Reappraisal of patterns of nonmarine cryptodiran turtle carotid circulation: evidence from osteological correlates and soft tissues

The turtle cranial circulation has been employed as an important source of phylogenetic information, but recent conflicting hypotheses of relationship within Testudinata suggest reevaluation of the utility of characters drawn from this complex. As a component of a comprehensive character analysis, the osteological correlates of the nonmarine cryptodiran turtle carotid circulation are herein subjected to high-resolution X-ray computed tomography, reassessed, and statistically investigated. Three different patterns of osteological correlates, indicating three disparate cranial circulatory patterns, are described, and this finding is corroborated by evidence from circulatory soft tissues. Members of the Trionychia and Kinosternoidea exhibit patterns that differ from the more widespread condition found in testudinoid taxa. This result differs from previous work, which has indicated the presence of only two major cranial circulatory patterns, and suggests that while cranial circulatory features may be phylogenetically informative, the information contained within them indicates patterns of relationship different from those previously hypothesized.     

Turtle phylogeny: insights from a novel nuclear intron

Introns have gained considerable popularity as markers for molecular phylogenetics. However, no primers exist for a nuclear intron that amplifies across all turtles. Available data from morphology and mitochondrial DNA have not unambiguously resolved relationships within the superfamily Trionychoidea and the family Chelidae, which together form a large portion of extant turtle diversity. We tested the phylogenetic utility of a novel intron from the RNA fingerprint protein 35 (R35) as applied to these two areas of turtle systematics. We found the intron to be a single-copy locus that provides excellent resolving power for lineages among turtles, though problems with alignment made it impossible to infer deeper amniote relationships. Maximum parsimony and maximum likelihood both demonstrated the polyphyly of Trionychoidea and the reciprocal monophyly of Australian/New Guinea and South American chelid turtles. This is the first study to resolve such relationships with strong statistical support, and we suggest that R35 holds great promise for resolving additional persistent problems in the phylogeny of living turtles.     

Taxonomy and sexual dimorphism of a new species of Loxoconcha (Podocopida: Ostracoda) from the Pleistocene of the Japan Sea

A new ostracod, Loxoconcha kamiyai sp. nov. in the Family Loxoconchidae, is described from the Pleistocene Omma Formation of Japan. Its geological and geographical distributions suggest that this species was once endemic to the Japan Sea, where it would have evolved until the Pliocene. Since the early Pleistocene, this species would have become extinct within this marginal sea during glacial maxima, probably due to its narrower salinity tolerances and geographical distributions than those of extant species inhabiting the euryhaline environments in other seas. The distributional patterns of pore systems in this species strongly suggest its closest phylogenetic affinities to a living species, Loxocorniculum mutsuense . These two species show a unique adult sexual dimorphism in the anterior element of the hingement. Taking the female hingement morphology as a standard, the male hingement can be explained in terms of heterochrony, i.e. paedomorphosis. Sexual hingement dimorphism with paedomorphosis occurs in only one phylogenetic group of the genus Loxoconcha , which is distinguished by the ontogenetic distributional patterns of pore systems. This morphology may represent relict primitive characters of ancient ostracods and could be an important character for evaluating the history of sexual dimorphism in ostracods since the Palaeozoic.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 239–251.     

Historical DNA from museum type specimens clarifies diversity of Asian leaf turtles (Cyclemys)

Species boundaries in Asian leaf turtles of the genus Cyclemys are difficult to define on the basis of morphology, primarily because many populations exhibit considerable ontogenetic variation in shell and head coloration. Two recent molecular phylogenetic hypotheses of Cyclemys species relationships, based largely on market and pet-trade samples of uncertain provenance, were highly incongruent. We used historical DNA methods to sequence fragments of the mitochondrial cytochrome  b gene from eight type specimens of Cyclemys (including one collected by Alfred Russel Wallace), and phylogenetically placed these type sequences into the context of published cytochrome  b variation. Our phylogenetic hypothesis supports the recognition of four named species ( Cyclemys atripons , Cyclemys dentata , Cyclemys oldhamii , and C. pulchristriata ), as well as a fifth species of unknown geographical provenance obtained from the Hong Kong pet trade. The type sequences show that previous molecular phylogenetic studies were hampered by misidentifications, supporting the notion that Cyclemys of unknown provenance are not reliably identified to species solely on the basis of morphology.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 131–141.     

