Resurrecting embryos of the tuatara,Sphenodon punctatus,to resolve vertebrate phallus evolution

The breadth of anatomical and functional diversity among amniote external genitalia has led to uncertainty about the evolutionary origins of the phallus. In several lineages, including the tuatara, Sphenodon punctatus, adults lack an intromittent phallus, raising the possibility that the amniote ancestor lacked external genitalia and reproduced using cloacal apposition. Accordingly, a phallus may have evolved multiple times in amniotes. However, similarities in development across amniote external genitalia suggest that the phallus may have a single evolutionary origin. To resolve the evolutionary history of amniote genitalia, we performed three-dimensional reconstruction of Victorian era tuatara embryos to look for embryological evidence of external genital initiation. Despite the absence of an intromittent phallus in adult tuataras, our observations show that tuatara embryos develop genital anlagen. This illustrates that there is a conserved developmental stage of external genital development among all amniotes and suggests a single evolutionary origin of amniote external genitalia.     

A Phylogenetic Perspective on Locomotory Strategies in Early Amniotes

Past approaches to understanding the evolution of locomotorystrategies among Paleozoic amniotes ("primitive reptiles" ofprevious parlance) have been influenced by preservational bias:early occurrences of some amniote taxa were used to polarizethe acquisition or development of locomotory structures amongthe earliest amniotes. Using a phylogeny representing the currentconsensus in the literature, we investigate the major locomotorystrategies that have been posited for Paleozoic amniotes (basalsynapsids on one hand and early reptiles on the other) by optimizingthe major locomotory styles identified for these taxa onto theconsensus tree, in order to present an overview of the patternof evolution of locomotory strategies inherited and adoptedby various amniote lineages.     

Origin of dental occlusion in tetrapods: signal for terrestrial vertebrate evolution?

Evolutionary changes of the dentition in tetrapods can be associated with major events in the history of terrestrial vertebrates. Dental occlusion, the process by which teeth from the upper jaw come in contact with those in the lower jaw, appears first in the fossil record in amniotes and their close relatives near the Permo-Carboniferous boundary approximately 300 million years ago. This evolutionary innovation permitted a dramatic increase in the level of oral processing of food in these early tetrapods, and has been generally associated with herbivory. Whereas herbivory in extinct vertebrates is based on circumstantial evidence, dental occlusion provides direct evidence about feeding strategies because jaw movements can be reconstructed from the wear patterns of the teeth. Examination of the evolution of dental occlusion in Paleozoic tetrapods within a phylogenetic framework reveals that this innovation developed independently in several lineages of amniotes, and is represented by a wide range of dental and mandibular morphologies. Dental occlusion also developed within diadectomorphs, the sister taxon of amniotes. The independent, multiple acquisition of this feeding strategy represents an important signal in the evolution of complex terrestrial vertebrate communities, and the first steps in the profound changes in the pattern of trophic interactions in terrestrial ecosystems.     

Prey processing in amniotes: biomechanical and behavioral patterns of food reduction

In this paper we examine the biomechanics of prey processing behavior in the amniotes. Whether amniotes swallow prey items whole or swallow highly processed slurries or boluses of food, they share a common biomechanical system where hard surfaces (teeth or beaks) are brought together on articulated jaws by the actions of adductor muscles to grasp and process food. How have amniotes modified this basic system to increase the chewing efficiency of the system? To address this question we first examine the primitive condition for prey processing representative of many of the past and present predatory amniotes. Because herbivory is expected to be related to improved prey processing in the jaws we review patterns of food processing mechanics in past and present herbivores. Herbivory has appeared numerous times in amniotes and several solutions to the task of chewing plant matter have appeared. Birds have abandoned jaw chewing in favor of a new way to chew--with the gut--so we will detour from the jaws to examine the appearance of gut chewing in the archosaurs. We will then fill in the gaps among amniote taxa with a look at some new data on patterns of prey processing behavior and jaw mechanics in lizards. Finally, we examine evolutionary patterns of amniote feeding mechanism and how correlates of chewing relate to the need to increase the efficiency of prey processing in order to facilitate increased metabolic rate and activity.     

