CHARACTER DIAGNOSIS, FOSSILS AND THE ORIGIN OF TETRAPODS

The rapid evolution of lungfish durophagy

Innovations relating to the consumption of hard prey are implicated in ecological shifts in marine ecosystems as early as the mid-Paleozoic. Lungfishes represent the first and longest-ranging lineage of durophagous vertebrates, but how and when the various feeding specializations of this group arose remain unclear. Two exceptionally preserved fossils of the Early Devonian lobe-finned fish Youngolepis reveal the origin of the specialized lungfish feeding mechanism. Youngolepis has a radically restructured palate, reorienting jaw muscles for optimal force transition, coupled with radiating entopterygoid tooth rows like those of lungfish toothplates. This triturating surface occurs in conjunction with marginal dentition and blunt coronoid fangs, suggesting a role in crushing rather than piercing prey. Bayesian tip-dating analyses incorporating these morphological data indicate that the complete suite of lungfish feeding specializations may have arisen in as little as 7 million years, representing one of the most striking episodes of innovation during the initial evolutionary radiations of bony fishes.

It is unclear how Lungfishes evolved durophagy, the consumption of hard prey, despite being the longest lineage of vertebrates with this feeding mechanism. Here, the authors describe exceptionally preserved fossils of Youngolepis from the Early Devonian, showing early adaptations to durophagy.

The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

Identifying the closest living relative(s) of tetrapods is an important, yet still contested question in vertebrate phylogenetics. Three hypotheses are possible and ruling out alternatives has proven difficult even with large molecular data sets due to weak phylogenetic signal coupled nonphylogenetic noise resulting from relatively rapid speciation events that occurred a long time ago ([Formula: see text]400 Ma). Here, we revisit the identity of the closest living relative of land vertebrates from a phylogenomic perspective and include new genomic data for all extant lungfish genera. RNA-seq proves to be a great alternative to genomic sequencing, which currently is technically not feasible in lungfishes due to their huge (50-130 Gb) and repetitive genomes. We examined the most important sources of systematic error, namely long-branch attraction (LBA), compositional heterogeneity and distribution of missing data and applied different correction techniques. A multispecies coalescent approach is used to account for deep coalescence that might come from the short and deep internodes separating early sarcopterygian splits. Concatenation methods favored lungfishes as the closest living relatives of tetrapods with strong statistical support. Amino acid profile mixture models can unambiguously resolve this difficult internode thanks to their ability to avoid systematic error. We assessed the performance of different site-heterogeneous models and data partitioning and compared the ability of different strategies designed to overcome LBA, including taxon manipulation, reduction of among-lineage rate heterogeneity and removal of fast-evolving or compositionally heterogeneous positions. The identification of lungfish as sister group of tetrapods is robust regarding the effects of nonstationary composition and distribution of missing data. The multispecies coalescent method reconstructed strongly supported topologies that were congruent with concatenation, despite pervasive gene tree heterogeneity. We reject alternative topologies for early sarcopterygian relationships by increasing the signal-to-noise ratio in our alignments. The analytical pipeline outlined here combines probabilistic phylogenomic inference with methods for evaluating data quality, model adequacy, and assessing systematic error, and thus is likely to help resolve similarly difficult internodes in the tree of life. [Coalescence; coelacanth; compositional heterogeneity; gene tree; long-branch attraction; lungfish; missing data; model misspecification; phylogenomic; species tree; systematic error.].

Phylogenetic Stability, Tree Shape, and Character Compatibility: A Case Study Using Early Tetrapods

Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades.

The origin and early phylogenetic history of jawed vertebrates

Fossils of early gnathostomes (or jawed vertebrates) have been the focus of study for nearly two centuries. They yield key clues about the evolutionary assembly of the group's common body plan, as well the divergence of the two living gnathostome lineages: the cartilaginous and bony vertebrates. A series of remarkable new palaeontological discoveries, analytical advances and innovative reinterpretations of existing fossil archives have fundamentally altered a decades-old consensus on the relationships of extinct gnathostomes, delivering a new evolutionary framework for exploring major questions that remain unanswered, including the origin of jaws.

