The evolutionary origins and significance of vertebrate left-right organisation

In the last few years, an understanding has emerged of the developmental mechanism for the consistent internal left-right structure, termed situs, that characterises vertebrate anatomy. This involves largely vertebrate-conserved (i.e. 'phylotypic') gene expression cascades that encode 'leftness' and 'rightness' in appropriate tissues either side of the embryo's midline soon after gastrulation. Recent evidence indicates that the initial, directional symmetry breaking that initiates these cascades utilises mechanisms that are conserved or at least closely related in different vertebrate types. I describe a scenario whereby the capacity for directional modification of an otherwise bilateral body plan can be viewed as an adaptive innovation rather closely connected with vertebrate origins, enabling optimal 'design' for very active lifestyles. But an alternative scenario, while retaining the view that situs and indeed other vertebrate functional lateralisations are deeply adaptive, proposes that they originated in the co-optation of left-right developmental information inherited from a very early stage in metazoan diversification. It is proposed that a remote chordate ancestor lost its original or 'ur-bilaterian' symmetry to pass through an altogether non-symmetrical stage, and that the vertebrate dorsoventral midline plane is not descended from that original one. I review the considerable evidence in favour of this scenario, and discuss its wider implications for directional asymmetries across the Metazoa.     

The evolution of metamorphosis in amphibians

A survey is provided of the external transformations that coincide with metamorphosis or a water-to-land transition, and of transformations during water-to-land transition in the retinal projection, the brain stem, the lateral-line system, and the inner ear of amphibians. Among the three orders of amphibians, the frogs are characterized by more pronounced transformations during the water-to-land transition than are the other two orders. Some of the progressive and regressive changes in the sensory and nervous system are presented and a scenario is suggested for the evolution of these transformations among amphibians. Suggestions that metamorphosis in frogs can recapitulate the water-to-land transition of ancestral amniotic vertebrates are refuted.     

The evolution of metamorphosis in temnospondyls

Temnospondyls, possible relatives of extant amphibians and crudely similar to recent salamanders, are known from larval, neotenic and metamorphosed stages. Here, ontogenetic data of various temnospondyl taxa are analysed in order to recognize metamorphosis. Here, metamorphosis is strictly defined as a shift from an aquatic to a terrestrial existence. Following a check-list of criteria, the most likely metamorphosis-induced changes are proved in three temnospondyl lineages: eryopids, zatrachydids and dissorophoids. In a few other, unrelated taxa, terrestrial adults are known but no larval or metamorphosing forms. The distribution of metamorphosis among the Temnospondyli does not strictly correlate with phylogeny, which highlights the widespread occurrence of neoteny. In each group, characteristic patterns of metamorphosis are described and compared. Among temnospondyls, dissorophoids had the most intensive type of metamorphosis, characterized by a condensed ontogeny and a relatively small body size. The result was a distinct transformed morphotype with far-reaching terrestrial adaptations.     

The evolution of vertebrate flight

Flight–defined as the ability to produce useful aerodynamic forces by flapping the wings–is one of the most striking adaptations in vertebrates. Its origin has been surrounded by considerable controversy, due in part to terminological inconsistencies, in part to phylogenetic uncertainty over the sister groups and relationships of birds, bats and pterosaurs, and in part to disagreement over the interpretation of the available fossil evidence and over the relative importance of morphological, mechanical and ecological specializations. Study of the correlation between functional morphology and mechanics in contemporary birds and bats, and in particular of the aerodynamics of flapping wings, clarifies the mechanical changes needed in the course of the evolution of flight. This strongly favours a gliding origin of tetrapod flight, and on mechanical and ecological grounds the alternative cursorial and fluttering hypotheses (neither of which is at present well-defined) may be discounted. The argument is particularly strong in bats, but weaker in birds owing to apparent inconsistencies with the fossil evidence. However, study of the fossils of the Jurassic theropod dinosaur Archaeopteryx , the sister-group of the stem-group proto-birds, supports this view. Its morphology indicates adaptation for flapping flight at the moderately high speeds which would be associated with gliding, but not for the slow speeds which would be required for incipient flight in a running cursor, where the wingbeat is aerodynamically and kinematically considerably more complex. Slow flight in birds and bats is a more derived condition, and vertebrate flapping flight apparently evolved through a gliding stage.     

