would have arisen from a single cell. Is there any reason to think that the
process of specification and differentiation, from egg to adult in the PDA, would
differ fundamentally from known bilaterians in its regulatory complexity?
Significantly, Erwin and Davidson (2002) omit one character from their PDA “parts
list” that functional logic suggests must have been present – namely, the formation of
gametes. Was the PDA reproducing by generating eggs and sperm? If the answer is
Yes (probably), then we invite the reader to try a simple thought experiment, the first
of two on this poster.
Let’s suppose the cell depicted in Figure 1 represents a fertilized PDA egg, about to
commence cleavage. Where is this egg going? – i.e., what specific morphology lies at
the adult (reproductively capable) end of its ontogenetic network?
The answer, of course, depends on how the structure of the egg was specified
maternally – i.e., on Mom. Was Mom, as Valentine argued recently, “a small, soft-
bodied worm,” with “about fifteen to twenty cell morphotypes” (2004, 483)?
4
However one answers this question, it is clear that the functioning bilaterian
ontogenetic networks that we know are specified in remarkable detail.
Here a parallel with C. elegans is instructive. “It has been estimated,” notes Golden
(2000, 418), “that 100-400 maternal gene products could be involved in cell-division
processes in the 1-cell embryo” of C. elegans. While it is unreasonable to expect that
one could give anything close to that level of detail for the developmental architecture
of the PDA, as one sketches more of its particulars, the organism will fall into one or
another specific ontogenetic network. And such networks, in our experience, are
constrained in their range of possible (viable) variation.
A generalized PDA is useful as a phylogenetic placeholder, anchoring the historical
relationships (cladograms) of what are very different types of organisms. But real
animals, such as those depicted below (see Figures 2-4), develop via ontogenetic
networks of remarkable specificity.
This brings us to our second simple thought experiment, to bring this evidential
difficulty home. Think of how – in particular, when during development – the
body plan begins to be specified in the model system you know best. Now ask
yourself which mutations are tolerated least well by that same model system, when
those mutations are expressed, and which morphological features they mainly affect.
Is there any reason to think that the body plan specification processes in the PDA
would be any different? If so, why? And how would its ontogenetic network
function?
Anterior-posterior axisA P
Thought experiment #1:
What will this PDA egg become?
Figure 1
5
The plain fact is that we do not now observe viable changes to body plan characters
(with the possible exception of losses of structures, e.g., the frequent loss of the tail in
ascidian larvae). This has led to the hypothesis of profound temporal asymmetries in
evolutionary processes.
Drosophila m elanogaster
Figure 2
(Law rence 1992)
Caenorhabditis elegans
Figure 3
(figure after Hodgk in 19 87, 135)
Halocynthia papillosa
Figure 4
(Burton 1980)
6
3. THE HYPOTHESIS OF TEMPORAL ASYMMETRIES IN ANIMAL
EVOLUTION
In light of the absence of viable macromutants today, some evolutionary theorists
contend that “patterns of intraspecific variation in modern phyla are qualitatively
different from those that must have existed in the taxa that lived during
Neoproterozoic and probably Early Cambrian times” (Shubin and Marshall 2000,
335). Many workers have argued that (in effect) had evolutionary biologists been
present at the Neoproterozoic-Cambrian boundary, they would have seen events in
populations then evolving that could not be replicated in laboratories or the field
today; see, for instance, Campbell and Marshall (1987), Foote and Gould (1992),
Arthur (1997) and Erwin (1994, 2000), among others. We may summarize this thesis
as follows:
Macroevolutionary processes acting over the history of the animals display
temporal asymmetries, such that at certain critical periods – e.g., the Cambrian
Explosion – adaptive changes in ontogenetic architectures (networks) were
possible that are no longer accessible to selection.
“Many of the characters that evolved during the origin of phyla,” argue Shubin and
Marshall (2000, 335), “are no longer able to change.” Thus, “there seems to be no
alternative but to seek some unusual feature of the primitive genome that would allow
it to change in such a way that large coordinated viable morphological changes could
take place over short periods of geological time” (Campbell and Marshall 1987, 97).