Phylogenetic relationships and biogeographical history of the genus Rhinoclemmys Fitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea)

Rhinoclemmys is an interesting genus of turtles biogeographically and ecologically, being the only genus of the family Geoemydidae that occurs in the New World and inhabiting a wide range of habitats from aquatic to highly terrestrial. Here we present a molecular phylogeny of Rhinoclemmys using both mitochondrial and nuclear genes. Our results strongly support the monophyletic and subfamilial status of Rhinoclemmys within the monophyletic family Geoemydidae. Within Rhinoclemmys , two clades are strongly supported, i.e. R. annulata  +  R. pulcherrima and R. areolata  +  R. punctularia  +  R. diademata  +  R. funerea  +  R. melanosterna , but the positions of R. nasuta and R. rubida are still weakly supported. In terms of the biogeographical history, the results of this study, coupled with palaeontological evidence, corroborate the hypothesis that this group migrated from Asia to the Americas across the Bering Strait during the early Eocene. The radiation of Rhinoclemmys in Central and South America corresponds well with vicariance events, including the emergence of the Sierra Madres of Mexico and the Nuclear Highland, and dispersals across the Panama land bridge. Interestingly, our resulting phylogeny suggests this group invaded South America at least four times and that dispersal of R. nasuta to South America probably took place in the early Miocene before the emergence of the Isthmus of Panama. We finally discuss our phylogenetic results with regard to the monophyly of the family Geoemydidae and in the context of previous morphological analyses. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 751–767.     

Phylogenetic analysis of non-stereotyped behavioural sequences with a successive event-pairing method

A new method is proposed which uses transitions among acts in non-stereotyped behavioural sequences as phylogenetic characters. This method is derived from the event-pairing method designed for the phylogenetic study of developmental sequences and from ethological analyses of transition matrices. It is applied to study the phylogenetic relationships within a well-known group, the presocial Zetoborinae cockroaches. The analysis is carried out with three data sets: a behavioural data set with transitions among acts in behavioural dyadic sequences, together with morphological and molecular data sets. Non-stereotyped behaviour proved to be phylogenetically informative and to display low homoplasy. This new method opens an avenue for studying the evolution of behaviour in the framework of phylogenetic analysis, which was restricted until now to the study of stereotyped sequences and/or isolated features involved in courting or building activities.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 853–867.     

A geometric morphometric assessment of the effects of environment and cladogenesis on the evolution of the turtle shell

In the largest group of extant turtles, the Testudinoidea, the acquisition of an aquatic or terrestrial way of life has occurred within two clades, allowing the study of homoplasy linked to environment (commonly named convergence). Here we appraise the respective importance of two sources of morphological variation: a major cladogenetic event and a major environmental shift (aquatic vs. terrestrial). The repeatability of the same evolutionary process (environmental change) allows an assessment of the weights of both natural selection and phylogenetic constraints on several morphological features of the shell. These sources of morphological variance on the complex shell structure were studied using geometric morphometrics. We depict the morphological variation of three parts of the turtle shell: epidermal carapace, bony carapace, and plastron. In the three structures, we found that both phylogeny and environment were significant sources of morphological variation, and geometric morphometrics allowed the pattern of morphological variation due to each effect to be assessed. The assessment of the homoplasy due to environment and of the pattern of morphological variability suggests that the carapace has undergone similar morphological changes between aquatic and terrestrial environments within the two clades. The radiation of the Testudinoidea is interpreted as an adaptive radiation.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 485–501.     

Morphological phylogenetics of Puya subgenus Puya (Bromeliaceae)

Puya , a large genus mostly from South America, has been taxonomically divided into two subgenera: Puyopsis and Puya. The latter includes only eight species distributed mainly in Chile, extending to Argentina, Bolivia, and Peru. The species of subgenus Puya are recognized by the presence of a sterile apex of the inflorescence branches, whereas those of subgenus Puyopsis have fertile flowers all along the branches. The objectives of this article were to determine whether this diagnostic character was synapomorphic for subgenus Puya , and to explore the relationships between its species. Parsimony analyses were performed for 43 taxa and 93 morphological characters, 87 of which were discrete and six continuous. In the analysis that included all characters, a single most parsimonious tree was found that supported subgenus Puya by two synapomorphic character states, including the diagnostic character of a sterile inflorescence branch apex and a blooming pattern in which flowers open gradually from base to apex. The trees were better supported when the continuous characters were included. Further studies are suggested to resolve the infrageneric classification of Puya and the relationships of the species belonging to subgenus Puya .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 93–110.     