Behavioral evidence for the evolution of walking and bounding before terrestriality in sarcopterygian fishes

Tetrapods evolved from sarcopterygian fishes in the Devonian and were the first vertebrates to colonize land. The locomotor component of this transition can be divided into four major events: terrestriality, the origins of digited limbs, solid substrate-based locomotion, and alternating gaits that use pelvic appendages as major propulsors. As the sister group to tetrapods, lungfish are a morphologically and phylogenetically relevant sarcopterygian taxon for understanding the order in which these events occurred. We found that a species of African lungfish (Protopterus annectens) uses a range of pelvic fin-driven, tetrapod-like gaits, including walking and bounding, in an aquatic environment, despite having a derived limb endoskeleton and primitively small, muscularly supported pelvis. Surprisingly, given these morphological traits, P. annectens also lifts its body clear of the substrate using its pelvic fins, an ability thought to be a tetrapod innovation. Our findings suggest that some fundamental features of tetrapod locomotion, including pelvic limb gait patterns and substrate association, probably arose in sarcopterygians before the origin of digited limbs or terrestriality. It follows that the attribution of some of the nondigited Devonian fossil trackways to limbed tetrapods may need to be revisited.

Lower jaws, lower tetrapods–a review based on the Devonian genus Acanthostega

The lower jaw of the Devonian tetrapod Acanthostega is described for the first time. Redescriptions are provided for the lower jaws of the elpistostegid Panderichthys, the Devonian tetrapods Elginerpeton, Obruchevichthys, Metaxygnathus, Ventastega and Ichthyostega, and the Carboniferous tetrapods Crassigyrinus, Megalocephalus and Gephyrostegus. The character distri- butions thus revealed differ considerably from previous accounts, particularly in the wide distribution of certain primitive characters. Meckelian ossification in the middle part of the jaw is widespread among Devonian tetrapods, being demonstrably absent only in Acanthostega. Among Carboniferous tetrapods, a tooth-bearing parasymphysial plate is shown to be present in Crassigyrinus and Megalocephalus (having already been demonstrated by other authors in Whatcheeria and Greererpeton). A phylogenetic analysis of 26 early tetrapods including all the aforementioned genera, scored for 51 lower jaw characters, produces at least 2,500 equally parsimonious trees. However, the lack of resolution lies largely in a big top end polychotomy containing anthracosaurs, temnospondyls, seymouriamorphs, microsaurs and a nectridean-amniote clade. Below this polycho- tomy, which may correspond approximately to the tetrapod crown group, there is a well-resolved stem-group containing, in descending order, Megalocephalus, Greererpeton, Crassigyrinus, (jaws associated with) Tulerpeton, Whatcheeria, Acanthostega, Metaxygnathus, Ichthyostega, Ventastega and Metaxygnathus (unresolved), an Elginerpeton-Obruchevichthys clade, and Panderichthys. This conflicts with recently published phylogenies by Coates and Lebedev & Coates, which place Tulerpeton and all post-Devonian tetrapods in the amphibian or amniote branches of the tetrapod crown group.

The Order Adelospondyli: Carboniferous lepospondyl amphibians

The Order Adelospondyli, an isolated group of amphibians from the Carboniferous of the Edinburgh area, is redescribed and distinguished from other early tetrapods. Although systematics of genera and species is unsatisfactory, the group seems monophyletic, since as far as they are known, all conform to a single overall structural plan. There is an entire skull roof with a reduced complement of bones in an unique pattern, a highly characteristic marginal dentition, a massive hyoid apparatus, at least 70 holospondylous trunk vertebrae, and (like some other Lower Carboniferous tetrapods) a shoulder region with a heavy dermal girdle but no trace of ossified limbs or endochondral girdle. Adelogyrinids show no special affinity with other Palaeozoic amphibians: the vertebral characters in which they resemble microsaurs, lysorophids, aïstopods, and nectrideans may have evolved more than once among early tetrapods, and the shoulder girdle and neural arch characters shared with labyrinthodonts are probably primitive. The adelogyrinids thus illustrate the more general problems of establishing interrelationships among early tetrapods. Their way of life is discussed.

The pelvic girdle and hind limb ofCrassigyrinus scoticus(Lydekker) from the Scottish Carboniferous and the origin of the tetrapod pelvic skeleton

Our knowledge of the primitive and aberrant early tetrapodCrassigyrinus scoticuswas based on a partial skull roof and mandibles from the Lower Carboniferous of Gilmerton, Edinburgh, plus a skeleton lacking the hind limb and tail from the Namurian, basal Upper Carboniferous, of Cowdenbeath, Fife. New specimens from Cowdenbeath include the pelvic girdle, presacral and sacral rib and most of the hind limb. The ilium of the girdle had a firm articulation with the vertebral column via the sacral rib. The ischium, separated from the ilium by cartilage, was, like that found with the Cowdenbeath skeleton, ornamented as though a dermal bone. No pubis is preserved. The femur lacks an adductor crest, but has a strongly developed internal trochanter. Tibia and fibula are short stout bones, but axial torsion is present in the fibula rather than the tibia. This, and the structure of the femur, suggests a swimming rather than a walking limb. Probable metatarsals and phalanges are recorded. A skeletal reconstruction and a life restoration ofCrassigyrinusare presented in the light of its reconstructed anatomy and physiology.

