Conserved anterior boundaries of Hox gene expression in the central nervous system of the leech Helobdella

Hox genes in spiders: Their significance for development and evolution

Hox genes are known for their role in the specification of typical body plan features in animals. Evolutionary changes in Hox gene function are believed to be involved in the emergence of the diverse body plans we observe in animals today. Spiders share many body plan features with other arthropods, but also have numerous unique traits of their own. Studies of spider Hox genes have already provided insights into evolutionarily conserved and derived features of the spider body plan and their genetic basis. However, many aspects of Hox gene biology have been insufficiently studied in spiders so far. In this review, we highlight previous comparative studies of Hox genes in spiders and their significance for our understanding of the evolution of the spider body plan. We also identify aspects of Hox gene biology that need to be studied in greater detail. Many spider Hox genes have not been investigated beyond their mRNA expression patterns, and the role of Hox genes with apparently plesiomorphic or dual functions, like ftz and Hox3 is still unclear. Spiders have a duplicated Hox gene cluster, but possible sub- or neofunctionalisation of duplicates have not yet been studied systematically. Future research should therefore focus on these issues, in addition to the role of Polycomb and trithorax-mediated regulation, the identification of regulatory regions, cofactors or spider-specific target genes, and the significance of non-coding RNAs transcribed from within the Hox cluster and even from the antisense strand of particular Hox genes.

Echiuran Hox genes provide new insights into the correspondence between Hox subcluster organization and collinearity pattern

In many bilaterians, Hox genes are generally clustered along the chromosomes and expressed in spatial and temporal order. In vertebrates, the expression of Hox genes follows a whole-cluster spatio-temporal collinearity (WSTC) pattern, whereas in some invertebrates the expression of Hox genes exhibits a subcluster-level spatio-temporal collinearity pattern. In bilaterians, the diversity of collinearity patterns and the cause of collinearity differences in Hox gene expression remain poorly understood. Here, we investigate genomic organization and expression pattern of Hox genes in the echiuran worm Urechis unicinctus (Annelida, Echiura). Urechis unicinctus has a split cluster with four subclusters divided by non-Hox genes: first subcluster (Hox1 and Hox2), second subcluster (Hox3), third subcluster (Hox4, Hox5, Lox5, Antp and Lox4), fourth subcluster (Lox2 and Post2). The expression of U. unicinctus Hox genes shows a subcluster-based whole-cluster spatio-temporal collinearity (S-WSTC) pattern: the anterior-most genes in each subcluster are activated in a spatially and temporally colinear manner (reminiscent of WSTC), with the subsequent genes in each subcluster then being very similar to their respective anterior-most subcluster gene. Combining genomic organization and expression profiles of Hox genes in different invertebrate lineages, we propose that the spatio-temporal collinearity of invertebrate Hox is subcluster-based.

Glossiphoniid leeches as a touchstone for studies of development in clitellate annelids

My goals in this chapter are to share my enthusiasm for studying the biology of leeches, to place this work in context by presenting my rationale for studying non-traditional biological models in general, and to sample just three of the questions that intrigue me in leech biology, namely segmentation, genome evolution and neuronal fate specification. I first became excited about the idea of using leeches as a subject of investigation as an undergraduate in 1970 and have been engaged in this work since I arrived at Berkeley as a postdoc in 1976, intending to study leech neurobiology. Both my research interests and the rationale for the work have expanded greatly since then. What follows is a fragmentary personal and historical account-the interested reader may find more comprehensive treatments elsewhere (Kuo et al., 2020; Shankland & Savage, 1997; Shain, 2009; Weisblat & Huang, 2001; Weisblat & Kuo, 2009, 2014; Weisblat & Winchell, 2020).

Dorsoventral decoupling of Hox gene expression underpins the diversification of molluscs

In contrast to the Hox genes in arthropods and vertebrates, those in molluscs show diverse expression patterns with differences reported among lineages. Here, we investigate 2 phylogenetically distant molluscs, a gastropod and a polyplacophoran, and show that the Hox expression in both species can be divided into 2 categories. The Hox expression in the ventral ectoderm generally shows a canonical staggered pattern comparable to the patterns of other bilaterians and likely contributes to ventral patterning, such as neurogenesis. The other category of Hox expression on the dorsal side is strongly correlated with shell formation and exhibits lineage-specific characteristics in each class of mollusc. This generalized model of decoupled dorsoventral Hox expression is compatible with known Hox expression data from other molluscan lineages and may represent a key characteristic of molluscan Hox expression. These results support the concept of widespread staggered Hox expression in Mollusca and reveal aspects that may be related to the evolutionary diversification of molluscs. We propose that dorsoventral decoupling of Hox expression allowed lineage-specific dorsal and ventral patterning, which may have facilitated the evolution of diverse body plans in different molluscan lineages.

On the origin of leeches by evolution of development

Leeches are a unique group of annelids arising from an ancestor that would be characterized as a freshwater oligochaete worm. Comparative biology of the oligochaetes and the leeches reveals that body plan changes in the oligochaete-to-leech transition probably occurred by addition or modification of the terminal steps in embryonic development and that they were likely driven by a change in the feeding behavior in the ancestor of leeches. In this review article, developmental changes that are associated with the evolution of several leech-specific traits are discussed. These include (1) the evolution of suckers, (2) the loss of chaetae, (3) the loss of septa, and (4) a fixed number of segments. An altered developmental fate of the teloblast is further proposed to be a key factor contributing to the fixation of the segment number, and the evolutionary change in teloblast development may also account for the loss of the ability to regenerate the lost body segments in the leech.

Staggered Hox expression is more widespread among molluscs than previously appreciated

Hox genes are expressed along the anterior-posterior body axis in a colinear fashion in the majority of bilaterians. Contrary to polyplacophorans, a group of aculiferan molluscs with conserved ancestral molluscan features, gastropods and cephalopods deviate from this pattern by expressing Hox genes in distinct morphological structures and not in a staggered fashion. Among conchiferans, scaphopods exhibit many similarities with gastropods, cephalopods and bivalves, however, the molecular developmental underpinnings of these similar traits remain unknown. We investigated Hox gene expression in developmental stages of the scaphopod Antalis entalis to elucidate whether these genes are involved in patterning morphological traits shared by their kin conchiferans. Scaphopod Hox genes are predominantly expressed in the foot and mantle but also in the central nervous system. Surprisingly, the scaphopod mid-stage trochophore exhibits a near-to staggered expression of all nine Hox genes identified. Temporal colinearity was not found and early-stage and late-stage trochophores, as well as postmetamorphic individuals, do not show any apparent traces of staggered expression. In these stages, Hox genes are expressed in distinct morphological structures such as the cerebral and pedal ganglia and in the shell field of early-stage trochophores. Interestingly, a re-evaluation of previously published data on early-stage cephalopod embryos and of the gastropod pre-torsional veliger shows that these developmental stages exhibit traces of staggered Hox expression. Considering our results and all gene expression and genomic data available for molluscs as well as other bilaterians, we suggest a last common molluscan ancestor with colinear Hox expression in predominantly ectodermal tissues along the anterior-posterior axis. Subsequently, certain Hox genes have been co-opted into the patterning process of distinct structures (apical organ or prototroch) in conchiferans.

