' 2008 Wiley-Liss, Inc.

genesis 46:575579 (2008)

EDITORIAL

Chordate Origins and Evolution

Billie J. Swalla1,2 and Jose Xavier-Neto3*
1 2

Department of Biology, Center for Developmental Biology, University of Washington, Seattle, Washington Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington 3 Laboratorio de Genetica e Cardiologia Molecular InCor, HC.FMUSP, Sao Paulo-SP, Brazil

INTRODUCTION Chordate origins is a subject that has intrigued and stymied scientists for nearly 200 years. However, recent studies that are combining developmental biology and evolutionary approaches to this complex question are beginning to make some headway into understanding the evolution of these unique animals. Developmental biology is traditionally studied with the aid of a few classic model species and some emerging model systems. Knowledge extracted from different models advances at different rates, fast in some, more slowly in others. As a consequence, data from the more prolic species have been particularly inuential in generating developmental syntheses. However, these syntheses are, by necessity, mosaics of information units acquired in different organisms, and therefore, represent only approximations to the ultimate goal of fully understanding development in a given species. The identication of signaling molecules and transcription factors as major players in the development of animals, as widely separated by evolution as insects and vertebrates, is testimony to the fact that the developmental processes of all animals can be understood on the same mechanistic bases. In the last 20 years the enormous success in cloning and characterizing expression patterns for homologs of major genes encoding these molecules in model species has stimulated research on the molecular basis of common features of animal development. However, there were times when similarities among organisms were often stretched beyond the supporting evidence, which, as a reaction, triggered renewed research in the developmental basis of animal diversity. Recently, interest in the specics of animal development has been facilitated by the decoding of genomes of organisms that occupy key positions in the phylogenetic tree and of species closely related to the classic model systems. The comparative study of development in these two complementary fronts is beginning to explain why animals can be so different, even though they utilize essentially the same developmental building blocks. These studies indicate that animals often use slightly different combinations of the same key players to build

homologous structures, but that, occasionally, homologous structures can be built using dramatically different molecules (Patel et al., 1992; Rudel and Sommer, 2003). Overall, it is apparent that new developmental syntheses are being made, reconciling research interests in common and in divergent aspects of animal development. In this view, the study of the commonalities of development is crucial to understand ontogeny at the level of a single organism and, simultaneously, to provide a backdrop to identify specic mechanisms that gave rise to the remarkable diversity of life forms that we encounter in nature. Ultimately, however, comparative analyses of development can only make sense if performed in an evolutionary context. Without an evolutionary framework it is impossible to ascertain whether certain striking similarities result from common descent or were acquired independently. The renewed interest in the comparative aspects of development indicated that some morphological similarities interpreted as homologies on the basis of shared genetic circuits, can sometimes be best understood as parallelisms or convergences, rather than homologies, stressing the fact that relationships between genomes and phenotypes are very plastic (Baguna and Garcia-Fernandez, 2003; Hall, 2003; Plachetzki and Oakley, 2007; Xavier-Neto et al., 2007). Therefore, the study of evolution is fast becoming a crucial aid to understand development. The diversity of structure, function, and developmental programs displayed by animals is encapsulated in the concept of body plan. The idea that animals can be described and analyzed as if they are the products of specic blueprints is a powerful abstraction that allows us to inquire whether different animals use the same basic instructions, when these directions rst appeared, or when they were lost in evolution. If the developmental biologist reaches this far in his or her analyses, it is likely that he or she will be compelled to pursue progressively deeper
* Correspondence to: Jose Xavier-Neto E-mail: Xavier.neto@incor.usp.br Published online 10 November 2008 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/dvg.20477

