Turtle origins: insights from phylogenetic retrofitting and molecular scaffolds

Adding new taxa to morphological phylogenetic analyses without substantially revising the set of included characters is a common practice, with drawbacks (undersampling of relevant characters) and potential benefits (character selection is not biased by preconceptions over the affinities of the ‘retrofitted’ taxon). Retrofitting turtles (Testudines) and other taxa to recent reptile phylogenies consistently places turtles with anapsid‐grade parareptiles (especially Eunotosaurus and/or pareiasauromorphs), under both Bayesian and parsimony analyses. This morphological evidence for turtle–parareptile affinities appears to contradict the robust genomic evidence that extant (living) turtles are nested within diapsids as sister to extant archosaurs (birds and crocodilians). However, the morphological data are almost equally consistent with a turtle–archosaur clade: enforcing this molecular scaffold onto the morphological data does not greatly increase tree length (parsimony) or reduce likelihood (Bayesian inference). Moreover, under certain analytic conditions, Eunotosaurus groups with turtles and thus also falls within the turtle–archosaur clade. This result raises the possibility that turtles could simultaneously be most closely related to a taxon traditionally considered a parareptile (Eunotosaurus) and still have archosaurs as their closest extant sister group.     

Temporal bone arrangements in turtles: an overview

The temporal region of turtles is characterized by significant anatomical diversity. Turtles show a pure anapsid morphotype that exhibits various different marginal reductions known as emarginations. As a result of this diversity, turtles can be taken as a model by which to understand the processes that may have resulted in the highly debated anatomy of the amniote temporal region in general. In this review on almost forgotten literature, I summarize ten potential factors that may act on the skull to shape the temporal region of turtles. These are: (1) phylogenetic constraints, (2) skull weights, (3) type of food, (4) skull dimensions, (5) muscle bulging, (6) ear anatomy and jaw muscle bending mechanisms, (7) extent and nature of muscle attachment sites, (8) internal forces within the jaw adductor chamber, (9) environmental pressure, and (10) neck bending mechanisms. Particular focus is laid on the interrelationship of the jaw musculature and the dermatocranial armour, which were assumed to influence each other to a certain degree. In the literature, cranial dimensions were assumed to influence temporal bone formation within major tetrapod groups. Among these, turtles seem to represent a kind of intermixture, a phenomenon that may be reflected in their specific anatomy. The references presented should be understood as product of the scientific environment in which they developed and the older literature does not always insist current empirical demands. However, the intuitive and creative ideas and the comprehensive anatomical considerations of these authors may inspire future studies in several fields related to this topic.     

Turtles as diapsid reptiles

Recent molecular studies of amniote relationships show turtles to be diapsid reptiles, related to the archosauromorph branch of saurian phylogeny. This conflicts with palaeontological data which shows turtles to be related either to anapsids, or to the lepidosauromorph branch within diapsids. Archosauromorph relationships of turtles have previously been proposed on the basis of neontological (mostly soft anatomy) characters. This paper reviews the neontological character evidence for turtle relationships and shows that most, but not all, of these characters are invalid in the reconstruction of turtle relationships within Amniota.     

Feeding mechanics in Triassic stem-group sauropterygians: the anatomy of a successful invasion of Mesozoic seas

The jaw adductor musculature in Triassic stem-group sauropterygians is reconstructed on the basis of a paradigmatic model of muscle architecture (functional equivalence of sarcomeres) and using invariant traits of the anatomy of the trigeminal jaw adductor muscles in extant reptiles. The reconstructed jaw adductor musculature predicts trophic specializations in stem-group sauropterygians. Suction feeding is a component in prey capture for some benthic feeding, as well as for some pelagic feeding taxa. The differentiation of 'pincer' jaws is correlated with the potential for rapid, snapping bites. There is some evidence for habitat partitioning among Triassic stem-group sauropterygians with respect to trophic specialization. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 135 , 33–63.     

Diversity of Middle Jurassic Turtles from the Berezovsk Quarry Locality,Krasnoyarsk Region,Russia: Morphology and Histological Study

Abstract—Morphology and histology of several fragmentary turtle specimens from the Middle Jurassic locality in the Berezovsk quarry (Krasnoyarsk Region, Russia) are described, including Testudines indet. 1 (costal VIII), Testudines indet. 2 (two ornamented shell fragments), and Testudines indet. 3 (distal part of a humerus), and also skeletal elements of Annemys sp. (Xinjiangchelyidae) represented by mass material in the same locality. It is shown that Testudines indet. 1 and 3 probably belong to one or two taxa of basal aquatic turtles, while Testudines indet. 2 is most likely an abnormal Annemys sp. The presumable presence of basal turtles in the Berezovsk Quarry Assemblage agrees with the fact that they are present in other Middle Jurassic turtle assemblages of Asia.     