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

Temporal collinearity is often considered the main force preserving Hox gene clusters in animal genomes. Studies that combine genomic and gene expression data are scarce, however, particularly in invertebrates like the Lophotrochozoa. As a result, the temporal collinearity hypothesis is currently built on poorly supported foundations. Here we characterize the complement, cluster, and expression of Hox genes in two brachiopod species, Terebratalia transversa and Novocrania anomalaT. transversa has a split cluster with 10 genes (lab, pb, Hox3, Dfd, Scr, Lox5, Antp, Lox4, Post2, and Post1), whereas N. anomala has 9 genes (apparently missing Post1). Our in situ hybridization, real-time quantitative PCR, and stage-specific transcriptomic analyses show that brachiopod Hox genes are neither strictly temporally nor spatially collinear; only pb (in T. transversa), Hox3 (in both brachiopods), and Dfd (in both brachiopods) show staggered mesodermal expression. Thus, our findings support the idea that temporal collinearity might contribute to keeping Hox genes clustered. Remarkably, expression of the Hox genes in both brachiopod species demonstrates cooption of Hox genes in the chaetae and shell fields, two major lophotrochozoan morphological novelties. The shared and specific expression of Hox genes, together with Arx, Zic, and Notch pathway components in chaetae and shell fields in brachiopods, mollusks, and annelids provide molecular evidence supporting the conservation of the molecular basis for these lophotrochozoan hallmarks.

Early mesodermal expression of Hox genes in the polychaete Alitta virens (Annelida, Lophotrochozoa)

Hox genes are the key regulators of axial regionalization of bilaterian animals. However, their main function is fulfilled differently in the development of animals from different evolutionary branches. Early patterning of the developing embryos by Hox gene expression in the representatives of protostomes (arthropods, mollusks) starts in the ectodermal cells. On the contrary, the instructive role of the mesoderm in the axial patterning was demonstrated for vertebrates. This makes it difficult to understand if during the axial regionalization of ancestral bilaterians Hox genes first expressed in the developing mesoderm or the ectoderm. To resolve this question, it is necessary to expand the number of models for investigation of the early axial patterning. Here, we show that three Hox genes of the polychaete Alitta virens (formerly Nereis virens, Annelida, Lophotrochozoa)-Hox2, Hox4, and Lox5-are expressed in the mesodermal anlagen of the three future larval chaetigerous segments in spatially colinear manner before the initiation of Hox expression in the larval ectoderm. This is the first evidence of sequential Hox gene expression in the mesoderm of protostomes to date.

Embryonic expression patterns of Hox genes in the oligochaete annelid Tubifex tubifex

We have cloned and characterized the expression of seven Hox genes (designated Ttu-lab, Ttu-Dfd, Ttu-Scr1, Ttu-Scr2, Ttu-Lox5, Ttu-Lox4 and Ttu-Lox2) from the oligochaete annelid Tubifex tubifex. RT-PCR analyses show that except for Ttu-Lox4 and Ttu-Lox2 which begin expression as early as cleavage stages, Tubifex Hox genes are expressed during stages 13-18 when embryos undergo germ band formation, segmentation and body elongation. In terms of combination of tissues (or organs) exhibiting positive cells, the Tubifex Hox genes examined in this study are classified into three groups. Ttu-lab, Ttu-Scr1 and Ttu-Lox5 are expressed only in the ventral nerve cord; Ttu-Scr2 and Ttu-Lox4 are expressed not only in the ventral nerve cord but also in distinct lateral segmental tissues; and Ttu-Dfd and Ttu-Lox2 are expressed not only in the segmental ectoderm along the length of the AP body axis but also in the prostomium. Anterior expression boundaries of Ttu-lab, Ttu-Scr1, Ttu-Lox5 and Ttu-Lox4 are at segments 3, 4, 5, and 9, respectively. Anterior expression boundary of Ttu-Scr2 is at segment 2, and Ttu-Dfd and Ttu-Lox2 are expressed even at the anteriormost portion, the prostomium. These observations suggest that as in other annelids, so-called "spatial colinearity" of anterior expression boundaries of Hox genes has been conserved in the oligochaetes. It is also evident that there are some oligochaete Hox genes which violate the spatial colinearity rule.

Hox and ParaHox gene expression in early body plan patterning of polyplacophoran mollusks

Molecular developmental studies of various bilaterians have shown that the identity of the anteroposterior body axis is controlled by Hox and ParaHox genes. Detailed Hox and ParaHox gene expression data are available for conchiferan mollusks, such as gastropods (snails and slugs) and cephalopods (squids and octopuses), whereas information on the putative conchiferan sister group, Aculifera, is still scarce (but see Fritsch et al., 2015 on Hox gene expression in the polyplacophoran Acanthochitona crinita). In contrast to gastropods and cephalopods, the Hox genes in polyplacophorans are expressed in an anteroposterior sequence similar to the condition in annelids and other bilaterians. Here, we present the expression patterns of the Hox genes Lox5, Lox4, and Lox2, together with the ParaHox gene caudal (Cdx) in the polyplacophoran A. crinita. To localize Hox and ParaHox gene transcription products, we also investigated the expression patterns of the genes FMRF and Elav, and the development of the nervous system. Similar to the other Hox genes, all three Acr‐Lox genes are expressed in an anteroposterior sequence. Transcripts of Acr‐Cdx are seemingly present in the forming hindgut at the posterior end. The expression patterns of both the central class Acr‐Lox genes and the Acr‐Cdx gene are strikingly similar to those in annelids and nemerteans. In Polyplacophora, the expression patterns of the Hox and ParaHox genes seem to be evolutionarily highly conserved, while in conchiferan mollusks these genes are co‐opted into novel functions that might have led to evolutionary novelties, at least in gastropods and cephalopods.