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comparisons in the quest for origins of developmental patterns, thus falling completely under evolutions spell. Unfortunately, this is when developmental biologists nd themselves in uncharted territory. At this stage, they will need to become familiar not only with a vast number of animal body plans, but also with various phylogenetic schemes that suggest competing evolutionary hypotheses (Swalla and Smith, 2008). Fortunately, the exponential accumulation of molecular data from genomes and animal models comes to the rescue. Molecular phylogenies are continually being constructed, recently incorporating multiple genes on a genomic scale, hopefully reducing sources of systematical errors (Bourlat, 2006; Delsuc et al., 2005; Dunn et al., 2008). The interested developmental biologist is also compelled to understand how fossils can and do change our views on the evolution of development (Conway-Morris, 1994; Hall, 2002). However, there are some creative researchers who, through collaborations and training, are combining results and ideas from different elds to create synthetic hypothesis on the evolution of animal body plans. The evolution of our own vertebrate subphylum among chordates and deuterostomes represents a case in point in which the recent urry of new data from bioinformatics, development, evolution, and paleontology has changed traditional paradigms and opened opportunities for new syntheses (Cameron et al., 2000). Therefore, the time has come when we can compare vertebrates to the rest of the invertebrate deuterostomes and ask insightful questions about the evolution and development of the successful vertebrate body plan. In this volume, we approached a number of different researchers who use different methods for insight into animal relationships, development, and evolution in order to see if there are particular themes that are emerging. Deuterostomes include Chordata (vertebrates, cephalochordates, tunicates) together with ambulacraria (echinoderms and hemichordates) (Cameron et al., 2000). In the last 4 years new phylogenetic ideas have been proposed, a new phylum, Xenoturbellida, has joined deuterostomes and been assigned to a position basal to ambulacraria (Bourlat et al., 2006), some proposed deuterostomes such as the lophophorates (Halanych et al., 1995) and enigmatic chaetognaths (Marletaz et al., 2006b) have now been rmly displaced to join protostomes and some paradigms such as the calcichordate hypothesis have been revisited (Delsuc et al., 2006 and references therein). There are two groups of deuterostomes where very little developmental information is available, the newest deuterostome phylum Xenoturbellida and the colonial pterobranch hemichordates, so we have articles on both of these fascinating groups. Max Telford has pioneered the molecular work that placed Xenoturbellids as deuterostomes (Bourlat et al., 2006) and brings us up to date on how this worm may answer questions of chordate origins (Telford, 2008). Then Atsuko Sato, working with John Bishop and Peter Holland, contributes a paper with photos of larvae of Rhabdopleura normani that summa-

rizes the importance that pterobranchs have played in classic views of deuterostome evolution (Sato et al., 2008), due to the extensive fossil record of Pterobranchs or graptolites (Swalla and Smith, 2008). Genomic approaches to chordate phylogenies suggested changes to the traditional euchordate viewvertebrates and cephalochordates as sister groups to the exclusion of basal tunicatesand placed vertebrates and tunicates as sister groups (the Olfactores hypothesis) (Blair and Hedges, 2005; Delsuc et al., 2006; Philippe et al., 2005). These novel ideas have been subjected to thorough testing and the Olfactores hypothesis has received further support (Bourlat et al., 2006; Delsuc et al., 2006, 2008; Dunn et al., 2008; Swalla and Smith, 2008). In contrast, the unorthodox assembly of cephalochordates and echinoderms, which initially raised suspicions about chordate monophyly (Delsuc et al., 2006), was not conrmed (Bourlat et al., 2006; Delsuc et al., 2008). Importantly, although chordate topologies may have changed, integrity of the subphylum has been reafrmed, albeit, perhaps, at the surprising price of destabilizing deuterostomes as a natural group (Delsuc et al., 2008). This point is discussed in this special issue along with the account of challenging morphological and molecular similarities observed between Xenoturbella and Acoelomorph atworms (Bourlat et al., 2003; Cameron et al., 2000; Delsuc et al., 2008; Philippe et al., 2007; Telford, 2008). It is interesting how these novel ideas are ltering through the eld of chordate evolution and biology. In this volume, Chen discusses the insights provided by the controversial Haikouella and Yunnanozoon fossils collected from the Doushantuo formation in China. These Precambrian fossils were dated to about 530 Mya (millions of years ago) and have been alternatively interpreted as a chordates, hemichordates, basal deuterostomes or precraniate representatives of Cristozoa (Chen, 2008 and references therein), a new proposed subphylum that includes all animals that display neural crest cells or their derivatives (Holland and Chen, 2001). The peculiar state of preservation of his material allows Chen to confront alternative hypotheses and to propose that both fossils provide missing links to an ancestral Chordate, which he pictures, in agreement with the Olfactores hypothesis, as an animal similar to the cephalochordate amphioxus. Chen goes on to remark that although tunicates display important molecular and morphological synapomorphies in their pumping organs, nervous systems, and photoreceptor apparatuses that link them to vertebrates (Jeffery et al., 2007; Schubert et al., 2006; Shimeld et al., 2005; Simoes-Costa et al., 2005), they display such derived bodies that few other characters will be useful to reconstruct the proximate ancestor of vertebrates, a task for which the Haikouella and Yunnanozoon fossils are better qualied. These interpretations sum up very well not only the potential that fossils have to inuence our thinking about the evolution of chordate development, but also the problems associated with them, since the afnities of both Hai-