The Oldest Caseid Synapsid from the Late Pennsylvanian of Kansas,and the Evolution of Herbivory in Terrestrial Vertebrates

The origin and early evolution of amniotes (fully terrestrial vertebrates) led to major changes in the structure and hierarchy of terrestrial ecosystems. The first appearance of herbivores played a pivotal role in this transformation. After an early bifurcation into Reptilia and Synapsida (including mammals) 315 Ma, synapsids dominated Paleozoic terrestrial vertebrate communities, with the herbivorous caseids representing the largest vertebrates on land. Eocasea martini gen. et sp. nov., a small carnivorous caseid from the Late Carboniferous, extends significantly the fossil record of Caseidae, and permits the first clade-based study of the origin and initial evolution of herbivory in terrestrial tetrapods. Our results demonstrate for the first time that large caseid herbivores evolved from small, non-herbivorous caseids. This pattern is mirrored by three other clades, documenting multiple, independent, but temporally staggered origins of herbivory and increase in body size among early terrestrial tetrapods, leading to patterns consistent with modern terrestrial ecosystem.     

The oldest known amniotic embryos suggest viviparity in mesosaurs

The earliest undisputed crown-group amniotes date back to the Late Carboniferous, but the fossil record of amniotic eggs and embryos is very sparse, with the oldest described examples being from the Triassic. Here, we report exceptional, well-preserved amniotic mesosaur embryos from the Early Permian of Uruguay and Brazil. These embryos provide the earliest direct evidence of reproductive biology in Paleozoic amniotes. The absence of a recognisable eggshell and the occurrence of a partially articulated, but well-preserved embryo within an adult individual suggest that mesosaurs were viviparous or that they laid eggs in advanced stages of development. Our finds represent the only known documentation of amniotic embryos in the Paleozoic and the earliest known case of viviparity, thus extending the record of these reproductive strategies by 90 and 60 Ma, respectively.     

Evolutionary genomics of chromoviruses in eukaryotes

The diversity, origin, and evolution of chromoviruses in Eukaryota were examined using the massive amount of genome sequence data for different eukaryotic lineages. A surprisingly large number of novel full-length chromoviral elements were found, greatly exceeding the number of the known chromoviruses. These new elements are mostly structurally intact and highly conserved. Chromoviruses in the key Amniota lineage, the reptiles, have been analyzed by PCR to explain their evolutionary dynamics in amniotes. Phylogenetic analyses provide evidence for a novel centromere-specific chromoviral clade that is widespread and highly conserved in all seed plants. Chromoviral diversity in plants, fungi, and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. The age of plant chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages, the green and the red algae. The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa. The evolutionary history and dynamics of chromoviruses can be explained simply by strict vertical transmission in plants, followed by more complex evolution in fungi and in Metazoa. The currently available data clearly show that chromoviruses indeed represent the oldest and the most widespread clade of Metaviridae.     

The importance of global parsimony and historical bias in understanding tetrapod evolution. Part I. Systematics,middle ear evolution and jaw suspension

A phylogenetic analysis based on a data matrix of 43 taxa and 155 osteological characters has produced a new hypothesis of tetrapod phylogeny that is drastically different from the established consensus. Among Paleozoic taxa, only diadectomorphs appear to be related to amniotes. In contrast to previous hypotheses, lissamphibians appear to have been derived from lepospondyls. Seymouriamorphs, gephyrostegids, embolomeres, temnospondyls, and loxommatids are stem-tetrapods. The new phylogeny suggests that the absence of a tympanic middle ear in salamanders and gymnophiones is a primitive character.     