After these critical periods, ontogenetic networks supposedly “hardened” (McKinney
and McNamara 1991, 363) and now resist fundamental perturbation.
This hypothesis places tremendous weight on the theory of common descent, at a high
cost to what we know from genetics and developmental biology. The “labile”
ontogenies from the hypothesized critical periods in evolutionary history are typically
uncharacterized (i.e., they are unarticulated beyond the level of postulates).
Furthermore, how exactly would a pre-Cambrian metazoan, such as the PDA, be free
to vary in ways that it (now) could not? “One cannot ignore the fact,” argues
Levinton (2001, 857), “that a stable developmental program was just as necessary for
survival in the Cambrian as it is today.”
4. CONCLUSIONS
It is likely that the ontogenetic complexity of Cambrian bilaterians was as great as
developing animals today. Indeed this would be the case for the hypothetical common
7
ancestor of the protostomes and deuterostomes (PDA). It is unclear, however, how the
ontogenetic network of this organism would have varied to allow it to give rise to the
disparate ontogenetic networks of the extant bilaterian phyla. That it did so vary
seems to be an inference supported, not by what we know from developmental
biology or genetics, but rather by the theory of common descent.
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Carroll, Robert L. 2000. Towards a new evolutionary synthesis. Trends in Ecology and Evolution
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Erwin, Douglas. 1999. The Origin of Bodyplans. American Zoologist 39:617-629.
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Jablonski, David. 2000. Micro- and macroevolution: scale and hierarchy in evolutionary biology and
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Ohno, Susumu. 1996. The notion of the Cambrian pananimalia genome. Proceedings of the National
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Peterson, Kevin J., Cameron, Andrew R., and Davidson, Eric C. 2000. Bilaterian Origins:
Significance of New Experimental Observations. Developmental Biology 21:1-17.
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Time (The Paleontological Society, 2000), pp. 324-340.
Valentine, James W. 1994. The Cambrian Explosion. In Early Life on Earth, ed. S. Bengston (New
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University of Chicago Press), pp. 231-273.
9
The Search for the Urbilaterian Ancestor
It is doubtful that we will find a fossilized representative of the ancestral lineage that gave rise to both the deuterostomes and the protostomes. This hypothetical animal is sometimes called the Urbilaterian ancestor or the PDA (protostome-deuterostome ancestor). Since it is doubtful that such an animal would have had either a bony endoskeleton (a deuterostome chordate trait) or a hard exoskeleton (characteristic of protostomate ecdysozoans), it would not have fossilized well. However, we can undertake what Sean Carroll has called “paleontology without fossils.”
Homologous genes with ancestral functions
The immediate aim of “paleontology without fossils” is to find homologous genes that perform the same functions in both a deuterostome (usually a chick or a mouse) and a protostome (generally an arthropod, such as Drosophila). Many such genes have been found (Table 1), and their similarities of structure and function in protostomes and deuterostomes make it likely that these genes emerged in an animal that is ancestral to both groups.
Table 1 (Click image to enlarge.) |
The Pax6 protein, for example, plays a role in forming eyes in both vertebrates and invertebrates (see Chapter 2). Ectopic expression of Pax6 results in extra eyes in both Drosophila and Xenopus—representatives of the protostomes and deuterostomes, respectively (Chow et al. 1999). Moreover, the ectopic expression of a deuterostome (mouse) Pax6 gene in a fly larva induces ectopic fly eyes (see Figure 1), and the ectopic expression of the Drosophila Pax6 gene in Xenopus ectoderm induces eye development in the frog tadpole (Halder et al. 1995; Onuma et al. 2002). Therefore, it is a safe assumption that the samePax6 gene is involved in eye production in both deuterostomes and protostomes. Moreover, at least three other genes—sine oculis, eyes absent, and dachshund—are also used to form eyes in both Drosophila and vertebrates (Jean et al. 1998; Relaix and Buckingham 1999). Since it is extremely unlikely that deuterostomes and protostomes would have evolved Pax6 and its partners independently—and used them independently for the same function—it is likely that the PDA possessed a Pax6 gene and used it for generating eyes.
