The Evolutionary Emergence of Vertebrates From Among Their Spineless Relatives

The evolutionary origin of vertebrates has been debated ad nauseam by anatomists, paleontologists, embryologists, and physiologists, but it is only now that molecular phylogenetics is providing a more rigorous framework for the placement of vertebrates among their invertebrate relatives that we can begin to arrive at concrete conclusions concerning the nature of ancient ancestors and the sequence in which characteristic anatomical features were acquired. Vertebrates tunicates and cephalochordates together comprise the chordate phylum, which along with echinoderms and hemichordates constitute the deuterostomes. The origin of vertebrates and of jawed vertebrates is characterized by a doubling of the vertebrate genome, leading to hypotheses that this genomic event drove organismal macroevolution. However, this perspective of evolutionary history, based on living organisms alone, is an artifact. Phylogenetic trees that integrate fossil vertebrates among their living relatives demonstrate the gradual and piecemeal assembly of the gnathostome body plan. Unfortunately, it has not been possible to demonstrate gradual assembly of the vertebrate body plan. This is not because vertebrates are irreducibly complex but because many of the characters that distinguish vertebrates from invertebrates are embryological and cellular and, therefore, inherently unfossilizable.

Discriminating signal from noise in the fossil record of early vertebrates reveals cryptic evolutionary history

The fossil record of early vertebrates has been influential in elucidating the evolutionary assembly of the gnathostome bodyplan. Understanding of the timing and tempo of vertebrate innovations remains, however, mired in a literal reading of the fossil record. Early jawless vertebrates (ostracoderms) exhibit restriction to shallow-water environments. The distribution of their stratigraphic occurrences therefore reflects not only flux in diversity, but also secular variation in facies representation of the rock record. Using stratigraphic, phylogenetic and palaeoenvironmental data, we assessed the veracity of the fossil records of the jawless relatives of jawed vertebrates (Osteostraci, Galeaspida, Thelodonti, Heterostraci). Non-random models of fossil recovery potential using Palaeozoic sea-level changes were used to calculate confidence intervals of clade origins. These intervals extend the timescale for possible origins into the Upper Ordovician; these estimates ameliorate the long ghost lineages inferred for Osteostraci, Galeaspida and Heterostraci, given their known stratigraphic occurrences and stem–gnathostome phylogeny. Diversity changes through the Silurian and Devonian were found to lie within the expected limits predicted from estimates of fossil record quality indicating that it is geological, rather than biological factors, that are responsible for shifts in diversity. Environmental restriction also appears to belie ostracoderm extinction and demise rather than competition with jawed vertebrates.     

First discovery of a primitive coelacanth fin fills a major gap in the evolution of lobed fins and limbs

The fossil record provides unique clues about the primitive pattern of lobed fins, the precursors of digit-bearing limbs. Such information is vital for understanding the evolutionary transition from fish fins to tetrapod limbs, and it guides the choice of model systems for investigating the developmental changes underpinning this event. However, the evolutionary preconditions for tetrapod limbs remain unclear. This uncertainty arises from an outstanding gap in our knowledge of early lobed fins: there are no fossil data that record primitive pectoral fin conditions in coelacanths, one of the three major groups of sarcopterygian (lobe-finned) fishes. A new fossil from the Middle-Late Devonian of Wyoming preserves the first and only example of a primitive coelacanth pectoral fin endoskeleton. The strongly asymmetrical skeleton of this fin corroborates the hypothesis that this is the primitive sarcopterygian pattern, and that this pattern persisted in the closest fish-like relatives of land vertebrates. The new material reveals the specializations of paired fins in the modern coelacanth, as well as in living lungfishes. Consequently, the context in which these might be used to investigate evolutionary and developmental relationships between vertebrate fins and limbs is changed. Our data suggest that primitive actinopterygians, rather than living sarcopterygian fishes and their derived appendages, are the most informative comparators for developmental studies seeking to understand the origin of tetrapod limbs.     

