Endoderm development appears extensively divergent across vertebrates, with the presence or absence of distinct extraembryonic components and the diversity of the cellular organization of the former when present (Takeuchi et al. 2009). In amniotes, which have developed overt extraembryonic tissues, the fact that endoderm specification takes place into two phases, respectively taking place at early blastula and gastrula stages and primarily contributing to extraembryonic membranes and definitive gut endoderm, has been known for a long time. Developmental genetics have unambiguously shown that the latter phase, but not the former one, is dependent on Nodal signaling (Hoodless et al. 2001; Yamamoto et al. 2001; Robertson et al. 2003; Vincent et al. 2003). Two successive endoderm specification phases, respectively dependent and independent of Nodal signaling, have more unexpectedly also been found in teleosts (Dickmeis et al. 2001; Kikuchi et al. 2001; Sakaguchi et al. 2001; Hong et al. 2010). In the zebrafish, the extraembryonic YSL is of endodermal identity, as assessed by expression of Sox32, which codes for a zinc finger transcription factor closely related to the general endoderm differentiation marker Sox17, and its specification precedes, and actually controls, embryonic gut formation (Sakaguchi et al. 2001; Aoki et al. 2002). Such a biphasic mode of endoderm specification may even also exist in amphibians, despite the absence of distinct extraembryonic tissues in this case (Luxardi et al. 2010; Skirkanich et al. 2011). In the dogfish, analysis of endoderm markers coupled to pharmacological treatments directed vs. Nodal/activin signaling indicate that, similarly, the deep mesenchyme and syncytial nuclei are of endodermal identity, already specified at early blastula stages, and there is no evidence for an involvement of Nodal in its formation, or maintenance. In contrast, the specification of the anterior mesendoderm only takes place at late blastula stages, in a Nodal-dependent fashion (Godard et al. manuscript in preparation). These data clearly bring support to the ancestrality of a biphasic mode of endoderm development in jawed vertebrates. While no evidence for such a two-step mode of endoderm specification has been reported either in amphioxus or tunicates, the presence of two distinct endoderm components, respectively corresponding to the extraembryonic nutritive yolk mass and an embryonic component contributing to the gut proper, has also been shown in the lamprey (Takeuchi et al. 2009). The relationship between the two phases described in the dogfish and the lamprey remains to be confirmed, but this raises the possibility that a biphasic mode of endoderm specification may be a vertebrate innovation. However, most apparent in the dogfish is that these two specification events do not concern compartmentalized, respectively extraembryonic and embryonic, cell populations. Nodal/activin signaling actually appears required for the formation of the thickened posterior margin, which at the earliest stage following its appearance also contributes to the extraembryonic deep mesenchyme (Godard et al. manuscript in preparation). Along the same line, Nodal/activin signaling controls the establishment of a regional pattern spanning a broad posterior (organizer side) sector of the deep mesenchyme and adjacent involuting mesendoderm (Fig. 3; (Coolen et al. 2007; Godard et al. manuscript in preparation). This molecular pattern is established following an accurate temporal regulation (Lim1, then Hex, followed by Brachyury and Chordin), which later translates along the antero-posterior axis possibly through a mechanism related to those demonstrated at trunk levels in amphibians (Wacker et al. 2004; Durston et al. 2010). But these expression territories show no evidence for a restriction to either extraembryonic or embryonic territories, the anterior-most ones (Lim1 and Hex) actually spanning the transition zone between the deep mesenchyme and anterior involuting mesendoderm, while the posterior-most ones (Brachyury and Chordin) lie posterior to it (Fig. 3; Coolen et al. 2007; Godard et al. manuscript in preparation). This molecular continuity suggests that in the dogfish, cell fate choices between extraembryonic vs. embryonic endoderm result from cell allocation to either territory related to differential cell behaviors, rather than from distinct specification events. Intriguingly, the earliest phases of Lim1 and Hex expressions in the dogfish are strikingly reminiscent by their relative timing and nested spatial organization to those of their orthologs in the mouse embryonic VE, which also depend on Nodal signaling (Fig. 4; Mesnard et al. 2006). In both species, they are also followed by Brachyury and Chordin expressions in the forming anterior mesendoderm (Bachiller et al. 2000). Although the chronology and relative organization may be less accurately defined, Lim1 and Hex are also expressed dorsally in the zebrafish YSL and the xenopus deep endoderm, while Brachyury and Chordin are restricted to adjacent nascent mesendoderm (Ho et al. 1999; Smithers & Jones, 2002). Taken together, these data support a strong conservation of endoderm patterning mechanisms across jawed vertebrates, independently of the presence or absence of extraembryonic components. We suggest that the molecular similarities between the mouse embryonic visceral endoderm and zebrafish dorsal YSL result from their common ontogenetic origin from a single ancestral territory of anterior mesendoderm regional identity, containing intermingling cells derived from the first and second phase of endoderm specification and allocated to extraembryonic or embryonic tissues as the result of differences in cell behaviors, such as motility or adhesiveness, exactly as is the case in the dogfish. In this view, the epithelial and syncytial organizations of the mouse VE and zebrafish YSL may be related to taxa-specific specializations obscuring the ancestral continuity between extraembryonic and embryonic components, which is most apparent in the dogfish. Analyses of the origin of the YSL of teleosts by comparative analyses across actinopterygians actually support this view (Cooper & Virta, 2007). In support of this model is also the fact that in the mouse, VE, long thought to exclusively contribute to extraembryonic annexes, actually also contributes to the gut (Kwon et al. 2008). This shows that, as in the dogfish, no strict segregation between embryonic and extraembryonic endoderm is established at the onset of gastrulation, which may be a remnant of the ancestral continuity between these tissues proposed here. Accurate analyses of cell behaviors from blastula to early gastrula stages will be important to assess the generality of this conclusion at the vertebrate scale.