HOX gene complement and expression in the planarian Schmidtea mediterranea

Background

Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi.

Results

Because the planarian Schmidteamediterranea (S. mediterranea) is unsegmented, appendage less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here, we argue against this hypothesis and show that S. mediterranea has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially restricted expression. Finally, we confirm HOX gene axial expression by RNA deep-sequencing 6 anterior–posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially restricted transcripts.

Conclusions

Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior–posterior axis of adult planarians.

Electronic supplementary material

The online version of this article (doi:10.1186/s13227-016-0044-8) contains supplementary material, which is available to authorized users.

An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality

Hox genes are regulators of animal embryonic development. Changes in the number and sequence of Hox genes as well as in their expression patterns have been related to the evolution of the body plan. Lophotrochozoa is a clade of Protostomia characterized by several phyla which show a wide morphological diversity. Despite that the works summarized in this review emphasize the fragmentary nature of the data available regarding the presence and expression of Hox genes, they also offer interesting insight into the evolution of the Hox cluster and the role played by Hox genes in several phyla. However, the number of genes involved in the cluster of the lophotrochozoan ancestor is still a question of debate. The data presented here suggest that at least nine genes were present while two other genes, Lox4 and Post-2, may either have been present in the ancestor or may have arisen as a result of duplication in the Brachiopoda-Mollusca-Annelida lineage. Spatial and temporal collinearity is a feature of Hox gene expression which was probably present in the ancestor of deuterostomes and protostomes. However, in Lophotrochozoa, it has been detected in only a few species belonging to Annelida and Mollusca.

Hox genes, evo-devo, and the case of the ftz gene

The discovery of the broad conservation of embryonic regulatory genes across animal phyla, launched by the cloning of homeotic genes in the 1980s, was a founding event in the field of evolutionary developmental biology (evo-devo). While it had long been known that fundamental cellular processes, commonly referred to as housekeeping functions, are shared by animals and plants across the planet-processes such as the storage of information in genomic DNA, transcription, translation and the machinery for these processes, universal codon usage, and metabolic enzymes-Hox genes were different: mutations in these genes caused "bizarre" homeotic transformations of insect body parts that were certainly interesting but were expected to be idiosyncratic. The isolation of the genes responsible for these bizarre phenotypes turned out to be highly conserved Hox genes that play roles in embryonic patterning throughout Metazoa. How Hox genes have changed to promote the development of diverse body plans remains a central issue of the field of evo-devo today. For this Memorial article series, I review events around the discovery of the broad evolutionary conservation of Hox genes and the impact of this discovery on the field of developmental biology. I highlight studies carried out in Walter Gehring's lab and by former lab members that have continued to push the field forward, raising new questions and forging new approaches to understand the evolution of developmental mechanisms.

Unexpected co-linearity of Hox gene expression in an aculiferan mollusk

BACKGROUND

Mollusca is an extremely diverse animal phylum that includes the aculiferans (worm-like aplacophorans and eight-shelled polyplacophorans) and their sister group, the conchiferans, comprising monoplacophorans, bivalves (clams, mussels), gastropods (snails, slugs), scaphopods (tusk shells) and cephalopods (squids, octopuses). Studies on mollusks have revealed an overall number of 11 Hox genes in seven out of eight molluscan "class"-level taxa, but expression data of key developmental regulators such as homeotic genes are only available for three gastropod and two cephalopod species. These show that Hox genes are involved in the formation of specific features including shell, foot, funnel or tentacles and not in antero-posterior body plan patterning as in most other bilaterian animals. The role of Hox genes in non-conchiferan (i.e., aculiferan) mollusks remains entirely unknown.

RESULTS

Here we present the first data on the expression of seven Hox genes in apolyplacophoran mollusk, Acanthochitona crinita. In A. crinita the Hox genes Acr-Hox1-5, Hox7 and Post2 are expressed in a co-linear pattern along the antero-posterior axis, but not in molluscan-specific features such as the shell or the foot. The expression pattern is restricted to the post-trochal region and the transcripts are present in ecto-, endo- and mesodermal cell layers. Contrary to the situation in gastropods and cephalopods, we did neither find Hox gene expression in distinct neural subsets of A. crinita, nor in its developing shell plates.

CONCLUSIONS

Our analysis and comparison with other lophotrochozoans indicate that the basal role of Hox genes is in antero-posterior axis patterning in mollusks, similar to the vast majority of bilaterian animals, and that this role has been conserved in polyplacophorans, while co-option into patterning of evolutionary novelties emerged either at the base of Conchifera or independently in gastropods and cephalopods. These morphological innovations most likely contributed to the evolutionary success of its representatives, as exemplified by, e.g., the wide ecological range and species richness of gastropods.

Hox genes pattern the anterior-posterior axis of the juvenile but not the larva in a maximally indirect developing invertebrate, Micrura alaskensis (Nemertea)

BACKGROUND

The pilidium larva is a novel body plan that arose within a single clade in the phylum Nemertea - the Pilidiophora. While the sister clade of the Pilidiophora and the basal nemerteans develop directly, pilidiophorans have a long-lived planktotrophic larva with a body plan distinctly different from that of the juvenile. Uniquely, the pilidiophoran juvenile develops inside the larva from several discrete rudiments. The orientation of the juvenile with respect to the larval body varies within the Pilidiophora, which suggests that the larval and juvenile anteroposterior (AP) axes are patterned differently. In order to gain insight into the evolutionary origins of the pilidium larva and the mechanisms underlying this implied axial uncoupling, we examined the expression of the Hox genes during development of the pilidiophoran Micrura alaskensis.

RESULTS

We identified sequences of nine Hox genes and the ParaHox gene caudal through a combination of transcriptome analysis and molecular cloning, and determined their expression pattern during development using in situ hybridization in whole-mounted larvae. We found that Hox genes are first expressed long after the pilidium is fully formed and functional. The Hox genes are expressed in apparently overlapping domains along the AP axis of the developing juvenile in a subset of the rudiments that give rise to the juvenile trunk. Hox genes are not expressed in the larval body at any stage of development.

CONCLUSIONS

While the Hox genes pattern the juvenile pilidiophoran, the pilidial body, which appears to be an evolutionary novelty, must be patterned by some mechanism other than the Hox genes. Although the pilidiophoran juvenile develops from separate rudiments with no obvious relationship to the embryonic formation of the larva, the Hox genes appear to exhibit canonical expression along the juvenile AP axis. This suggests that the Hox patterning system can maintain conserved function even when widely decoupled from early polarity established in the egg.