The compositional evolution of vertebrate genomes

The compositional evolution of vertebrate genomes is characterized: (i) by one predominant conservative mode, in which nucleotide changes occur, but the base composition of DNA sequences in general, and of coding sequences in particular, does not change; and (ii) by three different shifting or transitional modes, in which nucleotide changes are accompanied by changes in the base composition of sequences. Investigations on these evolutionary modes have shed new light on a central problem in molecular evolution, namely the role played by natural selection in modulating the mutational input.This review will present first the intragenomic shifts, the 'major shifts' and the 'minor shift', and then the 'whole-genome', or 'horizontal', shift. In each case, the shifts were preceded and followed by a conservative mode of evolution. This review expands on a previous one [Bernardi, Gene 241 (2000) 3-17], and summarizes the evidence that the changes of the compositional patterns of the genome and their maintenance are controlled by Darwinian natural selection.     

The evolution of early vertebrate photoreceptors

Meeting the challenge of sampling an ancient aquatic landscape by the early vertebrates was crucial to their survival and would establish a retinal bauplan to be used by all subsequent vertebrate descendents. Image-forming eyes were under tremendous selection pressure and the ability to identify suitable prey and detect potential predators was thought to be one of the major drivers of speciation in the Early Cambrian. Based on the fossil record, we know that hagfishes, lampreys, holocephalans, elasmobranchs and lungfishes occupy critical stages in vertebrate evolution, having remained relatively unchanged over hundreds of millions of years. Now using extant representatives of these ‘living fossils’, we are able to piece together the evolution of vertebrate photoreception. While photoreception in hagfishes appears to be based on light detection and controlling circadian rhythms, rather than image formation, the photoreceptors of lampreys fall into five distinct classes and represent a critical stage in the dichotomy of rods and cones. At least four types of retinal cones sample the visual environment in lampreys mediating photopic (and potentially colour) vision, a sampling strategy retained by lungfishes, some modern teleosts, reptiles and birds. Trichromacy is retained in cartilaginous fishes (at least in batoids and holocephalans), where it is predicted that true scotopic (dim light) vision evolved in the common ancestor of all living gnathostomes. The capacity to discriminate colour and balance the tradeoff between resolution and sensitivity in the early vertebrates was an important driver of eye evolution, where many of the ocular features evolved were retained as vertebrates progressed on to land.     

The origins and evolution of ubiquitination sites

Protein ubiquitination is central to the regulation of various pathways in eukaryotes. The process of ubiquitination and its cellular outcome were investigated in hundreds of proteins to date. Despite this, the evolution of this regulatory mechanism has not yet been addressed comprehensively. Here, we quantify the rates of evolutionary changes of ubiquitination and SUMOylation (Small Ubiquitin-like MOdifier) sites. We estimate the time at which they first appeared, and compare them to acetylation and phosphorylation sites and to unmodified residues. We observe that the various modification sites studied exhibit similar rates. Mammalian ubiquitination sites are weakly more conserved than unmodified lysine residues, and a higher degree of relative conservation is observed when analyzing bona fide ubiquitination sites. Various reasons can be proposed for the limited level of excess conservation of ubiquitination, including shifts in locations of the sites, the presence of alternative sites, and changes in the regulatory pathways. We observe that disappearance of sites may be compensated by the presence of a lysine residue in close proximity, which is significant when compared to evolutionary patterns of unmodified lysine residues, especially in disordered regions. This emphasizes the importance of analyzing a window in the vicinity of functional residues, as well as the capability of the ubiquitination machinery to ubiquitinate residues in a certain region. Using prokaryotic orthologs of ubiquitinated proteins, we study how ubiquitination sites were formed, and observe that while sometimes sequence additions and rearrangements are involved, in many cases the ubiquitination machinery utilizes an already existing sequence without significantly changing it. Finally, we examine the evolution of ubiquitination, which is linked with other modifications, to infer how these complex regulatory modules have evolved. Our study gives initial insights into the formation of ubiquitination sites, their degree of conservation in various species, and their co-evolution with other posttranslational modifications.     

The origins and ongoing evolution of viruses

Genome analyses of double strand DNA tailed bacteriophages argue that they evolve by recombinational reassortment of genes and by the acquisition of novel genes as simple genetic elements termed morons. These processes suggest a model for early virus evolution, wherein viruses can be regarded less as having derived from cells and more as being partners in their mutual co-evolution.     

The neural crest in vertebrate evolution

Vertebrates belong to the group of chordates characterized by a dorsal neural tube and an anteroposterior axis, the notochord. They are the only chordates to possess an embryonic and pluripotent structure associated with their neural primordium, the neural crest (NC). The NC is at the origin of multiple cell types and plays a major role in the construction of the head, which has been an important asset in the evolutionary success of vertebrates. We discuss here the contribution of the rostral domain of the NC to craniofacial skeletogenesis. Moreover, recent data show that cephalic NC cells regulate the activity of secondary brain organizers, hence being critical for preotic brain development, a role that had not been suspected before.     

