Turtle carotid circulation: a character analysis case study

The bony canals permeating the turtle skull associated with the cranial circulation have long been considered integral to an understanding of extinct and extant turtle systematics. Recent phylogenetic analyses, employing a variety of data sets, suggest alternatives to the traditional arrangement of crown turtles. Of particular note is the recent failure of investigations employing molecular techniques to retrieve a monophyletic Trionychoidea, a clade supported largely by shared circulatory features. These alternative phylogenies may also have implications for extinct forms. The turtle cranial arterial circulation therefore represents an ideal system upon which to conduct a detailed, multipronged analysis of a systematically influential character. In the present study, the theoretical underpinnings of character analysis are critically evaluated, and a new interpretation of circulatory variation in turtles is offered, including a revised phylogenetic character suite. This assessment indicates an autapomorphic circulatory pattern in Trionychia, whereas Trionychoidea is not supported.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 239–256.     

Macroecological patterns of sexual size dimorphism in turtles of the world

Sexual size dimorphism (SSD) is a well‐documented phenomenon in both plants and animals; however, the ecological and evolutionary mechanisms that drive and maintain SSD patterns across geographic space at regional and global scales are understudied, especially for reptiles. Our goal was to examine geographic variation of turtle SSD and to explore ecological and environmental correlates using phylogenetic comparative methods. We use published body size data on 135 species from nine turtle families to examine how geographic patterns and the evolution of SSD are influenced by habitat specialization, climate (annual mean temperature and annual precipitation) and climate variability, latitude, or a combination of these predictor variables. We found that geographic variation, magnitude and direction of turtle SSD are best explained by habitat association, annual temperature variance and annual precipitation. Use of semi‐aquatic and terrestrial habitats was associated with male‐biased SSD, whereas use of aquatic habitat was associated with female‐biased SSD. Our results also suggest that greater temperature variability is associated with female‐biased SSD. In contrast, wetter climates are associated with male‐biased SSD compared with arid climates that are associated with female‐biased SSD. We also show support for a global latitudinal trend in SSD, with females being larger than males towards the poles, especially in the families Emydidae and Geoemydidae. Estimates of phylogenetic signal for both SSD and habitat type indicate that closely related species occupy similar habitats and exhibit similar direction and magnitude of SSD. These global patterns of SSD may arise from sex‐specific reproductive behaviour, fecundity and sex‐specific responses to environmental factors that differ among habitats and vary systematically across latitude. Thus, this study adds to our current understanding that while SSD can vary dramatically across and within turtle species under phylogenetic constraints, it may be driven, maintained and exaggerated by habitat type, climate and geographic location.     

Cranial variation amongst independent lineages of the alligator snapping turtle (Macrochelys temminckii)

Recent interest in diagnoses and relationships between lineages of the alligator snapping turtle (Macrochelys temminckii) present conflicting patterns of molecular variation across the taxon's range. This study uses geometric morphometric techniques to test molecular hypotheses. We analyse alligator snapping turtle cranial variation amongst populations (i.e. drainages) with the hypothesis that populations of turtles recovered as monophyletic by previous molecular studies are more similar to each other in cranial shape. Dorsal, lateral and ventral cranial shape analyses corroborate the uniqueness of populations recovered by molecular genetic hypotheses. Additionally, analyses reveal near equal separation between drainages that were assigned to monophyletic clades by previous phylogenetic studies. These results reveal the potential for more independent lineages that have yet to be diagnosed, and unique cranial shapes are described for our three most heavily sampled drainages.     

The Holes of Moles: Osteological Correlates of the Trigeminal Nerve in Talpidae

Talpidae consists of small insectivorous mammals exhibiting a range of environmental preferences. As all its members rely on a highly developed somatosensation system, they are an ideal study-group for investigating osteological correlates of the trigeminal nerve. We quantitatively studied cranial anatomy in 22 species of desman, shrew-mole, and true mole using microscopy and micro-CT imaging to investigate whether the infraorbital foramina within Talpidae is enlarged in semiaquatic forms and more broadly associated with habitat preference. We also investigated whether associated foramina were covariant. In order to account for a phylogenetic basis for any correlations, we reconstructed the best taxonomically sampled phylogeny for talpids in the literature to date, based on cytochrome b. Relationships among genera and species are broadly congruent with previous analyses; however, we report new placements for Neurotrichus gibbsii and Mogera tokudae. Although no correlation was found between habitat and the caliber of the V₃ associated mandibular canal and foramen ovale, our results indicate that semiaquatic forms show larger infraorbital foramina in comparison to terrestrial species, and that the caliber of the sphenorbital fissure can also serve as a proxy for habitat preference. This work, therefore, supports the use of certain osteological features to infer habitat preferences in fossil species and indicates this can be achieved even when studying ecologically diverse, closely related species within the same family.     

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.     