Developmental biology of the leech Helobdella

Glossiphoniid leeches of the genus Helobdella provide experimentally tractable models for studies in evolutionary developmental biology (Evo-Devo). Here, after a brief rationale, we will summarize our current understanding of Helobdella development and highlight the near term prospects for future investigations, with respect to the issues of: D quadrant specification; the transition from spiral to bilaterally symmetric cleavage; segmentation, and the connections between segmental and non-segmental tissues; modifications of BMP signaling in dorsoventral patterning and the O-P equivalence group; germ line specification and genome rearrangements. The goal of this contribution is to serve as a summary of, and guide to, published work.

Regional and segmental differences in the embryonic expression of a putative leech Hox gene, Lox2, by central neurons immunoreactive to FMRFamide-like neuropeptides

We performed immunofluorescence experiments using a rat polyclonal antibody on formaldehyde-fixed whole-mount embryos to characterize the expression of a putative leech Hox gene, Lox2, during embryonic development. The main goal was to determine whether the differentiation of subsets of FMRFamide-like immunoreactive (FLI) neurons coincide with the expression domain of Lox2. The earliest expression of Lox2 was detected in relatively large, prominent nuclei in the posterior region at embryonic day 4, a very early stage. Lox2 expression was also detected in subsets of central neurons (neurons located in the CNS) located in midbody ganglia 6 (M6)-M21. In addition, Lox2 was expressed by a number of segment-specific and segmentally repeated central FLI neurons. Lox2-positive FLI neurons of interest included some of those previously identified: the rostral most ventral (RMV) neurons, the circular ventral (CV) neurons, and cell 261. The paired RMVs, which are located in all midbody ganglia, expressed Lox2 only in M7-M19. The CV neurons, specialized motor neurons that innervate the circular ventral muscles of the body wall, expressed Lox2 in M7-M19. The putative cell 261 expressed Lox2 in M7-M12, where Lox1 is also expressed. FMRFamide staining in putative segmental homologs of cell 261 was not detected in other segmental ganglia. Our results suggest a role for Lox2 in very early embryonic development (before the formation of the CNS), and in the differentiation of segmentally repeated and region-specific FLI neurons.

Hox gene expression during postlarval development of the polychaete Alitta virens

BACKGROUND

Hox genes are the family of transcription factors that play a key role in the patterning of the anterior-posterior axis of all bilaterian animals. These genes display clustered organization and colinear expression. Expression boundaries of individual Hox genes usually correspond with morphological boundaries of the body. Previously, we studied Hox gene expression during larval development of the polychaete Alitta virens (formerly Nereis virens) and discovered that Hox genes are expressed in nereid larva according to the spatial colinearity principle. Adult Alitta virens consist of multiple morphologically similar segments, which are formed sequentially in the growth zone. Since the worm grows for most of its life, postlarval segments constantly change their position along the anterior-posterior axis.

RESULTS

We studied the expression dynamics of the Hox cluster during postlarval development of the nereid Alitta virens and found that 8 out of 11 Hox genes are transcribed as wide gene-specific gradients in the ventral nerve cord, ectoderm, and mesoderm. The expression domains constantly shift in accordance with the changing proportions of the growing worm, so expression domains of most Hox genes do not have stable anterior or/and posterior boundaries.In the course of our study, we revealed long antisense RNA (asRNA) for some Hox genes. Expression patterns of two of these genes were analyzed using whole-mount in-situ hybridization. This is the first discovery of antisense RNA for Hox genes in Lophotrochozoa.

CONCLUSION

Hox gene expression in juvenile A. virens differs significantly from Hox gene expression patterns both in A. virens larva and in other Bilateria.We suppose that the postlarval function of the Hox genes in this polychaete is to establish and maintain positional coordinates in a constantly growing body, as opposed to creating morphological difference between segments.

Variation and constraint in Hox gene evolution

Despite enormous body plan variation, genes regulating embryonic development are highly conserved. Here, we probe the mechanisms that predispose ancient regulatory genes to reutilization and diversification rather than evolutionary loss. The Hox gene fushi tarazu (ftz) arose as a homeotic gene but functions as a pair-rule segmentation gene in Drosophila. ftz shows extensive variation in expression and protein coding regions but has managed to elude loss from arthropod genomes. We asked what properties prevent this loss by testing the importance of different protein motifs and partners in the developing CNS, where ftz expression is conserved. Drosophila Ftz proteins with mutated protein motifs were expressed under the control of a neurogenic-specific ftz cis-regulatory element (CRE) in a ftz mutant background rescued for segmentation defects. Ftz CNS function did not require the variable motifs that mediate differential cofactor interactions involved in homeosis or segmentation, which vary in arthropods. Rather, CNS function did require the shared DNA-binding homeodomain, which plays less of a role in Ftz segmentation activity. The Antennapedia homeodomain substituted for Ftz homeodomain function in the Drosophila CNS, but full-length Antennapedia did not rescue CNS defects. These results suggest that a core CNS function retains ftz in arthropod genomes. Acquisition of a neurogenic CRE led to ftz expression in unique CNS cells, differentiating its role from neighboring Hox genes, rendering it nonredundant. The inherent flexibility of modular CREs and protein domains allows for stepwise acquisition of new functions, explaining broad retention of regulatory genes during animal evolution.

Segmental and regional differences in neuronal expression of the leech Hox genes Lox1 and Lox2 during embryogenesis

Using double immunofluorescence experiments, we described the expression of the leech Hox genes, Lox1 and Lox2 by central neurons that stained for either serotonin or the leech-specific neuronal marker, Laz1-1. The goal is to determine whether the segmental boundaries of Lox1 and Lox2 expression in identified neurons coincide with segmental and regional differences in the differentiation of these cells. A number of neurons described here have been previously identified. The anteromedial serotonergic neurons are restricted to rostral ganglion 1 (R1) to midbody ganglion 3 (M3), but only express Lox1 in M2 and M3. The posteromedial serotonergic neurons which are situated in all segments as bilateral pairs early in development, but later become unpaired starting at M3, expressed Lox1 only in M2 and M3, and Lox2 in M8 to M21, in all paired and unpaired stages. The Retzius neurons, which stain for serotonin, express Lox2 in M7 to M21 where they exhibit different morphologies from their segmental homologs of the sex ganglia in M5 and M6. The Laz1-1 immunoreactive (Laz1-1+) heart accessory-like neurons express Lox1 in M4 and Lox2 in M7 to M17, but not in their segmental homologs of the heart accessory (HA) neurons located exclusively in M5 and M6. Also, Laz1-1+ neurons, which we named Lz3 expressed Lox1 in M4 to M8 where they are unpaired, but express Lox2 in M9 to M16 where they are bilaterally paired. Other Laz1-1 cells show more restricted and isolated Lox1 and Lox2 expression patterns. These results suggest a role of Lox1 and/or Lox2 in defining the anteroposterior boundaries of segmentally iterated neurons.