文昌鱼特异的基因倍增

进化生物学和发育生物学的结合产生了一门新兴学科——进化发育生物学,近年来该领域研究取得了丰硕的成果。头索动物文昌鱼是现存生物中最近似于脊椎动物直接祖先的生物,在与脊椎动物分化后形态改变很小,其基因组未曾经历大规模的基因组倍增,在一定程度上反映了脊椎动物祖先型基因组的特征,但在漫长的独立进化历程中基因组自身还是经历了一些变化。本文介绍了在几例在文昌鱼支系中独立发生的基因倍增事件(Hox; Evx; HNF-3; Calmodulin-like),有力地揭示了文昌鱼虽然与脊椎动物直接祖先极其接近,但其基因组有其自身特性,不能简单地将之等同于脊椎动物直接祖先。Abstract: The union of the two complementary disciplines, developmental biology and evolutionary biology resulted in a new division of evolutionary developmental biology, namely “Evo-Devo”. Recently, the research on this field has been fruitful in understanding the origin and development of vertebrates. The cephalochordate amphioxus, which remains in relatively invariant morphology since the divergence from the vertebrate lineage, is the closest living relative to vertebrates. The vertebrate-like simple body plan and preduplicative genome provide amphioxus genes the privilege to serve as key landmark to understand morphological evolution. However, the amphioxus genome has not escaped evolution. In this paper several examples of independent gene (Hox; Evx; HNF-3 and Calmodulin-like) duplications in the cephalochordate lineage were summarized. These particularities and oddities remind the fact that amphioxus is not an immediate ancestor of the vertebrates but ‘only’ the closest living relative to the ancestor, with a mix of prototypical and amphioxus-specific features in its genome.     

脊椎动物基因组与基因复制研究进展

脊椎动物的出现是动物进化历史上一次质的飞跃.由于所有的脊椎动物在其胚胎发育中都呈现连续的解剖学特征,因此过去很多学者都根据现存脊椎动物的形态特征和在其发育过程中的解剖学特征假想原始脊椎动物,并推导其进化过程和起源.近年来的研究表明,通过对脊椎动物和与之亲缘关系接近的物种之间进行基因家族、染色体结构分析,可以对脊椎动物进化提供很多线索和证据.更多的研究表明,脊椎动物在进化过程中很可能发生过整体基因组的复制, 基因和/或基因组的复制可能是引起脊椎动物形体结构复杂性增加的根本原因.因此,基因和基因组的复制正在成为生物进化研究的热点问题.但这两种复制方式中哪一种是产生动物形体结构和功能复杂性增加最重要的原因尚有争论.     

Les premiers vertébrés et les premières étapes de l’évolution du crâne

The earliest vertebrates and the first steps of the evolution of the skull. Vertebrates are one of the few metazoan taxa, which display a well-corroborated phylogenetic pattern, a good and anatomically informative fossil record, and a relatively slow ontogenetic development. They are thus a favourite taxon for illustrating evolution as a historical process, although the stem of the vertebrate tree remains poorly documented by fossils, except for some Early Cambrian forms. Therefore, the characterization of the vertebrates now rests essentially on a small number of developmental characters, mostly involved in the rise of the skull, and whose precursors may occur in other chordates. The tree of the crown-group vertebrates also shows some major morphological gaps due to early extinctions, but a number of Palaeozoic stem gnathostome taxa helps in documenting the agnathan-gnathostome evolutionary transition. However, stem cyclostomes remain elusive.     

Atlas of vertebrate decay: a visual and taphonomic guide to fossil interpretation

Like many other important evolutionary transitions, our knowledge of the origin of vertebrates is limited to windows of exceptional preservation of soft‐bodied fossils. Unfortunately, these fossils are rare and have been subjected to complex taphonomic filters including decay, collapse and distortion. To maximize our ability to utilize these crucial fossils to reconstruct the timing and sequence of evolutionary events, we are in the need of a robust taphonomic framework with in which to interpret them. Here, we report the results of a series of experiments designed to examine patterns of transformation and loss during decay of important anatomical characters of chordates and primitive vertebrates (ammocoete, adult lamprey, hagfish, juvenile chondrichthyans and a non‐vertebrate chordate, Branchiostoma). Complex and repeated patterns of transformation during decay are identified and figured for informative character complexes including eyes, feeding apparatus, skull and brain, muscles, branchial apparatus, axial structures, viscera, heart and fins. The resulting data regarding character decay and relative loss serve as a guide to recognition and interpretation of the anatomy of non‐biomineralized fossil vertebrates. The methods and techniques outlined are eminently applicable to other soft‐bodied groups and present a new way to interpret the exceptionally preserved fossil record.     