A detailed redescription of the mesoderm/neural crest cell boundary in the murine orbitotemporal region integrates the mammalian cranium into a pan-amniote cranial configuration

The morphology of the mammalian chondrocranium appears to differ significantly from those of other amniotes, since the former possesses uniquely developed brain and cranial sensory organs. In particular, a question has long remained unanswered as to the developmental and evolutionary origins of a cartilaginous nodule called the ala hypochiasmatica. In this study, we investigated the embryonic origin of skeletal elements in the murine orbitotemporal region by combining genetic cell lineage analysis with detailed morphological observation. Our results showed that the mesodermal embryonic environment including the ala hypochiasmatica, which appeared as an isolated mesodermal distribution in the neural crest-derived prechordal region, is formed as a part of the mesoderm that continued from the chordal region during early chondrocranial development. The mesoderm/neural crest cell boundary in the head mesenchyme is modified through development, resulting in the secondary mesodermal expansion to invade into the prechordal region. We thus revealed that the ala hypochiasmatica develops as the frontier of the mesodermal sheet stretched along the cephalic flexure. These results suggest that the mammalian ala hypochiasmatica has evolved from a part of the mesodermal primary cranial wall in ancestral amniotes. In addition, the endoskeletal elements in the orbitotemporal region, such as the orbital cartilage, suprapterygoid articulation of the palatoquadrate, and trabecula, some of which were once believed to represent primitive traits of amniotes and to be lost in the mammalian lineage, have been confirmed to exist in the mammalian cranium. Consequently, the mammalian chondrocranium can now be explained in relation to the pan-amniote cranial configuration.     

GPR15–C10ORF99 functional pairing initiates colonic Treg homing in amniotes

Regulatory T lymphocyte (Treg) homing reactions mediated by G protein‐coupled receptor (GPCR)–ligand interactions play a central role in maintaining intestinal immune homeostasis by restraining inappropriate immune responses in the gastrointestinal tract. However, the origin of Treg homing to the colon remains mysterious. Here, we report that the C10ORF99 peptide (also known as CPR15L and AP57), a cognate ligand of GPR15 that controls Treg homing to the colon, originates from a duplication of the flanking CDHR1 gene and is functionally paired with GPR15 in amniotes. Evolutionary analysis and experimental data indicate that the GPR15–C10ORF99 pair is functionally conserved to mediate colonic Treg homing in amniotes and their expression patterns are positively correlated with herbivore diet in the colon. With the first herbivorous diet in early amniotes, a new biological process (herbivorous diet short‐chain fatty acid‐C10ORF99/GPR15‐induced Treg homing colon immune homeostasis) emerged, and we propose an evolutionary model whereby GPR15–C10ORF99 functional pairing has initiated the first colonic Treg homing reaction in amniotes. Our findings also highlight that GPCR–ligand pairing leads to physiological adaptation during vertebrate evolution.     

Parsimony-based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg

The origin of the amniotic egg was a major event in vertebrate evolution and is thought to have contributed to the spectacular evolutionary radiation of amniotes. We test one of the most popular scenarios proposed by Carroll in 1970 to explain the origin of the amniotic egg using a novel method based on an asymmetric version of linear parsimony (aka Wagner parsimony) for identifying the most parsimonious split of a tree into two parts between which the evolution of the character is allowed to differ. The new method evaluates the cost of splitting a phylogenetic tree at a given node as the integral, over all pairs of asymmetry parameters, of the most parsimonious costs that can be achieved by using the first parameter on the subtree pending from this node and the second parameter elsewhere. By testing all the nodes, we then obtain the most parsimonious split of a tree with regard to the character values at its tips. Among the nine trees and two characters tested, our method yields a total of 517 parsimonious trend changes in Permo-Carboniferous stegocephalians, a single one of which occurs in a part of the tree (among stem-amniotes) where Carroll's scenario predicts that there should have been distinct changes in body size evolutionary trends. This refutes the scenario because the amniote stem does not appear to have elevated rates of evolutionary trend shifts. Our nodal body size estimates offer less discriminating power, but they likewise fail to find strong support for Carroll's scenario.     