The Head and Neck Anatomy of Sea Turtles (Cryptodira: Chelonioidea) and Skull Shape in Testudines

Background

Sea turtles (Chelonoidea) are a charismatic group of marine reptiles that occupy a range of important ecological roles. However, the diversity and evolution of their feeding anatomy remain incompletely known.

Methodology/Principal Findings

Using computed tomography and classical comparative anatomy we describe the cranial anatomy in two sea turtles, the loggerhead (Caretta caretta) and Kemp’s ridley (Lepidochelys kempii), for a better understanding of sea turtle functional anatomy and morphological variation. In both taxa the temporal region of the skull is enclosed by bone and the jaw joint structure and muscle arrangement indicate that palinal jaw movement is possible. The tongue is relatively small, and the hyoid apparatus is not as conspicuous as in some freshwater aquatic turtles. We find several similarities between the muscles of C. caretta and L. kempii, but comparison with other turtles suggests only one of these characters may be derived: connection of the m. adductor mandibulae internus into the Pars intramandibularis via the Zwischensehne. The large fleshy origin of the m. adductor mandibulae externus Pars superficialis from the jugal seems to be a characteristic feature of sea turtles.

Conclusions/Significance

In C. caretta and L. kempii the ability to suction feed does not seem to be as well developed as that found in some freshwater aquatic turtles. Instead both have skulls suited to forceful biting. This is consistent with the observation that both taxa tend to feed on relatively slow moving but sometimes armoured prey. The broad fleshy origin of the m. adductor mandibulae externus Pars superficialis may be linked to thecheek region being almost fully enclosed in bone but the relationship is complex.     

Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes

Several different groups of birds have been proposed as being the oldest or earliest diverging extant lineage within the avian phylogenetic tree, particularly ratites (Struthioniformes), waterfowl (Anseriformes), and shorebirds (Charadriiformes). Difficulty in resolving this issue stems from several factors, including the relatively rapid radiation of primary (ordinal) bird lineages and the lack of characters from an extant outgroup for birds that is closely related to them by measure of time. To help resolve this question, we have sequenced entire mitochondrial genomes for five birds (a rhea, a duck, a falcon, and two perching birds), one crocodilian, and one turtle. Maximum parsimony and maximum likelihood analyses of these new sequences together with published sequences (18 taxa total) yield the same optimal tree topology, in which a perching bird (Passeriformes) is sister to all the other bird taxa. A basal position for waterfowl among the bird study taxa is rejected by maximum likelihood analyses. However, neither the conventional view, in which ratites (including rhea) are basal to other birds, nor tree topologies with falcon or chicken basal among birds could be rejected in the same manner. In likelihood analyses of a subset of seven birds, alligator, and turtle (9 taxa total), we find that increasing the number of parameters in the model shifts the optimal topology from one with a perching bird basal among birds to the conventional view with ratites diverging basally; moreover, likelihood scores for the two trees are not significantly different. Thus, although our largest set of taxa and characters supports a tree with perching birds diverging basally among birds, the position of this earliest divergence among birds appears unstable. Our analyses indicate a sister relationship between a waterfowl/chicken clade and ratites, relative to perching birds and falcon. We find support for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis (birds and mammals as sister taxa) and the placement of turtles as basal within the phylogenetic tree for amniote animals.     

A new, nearly complete stem turtle from the Jurassic of South America with implications for turtle evolution

Turtles have been known since the Upper Triassic (210Myr old); however, fossils recording the first steps of turtle evolution are scarce and often fragmentary. As a consequence, one of the main questions is whether living turtles (Testudines) originated during the Late Triassic (210Myr old) or during the Middle to Late Jurassic (ca 160Myr old). The discovery of the new fossil turtle, Condorchelys antiqua gen. et sp. nov. from the Middle to Upper Jurassic (ca 160-146Myr old) of South America (Patagonia, Argentina), presented here sheds new light on early turtle evolution. An updated cladistic analysis of turtles shows that C. antiqua and other fossil turtles are not crown turtles, but stem turtles. This cladistic analysis also shows that stem turtles were more diverse than previously thought, and that until the Middle to Upper Jurassic there were turtles without the modern jaw closure mechanism.     