Genome duplication, extinction and vertebrate evolution

Vertebrate evolution has been punctuated by three episodes of widespread gene or genome duplication, which have been linked with the origin of vertebrates, gnathostomes and teleosts, respectively. These three events coincide with bursts of character acquisition and increases in phenotypic complexity, and many researchers have suggested a causal relationship between the two. However, this pattern is derived from data for living taxa only; we argue here that, when fossils are taken into account, bursts of character acquisition disappear and gen(om)e duplication in vertebrate phylogeny can no longer be correlated with the origin of body plans. If patterns of character acquisition or morphological gaps between higher taxa are a reflection of phenotypic complexity, then more inclusive data sets incorporating fossil taxa provide no support for hypotheses linking gen(om)e duplications and the evolution of complexity in vertebrates.     

Lamprey as an evo-devo model: lessons from comparative embryology and molecular phylogenetics

Lamprey, the living jawless vertebrate, has been regarded as one of the most primitive groups of vertebrates. The evolutionary phylogenetic position of the lamprey promises to provide hints about the origin of the vertebrate genome as well as the origin of the body plan, a part of which may be written in the genome. Since the lamprey split from the gnathostome lineage early in the history of vertebrates, the shared developmental mechanisms in lampreys and gnathostomes can be regarded as possessed by the hypothetical common ancestor of these animals, whereas the gnathostome-specific developmental mechanisms that are absent from lampreys indicate that they are relatively new, added to the developmental program only after the split of gnathostomes. Thus, the sequential establishment of the gnathostome body plan is inherently related to the history of genomic duplication events. In this review, recent molecular developmental and evolutionary molecular research on the living lampreys are summarized and discussed, taking vertebrate comparative morphology and embryology into consideration.     

Fossil apes from the vallès‐penedès basin

Currently restricted to Southeast Asia and Africa, extant hominoids are the remnants of a group that was much more diverse during the Miocene. Apes initially diversified in Africa during the early Miocene, but by the middle Miocene they extended their geographical range into Eurasia, where they experienced an impressive evolutionary radiation. Understanding the role of Eurasian hominoids in the origin and evolution of the great‐ape‐and‐human clade (Hominidae) is partly hampered by phylogenetic uncertainties, the scarcity and incompleteness of fossil remains, the current restricted diversity of the group, and pervasive homoplasy. Nevertheless, scientific knowledge of the Eurasian hominoid radiation has significantly improved during the last decade. In the case of Western Europe, this has been due to the discovery of new remains from the Vallès‐Penedès Basin (Catalonia, Spain). Here, I review the fossil record of Vallès‐Penedès apes and consider its implications. Although significant disagreements persist among scholars, some important lessons can be learned regarding the evolutionary history of the closest living relatives of humans. © 2012 Wiley Periodicals, Inc.     

Vertebrate cranial evolution: Contributions and conflict from the fossil record

In modern vertebrates, the craniofacial skeleton is complex, comprising cartilage and bone of the neurocranium, dermatocranium and splanchnocranium (and their derivatives), housing a range of sensory structures such as eyes, nasal and vestibulo-acoustic capsules, with the splanchnocranium including branchial arches, used in respiration and feeding. It is well understood that the skeleton derives from neural crest and mesoderm, while the sensory elements derive from ectodermal thickenings known as placodes. Recent research demonstrates that neural crest and placodes have an evolutionary history outside of vertebrates, while the vertebrate fossil record allows the sequence of the evolution of these various features to be understood. Stem-group vertebrates such as Metaspriggina walcotti (Burgess Shale, Middle Cambrian) possess eyes, paired nasal capsules and well-developed branchial arches, the latter derived from cranial neural crest in extant vertebrates, indicating that placodes and neural crest evolved over 500 million years ago. Since that time the vertebrate craniofacial skeleton has evolved, including different types of bone, of potential neural crest or mesodermal origin. One problematic part of the craniofacial skeleton concerns the evolution of the nasal organs, with evidence for both paired and unpaired nasal sacs being the primitive state for vertebrates.     