Of chicken wings and frog legs: a smorgasbord of evolutionary variation in mechanisms of tetrapod limb development

The tetrapod limb, which has served as a paradigm for the study of development and morphological evolution, is becoming a paradigm for developmental evolution as well. In its origin and diversification, the tetrapod limb has undergone a great deal of remodeling. These morphological changes and other evolutionary phenomena have produced variation in mechanisms of tetrapod limb development. Here, we review that variation in the four major clades of limbed tetrapods. Comparisons in a phylogenetic context reveal details of development and evolution that otherwise may have been unclear. Such details include apparent differences in the mechanisms of dorsal-ventral patterning and limb identity specification between mouse and chick and mechanistic novelties in amniotes, anurans, and urodeles. As we gain a better understanding of the details of limb development, further differences among taxa will be revealed. The use of appropriate comparative techniques in a phylogenetic context thus sheds light on evolutionary transitions in limb morphology and the generality of developmental models across species and is therefore important to both evolutionary and developmental biologists.     

Sesamoids and Morphological Variation: a Hypothesis on the Origin of Rod-like Skeletal Elements in Aerial Mammals

Enigmatic rod-like skeletal structures that support compliant membranes (patagia) in aerial mammals have been often considered as neomorphic elements or as evolutionary novelties, and their origin has remained poorly understood. A potential source of skeletal plasticity and, probably, of morphofunctional innovations are sesamoids, which were recently demonstrated to have a common cellular origin with bone eminences. In this review, I compile information regarding anatomy, evolution, and development of rod-like skeletal elements in extant gliding and flying mammals and propose a working hypothesis on the origin of these structures. Rod-like skeletal elements, namely, the calcar in bats (Chiroptera), the unciform element in Anomaluridae (Rodentia), and the styliform cartilage in Pteromyini (Rodentia: Sciuridae), would derive from sesamoids, which, in turn, would have the same origin as eminences of long bones (or bones with a long-bone-like growth), i.e., calcaneus, ulna, and pisiform, respectively. Rod-like skeletal elements exhibit several features of sesamoids. However, further developmental data are needed to confirm this hypothesis, particularly whether these structures share a cellular origin and molecular developmental pathways with sesamoids and bone eminences. If this hypothesis were supported, a new role for sesamoids in generating morphofunctional innovations in mammals and, potentially, in other aerial amniotes, would be recognized. Rod-like skeletal elements, which are key in the evolution of aerial locomotion, might constitute an example of pre-existing traits that acquire novel functions through relatively little developmental plasticity.

     

Evolution of closely linked gene pairs in vertebrate genomes

The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos). We show here that a lack of head-to-tail (h2t) gene duos is an even more distinctive characteristic of mammalian genomes, with the platypus genome as the only exception. In nonmammalian vertebrate and in nonvertebrate genomes, the frequency of h2h, h2t, and tail-to-tail (t2t) gene duos is close to random. In tetrapod genomes, the h2t and t2t gene duos are more likely to be part of a larger gene cluster of closely spaced genes than h2h gene duos; in fish and urochordate genomes, the reverse is seen. In human and mouse tissues, the expression profiles of gene duos were skewed toward positive coexpression, irrespective of orientation. The organization of orthologs of both members of about 40% of the human gene duos could be traced in other species, enabling a prediction of the organization at the branch points of gnathostomes, tetrapods, amniotes, and euarchontoglires. The accumulation of h2h gene duos started in tetrapods, whereas that of h2t and t2t gene duos only started in amniotes. The apparent lack of evolutionary conservation of h2t and t2t gene duos relative to that of h2h gene duos is thus a result of their relatively late origin in the lineage leading to mammals; we show that once they are formed h2t and t2t gene duos are as stable as h2h gene duos.     