The ornamentation of the ischium ofCrassigyrinus, and that of the colosteidGreererpeton, suggests that the bone may be at least in part dermal. Its homology wth the pelvic fin basal scute of osteolepiform fishes is proposed and the homologies of pectoral and pelvic fins, and thus limbs, discussed.

43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

BACKGROUND

Since the discovery of the "living fossil" in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed.

FINDINGS

We used the Bayesian method under the coalescence model with the latest published program (Bayesian Estimation of Species Trees, or BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear protein-coding genes with the jackknife method for taxon sub-sampling. The lungfish-coelacanth sister group was consistently reconstructed with the Bayesian method under the coalescence model in 17 out of 21 taxon sets with a Bayesian posterior probability as high as 99%. Lungfish-tetrapod was only inferred from BCLS and BACLS. Neither coelacanth-tetrapod nor lungfish-coelacanth-tetrapod was recovered out of all 21 taxon sets.

CONCLUSIONS

Our results provide strong evidence in favor of accepting the hypothesis that lungfishes and coelacanths form a monophyletic sister-group that is the closest living relative of tetrapods. This clade was supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.

Ever Since Owen: Changing Perspectives on the Early Evolution of Tetrapods

The traditional notion of a gap between fishes and amphibians has been closed by a wealth of fish-like fossil tetrapods, many discovered since the mid 1980s. This review summarizes these discoveries and explores their significance relative to changing ideas about early tetrapod phylogeny, biogeography, and ecology. Research emphasis can now shift to broader-based questions, including the whole of the early tetrapod radiation, from the divergence from other lobed-finned fishes to the origins of modern amphibians and amniotes. The fish-to-tetrapod morphological transition occurred within the Upper Devonian; the divergence of modern tetrapod groups is an Early Carboniferous event. Modern tetrapods emerged in the aftermath of one of the five major extinction episodes in the fossil record, but the earlier Devonian tetrapod radiation is not well understood. Tetrapod limbs, paired fins, and comparative developmental data are reviewed; again, research emphasis needs to change to explore the origins of tetrapod diversity.

Fish fingers: digit homologues in sarcopterygian fish fins

A defining feature of tetrapod evolutionary origins is the transition from fish fins to tetrapod limbs. A major change during this transition is the appearance of the autopod (hands, feet), which comprises two distinct regions, the wrist/ankle and the digits. When the autopod first appeared in Late Devonian fossil tetrapods, it was incomplete: digits evolved before the full complement of wrist/ankle bones. Early tetrapod wrists/ankles, including those with a full complement of bones, also show a sharp pattern discontinuity between proximal elements and distal elements. This suggests the presence of a discontinuity in the proximal-distal sequence of development. Such a discontinuity occurs in living urodeles, where digits form before completion of the wrist/ankle, implying developmental independence of the digits from wrist/ankle elements. We have observed comparable independent development of pectoral fin radials in the lungfish Neoceratodus (Osteichthyes: Sarcopterygii), relative to homologues of the tetrapod limb and proximal wrist elements in the main fin axis. Moreover, in the Neoceratodus fin, expression of Hoxd13 closely matches late expression patterns observed in the tetrapod autopod. This evidence suggests that Neoceratodus fin radials and tetrapod digits may be patterned by shared mechanisms distinct from those patterning the proximal fin/limb elements, and in that sense are homologous. The presence of independently developing radials in the distal part of the pectoral (and pelvic) fin may be a general feature of the Sarcopterygii.

The origin of the internal nostril of tetrapods

The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. However, there is no consensus on the origin of the choana despite decades of heated debate; some have claimed that it represents a palatally displaced external nostril, but others have argued that this is implausible because it implies breaking and rejoining the maxillary-premaxillary dental arcade and the maxillary branch of nerve V. The fossil record has not resolved the dispute, because the choana is fully developed in known tetrapod stem-group members. Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.