Early vertebrate evolution

Debate over the origin and evolution of vertebrates has occupied biologists and palaeontologists alike for centuries. This debate has been refined by molecular phylogenetics, which has resolved the place of vertebrates among their invertebrate chordate relatives, and that of chordates among their deuterostome relatives. The origin of vertebrates is characterized by wide‐ranging genomic, embryologic and phenotypic evolutionary change. Analyses based on living lineages suggest dramatic shifts in the tempo of evolutionary change at the origin of vertebrates and gnathostomes, coincident with whole‐genome duplication events. However, the enriched perspective provided by the fossil record demonstrates that these apparent bursts of anatomical evolution and taxic richness are an artefact of the extinction of phylogenetic intermediates whose fossil remains evidence the gradual assembly of crown gnathostome characters in particular. A more refined understanding of the timing, tempo and mode of early vertebrate evolution rests with: (1) better genome assemblies for living cyclostomes; (2) a better understanding of the anatomical characteristics of key fossil groups, especially the anaspids, thelodonts, galeaspids and pituriaspids; (3) tests of the monophyly of traditional groups; and (4) the application of divergence time methods that integrate not just molecular data from living species, but also morphological data and extinct species. The resulting framework will provide for rigorous tests of rates of character evolution and diversification, and of hypotheses of long‐term trends in ecological evolution that themselves suffer for lack of quantitative functional tests. The fossil record has been silent on the nature of the transition from jawless vertebrates to the jawed vertebrates that have dominated communities since the middle Palaeozoic. Elucidation of this most formative of episodes likely rests with the overhaul of early vertebrate systematics that we propose, but perhaps more fundamentally with fossil grades that await discovery.     

The evolution of insect/vertebrate associations

The evolution of close vertebrate associations has occurred in seven orders of insects, resulting in a great diversity of interactions which range from commensalism to true parasitism. The evolution of each taxon of vertebrate associates is discussed in turn, some new ideas on the development of certain groups are presented and, on a broader scale, a general model for the evolution of ectoparasitic insects is proposed. It argues that all vertebrate associates have evolved along one of two macroevolutionary pathways which differ only in the sequencing of adaptations facilitating host association and host feeding. These pathways lead to parasite types which differ greatly in their life history and intimacy of host association.
Some microevolutionary processes influencing the diversification of ectoparasites are discussed, in particular the process of insect/vertebrate coevolution and the forms this may take. Host specificity, one consequence of coevolution, is recognised as an important factor influencing the structure of ectoparasite communities, and a hypothesis is presented that competition between ectoparasite species, mediated by host defensive responses, is also important in determining community structure.     

The molecular evolution of the vertebrate behavioural repertoire

How the sophisticated vertebrate behavioural repertoire evolved remains a major question in biology. The behavioural repertoire encompasses the set of individual behavioural components that an organism uses when adapting and responding to changes in its external world. Although unicellular organisms, invertebrates and vertebrates share simple reflex responses, the fundamental mechanisms that resulted in the complexity and sophistication that is characteristic of vertebrate behaviours have only recently been examined. A series of behavioural genetic experiments in mice and humans support a theory that posited the importance of synapse proteome expansion in generating complexity in the behavioural repertoire. Genome duplication events, approximately 550 Ma, produced expansion in the synapse proteome that resulted in increased complexity in synapse signalling mechanisms that regulate components of the behavioural repertoire. The experiments demonstrate the importance to behaviour of the gene duplication events, the diversification of paralogues and sequence constraint. They also confirm the significance of comparative proteomic and genomic studies that identified the molecular origins of synapses in unicellular eukaryotes and the vertebrate expansion in proteome complexity. These molecular mechanisms have general importance for understanding the repertoire of behaviours in different species and for human behavioural disorders arising from synapse gene mutations.     