Hedgehog regulation of superficial slow muscle fibres in Xenopus and the evolution of tetrapod trunk myogenesis

In tetrapod phylogeny, the dramatic modifications of the trunk have received less attention than the more obvious evolution of limbs. In somites, several waves of muscle precursors are induced by signals from nearby tissues. In both amniotes and fish, the earliest myogenesis requires secreted signals from the ventral midline carried by Hedgehog (Hh) proteins. To determine if this similarity represents evolutionary homology, we have examined myogenesis in Xenopus laevis, the major species from which insight into vertebrate mesoderm patterning has been derived. Xenopus embryos form two distinct kinds of muscle cells analogous to the superficial slow and medial fast muscle fibres of zebrafish. As in zebrafish, Hh signalling is required for XMyf5 expression and generation of a first wave of early superficial slow muscle fibres in tail somites. Thus, Hh-dependent adaxial myogenesis is the likely ancestral condition of teleosts, amphibia and amniotes. Our evidence suggests that midline-derived cells migrate to the lateral somite surface and generate superficial slow muscle. This cell re-orientation contributes to the apparent rotation of Xenopus somites. Xenopus myogenesis in the trunk differs from that in the tail. In the trunk, the first wave of superficial slow fibres is missing, suggesting that significant adaptation of the ancestral myogenic programme occurred during tetrapod trunk evolution. Although notochord is required for early medial XMyf5 expression, Hh signalling fails to drive these cells to slow myogenesis. Later, both trunk and tail somites develop a second wave of Hh-independent slow fibres. These fibres probably derive from an outer cell layer expressing the myogenic determination genes XMyf5, XMyoD and Pax3 in a pattern reminiscent of amniote dermomyotome. Thus, Xenopus somites have characteristics in common with both fish and amniotes that shed light on the evolution of somite differentiation. We propose a model for the evolutionary adaptation of myogenesis in the transition from fish to tetrapod trunk.     

Inner ear morphology of diadectomorphs and seymouriamorphs (Tetrapoda) uncovered by high-resolution x-ray microcomputed tomography,and the origin of the amniote crown group

The origin of amniotes was a key event in vertebrate evolution, enabling tetrapods to break their ties with water and invade terrestrial environments. Two pivotal clades of early tetrapods, the diadectomorphs and the seymouriamorphs, have played an unsurpassed role in debates about the ancestry of amniotes for over a century, but their skeletal morphology has provided conflicting evidence for their affinities. Using high-resolution X-ray microcomputed tomography, we reveal the three-dimensional architecture of the well preserved endosseous labyrinth of the inner ear in representative species belonging to both groups. Data from the inner ear are coded in a new cladistic matrix of stem and primitive crown amniotes. Both maximum parsimony and Bayesian inference analyses retrieve seymouriamorphs as derived non-crown amniotes and diadectomorphs as sister group to synapsids. If confirmed, this sister group relationship invites re-examination of character polarity near the roots of the crown amniote radiation. Major changes in the endosseous labyrinth and adjacent braincase regions are mapped across the transition from non-amniote to amniote tetrapods and include: a ventral shift of the cochlear recess relative to the vestibule and the semicircular canals; cochlear recess (primitively housed exclusively within the opisthotic) accommodated within both the prootic and the opisthotic; development of a distinct fossa subarcuata. The inner ear of seymouriamorphs foreshadows conditions of more derived groups, whereas that of diadectomorphs shows a mosaic of plesiomorphic and apomorphic traits, some of which are unambiguously amniote-like, including a distinct and pyramid-like cochlear recess.     

The Evolutionary Implications of Hemipenial Morphology of Rattlesnake Crotalus durissus terrificus (Laurent, 1768) (Serpentes: Viperidae: Crotalinae)