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kouella and Yunnanozoon are still hotly debated (Mallat and Chen, 2003; Mallat et al., 2003; Shu and ConwayMorris, 2003; Shu et al., 2003), with alternative views linking them to possible basal deuterostomes such as vetulicolians, precambrian fossils with divergent and even bizarre bodies that, have, so far, deed attempts to establish a consensual classication (Shu et al., 2001; Lacalli, 2002). Also inuenced by the new view of chordate evolution, Satoh (2008) and Swalla and Smith (2008) both enumerate the major ontogenetic and morphological features that place cephalochordates between all other nonchordate deuterostomes and vertebrates plus tunicates. Accordingly, Satoh (2008) suggests that the chordate ancestor was comparable to extant cephalochordates such as amphioxus and then proposes that this amphioxus-like animal evolved from a free-living ancestor similar to enteropneust hemichordates (Cameron et al., 2000; Swalla and Smith, 2008) through changes that fashioned a swimming, skeletal muscle driven, larva out of a ciliated larva similar to those of hemichordates and echinoderms. Satoh pictures this swimming larva as tadpole-like, but different, more primitive, than the tunicate tadpole, with only a trunk and a tail region. With amphioxus embryogenesis in mind Satoh proposes that both notochord and neural tube originated in the dorsal side of this due to spatial constraints of an anterior mouth, a posterior anus, a ventral bending of the gut to fuse to the mouth primordium, as well as due to proposed poor tness for larvae tted with asymmetric neural tube and notochord on the left or on the right side. An important feature of the scheme devised and dubbed by Satoh as Aboral-Dorsalization hypothesis is the link between dorsal location and the independent, de novo, origin for two of the ve major shared derived characters of chordates, namely the hollow neural tube and the notochord. As such, Satohs hypothesis questions nothing less than two celebrated paradigms concerning chordate Origins: Garstangs dipleurula theory (Garstang 1928a, b) and the DorsalVentral inversion hypothesis (Arendt and Nubler-Jung, 1994; De Robertis and Sasai, 1996; Gerhart, 2000 and references therein). Garstangs dipleurula theory (Garstang 1928a, b) and Romers widely accepted Deuterostome pterobranch ancestor (Romer 1967) are also discussed in the Brown et al. (2008) paper in this issue. This article further modies the view of a benthic vermiform deuterostome ancestor that was rst proposed by Swalla and coauthors in 2000, after working on both tunicate and hemichordate phylogenies (Cameron et al., 2000). This article also presents new data on the nerve cord of Ptychoderid hemichordates, those likely to have been the ancestral hemichordate. Several papers examine the evolution of specic gene networks in shaping vertebrate and chordate evolution. Paris and Laudet (2008) review the role of thyroid hormone in the evolution of chordate metamorphosis. Based on the patterns of conservation of this nuclear receptor they suggest that all chordates and, perhaps,