Evolutionary patterns of shape and functional diversification in the skull and jaw musculature of triggerfishes (Teleostei: Balistidae)

The robust skull and highly subdivided adductor mandibulae muscles of triggerfishes provide an excellent system within which to analyze the evolutionary processes underlying phenotypic diversification. We surveyed the anatomical diversity of balistid jaws using Procrustes‐based geometric morphometric analyses and a phylomorphospace approach to quantifying morphological transformation through evolution. We hypothesized that metrics of interspecific cranial shape would reveal patterns of phylogenetic diversification that are congruent with functional and ecological transformation. Morphological landmarks outlining skull and adductor mandibulae muscle shape were collected from 27 triggerfish species. Procrustes‐transformed skull shape configurations revealed significant phylogenetic and size‐influenced structure. Phylomorphospace plots of cranial shape diversity reveal groupings of shape between different species of triggerfish that are mostly consistent with phylogenetic relatedness. Repeated instances of convergence upon similar cranial shape by genetically disparate taxa are likely due to the functional demands of shared specialized dietary habits. This study shows that the diversification of triggerfish skulls occurs via modifications of cranial silhouette and the positioning of subdivided jaw adductor muscles. Using the morphometric data collected here as input to a biomechanical model of triggerfish jaw function, we find that subdivided jaw adductors, in conjunction with a unique cranial skeleton, have direct biomechanical consequences that are not always congruent with phylomorphospace patterns in the triggerfish lineage. The integration of geometric morphometrics with biomechanical modeling in a phylogenetic context provides novel insight into the evolutionary patterns and ecological role of muscle subdivisions in triggerfishes. J. Morphol. 277:737–752, 2016. © 2016 Wiley Periodicals, Inc.     

Exploring the Relationship between Skeletal Mass and Total Body Mass in Birds

Total body mass (TBM) is known to be related to a number of different osteological features in vertebrates, including limb element measurements and total skeletal mass. The relationship between skeletal mass and TBM in birds has been suggested as a way of estimating the latter in cases where only the skeleton is known (e.g., fossils). This relationship has thus also been applied to other extinct vertebrates, including the non-avian pterosaurs, while other studies have used additional skeletal correlates found in modern birds to estimate TBM. However, most previous studies have used TBM compiled from the literature rather than from direct measurements, producing values from population averages rather than from individuals. Here, we report a new dataset of 487 extant birds encompassing 79 species that have skeletal mass and TBM recorded at the time of collection or preparation. We combine both historical and new data for analyses with phylogenetic control and find a similar and well-correlated relationship between skeletal mass and TBM. Thus, we confirm that TBM and skeletal mass are accurate proxies for estimating one another. We also look at other factors that may have an effect on avian body mass, including sex, ontogenetic stage, and flight mode. While data are well-correlated in all cases, phylogeny is a major control on TBM in birds strongly suggesting that this relationship is not appropriate for estimating the total mass of taxa outside of crown birds, Neornithes (e.g., non-avian dinosaurs, pterosaurs). Data also reveal large variability in both bird skeletal and TBM within single species; caution should thus be applied when using published mass to test direct correlations with skeletal mass and bone lengths.     

Phylogeny and biogeography of the extant species of triplespine fishes (Triacanthidae, Tetraodontiformes)

A new phylogenetic hypothesis for the living species of triplespine fishes of the Indo-Western Pacific family Triacanthidae (Tetraodontiformes, Teleostei) is proposed. A data set of 55 morphological characters (34 osteological and 21 morphometric) was constructed. A cladistic analysis of the osteological data set yielded a single most-parsimonious tree. This cladogram does not support the monophyly of one of the four genera, Tripodichthys , but Bremer values for this analysis are low. The osteological data set was then combined with a data set of 21 morphometric characters that had previously been used to diagnose the four genera. The analysis of the combined data set produced the same phylogenetic hypothesis, but with greater nodal support. The biogeographical distribution of the living species is then interpreted with the use of this new phylogenetic information.     

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.     

The origin of the turtle body plan: evidence from fossils and embryos

The origin of the unique body plan of turtles has long been one of the most intriguing mysteries in evolutionary morphology. Discoveries of several new stem-turtles, together with insights from recent studies on the development of the shell in extant turtles, have provided crucial new information concerning this subject. It is now possible to develop a comprehensive scenario for the sequence of evolutionary changes leading to the formation of the turtle body plan within a phylogenetic framework and evaluate it in light of the ontogenetic development of the shell in extant turtles. The fossil record demonstrates that the evolution of the turtle shell took place over millions of years and involved a number of steps.     

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.     

Relationship between tropical cyclones and the distribution of sea turtle nesting grounds