MicroRNAs support a turtle + lizard clade

Despite much interest in amniote systematics, the origin of turtles remains elusive. Traditional morphological phylogenetic analyses place turtles outside Diapsida-amniotes whose ancestor had two fenestrae in the temporal region of the skull (among the living forms the tuatara, lizards, birds and crocodilians)-and allied with some unfenestrate-skulled (anapsid) taxa. Nonetheless, some morphological analyses place turtles within Diapsida, allied with Lepidosauria (tuatara and lizards). Most molecular studies agree that turtles are diapsids, but rather than allying them with lepidosaurs, instead place turtles near or within Archosauria (crocodilians and birds). Thus, three basic phylogenetic positions for turtles with respect to extant Diapsida are currently debated: (i) sister to Diapsida, (ii) sister to Lepidosauria, or (iii) sister to, or within, Archosauria. Interestingly, although these three alternatives are consistent with a single unrooted four-taxon tree for extant reptiles, they differ with respect to the position of the root. Here, we apply a novel molecular dataset, the presence versus absence of specific microRNAs, to the problem of the phylogenetic position of turtles and the root of the reptilian tree, and find that this dataset unambiguously supports a turtle + lepidosaur group. We find that turtles and lizards share four unique miRNA gene families that are not found in any other organisms' genome or small RNA library, and no miRNAs are found in all diapsids but not turtles, or in turtles and archosaurs but not in lizards. The concordance between our result and some morphological analyses suggests that there have been numerous morphological convergences and reversals in reptile phylogeny, including the loss of temporal fenestrae.     

A new stem craniate from the Ordovician of Morocco and the search for the sister group of the craniata

The investigation of the development of the trigeminal jaw adductor musculature in the turtle Chelydra serpentina documents the early aggregation of muscle rudiments around the innervating nerve branches, probably a consequence of inductive interaction. This may explain the early continuity of the intramandibularis with the intermandibularis muscle. Several aspects of muscle development differ in the turtle as compared to lizards. These differences highlight the fact that conjectures of homology, based on a static topographical correspondence of adult structures, cannot capture the dynamics of the developmental process. The intramandibularis muscle of turtles, comparable to that of crocodiles, represents a plesiomorphous structure which is not homologous to the intramandibularis muscle of lacertoid lizards, a derived feature of the Lacertoidea. A derived feature of the chelonian jaw adductor musculature is the posterodorsal expansion of the external adductor along a supraoccipital crest, developing according to a pattern of Haeckelian recapitulation. Muscle development serves to corroborate the concept of a monophyletic Eureptilia, including diapsids and synapsids, as opposed to the (paraphyletic) Anapsida. The impact of the differentiation of the external adductor into a pulley system on cranial kinesis is analysed in biomechanical terms.     

The structure and development of the jaw adductor musculature in the turtle Chelydra serpentina

The investigation of the development of the trigeminal jaw adductor musculature in the turtle Chelydra serpentina documents the early aggregation of muscle rudiments around the innervating nerve branches, probably a consequence of inductive interaction. This may explain the early continuity of the intramandibularis with the intermandibularis muscle. Several aspects of muscle development differ in the turtle as compared to lizards. These differences highlight the fact that conjectures of homology, based on a static topographical correspondence of adult structures, cannot capture the dynamics of the developmental process. The intramandibularis muscle of turtles, comparable to that of crocodiles, represents a plesiomorphous structure which is not homologous to the intramandibularis muscle of lacertoid lizards, a derived feature of the Lacertoidea. A derived feature of the chelonian jaw adductor musculature is the posterodorsal expansion of the external adductor along a supraoccipital crest, developing according to a pattern of Haeckelian recapitulation. Muscle development serves to corroborate the concept of a monophyletic Eureptilia, including diapsids and synapsids, as opposed to the (paraphyletic) Anapsida. The impact of the differentiation of the external adductor into a pulley system on cranial kinesis is analysed in biomechanical terms.     

Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae)

We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously published morphological characters for a complimentary set of 24 species. The combined data set provided complete taxonomic coverage for this globally distributed clade of turtles, with incomplete data for a few taxa. Although our taxonomic sampling is complete, most of the modern taxa are representatives of old and very divergent lineages. Thus, due to biological realities, our sampling consists of one or a few representatives of several ancient lineages across a relatively deep phylogenetic tree. Our analyses of the combined data set converge on a set of well-supported relationships, which is in accord with many aspects of traditional softshell systematics including the monophyly of the Cyclanorbinae and Trionychinae. However, our results conflict with other aspects of current taxonomy and indicate that most of the currently recognized tribes are not monophyletic. We use this strong estimate of the phylogeny of softshell turtles for two purposes: (1) as the basis for a novel rank-free classification, and (2) to retrospectively examine strategies for analyzing highly homoplasious mtDNA data in deep phylogenetic problems where increased taxon sampling is not an option. Weeded and weighted parsimony, and model-based techniques, generally improved the phylogenetic performance of highly homoplasious mtDNA sequences, but no single strategy completely mitigated the problems of associated with these highly homoplasious data. Many deep nodes in the softshell turtle phylogeny were confidently recovered only after the addition of largely nonhomoplasious data from the nuclear intron.     

Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling

Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a data set compiled from published sources and data original to this study supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.     

Myological variability in a decoupled skeletal system: Batoid cranial anatomy

Chondrichthyans (sharks, batoids, and chimaeras) have simple feeding mechanisms owing to their relatively few cranial skeletal elements. However, the indirect association of the jaws to the cranium (euhyostylic jaw suspension) has resulted in myriad cranial muscle rearrangements of both the hyoid and mandibular elements. We examined the cranial musculature of an abbreviated phylogenetic representation of batoid fishes, including skates, guitarfishes and with a particular focus on stingrays. We identified homologous muscle groups across these taxa and describe changes in gross morphology across developmental and functional muscle groups, with the goal of exploring how decoupling of the jaws from the skull has effected muscular arrangement. In particular, we focus on the cranial anatomy of durophagous and nondurophagous batoids, as the former display marked differences in morphology compared to the latter. Durophagous stingrays are characterized by hypertrophied jaw adductors, reliance on pennate versus fusiform muscle fiber architecture, tendinous rather than aponeurotic muscle insertions, and an overall reduction in mandibular kinesis. Nondurophagous stingrays have muscles that rely on aponeurotic insertions onto the skeletal structure, and display musculoskeletal specialization for jaw protrusion and independent lower jaw kinesis, relative to durophagous stingrays. We find that among extant chondrichthyans, considerable variation exists in the hyoid and mandibular muscles, slightly less so in hypaxial muscles, whereas branchial muscles are overwhelmingly conserved. As chondrichthyans occupy a position sister to all other living gnathostomes, our understanding of the structure and function of early vertebrate feeding systems rests heavily on understanding chondrichthyan cranial anatomy. Our findings highlight the incredible variation in muscular complexity across chondrichthyans in general and batoids in particular. J. Morphol. 275:862–881, 2014. © 2014 Wiley Periodicals, Inc.     

Shell bone histology indicates terrestrial palaeoecology of basal turtles

The palaeoecology of basal turtles from the Late Triassic was classically viewed as being semi-aquatic, similar to the lifestyle of modern snapping turtles. Lately, this view was questioned based on limb bone proportions, and a terrestrial palaeoecology was suggested for the turtle stem. Here, we present independent shell bone microstructural evidence for a terrestrial habitat of the oldest and basal most well-known turtles, i.e. the Upper Triassic Proterochersis robusta and Proganochelys quenstedti. Comparison of their shell bone histology with that of extant turtles preferring either aquatic habitats or terrestrial habitats clearly reveals congruence with terrestrial turtle taxa. Similarities in the shell bones of these turtles are a diploe structure with well-developed external and internal cortices, weak vascularization of the compact bone layers and a dense nature of the interior cancellous bone with overall short trabeculae. On the other hand, 'aquatic' turtles tend to reduce cortical bone layers, while increasing overall vascularization of the bone tissue. In contrast to the study of limb bone proportions, the present study is independent from the uncommon preservation of appendicular skeletal elements in fossil turtles, enabling the palaeoecological study of a much broader range of incompletely known turtle taxa in the fossil record.     

Testing phylogenetic implications of eggshell characters in side-necked turtles (Testudines: Pleurodira)

Amniote egg and eggshell morphology is a rich source of characters to link aspects of reproductive biology with systematics. Extensive work concerning both anatomy and phylogenetic assignability has been done on fossil bird and dinosaur eggs, but little is known for extant sauropsids. The utility of eggshell characters for phylogenetic analyses is tested and discussed for extant side-necked turtles (Pleurodira), and the diversity of egg ultrastructure is examined in several species. Egg gross morphology and eggshell ultrastructure of 12 species of extant side-necked turtles was documented using scanning electron microscopy. Thirteen eggshell characters were scored and mapped on a composite phylogeny and ancestral character states were reconstructed. Many of the characters do not show a phylogenetic signal according to a test comparing the number of steps on the chosen phylogeny with that on randomly generated trees. The presence of conservative, clade-supporting features could be demonstrated, and the following clades are supported by several characters: the Elseya-Emydura entity, short-necked Australasian chelids, is backed by two characters, and two additional characters could potentially support this group. Three characters support the monophyly of South American chelids, whereas two characters argue for the exclusion of Hydromedusa, a long-necked form resembling Australian chelids rather than South American forms, from this clade.     