POTENTIAL PITFALLS OF RECONSTRUCTING DEEP TIME EVOLUTIONARY HISTORY WITH ONLY EXTANT DATA,A CASE STUDY USING THE CANIDAE (MAMMALIA,CARNIVORA)

Reconstructing evolutionary patterns and their underlying processes is a central goal in biology. Yet many analyses of deep evolutionary histories assume that data from the fossil record is too incomplete to include, and rely solely on databases of extant taxa. Excluding fossil taxa assumes that character state distributions across living taxa are faithful representations of a clade's entire evolutionary history. Many factors can make this assumption problematic. Fossil taxa do not simply lead‐up to extant taxa; they represent now‐extinct lineages that can substantially impact interpretations of character evolution for extant groups. Here, we analyze body mass data for extant and fossil canids (dogs, foxes, and relatives) for changes in mean and variance through time. AIC‐based model selection recovered distinct models for each of eight canid subgroups. We compared model fit of parameter estimates for (1) extant data alone and (2) extant and fossil data, demonstrating that the latter performs significantly better. Moreover, extant‐only analyses result in unrealistically low estimates of ancestral mass. Although fossil data are not always available, reconstructions of deep‐time organismal evolution in the absence of deep‐time data can be highly inaccurate, and we argue that every effort should be made to include fossil data in macroevolutionary studies.     

Regulatory genes in the ancestral chordate genomes

Changes or innovations in gene regulatory networks for the developmental program in the ancestral chordate genome appear to be a major component in the evolutionary process in which tadpole-type larvae, a unique characteristic of chordates, arose. These alterations may include new genetic interactions as well as the acquisition of new regulatory genes. Previous analyses of the Ciona genome revealed that many genes may have emerged after the divergence of the tunicate and vertebrate lineages. In this paper, we examined this possibility by examining a second non-vertebrate chordate genome. We conclude from this analysis that the ancient chordate included almost the same repertory of regulatory genes, but less redundancy than extant vertebrates, and that approximately 10% of vertebrate regulatory genes were innovated after the emergence of vertebrates. Thus, refined regulatory networks arose during vertebrate evolution mainly as preexisting regulatory genes multiplied rather than by generating new regulatory genes. The inferred regulatory gene sets of the ancestral chordate would be an important foundation for understanding how tadpole-type larvae, a unique characteristic of chordates, evolved.     

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.     

It's a long way from amphioxus: descendants of the earliest chordate

The origin of chordates and the consequent genesis of vertebrates were major events in natural history. The amphioxus (lancelet) is now recognised as the closest extant relative to the stem chordate and is the only living invertebrate that retains a vertebrate‐like development and body plan through its lifespan, despite more than 500 million years of independent evolution from the stem vertebrate. The inspiring data coming from its recently sequenced genome confirms that amphioxus has a prototypical chordate genome with respect to gene content and structure, and even chromosomal organisation. Pushed by joint efforts of amphioxus researchers, amphioxus is now entering a new era, namely its maturation as a laboratory model, through the availability of a large amount of molecular data and the advent of experimental manipulation of the embryo. These two facts may well serve to illuminate the hidden secrets of the genetic changes that generated, among other vertebrates, ourselves.     

Impact of gene gains,losses and duplication modes on the origin and diversification of vertebrates

The study of the evolutionary origin of vertebrates has been linked to the study of genome duplications since Susumo Ohno suggested that the successful diversification of vertebrate innovations was facilitated by two rounds of whole-genome duplication (2R-WGD) in the stem vertebrate. Since then, studies on the functional evolution of many genes duplicated in the vertebrate lineage have provided the grounds to support experimentally this link. This article reviews cases of gene duplications derived either from the 2R-WGD or from local gene duplication events in vertebrates, analyzing their impact on the evolution of developmental innovations. We analyze how gene regulatory networks can be rewired by the activity of transposable elements after genome duplications, discuss how different mechanisms of duplication might affect the fate of duplicated genes, and how the loss of gene duplicates might influence the fate of surviving paralogs. We also discuss the evolutionary relationships between gene duplication and alternative splicing, in particular in the vertebrate lineage. Finally, we discuss the role that the 2R-WGD might have played in the evolution of vertebrate developmental gene networks, paying special attention to those related to vertebrate key features such as neural crest cells, placodes, and the complex tripartite brain. In this context, we argue that current evidences points that the 2R-WGD may not be linked to the origin of vertebrate innovations, but to their subsequent diversification in a broad variety of complex structures and functions that facilitated the successful transition from peaceful filter-feeding non-vertebrate ancestors to voracious vertebrate predators.     