Activation of Hox genes during caudal regeneration of the polychaete annelid Platynereis dumerilii

The capability of regenerating posterior segments and pygidial structures is ancestral for annelids and has been lost only a few times within this phylum. As one of the three major segmented taxa, annelids enable us to monitor reconstruction of lost tissues and organs. During regeneration, regional identities have to be imprinted onto the newly formed segments. In this study, we show spatial and temporal localization of expression of nine Hox genes during caudal regeneration of the polychaete annelid Platynereis dumerilii. Hox genes are homeodomain genes encoding transcriptional regulators of axial patterning in bilaterian animals during development. We demonstrate that five Platynereis Hox genes belonging to paralog groups (PG) 1, 4, 5, 6, and 9-14 are expressed in domains of the regenerating nervous system consistent with providing positional information along the anteroposterior axis of the regenerate. We report that expression in regenerating neuromeres is limited to varying subsets of perikarya, called gangliosomes. Four of nine genes analyzed do not appear to be involved in axial patterning. Two genes, Pdu-Hox2 and Pdu-Hox3, are predominantly expressed in the growth zone region. For some Hox genes expression in newly formed coelomic epithelia can be observed. Platynereis Hox genes do not exhibit temporal or spatial colinearity. Although there are some similarities to previously reported expression patterns during larval and postlarval development in Nereididae (Kulakova et al. 2007), expression patterns observed during caudal regeneration also show unique patterns.

The segmental pattern of otx, gbx, and Hox genes in the annelid Platynereis dumerilii

SUMMARY Annelids and arthropods, despite their distinct classification as Lophotrochozoa and Ecdysozoa, present a morphologically similar, segmented body plan. To elucidate the evolution of segmentation and, ultimately, to align segments across remote phyla, we undertook a refined expression analysis to precisely register the expression of conserved regionalization genes with morphological boundaries and segmental units in the marine annelid Platynereis dumerilii. We find that Pdu-otx defines a brain region anterior to the first discernable segmental entity that is delineated by a stripe of engrailed-expressing cells. The first segment is a "cryptic" segment that lacks chaetae and parapodia. This and the subsequent three chaetigerous larval segments harbor the anterior expression boundary of gbx, hox1, hox4, and lox5 genes, respectively. This molecular segmental topography matches the segmental pattern of otx, gbx, and Hox gene expression in arthropods. Our data thus support the view that an ancestral ground pattern of segmental identities existed in the trunk of the last common protostome ancestor that was lost or modified in protostomes lacking overt segmentation.

Expression of Hox genes during the larval development of the snail, Gibbula varia (L.)-further evidence of non-colinearity in molluscs

Hox transcription factors, a subfamily of homeobox genes, are expressed in distinct, often overlapping domains along the anterior-posterior body axis of animal embryos. Here, we report the sequence and expression pattern of Hox2, Hox3, Hox4, Hox5, Lox5, Hox7, Lox4, and Lox2 in different larval stages during the encapsulated development of the marine gastropod Gibbula varia. Our results show that all Gva-Hox genes are expressed in ectoderm-derived cells. Hox2, Hox3, Hox4, Hox5, and Hox7 are expressed in overlapping patterns in the pedal, pleural, oesophageal, and visceral ganglia, supporting the ancestral role of Hox genes in the neurogenesis processes in bilaterians. Gva-Hox1, Gva-Post2, and Gva-Post1 genes are involved in shell morphogenesis and have apparently lost their role in neurogangliogenesis. Lox5, Lox4, and Lox2 are expressed in different cells of the apical organ during the earlier larval stage (trochophore) and the cerebral ganglia during later larval stages (veliger). These results support the hypothesis that apical organ neurosensory cells contribute to the formation of cerebral ganglia commissures during metamorphosis. Gva-Hox7 and Gva-Lox4 are additionally expressed in the prototroch of the trochophore and in the velar area of the veliger larvae. This contradicts with the expression of these genes in the annelids, where most of Hox genes are expressed in the posttrochal area and are involved in segmental determination. Therefore, expression of Hox genes may serve as an example of co-option and plasticity of gene function during evolution of gastropods.

Hox genes and brain development in Drosophila

Hox genes are prominently expressed in the developing brain and ventral ganglia of Drosophila. In the embryonic brain, the Hox genes labial and Deformed are essential for the establishment of regionalized neuronal identity; in their absence cells are generated in the brain but fail to acquire appropriate neuronal features. Genetic analyses reveal that Hox proteins are largely equivalent in their action in embryonic brain development and that their expression is under the control of cross-regulatory interactions among Hox genes that are similar to those found in embryogenesis of trunk segments. Hox genes have a different role in postembryonic brain development. During the larval phase of CNS development, reactivation of specific Hox genes terminates neural proliferation by induction of apoptotic cell death in neural stem cell-like progenitors called neuroblasts. This reactivation process is tightly controlled by epigenetic mechanisms requiring the Polycomb group of genes. Many features of Hox gene action in Drosophila brain development are evolutionarily conserved and are manifest in brain development of vertebrates.

Coordinated spatial and temporal expression of Hox genes during embryogenesis in the acoel Convolutriloba longifissura

Background

Hox genes are critical for patterning the bilaterian anterior-posterior axis. The evolution of their clustered genomic arrangement and ancestral function has been debated since their discovery. As acoels appear to represent the sister group to the remaining Bilateria (Nephrozoa), investigating Hox gene expression will provide an insight into the ancestral features of the Hox genes in metazoan evolution.

Results

We describe the expression of anterior, central and posterior class Hox genes and the ParaHox ortholog Cdx in the acoel Convolutriloba longifissura. Expression of all three Hox genes begins contemporaneously after gastrulation and then resolves into staggered domains along the anterior-posterior axis, suggesting that the spatial coordination of Hox gene expression was present in the bilaterian ancestor. After early surface ectodermal expression, the anterior and central class genes are expressed in small domains of putative neural precursor cells co-expressing ClSoxB1, suggesting an evolutionary early function of Hox genes in patterning parts of the nervous system. In contrast, the expression of the posterior Hox gene is found in all three germ layers in a much broader posterior region of the embryo.