Phylogeography and morphological variability in land snails: the Sicilian Marmorana (Pulmonata, Helicidae)

Land snails have long been recognized as suitable organisms for studying phenotypic differentiation and phylogeny in relation to geographical distribution. Morphological data (shell and anatomy biometry on different geographical scales) and partial sequences from mitochondrial genes (cytochrome oxidase subunit I , 16S rDNA) were used to test whether morphological patterns match phylogeny in a diversified group of Sicilian rock-dwelling land snails belonging to the genus Marmorana . The taxonomic implications of the three character sets (shell and anatomical biometry and molecular data) were also considered. The inferred phylogenetic relationships do not match morphological (shell and genitalia) patterns. This result may significantly modify the current taxonomy. Mitochondrial based reconstructions define several supported clades well correlated with geographic distribution and populations were found to be distributed parapatrically. The progressive decline in mitochondrial DNA sequence similarity over a distance of 250 km is consistent with a model of isolation by distance, a pattern previously recognized for other groups of land snails. For one clade of Marmorana , colonization along Mediterranean trade routes appears to be a possibility.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 809–823.     

Evidence for speciational change in the evolution of ratites (Aves: Palaeognathae)

To perform a comparative analysis of character associations framed in a phylogenetic context (e.g. independent contrasts), a model of character evolution must be assumed. According to phyletic gradualism, morphological change accumulates gradually over time within lineages, and speciation events do not have a major role. Under speciational models, morphological change is assumed to occur during or just after cladogenesis in both daughter species, and the resulting morphologies do not change over long periods of time (stasis), until the next cladogenetic event. A novel method is presented for comparing these models of character evolution that uses permutational multiple phylogenetic regressions. The addition of divergence times to well-corroborated phylogenetic trees and the utilization of the method developed in this paper allows the estimation of relative frequency of gradual change and speciational change from living organisms. This method is applied to a dataset from ratites with the conclusion that, for a range of morphological features, change tends to have been speciational rather than gradual.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 99–106.     

Ecological diversification and phylogeny of emydid turtles

Ecological diversification is a central topic in ecology and evolutionary biology. We undertook the first comprehensive species-level phylogenetic analysis of Emydidae (an ecologically diverse group of turtles), and used the resulting phylogeny to test four general hypotheses about ecological diversification. Phylogenetic analyses were based on data from morphology (237 parsimony-informative characters) and mitochondrial DNA sequences (547 parsimony-informative characters) and included 39 of the 40 currently recognized emydid species. Combined analyses of all data provide a well-supported hypothesis for intergeneric relationships, and support monophyly of the two subfamilies (Emydinae and Deirochelyinae) and most genera (with the notable exception of Clemmys and Trachemys ). Habitat and diet were mapped onto the combined-data tree to test fundamental hypotheses about ecological diversification. Using continuous coding of ecological characters showed that lineages changed in habitat before diet, ecological change was most frequently from generalist to specialist, and habitat and diet rarely changed on the same branch of the phylogeny. However, we also demonstrate that the results of ancestral trait reconstructions can be highly sensitive to character coding method (i.e. continuous vs. discrete). Finally, we propose a simple model to describe the pattern of ecological diversification in emydid turtles and other lineages, which may reconcile the (seemingly) conflicting conclusions of our study and two recent reviews of ecological diversification.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 577–610.     

Phylogenetic relationships based on morphology among the Diospyros (Ebenaceae) species endemic to the Mascarene Islands

The Diospyros (Ebenaceae) species which colonized the Mascarene Islands, namely Mauritius, Reunion and Rodrigues, have been decimated over the years by human settlements. Of the 14 endemic species that have been described and collected for herbaria, Diospyros angulata is now believed to be extinct in Mauritius. The phylogenetic relationships of the 14 Diospyros species were determined using maximum parsimony analysis of 35 morphological characters. This analysis separated the Mascarene Diospyros into two major clades, with D. revaughanii , D. egrettarum and D. leucomelas grouped in the same strongly supported most basal clade while the rest of the species formed the other major clade. High bootstrap values were obtained for the sister species D. angulata and D. boutonania , and the clade clustering the upland species D. neraudii , D. nodosa and D. pterocalyx . There was also relatively strong support for the clade comprising D. hemiteles and D. melanida , which are located in mid altitude regions. These results indicate that Diospyros species most probably colonized the coastal areas of Mauritius and then moved to mid altitude habitats before finally reaching the upland regions. There are also strong indications that D. borbonica and D. diversifolia , endemic to Reunion and Rodrigues, respectively, resulted from migrations from Mauritius.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 307–313.     

