Protochordate Genomics    Tunicates    Amphioxus    Early Behavior       
Protochordates  (
Tunicates & Amphioxus)

Although the amphioxus and the tunicates are quite different, at one time it was believed that the amphioxus was a descendant of the tunicate larva.  Recent genome analysis has called that view into question, but there are still many articles which consider both genera together.   

Protochordate (invertebrate) -- Britannica Online Encyclopedia (Goog)
any member of either of two invertebrate subphyla of the phylum Chordata: the Tunicata (sea squirts, salps, etc.) and the Cephalochordata (amphioxus). Like the remaining subphylum of the chordates, the Vertebrata, the protochordates have a hollow dorsal nerve cord, gill slits, and a stiff supporting rod, the notochord, the forerunner of the backbone. The protochordates differ chiefly from the vertebrates in not having a backbone. Recent protochordates are thought to have evolved from the same ancestral stock as that which gave rise to the vertebrates."   

New perspectives on the evolution of protochordate sensory and locomotory systems, and the origin of brains and heads.
Cladistic analyses generally place tunicates close to the base of the chordate lineage, consistent with the assumption that the tunicate tail is primitively simple, not secondarily reduced from a segmented trunk.
    Cephalochordates (i.e. amphioxus) are segmented and resemble vertebrates in having two distinct locomotory modes, slow for distance swimming and fast for escape, that depend on separate sets of motor neurons and muscle cells. The sense organs of both amphioxus and tunicate larvae serve essentially as navigational aids and, despite some uncertainty as to homologies, current molecular and ultrastructural data imply a close relationship between them. There are far fewer signs of modification and reduction in the amphioxus central nervous system (CNS), however, so it is arguably the closer to the ancestral condition.  
    Similarities between amphioxus and tunicate sense organs are then most easily explained if distance swimming evolved before and escape behaviour after the two lineages diverged, leaving tunicates to adopt more passive means of avoiding predation. Neither group has the kind of sense organs or sensory integration centres an organism would need to monitor predators, yet mobile predators with eyes were probably important in the early Palaeozoic. For a predator, improvements in vision and locomotion are mutually reinforcing. Both features probably evolved rapidly and together, in an 'arms race' of eyes, brains and segments that left protochordates behind, and ultimately produced the vertebrate head."  
    See:  Amphioxus Fast-Slow Twitch 
    Full length PDF available online for free. 

Urochordata (Ascidians - Tunicates) 

Ciona intestinalis (Wiki)   

Vase tunicate Cionaintestinalis.jpg

Biology of Neglected Groups: Protochordata  (NRC) 
16 papers.  I expect that none of them are still available online.  The link, above, is no longer active.    
Ten relate directly to the protocordates, but five are focused specifically on the
Tunicates , and I've moved them to that page.  The remaining five plus one are below. 

2005    4. 
Ecology and natural history of the protochordates  
The last comprehensive reviews of ecology and natural history of ascidians were included in the excellent 1971 publication by Millar on the biology of ascidians and the 1991 treatise on New Caledonia ascidians by Monniot, Monniot, and Laboute. Several hundred papers have been published since that time, greatly expanding our knowledge of environmental tolerances and responses to increasing levels of anthropogenically derived toxins in marine waters, energetics and feeding strategies, predator–prey relationships, competition both intra- and inter-specific that include many studies of self–nonself recognition in colonial species, modes and environmental regulation of reproduction and development, symbionts, natural-product chemistry as antifouling and antipredator defenses, and dispersal mechanisms.  
    The relatively new field of molecular genetics is revealing the presence of cryptic species and is helping to determine the origin of anthropogenically transported individuals, an important and growing problem that affects natural ecological relationships in marine communities worldwide.  
    We are learning more about the difficult-to-study abyssal and Antarctic species. There have been great advances in our understanding of the importance in open-ocean food webs of the planktonic Appendicularia and Thaliacea. Also included in this review is a brief discussion of recent work on the Cephalochordata and Hemichordata."  
    Cited by's: 
View all 66 citing articles   

2005    6. 
Endocrinology of protochordates    
    See:  Protochordate Hormones 

2005    8.     
Environmental factors affecting reproduction and development in ascidians and other protochordates   
    "Protochordate reproduction and development are influenced by many kinds of environmental factors. For example, spawning, sexual and asexual reproduction, larval behaviour, and life-cycle transitions (metamorphosis) are key processes known to be affected by environmental factors. This review must be restricted primarily to only one group of protochordates, the ascidians or "sea squirts", because information on the reproductive ecology of hemichordates and cephalochordates is limited to only a few studies. Topics discussed in the present review include (i) environmental factors that regulate larval settlement, (ii) how pelagic embryos avoid damage to DNA caused by UV radiation, (iii) the effect of water temperature and food availability on sexual reproduction in colonial ascidians, (iv) environmental regulation of asexual budding, (v) environmental regulation of metamorphosis, and (vi) the possible role of the environment in the evolution of direct-developing ascidians. A novel role for HSP90 and nitric oxide signaling in the integration of environmental factors with cell signaling pathways in ascidians is discussed near the end of this review. Throughout this review, the multiple roles of environmental stress on ascidian reproduction and development are emphasized."      
    Cited by's:
View all 21 citing articles