even all deuterostomes, have a homologous metamorphosis stage during their postembryonic development. Paris and Laudet also present the intriguing view that mammalian metamorphosis may be the act of weaning of the young. Campo-Paysaa et al. (2008) discuss the evolution of our views on retinoic acid (RA) signaling across animals. First considered a vertebrate-specic and then a chordate-specic system operating in the elaboration of the AnteriorPosterior axis, RA signaling is now increasingly perceived as an ancestral system that dates back to the bilaterian ancestor, owing to the characterization of some of its key players in the genomes of an echinoderm and one hemichordate, among deuterostomes, as well of a gastropod mollusk and an annelid, among protostomes (Campo-Paysaa et al. 2008; Canestro et al., 2006; Howard-Ashby et al. 2006; Marletaz et al., 2006a; Simoes-Costa et al., 2008 and references therein; see also Albalat and Canestro, 2008). Campo-Paysaa et al. speculate that RA signaling may have played a role in neurite outgrowth and neuronal survival during development of the bilaterian ancestor, a role echoed by related actions of the RA in vertebrates and mollusks, but that it was subsequently lost in the lineage leading to ecdysozoan protostomes. Loss of RA signaling has indeed been a feature of bilaterian evolution, as demon strated by Canestro and Postlethwait 2007 in appendicularian tunicates, which further underscores the fact that tunicates have an evolutionarily derived body plan compared with the rest of the chordates. Sauka-Spengler and Bronner-Fraser (2008) discuss the gene regulatory networks underlying neural crest, which are found in vertebrates and perhaps some tunicates, but not in lancelets. These three papers all underscore the continued evolution of the vertebrate lineage from the ancestral chordates, by showing not only the conservation of important developmental gene networks, but also their modication for specifying body plans across all of the vertebrate groups. Analysis of the molecular underpinnings of shared derived developmental characters is an established approach to understand evolution. In this number Capellini et al., from the Di Gregorio laboratory, used the Brachyury-regulated Ci-Leprecan gene encoding a prolyl hydroxilase as a target to study the evolutionary history of a notochord-specic tunicate gene (Capellini et al., 2008). They show that Leprecan genes are single copy in diploblastic animals and invertebrate bilaterians and suggest that, after being co-opted to the notochord in an ancestral chordate, Leprecan was duplicated to give rise to the multiple Leprecan genes of vertebrates, which in turn acquired additional modules of expression for other domains in paraxial mesoderm, limb, craniofacial tissues, branchial arches and otic capsule. Kugler and colleagues, also from the Di Gregorio laboratory, dened a minimum complement of notochord genes conserved in vertebrates and in the tunicate Ciona intestinalis. Kugler et al. (2008) indicate that structural genes such as those encoding extracellular matrix proteins are more often found to be expressed in both C. intestinalis and verte-

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brates than transcription factors. Using transgenic embryos that express Ci-Brachyury, or its repressor form, they provide evidence for a class of notochord-specic genes that do not seem to be affected by Brachyury, suggesting the presence of further, unknown, notochord gene regulatory networks (Kugler et al., 2008). In summary, the picture of chordate evolution that is emerging from the last 4 years is one drastically different from the apparent stability suggested by the classic textbook Euchordate view. New ideas have been proposed and tested, but it is evident that important advances are on the corner. This is why we assembled a group of authors with expertise in a variety of these techniques and invited them to contribute to this authoritative, high quality collection of state of the art reviews that will help students, teachers, and researchers to grasp the important facts, direct them more easily to the primary literature and to stimulate new research to face the major challenges ahead. ACKNOWLEDGMENTS We wish to thank Richard Behringer and Terry Magnuson for continued support for the realization of this special issue. We are also indebted to the authors and reviewers for their excellent contributions. Work in the Xavier-Neto laboratory is supported by grants from FAPESP and CNPq. LITERATURE CITED
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