Most amniotes vertebrates have an intromittent organ to deliver semen. The reptile Sphenodon and most birds lost the ancestral penis and developed a cloaca-cloaca mating. Known as hemipenises, the copulatory organ of Squamata shows unique features between the amniotes intromittent organ. They are the only paired intromittent organs across amniotes and are fully inverted and encapsulated in the tail when not in use. The histology and ultrastructure of the hemipenes of Crotalus durissus rattlesnake is described as the evolutionary implications of the main features discussed. The organization of hemipenis of Crotalus durissus terrificus in two concentric corpora cavernosa is similar to other Squamata but differ markedly from the organization of the penis found in crocodilians, testudinata, birds and mammals. Based on the available data, the penis of the ancestral amniotes was made of connective tissue and the incorporation of smooth muscle in the framework of the sinusoids occurred independently in mammals and Crotalus durissus. The propulsor action of the muscle retractor penis basalis was confirmed and therefore the named should be changed to musculus hemipenis propulsor.The retractor penis magnus found in Squamata has no homology to the retractor penis of mammals, although both are responsible for the retraction of the copulatory organ.     

Histological microstructure of the claws of the African clawed frog, Xenopus laevis (Anura: Pipidae): implications for the evolution of claws in tetrapods

Claws are consistent components of amniote anatomy and may thus be implicated in the success of the amniote invasion of land. However, the evolutionary origin of these structures in tetrapods is unclear. Claws are present in certain extant non-amniotes, such as Xenopus laevis, the African clawed frog. The histology of the soft tissue component of the claws of X. laevis is described and compared with the amniote condition in order to gain new information on the question of homology of claws in these two groups based on patterns of keratinization.The X. laevis claw sheath is composed of a localized thickening of the corneous region of the epidermis that envelops the terminal phalanx. Noted differences between the non-cornified layers of the epidermis of the claw and non-claw region are the overall grainier appearance of the cells and an increased abundance of desmosomes in the intermediate spinosus cells. The biochemical identity of the sheath keratin(s) is inferred to be different from that of non-claw region epidermis, based on histological differences and differences in stain affinity between the two regions. The microstructure of the frog claw differs from that of amniotes in several respects, including the lack of a specified zone of growth near the base of the claw. Amphibians and amniotes, therefore, have very different patterns of claw sheath growth. Observations do not support homology of claws on a structural level in these two groups; however, further experimental work may confirm a conserved pattern of cornification in these structures in tetrapods.     

Endocrine Activity of Extraembryonic Membranes Extends beyond Placental Amniotes

Background

During development, all amniotes (mammals, reptiles, and birds) form extraembryonic membranes, which regulate gas and water exchange, remove metabolic wastes, provide shock absorption, and transfer maternally derived nutrients. In viviparous (live-bearing) amniotes, both extraembryonic membranes and maternal uterine tissues contribute to the placenta, an endocrine organ that synthesizes, transports, and metabolizes hormones essential for development. Historically, endocrine properties of the placenta have been viewed as an innovation of placental amniotes. However, an endocrine role of extraembryonic membranes has not been investigated in oviparous (egg-laying) amniotes despite similarities in their basic structure, function, and shared evolutionary ancestry. In this study, we ask whether the oviparous chorioallantoic membrane (CAM) of chicken (Gallus gallus) has the capability to synthesize and receive signaling of progesterone, a major placental steroid hormone.

Methodology/Principal Findings

We quantified mRNA expression of key steroidogenic enzymes involved in progesterone synthesis and found that 3β-hydroxysteroid dehydrogenase, which converts pregnenolone to progesterone exhibited a 464 fold increase in the CAM from day 8 to day 18 of embryonic development (F_{5, 68} = 89.282, p<0.0001). To further investigate progesterone synthesis, we performed explant culture and found that the CAM synthesizes progesterone in vitro in the presence of a steroid precursor. Finally, we quantified mRNA expression and performed protein immunolocalization of the progesterone receptor in the CAM.

Conclusions/Significance

Collectively, our data indicate that the chick CAM is steroidogenic and has the capability to both synthesize progesterone and receive progesterone signaling. These findings represent a paradigm shift in evolutionary reproductive biology by suggesting that endocrine activity of extraembryonic membranes is not a novel characteristic of placental amniotes. Rather, we hypothesize that these membranes may share an additional unifying characteristic, steroidogenesis, across amniotes at large.