Figure 1 The Pax6 gene for eye development is an example of a gene ancestral to both protostomes and deuterostomes. The micrograph shows ommatidia emerging in the leg of a fruit fly (a protostome) in which mouse (deuterostome) Pax6 cDNA was expressed in the leg disc. (From Halder et al. 1995, courtesy of W. J. Gehring and G. Halder.) (Click image to enlarge.) |
Another gene shared by deuterostomes and protostomes is the homeobox-containing gene tinman. The Tinman protein is expressed in the Drosophilasplanchnic mesoderm, eventually residing in the region of the cardiac mesoderm. Loss-of-function mutants of tinman lack a heart (hence its name). In mice, the homologous gene is Nkx2-5, and it too is originally expressed in the splanchnic mesoderm and continues to be expressed in those cells that form the heart tubes (see Chapter 12; Manak and Scott 1994). Thus, even though the hearts of vertebrates and of insects have little in common except their ability to pump fluids, they both appear to be predicated on the expression of the same gene, and it is therefore probable that the PDA had a circulatory system with a pump based on the expression of the ancestral Nkx2-5/tinman gene.
Another set of genes shared by deuterostomes and protostomes are those for the transcription factors involved in head formation (Finkelstein and Boncinelli 1994; Hirth and Reichert 1999). In Drosophila, the brain is composed of three segments, called neuromeres. These neuromeres are specified by three transcription factors. The genes encoding these factors are tailless (tll) andorthodenticle (otd), which are expressed predominantly in the anteriormost neuromere, and empty spiracles (ems), which is expressed in the posterior two neuromeres (Monaghan et al. 1995; Hirth et al. 1998). Loss-of-function mutations of otd eliminate the anteriormost neuromere of the developingDrosophila embryo, and loss-of-function mutations of ems eliminate the second and third neuromeres (Hirth et al. 1995). In frogs and mice, the homologues of these genes (Otx1, Otx2, Emx1, Emx2) are also expressed in the brain (Simeone et al. 1992), although the exact patterns of transcription are not identical (see Figure 8.30). When the Otx2 gene is experimentally knocked out (Acampora et al. 1995; Matsuo et al. 1995; Ang et al. 1996), the resulting mice have neural and mesodermal head deficiencies anterior to rhombomere 3. In humans, mutations of EMX2 lead to a rare condition known as schizencephaly, in which clefts rip through the entire cerebral cortex (Brunelli et al. 1996). Even though the Drosophila otd and ems genes are specified by the Bicoid and Hunchback gradients and the mammalian Otx and Emx genes are induced by the anterior dorsal mesoderm and endoderm, it appears that the same genes are used for determining the anterior brain regions. It is therefore likely that the ancestor of all bilaterian organisms had sensory organs based on Pax6, a heart based on tinman, and a head based on otd, ems, and tll. It also had something else: an anterior-posterior polarity based on the expression of Hox genes.
Anatomical similarities: Larval forms
Features held in common between protostomes and deuterostomes are thought to be derived from the PDA. In addition to the molecular similarities, there are also structural similarities between these two groups. The most basal forms of both deuterostomes and protostomes arise from ciliated larvae. These larvae might form in different ways—the protostomes using the blastopore region as their foregut and mouths, and the deuterostomes using the blastopore region as their anal hindgut—but recent molecular evidence suggests that even this morphological distinction may have underlying similarities. Arendt and colleagues (2001) have shown that the Brachyury (T) gene is expressed in the ventral foreguts of pluteus and hemichordate larvae of basal deuterostomes and in the trochophore larvae of annelid worms (Figure 2). Goosecoid and Otx are also found in the foregut regions of deuterostome and protostome larvae. Convergent evolution of these three genes would be unlikely (especially considering how specific their localizations are), suggesting that both protostomes and deuterostomes inherited a ciliated larval form from the PDA. Indeed, Arendt and colleagues (2001, 2004) have proposed that the Urbilaterian ancestor had a single blastoporal opening that extended along the surface of the embryo (like the blastopores of certain annelid embryos today), becoming a mouth in the protostomes and an anus in the deuterostomes.