Complete Mitochondrial Genome Sequences of the South American and the Australian Lungfish: Testing of the Phylogenetic Performance of Mitochondrial Data Sets for Phylogenetic Problems in Tetrapod Relationships

We determined the complete nucleotide sequences (16403 and 16572 base pairs, respectively) of the mitochondrial genomes of the South American lungfish, Lepidosiren paradoxa, and the Australian lungfish, Neoceratodus forsteri (Sarcopterygii, Dipnoi). The mitochondrial DNA sequences were established in an effort to resolve the debated evolutionary positions of the lungfish and the coelacanth relative to land vertebrates. Previous molecular phylogenetic studies based on complete mtDNA sequences, including only the African lungfish, Protopterus dolloi, sequence were able to strongly reject the traditional textbook hypothesis that coelacanths are the closest relatives of land vertebrates. However, these studies were unable to statistically significantly distinguish between the two remaining scenarios: lungfish as the closest relatives to land vertebrates and lungfish and coelacanths jointly as their sister group (Cao et al. 1998; Zardoya et al. 1998; Zardoya and Meyer 1997a). Lungfish, coelacanths, and the fish ancestors of the tetrapod lineage all originated within a short time window of about 20 million years, back in the early Devonian (about 380 to 400 million years ago). This short divergence time makes the determination of the phylogenetic relationships among these three lineages difficult. In this study, we attempted to break the long evolutionary branch of lungfish, in an effort to better resolve the phylogenetic relationships among the three extant sarcopterygian lineages. The gene order of the mitochondrial genomes of the South American and Australian lungfish conforms to the consensus gene order among gnathostome vertebrates. The phylogenetic analyses of the complete set of mitochondrial proteins (without ND6) suggest that the lungfish are the closest relatives of the tetrapods, although the support in favor of this scenario is not statistically significant. The two other smaller data sets (tRNA and rRNA genes) give inconsistent results depending on the different reconstruction methods applied and cannot significantly rule out any of the three alternative hypotheses. Nuclear protein-coding genes, which might be better phylogenetic markers for this question, support the lungfish-tetrapod sister-group relationship (Brinkmann et al. 2004).

The Greatest Step in Vertebrate History: A Paleobiological Review of the Fish‐Tetrapod Transition

Recent discoveries of previously unknown fossil forms have dramatically transformed understanding of many aspects of the fish-tetrapod transition. Newer paleobiological approaches have also contributed to changed views of which animals were involved and when, where, and how the transition occurred. This review summarizes major advances made and reevaluates alternative interpretations of important parts of the evidence. We begin with general issues and concepts, including limitations of the Paleozoic fossil record. We summarize important features of paleoclimates, paleoenvironments, paleobiogeography, and taphonomy. We then review the history of Devonian tetrapods and their closest stem group ancestors within the sarcopterygian fishes. It is now widely accepted that the first tetrapods arose from advanced tetrapodomorph stock (the elpistostegalids) in the Late Devonian, probably in Euramerica. However, truly terrestrial forms did not emerge until much later, in geographically far-flung regions, in the Lower Carboniferous. The complete transition occurred over about 25 million years; definitive emergences onto land took place during the most recent 5 million years. The sequence of character acquisition during the transition can be seen as a five-step process involving: (1) higher osteichthyan (tetrapodomorph) diversification in the Middle Devonian (beginning about 380 million years ago [mya]), (2) the emergence of "prototetrapods" (e.g., Elginerpeton) in the Frasnian stage (about 372 mya), (3) the appearance of aquatic tetrapods (e.g., Acanthostega) sometime in the early to mid-Famennian (about 360 mya), (4) the appearance of "eutetrapods" (e.g., Tulerpeton) at the very end of the Devonian period (about 358 mya), and (5) the first truly terrestrial tetrapods (e.g., Pederpes) in the Lower Carboniferous (about 340 mya). We discuss each of these steps with respect to inferred functional utility of acquired character sets. Dissociated heterochrony is seen as the most likely process for the evolutionarily rapid morphological transformations required. Developmental biological processes, including paedomorphosis, played important roles. We conclude with a discussion of phylogenetic interpretations of the evidence.

The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes

The origin of tetrapods is a major outstanding issue in vertebrate phylogeny. Each of the three possible principal hypotheses (coelacanth, lungfish, or neither being the sister group of tetrapods) has found support in different sets of data. In an attempt to resolve the controversy, sequences of 44 nuclear genes encoding amino acid residues at 10,404 positions were obtained and analyzed. However, this large set of sequences did not support conclusively one of the three hypotheses. Apparently, the coelacanth, lungfish, and tetrapod lineages diverged within such a short time interval that at this level of analysis, their relationships appear to be an irresolvable trichotomy.

Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates

The colonization of land by tetrapod ancestors is one of the major questions in the evolution of vertebrates. Despite intense molecular phylogenetic research on this problem during the last 15 years, there is, until now, no statistically supported answer to the question of whether coelacanths or lungfish are the closest living relatives of tetrapods. We determined DNA sequences of the nuclear-encoded recombination activating genes (Rag1 and Rag2) from all three major lungfish groups, the Australian Neoceratodis forsteri, the South American Lepidosiren paradoxa and the African lungfish Protopterus dolloi, and the Indonesian coelacanth Latimeria menadoensis. Phylogenetic analyses of both the single gene and the concatenated data sets of RAG1 and RAG2 found that the lungfishes are the closest living relatives of the land vertebrates. These results are supported by high bootstrap values, Bayesian posterior probabilities, and likelihood ratio tests.