2005    9.     
Historical introduction, overview, and reproductive biology of the protochordates  
This issue of the Canadian Journal of Zoology exhaustively reviews most major aspects of protochordate biology by specialists in their fields. Protochordates are members of two deuterostome phyla that are exclusively marine. The Hemichordata, with solitary enteropneusts and colonial pterobranchs, share a ciliated larva with echinoderms and appear to be closely related, but they also have many chordate-like features. The invertebrate chordates are composed of the exclusively solitary cephalochordates and the tunicates with both solitary and colonial forms. The cephalochordates are all free-swimming, but the tunicates include both sessile and free-swimming forms. Here I explore the history of research on protochordates, show how views on their relationships have changed with time, and review some of their reproductive and structural traits not included in other contributions to this special issue."  
    Cited by's: 
View all 12 citing articles   

2005    10.    
Protochordate body plan and the evolutionary role of larvae: old controversies resolved?   
Motile larvae figure prominently in a number of past scenarios for chordate and vertebrate origins, notably in the writings of Garstang, Berrill, and Romer. All three focus on the motile larva of a primitively sessile tunicate ancestor as a vertebrate progenitor; Garstang went further in deriving chordates themselves by neoteny from a yet more ancient larva of the dipleurula type.  
    Yet the molecular evidence currently available shows convincingly that the part of the tunicate larva that persists to the adult expresses only a subset of the genes required to specify a complete bilaterian body axis, and essentially the same appears to be true of dipleurula larvae. Specifically, both are essentially heads without trunks. Hence, both are highly derived and as such are probably poor models for any real ancestor.  
    mA more convincing case can be made for a sequence of ancestral forms that throughout their evolution were active, motile organisms expressing a full complement of axial patterning genes. This implies a basal, ancestral form resembling modern enteropneusts, although a pelagic organism at a hemichordate level of complexity is also possible.  
    A reassessment is thus required of the role played by adult and larval tunicates, and of larvae more generally, in chordate evolution. Tunicates need to be interpreted with caution, since the extreme degree of modification in the adult may have been accompanied by reductions to the larva. Dipleurula larvae may retain some ancestral features (e.g., of apical, oral, and anal organization), but are otherwise probably too specialized to be central players in chordate evolution. Garstang nevertheless remains a key figure in the history of evolutionary thought for his innovative ideas on the relation between ontogeny and phylogeny, and the way in which major innovations in morphology and body plan arise."  
    Cited by's: 
View all 29 citing articles   


2005    11.    
Molecular phylogeny of the protochordates: chordate evolution  
The deuterostomes are a monophyletic group of multicellular animals that include the Chordata, a phylum that exhibits a unique body plan within the metazoans.  
    Deuterostomes classically contained three phyla, Echinodermata, Hemichordata, and Chordata.  
    Protochordata describes two invertebrate chordate subphyla, the Tunicata (Urochordata) and the Cephalochordata. Tunicate species are key to understanding chordate origins, as they have tadpole larvae with a chordate body plan. However, molecular phylogenies show only weak support for the Tunicata as the sister-group to the rest of the chordates, suggesting that they are highly divergent from the Cephalochordata and Vertebrata.  
    We believe that members of the Tunicata exhibit a unique adult body plan and should be considered a separate phylum rather than a subphylum of Chordata.  
     The molecular phylogeny of the deuterostomes is reviewed and discussed in the context of likely morphological evolutionary scenarios and the possibility is raised that the ancestor of the Tunicata was colonial. In this scenario, the colonial tadpole larva would more resemble an ancestral chordate than the solitary tadpole larva.  
    In contrast, the true chordates (vertebrates and cephalochordates) would have evolved from filter-feeding benthic worms with cartilaginous gill slits, similar to extant enteropneust hemichordates."    
    Cited by's: 
View all 60 citing articles   

Head organization and the head/trunk relationship in protochordates: problems and prospects 
The fossil record has been an invaluable aid for reconstructing the major events of vertebrate evolution.  
    There is no comparable record for protochordates, however, which severely limits our knowledge of their ancestral morphology, habits, and mode of life. The alternative is inference based on an interpretation of living protochordates but this is fraught with problems, not least being our own biases of what we think an ancestral chordate ought to look like.
    Relevant to the present symposium is the problem of head/trunk relationships and whether or not the myotomes of the trunk originally extended into the head in vertebrates. I will review what is currently known of patterns of innervation in tunicates and amphioxus in relation to Romer's somaticovisceral concept of the vertebrate body to show how little progress has been made in resolving this problem.  
    There are, in contrast, surprisingly good prospects for solving some other puzzles concerning chordate origins. Dorsoventral inversion provides a good example. A consensus is now emerging, based largely on molecular data from hemichordates that casts new light on the asymmetry of the head in amphioxus. Specifically, the morphogenetic growth process that reestablishes symmetry in late-stage larvae can now be seen, at least in part, as a recapitulation of past evolutionary events, and this has important implications for the origin and basic organization of the brain."  
    Full length HTML available online for free:   
  I also got PDF through library.

Cephalochordates  (Amphioxus)
    See:   Amphioxus