Introduction to ‘Origin and evolution of the nervous system’

In 1665, Robert Hooke demonstrated in Micrographia the power of the microscope and comparative observations, one of which revealed similarities between the arthropod and vertebrate eyes. Utilizing comparative observations, Saint-Hilaire in 1822 was the first to propose that the ventral nervous system of arthropods corresponds to the dorsal nervous system of vertebrates. Since then, studies on the origin and evolution of the nervous system have become inseparable from studies about Metazoan origins and the origins of organ systems. The advent of genome sequence data and, in turn, phylogenomics and phylogenetics have refined cladistics and expanded our understanding of Metazoan phylogeny. However, the origin and evolution of the nervous system is still obscure and many questions and problems remain. A recurrent problem is whether and to what extent sequence data provide reliable guidance for comparisons across phyla. Are genetic data congruent with the geological fossil records? How can we reconcile evolved character loss with phylogenomic records? And how informative are genetic data in relation to the specification of nervous system morphologies? These provide some of the background and context for a Royal Society meeting to discuss new data and concepts that might achieve insights into the origin and evolution of brains and nervous systems.     

Decay of vertebrate characters in hagfish and lamprey (Cyclostomata) and the implications for the vertebrate fossil record

The timing and sequence of events underlying the origin and early evolution of vertebrates remains poorly understood. The palaeontological evidence should shed light on these issues, but difficulties in interpretation of the non-biomineralized fossil record make this problematic. Here we present an experimental analysis of decay of vertebrate characters based on the extant jawless vertebrates (Lampetra and Myxine). This provides a framework for the interpretation of the anatomy of soft-bodied fossil vertebrates and putative cyclostomes, and a context for reading the fossil record of non-biomineralized vertebrate characters. Decay results in transformation and non-random loss of characters. In both lamprey and hagfish, different types of cartilage decay at different rates, resulting in taphonomic bias towards loss of 'soft' cartilages containing vertebrate-specific Col2α1 extracellular matrix proteins; phylogenetically informative soft-tissue characters decay before more plesiomorphic characters. As such, synapomorphic decay bias, previously recognized in early chordates, is more pervasive, and needs to be taken into account when interpreting the anatomy of any non-biomineralized fossil vertebrate, such as Haikouichthys, Mayomyzon and Hardistiella.     

Tempo does not correlate with mode in the fossil record

The dominating view of evolution based on the fossil record is that established species remain more or less unaltered during their existence. Substantial evolution is on the other hand routinely reported for contemporary populations, and most quantitative traits show high potential for evolution. These contrasting observations on long‐ and short‐time scales are often referred to as the paradox of stasis, which rests on the fundamental assumption that periods of morphological stasis in the fossil record represent minimal evolutionary change. Investigating 450 fossil time series, I demonstrate that the nonaccumulating morphological fluctuations during stasis travel similar distances in morphospace compared to lineages showing directional change. Hence, lineages showing stasis are commonly undergoing considerable amounts of evolution, but this evolution does not accumulate to produce large net evolutionary changes over time. Rates of evolutionary change across modes in the fossil record may be more homogenous than previously assumed and advocated, supporting the claim that substantial evolution is not exclusively or causally linked to the process of speciation. Instead of exemplifying minimal evolution, stasis likely represents information on the dynamics of the adaptive landscape on macroevolutionary time scales, including the persistence of adaptive zones and ecological niches over millions of years.     

The Origin of the Vertebrate Eye

In his considerations of “organs of extreme perfection,” Charles Darwin described the evidence that would be necessary to support the evolutionary origin of the eye, namely, demonstration of the existence of “numerous gradations” from the most primitive eye to the most perfect one, where each such tiny change had provided a survival advantage (however slight) to the organism possessing the subtly altered form. In this paper, we discuss evidence indicating that the vertebrate eye did indeed evolve through numerous subtle changes. The great majority of the gradual transitions that did occur have not been preserved to the present time, either in the fossil record or in extant species; yet clear evidence of their occurrence remains. We discuss the remarkable “eye” of the hagfish, which has features intermediate between a simple light detector and an image-forming camera-like eye and which may represent a step in the evolution of our eye that can now be studied by modern methods. We also describe the important clues to the evolutionary origin of the vertebrate eye that can be found by studying the embryological development of our own eye, by examining the molecular genetic record preserved in our own genes and in the genes of other vertebrates, and through consideration of the imperfections (or evolutionary “scars”) in the construction of our eye. Taking these findings together, it is possible to discuss in some detail how the vertebrate eye evolved.