Reptile phylogeny and the interrelationships of turtles

A comprehensive analysis of amniote interrelationships is presented in an attempt to test turtle interrelationships. The results refute earlier hypotheses that turtles are related to parareptiles, i.e. to procolophonids or pareiasaurs. Instead, turtles are shown to be the sister-group of Sauropterygia, the two clades being nested within Sauria as sister-group of Lepidosauriformes. This scenario is also supported by several developmental and soft tissue characters which are shown to be congruent with the current phylogeny. The analysis strongly supports a monophyletic Parareptilia, sister-group of a monophylctic Eurcptilia. The Diapsida, however, is paraphyletic unless it includes turtles and sauropterygians. Additionally, the position of turtles within Diapsida has major implications for the evolutionary history and/or significance of many characters, i.e. temporal fenestration.     

What makes an ophiuroid? A morphological study of the problematic Ordovician stelleroid Stenaster and the palaeobiology of the earliest asteroids and ophiuroids

Extant asteroids and ophiuroids [EchinodermataJ are distinguished by differences in arm support, water vascular system structures and in details of arm and jaw structure. However, some lower Palaeozoic taxa show combinations of both asteroid-like and ophiuroid-like characters and their morphology and functional biology is poorly understood. This paper redescribes one such taxon, the middle-upper Ordovician stellate echinoderm Stenaster and clarifies its phylogenetic status. Characters in common with extant and Ordovician ophiuroids, include arm support due primarily to ambulacral ossicles, presence of extensive longitudinal arm musculature, a mobile jaw and an internalised radial water vessel with internalised podial pores. In addition, Stenaster lacks several characters which are conventionally considered to be asteroid-like, for example an axillary, madreporitc, marginal ossicles and a true ambulacral groove. However, in overall shape Stenaster is remarkably asteroid-like, showing short, broad-based arms shared podial basins and a small disc. A cladistic analysis of early asteroids, ophiuroids and somasteroid taxa consistently places Stenaster within the ophiuroids and suggests secondary convergence to asteroids. In functional terms, Stenaster is interpreted as an ophiuroid which has secondarily adopted a semi-infaunal, deposit-feeding mode of life, analogous to that of some extant paxillosid asteroids.     

Congruence,non‐homology,and the phylogeny of basal turtles

Joyce, W.G. and Sterli J. 2010. Congruence, non‐homology, and the phylogeny of basal turtles.–Acta Zoologica (Stockholm) Modern cladistic analysis is characterized by the assembly of increasingly larger data sets coupled with the use of congruence as the final test of homology. Some critics of this development have recently called for a return to more detailed primary homology analysis while questioning the utility of congruence. This discussion appears to be central to the debate regarding the phylogenetic relationships of basal turtles, as the large data sets developed by us have been criticized recently for utilizing poorly constructed characters and including too many homoplasy‐prone characters. Our analysis of this critique reveals that (1) new information regarding poorly understood taxa has a greater impact on the outcome of turtle phylogenies than the characters under dispute; (2) most current turtle phylogenies differ in taxon sampling, not character sampling, and so it appears illogical to condemn a particular analysis for its character sampling; (3) even evolutionary taxonomists should agree that key characters utilized to resolve basal turtle relationships cannot be thought to be ‘infallible’; (4) whereas various criteria provide positive evidence for homology, only congruence provides positive evidence for non‐homology; and (5) a stalemate between conflicting camps within a congruence frame work is preferable to the ad hoc dismissal of data sets, because authoritative statements are untestable.     

Skull shape variation in extant and extinct Testudinata and its relation to habitat and feeding ecology

Turtles (Testudinata) are a diverse group of reptiles that conquered a broad set of habitats and feeding ecologies over the course of their well‐documented evolutionary history. We here investigate the cranial shape of 171 representatives of the turtle lineage and the relationship of shape to different habitat and diet preferences using two‐dimensional geometric morphometrics. The skull shape of extant turtles correlates with both ecological proxies, but is more affected by habitat than diet. However, the application of these correlations to extinct turtles produces mostly flawed results, as least when compared to external data such as sedimentary environment, highlighting that the morphospace held by extant turtles is not necessarily the optimal location in tree space for a particular ecology. The inability of this study to correctly predict the ecology of extinct turtles is likely related to the fact that the shape of turtle skulls is dominated by the emarginations and jaw closure mechanisms, two shape features unrelated to habitat or feeding ecology. This indicates that various specializations that are apparent in the skull only contribute little to overall shape.