Early tetrapod relationships revisited

In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relationships, we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod clades. A stem-based (total-group) definition of Tetrapoda is preferred over apomorphy- and node-based (crown-group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP* search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differences between these trees concern: (1) the internal relationships of aïstopods, the three selected species of which form a trichotomy; (2) the internal relationships of embolomeres, with Archeria crassidisca and Pholiderpeton scut collapsed in a trichotomy with a clade formed by Anthracosaurus russelli and Pholiderpeton attheyi; (3) the internal relationships of derived dissorophoids, with four amphibamid species forming an unresolved node with a clade consisting of micromelerpetontids and branchiosaurids and a clade consisting of albanerpetontids plus basal crown-group lissamphibians; (4) the position of albenerpetontids and Eocaecilia micropoda, which form an unresolved node with a trichotomy subtending Karaurus sharovi, Valdotriton gracilis and Triadobatrachus massinoti; (5) the branching pattern of derived diplocaulid nectrideans, with Batrachiderpeton reticulatum and Diceratosaurus brevirostris collapsed in a trichotomy with a clade formed by Diplocaulus magnicornis and Diploceraspis burkei. The results of the original parsimony run--as well as those retrieved from several other treatments of the data set (e.g. exclusion of postcranial and lower jaw data; character reweighting; reverse weighting)--indicate a deep split of early tetrapods between lissamphibian- and amniote-related taxa. Colosteids, Crassigyrinus, Whatcheeria and baphetids are progressively more crownward stem-tetrapods. Caerorhachis, embolomeres, gephyrostegids, Solenodonsaurus and seymouriamorphs are progressively more crownward stem-amniotes. Eucritta is basal to temnospondyls, with crown-lissamphibians nested within dissorophoids. Westlothiana is basal to Lepospondyli, but evidence for the monophyletic status of the latter is weak. Westlothiana and Lepospondyli form the sister group to diadectomorphs and crown-group amniotes. Tuditanomorph and microbrachomorph microsaurs are successively more closely related to a clade including proximodistally: (1) lysorophids; (2) Acherontiscus as sister taxon to adelospondyls; (3) scincosaurids plus diplocaulids; (4) urocordylids plus aïstopods. A data set employing cranial characters only places microsaurs on the amniote stem, but forces remaining lepospondyls to appear as sister group to colosteids on the tetrapod stem in several trees. This arrangement is not significantly worse than the tree topology obtained from the analysis of the complete data set. The pattern of sister group relationships in the crownward part of the temnospondyl-lissamphibian tree re-emphasizes the important role of dissorophoids in the lissamphibian origin debate. However, no specific dissorophoid can be identified as the immediate sister taxon to crown-group lissamphibians. The branching sequence of various stem-group amniotes reveals a coherent set of internested character-state changes related to the acquisition of progressively more terrestrial habits in several Permo-Carboniferous forms.

The tetrapod limb: a hypothesis on its origin

A wrist joint and structures typical of the hand, such as digits, however, are absent in [Eustenopteron] (Andrews and Westoll, '68, p 240). Great changes must have been undergone during evolution of the ankle joint; the small number of large bones in the fin must somehow have developed into a large number of small bones, and it is very difficult to draw homologies in this region, or even be certain of what is being compared (Andrews and Westoll, '68, p 268). The tetrapod limb is one of the major morphological adaptations that facilitated the transition from an aquatic to a terrestrial lifestyle in vertebrate evolution. We review the paleontological evidence for the fin-limb transition and conclude that the innovation associated with evolution of the tetrapod limb is the zeugopodial-mesopodial transition, i.e., the evolution of the developmental mechanism that differentiates the distal parts of the limb (the autopodium, i.e., hand or foot) from the proximal parts. Based on a review of tetrapod limb and fish fin development, we propose a genetic hypothesis for the origin of the autopodium. In tetrapods the genes Hoxa-11 and Hoxa-13 have locally exclusive expression domains along the proximal-distal axis of the limb bud. The junction between the distal limit of Hoxa-11 expression and of the proximal limit of Hoxa-13 expression is involved in establishing the border between the zeugopodial and autopodial anlagen. In zebrafish, the expression domains of these genes are overlapping and there is no evidence for an autopodial equivalent in the fin skeleton. We propose that the evolution of the derived expression patterns of Hoxa-11 and Hoxa-13 may be causally involved in the origin of the tetrapod limb.