Aim This study examines the relationship between the distribution of existing sea turtle nesting sites and historical patterns of tropical cyclone events to investigate whether cyclones influence the current distribution of sea turtle nesting sites. The results, together with information on predicted cyclone activity and other key environmental variables, will help in the identification and prediction of future nesting sites for sea turtles as changes to the coastal environment continue. Location Queensland, Australia. Methods We used data on the nesting distribution of seven populations of four species of sea turtles [green (Chelonia mydas), flatback (Natator depressus), hawksbill (Eretmochelys imbricata) and loggerhead (Caretta caretta)] from the eastern Queensland coast, and tropical cyclone track data from 1969 to 2007 to explore the relationship between (1) sea turtle nesting phenology and cyclone season, and (2) sea turtle nesting sites and cyclone distribution. Furthermore, using two green turtle populations as a case study, we investigated the relationship between cyclone disturbance and sea turtle reproductive output, nesting site and season. Bootstrapping was used to explore if current sea turtle nesting sites are located in areas with lower or higher cyclone frequency than areas where turtles are currently not nesting. Results All populations of sea turtles studied here were disturbed by cyclone activity during the study period. The exposure (frequency) of tropical cyclones that crossed each nesting site varied greatly among and within the various sea turtle populations. This was mainly a result of the spatial distribution of each population’s nesting sites. Bootstrapping indicated that nesting sites generally have experienced lower cyclone activity than other areas that are available for nesting. Main conclusions Tropical cyclones might have been sufficiently detrimental to sea turtle hatching success on the eastern Queensland coast that through a natural selection process turtles in this region are now nesting in areas with lower cyclone activity. Therefore, it is important that future studies that predict climate or range shifts for sea turtle nesting distributions consider future cyclone activity as one of the variables in their model.     

The phylogenetic relationships of the Early Miocene stork Grallavis edwardsi,with comments on the interrelationships of living Ciconiidae (Aves)

The fossil record of storks (Aves, Ciconiidae) includes a relatively large number of specimens from the Middle Eocene onwards, but no taxon is as well represented as Grallavis edwardsi form the Early Miocene of the Allier region in central France. Despite this, the phylogenetic placement of G. edwardsi among other storks has remained elusive not least because of the lack of a robust phylogenetic framework for living storks. To find out how G. edwardsi relates to recent Ciconiidae, we performed a phylogenetic analysis based on osteological features including all living genus‐level taxa of the Ciconiidae. We show that the previously reported similarities to the extant taxa Ephippiorhynchus and Jabiru are based on plesiomorphic features, and our analysis supports a sister group relationship between Grallavis edwardsi and Leptoptilos. Our results are also consistent with a basal divergence within Ciconiidae between Mycteria and Anastomus, which are among the smallest storks, and all other storks. A sister group relationship between storks of the genus Ciconia and all large storks (Leptoptilini) is recovered albeit with weak support, which may be due to homoplastic features linked to their large size. Grallavis edwardsi possessed several osteological adaptations suited for scavenging, and despite lacking some derived traits characteristic of Leptoptilos, it is likely to have been a precursor of large marabou and adjutant storks.     

Ecological and evolutionary factors in the morphological diversification of South American spiny rats

Understanding the processes underlying morphological diversification is a central goal in ecology and evolutionary biology and requires the integration of information about phylogenetic divergence and ecological niche diversity. In the present study, we use geometric morphometrics and comparative methods to investigate morphological diversification in Neotropical spiny rats of the family Echimyidae. Morphological diversification is studied as shape variation in the skull, comprising a structure composed of four distinct units: vault, base, orognathofacial complex, and mandible. We demonstrate association among patterns of variation in shape in different cranial units, levels of phylogenetic divergence, and ecological niche diversification. At the lower level of phylogenetic divergence, there is significant and positive concordance between patterns of phylogenetic divergence and cranial shape variation in all cranial units. This concordance may be attributable to the phylogenetic and shape distances being calculated between species that occupy the same niche. At higher phylogenetic levels of divergence and with ecological niche diversity, there is significant concordance between shape variation in all four cranial units and the ecological niches. In particular, the orognathofacial complex revealed the most significant association between shape variation and ecological niche diversity. This association may be explained by the great functional importance of the orognathofacial complex.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 646–660.     

Phylogeny and paraphyly among tetrapod blood flukes (Digenea: Schistosomatidae and Spirorchiidae)

The blood flukes of turtles (Digenea: Spirorchiidae) and the blood flukes of crocodilians, birds and mammals (Digenea: Schistosomatidae) have long been considered as closely related, but distinct evolutionary lineages. Recent morphological and molecular studies have considered these families as sister taxa within the Schistosomatoidea. Representatives of both families have similar furcocercous cercariae and similar two-host life cycles, but have different definitive hosts, distinct reproductive patterns and different morphologies. Sequences including approximately 1800 bases of the small subunit ribosomal DNA and 1200 bases of the large subunit ribosomal DNA were generated from representatives of eight spirorchiid genera. These sequences were aligned with pre-existing sequences of Schistosomatidae and other representatives of the Diplostomida and analysed for phylogenetic signal using maximum parsimony and Bayesian inference. These analyses revealed that the Spirorchiidae is paraphyletic and that the turtle blood flukes are basal to the highly derived schistosomatids. Three genera of spirorchiids from marine turtles form a sister group to the Schistosomatidae and five genera of spirorchiids from freshwater turtles occupy basal positions in the phylogeny of tetrapod blood flukes. Marine turtles are considered to be derived from freshwater turtles and the results of the current study indicate that the spirorchiid parasites of marine turtles are similarly derived from a freshwater ancestor. The close relationship of the marine spirorchiids to schistosomatids and the basal position of the marine transmitted Austrobilharzia and Ornithobilharzia in the schistosomatid clade suggests that schistosomatids arose after a marine turtle blood fluke ancestor successfully colonised birds.