Morphological, functional and evolutionary aspects of tail autotomy and regeneration in the 'living fossil'Sphenodon (Reptilia: Rhynchocephalia)

Tail autotomy and regeneration are less known in Sphenodon ('Reptilia': Rhynchocephalia) than in Squamata. We examined museum specimens, Sphenodon guntheri ( N  = 8) and Sphenodon punctatus ( N  = 172), wild Sphenodon punctatus ( N  = 19) and Sphenodon sp. skeletons ( N  = 8). In S. punctatus , unlike in typical Squamata, sexes had similar relative (intact) tail lengths, and regeneration frequencies; tail and body growth was isometric. Tail breakage was usually intravertebral, usually followed by ablation of a variably sized terminal vertebral piece, partly deviating from lizards. Hypothetically, imperfect autotomy results from sphenodon's primitiveness. As in squamates, tail-losers were morphologically more left-side dominant than tail-retainers. Individual directional asymmetries in digit morphology and in digit injury were correlated (in lizards observed only at population level); tail-losers had more fluctuating asymmetry but their exclusion did not facilitate morphological taxonomic distinctions (no 'Seligmann effect'). In S. punctatus , extents and directions of sexual dimorphism paralleled differences between tail-retainers and tail-losers, females resembling tail-losers, also accounting for character interdependence (developmental constraints; employing a method similar to phylogenetic contrasts). The variation in the location of tail injury was correlated with the continuum of variation between injured and intact (pholidotic) morphotypes. These last two phenomena remain to be explored in Squamates.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 721–743.     

Pollen morphology of the Swertiinae (Gentianaceae): phylogenetic implications

Recent molecular surveys of the Swertiinae (Gentianaceae–Gentianeae) revealed unexpected phylogenetic relationships, including polyphyly of the genera Gentianella , Jaeschkea , Lomatogonium and Swertia . To find new non-molecular characters supporting the phylogeny, we examined the exine variation of 73 species of all major lineages of subtribe Swertiinae using environmental scanning electron miscroscopy supplementing older, mainly light microscopical, studies. In contrast to previous studies, we were able to pick out taxa from phylogenetic key positions with particular focus on Swertia . Many distantly related taxa such as parts of Frasera , Gentianopsis , Halenia , Gentianella , Megacodon and several lineages of Swertia share a striate–reticulate or reticulate exine pattern. This is interpreted as the plesiomorphic character state of Swertiinae. There is also considerable variation of derived patterns; for example, different types of microechinate or almost smooth pollen was repeatedly observed in distantly related groups. Another extreme was the ring-shaped reticulation found in a North American species of Gentianopsis . Unfortunately, major relationships as revealed by molecular analyses were rarely supported because of the abundance of the plesiomorphic type and homoplasy even on low taxonomic levels; for example, within Lomatogonium . Exine variation was particularly useful in characterizing independent lineages of Swertia . For example, according to pollen characters and in agreement with other data, the Asian Swertia cuneata is a sister group of a strongly diversified African lineage and Swertia yunnanensis , which is rather aberrant in flower morphology, seems close to parts of Lomatogonium .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 323–341.     

Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights

Comprehensive taxonomic sampling can vastly improve the accuracy of phylogenetic reconstruction. Here, we present the most inclusive phylogenetic analysis of Arvicolinae (Mammalia, Rodentia) to date, combining all published cytochrome  b gene sequences of greater than 1097 bp and new sequences from two monotypic genera. Overall, the phylogenetic relationships between 69 species of voles and lemmings, representing 18 genera and 10 tribes, were studied. By applying powerful modern approaches to phylogenetic reconstruction, such as maximum likelihood and Bayesian analysis, we provide new information on the early pulse of evolution within the Arvicolinae. While the position of two highly divergent lineages, Phenacomys and Ondatra , could not be resolved, the tribe Lemmini, appeared as the most basal group of voles. The collared lemmings (Dicrostonychini) grouped together with all of the remaining tribes. The two previously unstudied monotypic genera Dinaromys and Prometheomys form a moderately well-supported monophyletic clade, possibly a sister group to Ellobius (Ellobiusini). Furthermore, with one exception, all tribes ( sensu Musser & Carleton, 2005) proved to be monophyletic and can thus be regarded as meaningful evolutionary entities. Only the tribe Arvicolini emerged as paraphyletic in both analyses because of the unresolved phylogenetic position of Arvicola terrestris . Steppe voles of the genus Lagurus were solidly supported as a sister group to the Microtus and allies clade.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 825–835.     

Microanatomy of the amniote femur and inference of lifestyle in limbed vertebrates

The femoral microanatomy of 155 species of extant amniotes (57 species of mammals, 15 species of turtles, 56 species of lepidosaurs, and 27 species of birds) of known lifestyle is studied to demonstrate a possible link between some basic parameters of bone structure and specific lifestyles, as well as phylogenetic relationships between taxa. Squared change parsimony with random taxon reshuffling and pairwise comparisons reveal that most compactness and size parameters exhibit both phylogenetic and ecological signals. A discriminant analysis produces several inference models, including a ternary model (aquatic, amphibious, terrestrial) that yield the correct lifestyle in 88% of the cases. These models are used to infer the lifestyle of three extinct Permian temnospondyls: Eryops megacephalus, Acheloma dunni, and Trimerorhachis insignis. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 644–655.