On the origin of and phylogenetic relationships among living amphibians

The phylogenetic relationships among the three orders of modern amphibians (Caudata, Gymnophiona, and Anura) have been estimated based on both morphological and molecular evidence. Most morphological and paleontological studies of living and fossil amphibians support the hypothesis that salamanders and frogs are sister lineages (the Batrachia hypothesis) and that caecilians are more distantly related. Previous interpretations of molecular data based on nuclear and mitochondrial rRNA sequences suggested that salamanders and caecilians are sister groups to the exclusion of frogs. In an attempt to resolve this apparent conflict, the complete mitochondrial genomes of a salamander (Mertensiella luschani) and a caecilian (Typhlonectes natans) were determined (16,656 and 17,005 bp, respectively) and compared with previously published sequences from a frog (Xenopus laevis) and several other groups of vertebrates. Phylogenetic analyses of the mitochondrial data supported with high bootstrap values the monophyly of living amphibians with respect to other living groups of tetrapods, and a sister group relationship of salamanders and frogs. The lack of phylogenetically informative sites in the previous rRNA data sets (because of its shorter size and higher among-site rate variation) likely explains the discrepancy between our results and those based on previous molecular data. Strong support of the Batrachia hypothesis from both molecule- and morphology-based studies provides a robust phylogenetic framework that will be helpful to comparative studies among the three living orders of amphibians and will permit better understanding of the considerably divergent vertebral, brain, and digit developmental patterns found in frogs and salamanders.

Structural and Biochemical Characterization of the Lungfish (Lepidosiren paradoxa) Liver Basic Fatty Acid Binding Protein

Only one fatty acid-binding protein (FABP) from the liver of the lungfish (Lepidosiren paradoxa) was isolated and characterized. The sequence comparison of lungfish FABP with that of the known members of the liver FABP (L-FABP) and liver basic FABP (Lb-FABP) subfamilies indicates that it is more closely related to chicken, iguana, frog, axolotl, catfish, and shark Lb-FABPs than to mammalian and axolotl L-FABPs. Lungfish liver expression of this single Lb-FABP contrasts with the other fish studied so far which coexpress an Lb-FABP with heart-adipocyte and/or intestinal FABP types. The lungfish liver FABP expression pattern resembles that of tetrapods, which only expresses liver type FABPs. Lungfish Lb-FABP is one of the two FABPs reported to have a disulfide bridge. The molecular modeling of lungfish Lb-FABP predicts that nine of the conserved residues of Lb-FABPs are oriented toward the binding cavity, thus suggesting they are related to the protein binding characteristics.

Purification and characterization of insulin from the Australian lungfish, Neoceratodus forsteri (Dipnoi)

The Australian lungfish Neoceratodus forsteri, a facultative air breather, is considered to be the most primitive of the extant Dipnoi and so occupies a uniquely important evolutionary position in the transition from fish to tetrapods. Insulin was isolated from an extract of the pancreas of N. forsteri and its primary structure established as: A-Chain, Gly-Ile-Val-Glu-Gln-Cys-Cys-His-Thr-Pro(10)-Cys-Ser-Leu-Tyr-Gln-Leu-G lu-Asn-Tyr-Cys(20)-Asn-Glu-Thr-Glu; B-Chain, Ala-Ala-Val-Asn-Gln-His-Leu-Cys-Gly-Ser(10)-His-Leu-Val-Glu-Ala-Leu- Tyr-Phe-Val-Cys(20)-Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Leu-Pro- Lys(30)-Gly. This amino acid sequence is more similar to that of human insulin than to insulins from present-day amphibians. All the residues in human insulin that are considered to be important in receptor binding, dimerization, and hexamerization are conserved in lungfish insulin except for the substitution (Leu --> Phe) at the position corresponding to B17 in human insulin. Consistent with the assertion that the Dipnoi is a monophyletic group, insulins from N. forsteri and from the African lungfish Protopterus annectens contain extensions to the C-terminus of the A-chain and to the N-terminus of the B-chain that have not been found in other sarcopterygian species. However, the unusual amino acid substitutions found in insulin from P. annectens (e.g., GlyB21 --> Ala, GluB22 --> Asp, and ArgB23 --> Asn) are not present in N. forsteri insulin, suggesting that they occurred in the Protopterus lineage after divergence of the genera.