Conclusion

Our results suggest that the ancestral set of Hox genes was involved in the anterior-posterior patterning of the nervous system of the last common bilaterian ancestor and were later co-opted for patterning in diverse tissues in the bilaterian radiation. The lack of temporal colinearity of Hox expression in acoels may be due to a loss of genomic clustering in this clade or, alternatively, temporal colinearity may have arisen in conjunction with the expansion of the Hox cluster in the Nephrozoa.

Genomic organization and expression demonstrate spatial and temporal Hox gene colinearity in the lophotrochozoan Capitella sp. I

Hox genes define regional identities along the anterior–posterior axis in many animals. In a number of species, Hox genes are clustered in the genome, and the relative order of genes corresponds with position of expression in the body. Previous Hox gene studies in lophotrochozoans have reported expression for only a subset of the Hox gene complement and/or lack detailed genomic organization information, limiting interpretations of spatial and temporal colinearity in this diverse animal clade. We studied expression and genomic organization of the single Hox gene complement in the segmented polychaete annelid Capitella sp. I. Total genome searches identified 11 Hox genes in Capitella, representing 11 distinct paralog groups thought to represent the ancestral lophotrochozoan complement. At least 8 of the 11 Capitella Hox genes are genomically linked in a single cluster, have the same transcriptional orientation, and lack interspersed non-Hox genes. Studying their expression by situ hybridization, we find that the 11 Capitella Hox genes generally exhibit spatial and temporal colinearity. With the exception of CapI-Post1, Capitella Hox genes are all expressed in broad ectodermal domains during larval development, consistent with providing positional information along the anterior–posterior axis. The anterior genes CapI-lab, CapI-pb, and CapI-Hox3 initiate expression prior to the appearance of segments, while more posterior genes appear at or soon after segments appear. Many of the Capitella Hox genes have either an anterior or posterior expression boundary coinciding with the thoracic–abdomen transition, a major body tagma boundary. Following metamorphosis, several expression patterns change, including appearance of distinct posterior boundaries and restriction to the central nervous system. Capitella Hox genes have maintained a clustered organization, are expressed in the canonical anterior–posterior order found in other metazoans, and exhibit spatial and temporal colinearity, reflecting Hox gene characteristics that likely existed in the protostome–deuterostome ancestor.

Anteroposterior regionalization of the brain: genetic and comparative aspects

Developmental genetic analyses of embryonic CNS development in Drosophila have uncovered the role of key, high-order developmental control genes in anteroposterior regionalization of the brain. The gene families that have been characterized include the otd/Otx and ems/Emx genes which are involved in specification of the anterior brain, the Hox genes which are involved in the differentiation of the posterior brain and the Pax genes which are involved in the development of the anterior/posterior brain boundary zone. Taken together with work on the genetic control of mammalian CNS development, these findings indicate that all three gene sets have evolutionarily conserved roles in brain development, revealing a surprising evolutionary conservation in the molecular mechanisms of brain regionalization.

Muscle formation during embryogenesis of the polychaete Ophryotrocha diadema (Dorvilleidae) - new insights into annelid muscle patterns

Background

The standard textbook information that annelid musculature consists of oligochaete-like outer circular and inner longitudinal muscle-layers has recently been called into question by observations of a variety of complex muscle systems in numerous polychaete taxa. To clarify the ancestral muscle arrangement in this taxon, we compared myogenetic patterns during embryogenesis of Ophryotrocha diadema with available data on oligochaete and polychaete myogenesis. This work addresses the conflicting views on the ground pattern of annelids, and adds to our knowledge of the evolution of lophotrochozoan taxa.

Results

Somatic musculature in Ophryotrocha diadema can be classified into the trunk, prostomial/peristomial, and parapodial muscle complexes. The trunk muscles comprise strong bilateral pairs of distinct dorsal and ventral longitudinal strands. The latter are the first to differentiate during myogenesis. They originate within the peristomium and grow posteriorly through the continuous addition of myocytes. Later, the longitudinal muscles also expand anteriorly and form a complex arrangement of prostomial muscles. Four embryonic parapodia differentiate in an anterior-to-posterior progression, significantly contributing to the somatic musculature. Several diagonal and transverse muscles are present dorsally. Some of the latter are situated external to the longitudinal muscles, which implies they are homologous to the circular muscles of oligochaetes. These circular fibers are only weakly developed, and do not appear to form complete muscle circles.

Conclusion

Comparison of embryonic muscle patterns showed distinct similarities between myogenetic processes in Ophryotrocha diadema and those of oligochaete species, which allows us to relate the diverse adult muscle arrangements of these annelid taxa to each other. These findings provide significant clues for the interpretation of evolutionary changes in annelid musculature.

Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis

BACKGROUND

Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no "true" Hox genes exist in the phylum Cnidaria.

METHODOLOGY/PRINCIPAL FINDINGS

Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in "dorsoventral" patterning.

CONCLUSIONS/SIGNIFICANCE

A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today.

Missing link in the evolution of Hox clusters

Hox cluster has key roles in regulating the patterning of the antero-posterior axis in a metazoan embryo. It consists of the anterior, central and posterior genes; the central genes have been identified only in bilaterians, but not in cnidarians, and are responsible for archiving morphological complexity in bilaterian development. However, their evolutionary history has not been revealed, that is, there has been a "missing link". Here we show the evolutionary history of Hox clusters of 18 bilaterians and 2 cnidarians by using a new method, "motif-based reconstruction", examining the gain/loss processes of evolutionarily conserved sequences, "motifs", outside the homeodomain. We successfully identified the missing link in the evolution of Hox clusters between the cnidarian-bilaterian ancestor and the bilaterians as the ancestor of the central genes, which we call the proto-central gene. Exploring the correspondent gene with the proto-central gene, we found that one of the acoela Hox genes has the same motif repertory as that of the proto-central gene. This interesting finding suggests that the acoela Hox cluster corresponds with the missing link in the evolution of the Hox cluster between the cnidarian-bilaterian ancestor and the bilaterians. Our findings suggested that motif gains/diversifications led to the explosive diversity of the bilaterian body plan.