Figure 2 Late gastrula embryos (top) develop into ciliated larvae (bottom). (A) In the polychaete annelid worms (Protostomia), the lateral blastopore lips fuse along the later ventral midline. The blastopore gives rise to mouth and anus at opposite ends. In the trochophore larva produced by these embryos, the Brachyury gene (green) is expressed in the ventral portion of the stomodeum (i.e., the mouth) and in the proctodeum (anus), whileotx (gold) is expressed in two bands of cells along the ciliated bands. (B) In the hemichordates (a deuterostome lineage that includes the acorn worms), the tip of the gastrulation cavity touches the lateral body wall on the future ventral side, where the mouth later breaks through. The blastopore gives rise to the anus only. In the early tornaria larva produced by these embryos, Brachyury is expressed in the ventral portion of the stomodeum and in the proctodeum, and otx is expressed in two upper bands parallel to the pre-oral ciliated band and in two lower bands parallel to the post-oral ciliated band. (After Arendt et al. 2004.) (Click image to enlarge.) |
Cnidarians and their larvae as Urbilaterian candidates
Current research has focused on cnidarians and their planula larvae as the possible bilaterian ancestor. The planula larva of cnidarians resembles the acoelomic flatworms of the taxon Acoelomorpha. These animals are now thought to represent the sister group to the protostomes and deuterostomes (Baguña et al. 2008). While not within either of these two large groups, they do exhibit bilateral symmetry. If this placement of taxa is correct, many ideas have to be reconsidered. First, according to this scheme, the Urbilaterian ancestor is a different organism than the PDA (Figure 3). Second, recent phylogenies have indicated that the Xenoturbella is probably the most basal deuterostome clade, and that the unsegmented Chaetognathans are sister group to all the lophotrochozoans. This would suggest that both protostomes and deuterostomes originated from simple, unsegmented, wormlike creatures with only one body opening and a non-centralized nervous system at its base (Hejnol and Martindale 2008). The direct-developing acoel flatworms and the planula larvae of cnidarians may represent this type of organization. This would argue for a much simpler Urbilaterian that pre-dated the PDA. This Urbilaterian would be an unsegmented wormlike organism without feet and heart and with a decentralized nervous system. Its gut would have one opening, not two. The big difference between the cnidarians and the bilaterians would be the position of the site of gastrulation in relation to the egg. In bilaterians, gastrulation occurs ventrally (in what would normally become endoderm), while in cnidarians it occurs at the animal pole. In acoel flatworms, gastrulation takes place vegetally, in the macromeres that become the endomesoderm (Henry et al. 2000).
Figure 3 Phylogenetic position of the Acoelomorpha, based on molecular and morphological evidence from several recent sources. In this model, the position of the “Urbilaterian”—the stem species of the Bilateria—is distinct from that of the eubilaterian stem species (“protostome-deuterostome ancestor,” or PDA). Synapomorphies are indicated by filled squares. (After Hejnol and Martidale 2008.) (Click image to enlarge.) |
This would mean that the genes corresponding to heart or eye development arose only later. Genes specifying “mesoderm” appear to exist in cnidarians that lack mesoderm (Martindale et al. 2004), and the Pax6 gene appears to have evolved after the eyes of cnidarian medusae (Matus et al. 2007). The presence and expression of Hox clusters in cnidarians (Ryan et al. 2007; Hejnol and Martindale 2009), and the discovery that the Bmp4/dpp homologue in cnidarians is expressed on only one side of the blastopore (indicating bilateral symmetry; Hayward et al. 2002; Finnerty et al. 2004), indicates that cnidarians and bilaterians probably follow the same developmental rules, originating from an ancestor 570–700 million years ago.
Our new phylogenies and new abilities to determine gene expression patterns are enabling us to return to one of those old questions that Roux had promised we would come back to solve. One of the biggest of these questions concerned the origin of bilateral symmetry. There were several hypotheses (see Martidale and Hejnol 2009), but one of them, the acoeloid-planuloid hypothesis (von Graff 1891), predicted that the cnidarian planula larvae underwent a heterochronic change to give rise to the ancestor of acoel bilateral flatworms. The combination of molecular and anatomical investigations offers us provocative clues as to what the proverbial Urbilatarian ancestor might have been and may provide evidence for the ways that some of the most crucial features of the animal kingdom evolved.