Bradykinin and its receptors in non-mammalian vertebrates

The generation of bradykinin (BK) in blood by the action of the kallikrein-kinin system has been studied intensively in mammals but the system has received relatively little attention in non-mammalian vertebrates. The plasma of crocodilians and Testudines (turtles and tortoises) contains all the components of the kallikrein-kinin system found in mammals (prekallikrein activator, prekallikrein, kininogen, and kininases) and activation results in generation of [Thr6]-BK. Plasma of birds and snakes probably lacks a prekallikrein activator analogous to mammalian Factor XII but treatment with exogenous proteases (pig pancreatic kallikrein and/or trypsin) generates [Thr6, Leu8]-BK (chicken), [Ala1, Thr6]-BK (python) and [Val1, Thr6]-BK (colubrid snakes). The skins of certain frogs, particularly of the genus Rana, contain very high concentrations of BK-related peptides but their pathway of biosynthesis involves the action of cellular endoproteinase(s) cleaving at the site of single arginyl residues rather than by the action of the kallikrein-kinin system. Evidence for a prekallikrein activator in fish plasma is lacking but treatment with exogenous proteases generates [Arg0, Trp5, Leu8]-BK (trout and cod), [Trp5]-BK (bowfin and gar), [Met1, Met5]-BK (sturgeon). The cardiovascular actions and effects upon gastrointestinal smooth muscle of these peptides in their species of origin differ markedly. For example, intra-arterial injections of the native BK peptides into unanesthetized fish produce transient hypertension in the cod, complex depressor and pressor responses in the trout and bowfin and hypotension in the sturgeon. Pharmacological studies in snakes and fish and with the recombinantally expressed chicken BK receptor have demonstrated that the BK receptors in the tissues of non-mammalian vertebrates have appreciably different ligand binding properties from the well-characterized mammalian B1 and B2 receptors.

Characterization of bradykinin-related peptides generated in the plasma of six sarcopterygian species (African lungfish, amphiuma, coachwhip, bullsnake, gila monster, and Gray's monitor)

Incubation of heat-denatured plasma from six species occupying different evolutionary positions within the Sarcopterygian lineage [the dipnoan, Protopterus annectens (African lungfish); the urodele, Amphiuma tridactylum (three-toed amphiuma); the colubrid snakes, Pituophis melanoleucus sayi (bullsnake) and Masticophis flagellum (coachwhip); and the lizards Heloderma suspectum (Gila monster) and Varanus Grayi (Gray's monitor)] with trypsin generated bradykinin-related peptides that were detected by radioimmunoassay using an antiserum raised against mammalian bradykinin (BK). The peptides were purified by HPLC and their primary structures were established as lungfish [Tyr1,Gly2,Ala7,Pro8]BK, amphiuma [Phe1,Ile2, Leu5]BK, bullsnake and coachwhip [Val1,Thr6]BK, Gila monster [Leu2, Thr6]BK, and Gray's monitor [Thr6]BK. Monitor BK is identical to the peptide generated in turtle and alligator plasma and coachwhip/bullsnake BK shows one amino acid substitution (Ala1 --> Val) compared with the peptide generated in the plasma of the python. The data provide further evidence for the widespread occurrence of a kallikrein-kininogen system in nonmammalian vertebrates but indicate that the primary structure of BK has been poorly conserved during evolution.

Non-respiratory blood vessels in Latimeria gill filaments

A study of the blood pathways within the gills ofLatimeriahas been carried out using light and transmission electron microscopy. Clear evidence has been found for the presence of a secondary non–respiratory circulation in addition to the well–established respiratory pathway through the gill lamellae. All essential components of this system have been observed and have the same relationships and basic structure as comparable secondary systems in actinopterygian and elasmobranch fishes. These include a central venous sinus (CVS), arterio–venous anastomoses (AVAs) and central filament arteries (CFAs). AVAs connect both arterial vessels of the primary circulation and CFAs of the secondary circulation to the CVS. The latter contained many red blood cells. The presence of this secondary circulation inLatimeriagills contrasts with the situation in the gills of the three living genera of lungfishes where a system possessing the essential features of the tetrapod lymphatic vessel system has been recognized. No suggestions of a true lymphatic vessel system were observed inLatimeria. Other features of gill and vascular anatomy inLatimeriashow its closer relationship to dipnoans than other groups of living fishes but evidence derived from this study of the secondary circulation clearly supports the view that the Dipnoi rather thanLatimeriarepresent the living fishes most closely related to the tetrapods.