Pattern of body-wall muscle differentiation during embryonic development ofEnchytraeus coronatus (Annelida: Oligochaeta; Enchytraeidae)

The plesiomorphic arrangement of body-wall musculature within the annelids is still under discussion. While polychaete groups show a great variety of patterns in their somatic muscles, the musculature of soil-living oligochaetes was thought to represent the characteristic pattern in annelids. Oligochaete body-wall muscles consist of an outer continuous layer of circular and an inner continuous layer of longitudinal muscles, forming a closed tube. Since designs of adult body musculature are influenced by evolutionary changes, additional patterns found during embryogenesis can give further information about possible plesiomorphic features. In oligochaetes, detailed cell-lineage analyses document the origin of the mesoderm and consequently the muscles, but later processes of muscle formation remain unclear. In the present work, body-wall muscle differentiation was monitored during embryogenesis of thesoil-living oligochaete Enchytraeus coronatus (Annelida) by phalloidin staining. Primary circular muscles form in a discrete anterior-to-posterior segmental pattern, whereas emerging longitudinal muscles are restricted to one ventral and one dorsal pair of primary strands, which continuously elongate towards posterior. These primary muscles establish an initial muscle-template. Secondary circular and longitudinal muscles subsequently differentiate in the previous spaces later in development. The prominent ventral primary longitudinal muscle strands on both sides eventually meet at the ventral midline due to neurulation, which moves the ventral nerve cord into a coelomic position, closing the muscle layers into a complete tube. This early embryonic pattern in E. coronatus resembles the adult body-wall muscle arrangements in several polychaete groups as well as muscle differentiation during embryonic development of the polychaete Capitella sp. I.

Hox gene expression in larval development of the polychaetes Nereis virens and Platynereis dumerilii (Annelida, Lophotrochozoa)

The bilaterian animals are divided into three great branches: the Deuterostomia, Ecdysozoa, and Lophotrochozoa. The evolution of developmental mechanisms is less studied in the Lophotrochozoa than in the other two clades. We have studied the expression of Hox genes during larval development of two lophotrochozoans, the polychaete annelids Nereis virens and Platynereis dumerilii. As reported previously, the Hox cluster of N. virens consists of at least 11 genes (de Rosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, Akam M, Carroll SB, Balavoine G, Nature, 399:772-776, 1999; Andreeva TF, Cook C, Korchagina NM, Akam M, Dondua AK, Ontogenez 32:225-233, 2001); we have also cloned nine Hox genes of P. dumerilii. Hox genes are mainly expressed in the descendants of the 2d blastomere, which form the integument of segments, ventral neural ganglia, pre-pygidial growth zone, and the pygidial lobe. Patterns of expression are similar for orthologous genes of both nereids. In Nereis, Hox2, and Hox3 are activated before the blastopore closure, while Hox1 and Hox4 are activated just after this. Hox5 and Post2 are first active during the metatrochophore stage, and Hox7, Lox4, and Lox2 at the late nectochaete stage only. During larval stages, Hox genes are expressed in staggered domains in the developing segments and pygidial lobe. The pattern of expression of Hox cluster genes suggests their involvement in the vectorial regionalization of the larval body along the antero-posterior axis. Hox gene expression in nereids conforms to the canonical patterns postulated for the two other evolutionary branches of the Bilateria, the Ecdysozoa and the Deuterostomia, thus supporting the evolutionary conservatism of the function of Hox genes in development.

Restricted expression of a median Hox gene in the central nervous system of chaetognaths

Hox genes encode a set of evolutionarily conserved transcription factors that regulate anterior-posterior patterning. Here we report the first developmental expression of a Hox gene from Chaetognatha. These metazoans have been shown recently to be part of the protostome group of bilaterians. We describe the analysis of the SceMed4 gene (a Spadella cephaloptera Median Hox gene) including its expression from late stages of egg development to 7 days after hatching. In all of these stages, SceMed4 is expressed in two lateral stripes in a restricted region of the developing ventral ganglion.

Evidence from Hox genes that bryozoans are lophotrochozoans

Bryozoans, or moss animals, are small colonial organisms that possess a suspension-feeding apparatus called a lophophore. Traditionally, this "phylum" has been grouped with brachiopods and phoronids because of the feeding structure. Available molecular and morphological data refute this notion of a monophyletic "Lophophorata." Alternative hypotheses place bryozoans either at the base of the Lophotrochozoa or basal to the Lophotrochozoa/Ecdysozoa split. Surprisingly, the only molecular data bearing on this issue are from the 18S nuclear ribosomal gene. Here we report the results of a Hox gene survey using degenerate polymerase chain reaction primers in a gymnolaemate bryozoan, Bugula turrita. Putative orthologs to both the Post2 and the Lox5 genes were found, suggesting that bryozoans are not a basal protostome group but closely allied to other lophotrochozoan taxa. We also found the first definitive evidence of two Deformed/Hox4 class genes in a nonvertebrate animal.

Expression of anterior Hox genes during larval development of the gastropod Haliotis asinina

We report the spatial expression patterns of five anterior Hox genes during larval development of the gastropod mollusc Haliotis asinina, an unsegmented spiralian lophotrochozoan. Molecular alignments and phylogenetic analysis indicate that these genes are homologues of Drosophila HOM-C genes labial, proboscipedia, zen, Deformed, and Sex combs reduced; the abalone genes are named Has-Hox1, -Hox2, -Hox3, -Hox4, and -Hox5. Has-Hox transcripts are first detected in the free-swimming trochophore larval stage and restricted to the posttrochal ectoderm. Has-Hox2, -Hox3, and -Hox4 are expressed in bilaterally symmetrical and overlapping patterns in presumptive neuroectodermal cells on the ventral side of the trochophore. Has-Hox1 expression is restricted to a ring of cells on the dorsoposterior surface, corresponding to the outer mantle edge where new larval shell is being synthesized. There appears to be little change in the expression domains of these Has-Hox genes in pre- and posttorsional veliger larvae, with expression maintained in ectodermal and neuroectodermal tissues. Has-Hox2, -Hox3, -Hox4, and-Hox5 appear to be expressed in a colinear manner in the ganglia and connectives in the twisted nervous system. This pattern is not evident in older larvae. Has-Hox1 and-Hox4 are expressed in the margin of the mantle in the posttorsional veliger, suggesting that Hox genes play a role in gastropod shell formation.