The evolution of the vertebrate beta-globin gene promoter

Complexity analysis is capable of highlighting those gross evolutionary changes in gene promoter regions (loosely termed "promoter shuffling") that are undetectable by conventional DNA sequence alignment. Complexity analysis was therefore used here to identify the modular components (blocks) of the orthologous beta-globin gene promoter sequences of 22 vertebrate species, from zebrafish to humans. Considerable variation between the beta-globin gene promoters was apparent in terms of block presence/absence, copy number, and relative location. Some sequence blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Block similarities were also evident between the promoters of the paralogous human beta-like globin genes. It may be inferred that a wide variety of different mutational mechanisms have operated upon the beta-globin gene promoter over evolutionary time. Because these include gross changes such as deletion, duplication, amplification, elongation, contraction, and fusion, as well as the steady accumulation of single base-pair substitutions, it is clear that some redefinition of the term "promoter shuffling" is required. This notwithstanding, and as previously described for the vertebrate growth hormone gene promoter, the modular structure of the beta-globin promoter region and those of its paralogous counterparts have continually been rearranged into new combinations through the alteration, or shuffling, of preexisting blocks. Some of these changes may have had no influence on promoter function, but others could have altered either the level of gene expression or the responsiveness of the promoter to external stimuli. The comparative study of vertebrate beta-globin gene promoter regions described here confirms the generality of the phenomenon of sequence block shuffling and thus supports the view that it could have played an important role in the evolution of differential gene expression.     

Understanding vertebrate brain evolution

Four major questions can be asked about vertebrate brain evolution:1) What major changes have occurred in neural organization andfunction? 2) When did these changes occur? 3) By what mechanismsdid these changes occur? 4) Why did these changes occur? Comparativeneurobiologists have been very successful in recognizing majorchanges in brain structure. They have also made progress inunderstanding the functional significance of these changes,although this understanding is primarily limited to sensorycenters, rather than integrative or motor centers, because ofthe relative ease of manipulating the relevant stimuli. Althoughneuropaleontology continues to provide important insights intowhen changes occurred, this approach is generally limited torecognizing variation in overall brain size, and sometimes brainregions, as interpreted from the surface of an endocranial cast.In recent years, most new information regarding when neuralchanges occurred has been based on cladistical analysis of neuralfeatures in extant taxa. Historically, neurobiologists havemade little progress in understanding how and why brains evolve.The emerging field of evolutionary developmental biology appearsto be the most promising approach for revealing how changesin development and its processes produce neural changes, includingthe emergence of novel features. Why neural changes have occurredis the most difficult question and one that has been the mostignored, in large part because its investigation requires abroad interdisciplinary approach involving both behavior andecology.     

The evolution of milk secretion and its ancient origins

Lactation represents an important element of the life history strategies of all mammals, whether monotreme, marsupial, or eutherian. Milk originated as a glandular skin secretion in synapsids (the lineage ancestral to mammals), perhaps as early as the Pennsylvanian period, that is, approximately 310 million years ago (mya). Early synapsids laid eggs with parchment-like shells intolerant of desiccation and apparently dependent on glandular skin secretions for moisture. Mammary glands probably evolved from apocrine-like glands that combined multiple modes of secretion and developed in association with hair follicles. Comparative analyses of the evolutionary origin of milk constituents support a scenario in which these secretions evolved into a nutrient-rich milk long before mammals arose. A variety of antimicrobial and secretory constituents were co-opted into novel roles related to nutrition of the young. Secretory calcium-binding phosphoproteins may originally have had a role in calcium delivery to eggs; however, by evolving into large, complex casein micelles, they took on an important role in transport of amino acids, calcium and phosphorus. Several proteins involved in immunity, including an ancestral butyrophilin and xanthine oxidoreductase, were incorporated into a novel membrane-bound lipid droplet (the milk fat globule) that became a primary mode of energy transfer. An ancestral c-lysozyme lost its lytic functions in favor of a role as α-lactalbumin, which modifies a galactosyltransferase to recognize glucose as an acceptor, leading to the synthesis of novel milk sugars, of which free oligosaccharides may have predated free lactose. An ancestral lipocalin and an ancestral whey acidic protein four-disulphide core protein apparently lost their original transport and antimicrobial functions when they became the whey proteins β-lactoglobulin and whey acidic protein, which with α-lactalbumin provide limiting sulfur amino acids to the young. By the late Triassic period (ca 210 mya), mammaliaforms (mammalian ancestors) were endothermic (requiring fluid to replace incubatory water losses of eggs), very small in size (making large eggs impossible), and had rapid growth and limited tooth replacement (indicating delayed onset of feeding and reliance on milk). Thus, milk had already supplanted egg yolk as the primary nutrient source, and by the Jurassic period (ca 170 mya) vitellogenin genes were being lost. All primary milk constituents evolved before the appearance of mammals, and some constituents may have origins that predate the split of the synapsids from sauropsids (the lineage leading to 'reptiles' and birds). Thus, the modern dairy industry is built upon a very old foundation, the cornerstones of which were laid even before dinosaurs ruled the earth in the Jurassic and Cretaceous periods.