Primary structure of insulin from the african lungfish, Protopterus annectens

Among the extant Sarcopterygii, the interrelationship between the Dipnoi (lungfishes), Actinistia (coelacanths), and Tetrapoda (tetrapods) is controversial. Insulin has been purified from an extract of the pancreas of the African lungfish Protopterus annectens and its primary structure established as A-chain, Gly-Ile-Val-Glu-Gln-Cys-Cys-His-Lys-Pro10-Cys-Ser-Leu- Tyr -Glu-Leu-Glu-Asn-Tyr-Cys20-Asn-Val-Pro; and B-chain, Ala-Val-Leu-Asn-Gln-His-Leu-Cys-Gly-Ser10-His-Leu-Val- Glu- Ala-Leu-Tyr-Leu-Val-Cys20-Ala-Asp-Asn-Gly-Phe- Phe-Tyr-Lys-Pro-Ser30-Gly. Lungfish insulin contains unusual structural features, such as the dipeptide extension to the C-terminus of the A-chain and the substitution Arg --> Asn at position B-23 in the putative receptor binding region of insulin, which may be expected to influence appreciably its biological potency relative to mammalian insulins. Lungfish insulin also contains amino acid substitutions such as Gly --> Ala at position B-21, Glu --> Asp at position B-22, and a Lys --> Ser residue at position B-30, previously found in insulins from amphibia. This observation is consistent with paleontological data suggesting that lungfish and amphibia share a close phylogenetic relationship.

Homologies in the fossil record: the middle ear as a test case

This paper examines the middle ear of fossil living animals in terms of the homologies which have been drawn between its parts in different vertebrate groups. Seven homologies are considered: 1, the middle ear cavity/spiracular pouch; 2, the stapes/hyomandibula; 3, the stapedial/hyomandibular processes; 4 the tympanic membrane; 5, the otic notch; 6, the fenestra ovalis; 7, and the stapedial/hyomandibular foramen. The reasons leading to assessments of homology are reviewed. Homologies 1 and 2, based largely on embryological evidence, are fairly robust, though there are arguments about the details. Homologies 3, 4 and 5 stem from ideas about early tetrapod evolution, and were influenced by contingent factors including the order and time of discovery of early fossil taxa, and perceptions of their phylogeny which resulted from this. They were also influenced by ideas of the evolution of terrestriality among tetrapods. Most of the conceptions have been overturned in recent years by new fossil discoveries and new ways of looking at old data. Homology 6 has been little considered. One possible hypothesis, placed in a strictly 'archetypal' theoretical framework has been ignored but deserves consideration on other grounds. Homology 7 depends on how tetrapods are characterised, not a question which has posed difficulties until recently, but which is likely to with the discovery of intermediate fossil forms.

Edgeworth's legacy of cranial muscle development with an analysis of muscles in the ventral gill arch region of batoid fishes (Chondrichthyes: Batoidea)

A series of studies by Edgeworth demonstrated that cranial muscles of gnathostome fishes are embryologically of somitic origin, originating from the mandibular, hyoid, branchial, epibranchial, and hypobranchial muscle plates. Recent experimental studies using quail-chick chimeras support Edgeworth's view on the developmental origin of cranial muscles. One of his findings, the existence of the premyogenic condensation constrictor dorsalis in teleost fishes, has also been confirmed by molecular developmental studies. Therefore, developmental mechanisms for patterning of cranial muscles, as described and implicated by Edgeworth, may serve as structural entities or regulatory phenomena responsible for developmental and evolutionary changes. With Edgeworth's and other studies as background, muscles in the ventral gill arch region of batoid fishes are analyzed and compared with those of other gnathostome fishes. The spiracularis is regarded as homologous at least within batoid fishes, but its status within elasmobranchs remains unclear; developmental modifications of the spiracularis proper are evident in some batoid fishes and in several shark groups. The peculiar ventral extension of the spiracularis in electric rays and some stingrays may represent convergence, probably facilitating ventilation and/or feeding in both groups. The evolutionary origin of the "internus" and "externus" remains uncertain, despite the fact that a variety of forms of the constrictor superficiales ventrales in batoid fishes indicates an actual medio-ventral extension of the "externus." The intermandibularis is probably present only in electric rays. The "X" muscle occurs only in electric rays and is considered to be Edgeworth's intermandibularis profundus. Its association with the adductor mandibular complex in narkinidid and narcinidid electric rays may relate to its functional role in lower jaw movement. Contrary to common belief, in most batoid fishes as well as some sharks, muscles that originate from the branchial muscle plate and extend medially in the ventral gill arches do exist: the medial extension of the interbranchiales in most batoid fishes and some sharks and the "Y" muscle in the pelagic stingrays Myliobatos and Rhinoptera. The latter is another example of the medial extension of the "internus." Whether the interbranchiales and "Y" muscle are homologous within elasmobranchs and whether homologous with the obliques ventrales and/or transversi ventrales of osteichthyan fishes await further research. Four hypobranchial muscles are recognized in batoid fishes: the coracomandibularis, coracohyoideus, coracoarcualis, and coracohyomandibularis. The coracohyoideus is discrete from the coracoarcualis; its complete structural separation from the latter occurs in several groups of batoid fishes.(ABSTRACT TRUNCATED AT 400 WORDS)