An urbilaterian origin of the tripartite brain: developmental genetic insights from Drosophila

Studies on expression and function of key developmental control genes suggest that the embryonic vertebrate brain has a tripartite ground plan that consists of a forebrain/midbrain, a hindbrain and an intervening midbrain/hindbrain boundary region, which are characterized by the specific expression of the Otx, Hox and Pax2/5/8 genes, respectively. We show that the embryonic brain of the fruitfly Drosophila melanogaster expresses all three sets of homologous genes in a similar tripartite pattern. Thus, a Pax2/5/8 expression domain is located at the interface of brain-specific otd/Otx2 and unpg/Gbx2 expression domains anterior to Hox expression regions. We identify this territory as the deutocerebral/tritocerebral boundary region in the embryonic Drosophila brain. Mutational inactivation of otd/Otx2 and unpg/Gbx2 result in the loss or misplacement of the brain-specific expression domains of Pax2/5/8 and Hox genes. In addition, otd/Otx2 and unpg/Gbx2 appear to negatively regulate each other at the interface of their brain-specific expression domains. Our studies demonstrate that the deutocerebral/tritocerebral boundary region in the embryonic Drosophila brain displays developmental genetic features similar to those observed for the midbrain/hindbrain boundary region in vertebrate brain development. This suggests that a tripartite organization of the embryonic brain was already established in the last common urbilaterian ancestor of protostomes and deuterostomes.

The abdominal-B-like gene expression during larval development of Nereis virens (polychaeta)

We have studied the posterior Hox gene Nvi-Post1 expression in the early development of the polychaete Nereis virens. This is the first evidence of the posterior group Hox genes expression during the larval development of a Lophotrochozoan. The expression begins in the trochophore hyposphere at the prospective sites of larval parapodia. As the larva develops the expression weakens and finally becomes undetectable in the nectochaete stage and juvenile worm. The Nvi-Post1 expression appears to be important for larval, but not postlarval development.

Segment-specific expression of alkaline phosphatase in the Tubifex embryo requires DNA replication and mRNA synthesis

During embryogenesis of the oligochaete annelid Tubifex, segments VII and VIII specifically express mesodermal alkaline phosphatase (ALP) activity in the ventrolateral region. In this study, using specific inhibitors, we examined whether this segment-specific expression of ALP activity depends on DNA replication and RNA transcription. BrdU-incorporation experiments showed that presumptive ALP-expressing cells undergo the last round of DNA replication at 12-24 hr prior to emergence of ALP activity. When this DNA replication was inhibited by aphidicolin, ALP development was completely abrogated in the ventrolateral mesoderm. Similar inhibition of ALP development was also observed in alpha-amanitin-injected embryos. While injection of alpha-amanitin at 24 hr prior to the emergence of ALP activity exerted inhibitory effects on ALP development, injection at 14 hr was no longer effective. In contrast, ALP activity developed normally in cytochalasin-D-treated embryos in which cytokinesis was prevented from occurring for 36 hs prior to appearance of ALP activity. These results suggest that the segment-specific development of ALP activity in the Tubifex embryo depends on DNA replication and mRNA transcription, both of which occur long before the emergence of ALP activity.

Hox cluster organization in the jawless vertebrate Petromyzon marinus

Large-scale gene amplifications may have facilitated the evolution of morphological innovations that accompanied the origin of vertebrates. This hypothesis predicts that the genomes of extant jawless fish, scions of deeply branching vertebrate lineages, should bear a record of these events. Previous work suggests that nonvertebrate chordates have a single Hox cluster, but that gnathostome vertebrates have four or more Hox clusters. Did the duplication events that produced multiple vertebrate Hox clusters occur before or after the divergence of agnathan and gnathostome lineages? Can investigation of lamprey Hox clusters illuminate the origins of the four gnathostome Hox clusters? To approach these questions, we cloned and sequenced 13 Hox cluster genes from cDNA and genomic libraries in the lamprey, Petromyzon marinus. The results suggest that the lamprey has at least four Hox clusters and support the model that gnathostome Hox clusters arose by a two-round-no-cluster-loss mechanism, with tree topology [(AB)(CD)]. A three-round model, however, is not rigorously excluded by the data and, for this model, the tree topologies [(D(C(AB))] and [(C(D(AB))] are most parsimonious. Gene phylogenies suggest that at least one Hox cluster duplication occurred in the lamprey lineage after it diverged from the gnathostome lineage. The results argue against two or more rounds of duplication before the divergence of agnathan and gnathostome vertebrates. If Hox clusters were duplicated in whole-genome duplication events, then these data suggest that, at most, one whole genome duplication occurred before the evolution of vertebrate developmental innovations.

HOX genes in the sepiolid squid Euprymna scolopes: implications for the evolution of complex body plans

Molluscs display a rich diversity of body plans ranging from the wormlike appearance of aplacophorans to the complex body plan of the cephalopods with highly developed sensory organs, a complex central nervous system, and cognitive abilities unrivaled among the invertebrates. The aim of the current study is to define molecular parameters relevant to the developmental evolution of cephalopods by using the sepiolid squid Euprymna scolopes as a model system. Using PCR-based approaches, we identified one anterior, one paralog group 3, five central, and two posterior group Hox genes. The deduced homeodomain sequences of the E. scolopes Hox cluster genes are most similar to known annelid, brachiopod, and nemertean Hox gene homeodomain sequences. Our results are consistent with the presence of a single Hox gene cluster in cephalopods. Our data also corroborate the proposed existence of a differentiated Hox gene cluster in the last common ancestor of Bilaterians. Furthermore, our phylogenetic analysis and in particular the identification of Post-1 and Post-2 homologs support the Lophotrochozoan clade.

Testing the vulnerability of the phylotypic stage: on modularity and evolutionary conservation

The phylotypic stage is the developmental stage at which vertebrates most resemble each other. In this study we test the plausibility of the hypotheses of Sander [1983, Development and Evolution, Cambridge University Press] and Raff [1994, Early Life on Earth, Columbia University Press; 1996, The Shape of Life, University of Chicago Press] that the phylotypic stage is conserved due to the intense and global interactivity occurring during that stage. First, we test the prediction that the phylotypic stage is much more vulnerable than any other stage. A search of the teratological literature shows that disturbances at this stage lead to a much higher mortality than in other stages, in accordance with the prediction. Second, we test whether that vulnerability is indeed caused by the interactiveness and lack of modularity of the inductions or, alternatively, is caused by some particularly vulnerable process going on at that time. From the pattern of multiple induced anomalies we conclude that it is indeed the interactiveness that is the root cause of the vulnerability. Together these results support the hypotheses of Sander and Raff. We end by presenting an argument on why the absence of modularity in the inductive interactions may also be the root cause of the conservation of the much discussed temporal and spatial colinearity of the Hox genes. J. Exp. Zool. (Mol. Dev. Evol.) 291:195-204, 2001.

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences

Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1,000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.