Tracing the evolution of the holothurian body plan through stem‐group fossils

The fossil echinoderm Palaeocucumaria, from the early Devonian Hunsrück Slate of southwestern Germany, has been studied using both traditional techniques and X‐ray microtomography, and its anatomy clarified. Phylogenetic analysis shows that it is a stem‐group holothurian with a combination of characters that help understand how the modern (crown‐group) holothurian body plan developed. Echinoids and holothurians have evolved along different paths, by differential growth of the larval‐ and rudment‐derived body regions. Palaeocucumaria shows that late stem‐group holothurians had a water vascular organization with a single external madreporite and calcified stone canal leading to the aboral end of the peripharyngeal coelom, and five primary radial water vessels that gave rise to tentacle‐like tube‐feet. This fossil data, in combination with a molecular phylogeny based on 18 s‐like rRNA gene sequence data, is used to order evolutionary steps in the making of the crown‐group holothurian body plan. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 670–681.     

Three‐dimensional geometry of a pterosaur wing skeleton,and its implications for aerial and terrestrial locomotion

This study reports on the three‐dimensional spatial arrangement and movements of the skeleton of Anhanguera santanae (Pterodactyloidea: Ornithocheiridae), determined using exceptionally well‐preserved uncrushed fossil material, and a rigid‐body method for analysing the joints of extinct animals. The geometric results of this analysis suggest that the ornithocheirids were inherently unstable in pitch and yaw. As a result, pitch control would probably have been brought about by direct adjustment of the angle of attack of the wing, by raising or lowering the trailing edge from the root using the legs if, as is indicated in soft‐tissue specimens of a number of unrelated pterosaur species, the legs were attached to the main wing membrane, or by using long‐axis rotations at the shoulder or wrist to raise and lower the trailing edge from the wingtip. An analysis of the three‐dimensional morphology of the wrist lends support to the idea that the pteroid – a long, slender wrist bone unique to pterosaurs that supported a membranous forewing – was directed forwards in flight, not towards the body. As a result, the forewing could have fulfilled the function of an air‐brake and high‐lift device, and may also have had an important role in pitch, yaw, and roll control. The joint analysis is consistent with a semi‐erect quadrupedal model of terrestrial locomotion in the ornithocheirids. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 27–69.     

Resource tracking and its conservation implications for an obligate frugivore (Procnias tricarunculatus,the three‐wattled bellbird)

In Monteverde, Costa Rica, the vulnerable Three‐wattled Bellbird (Procnias tricarunculatus) feeds primarily upon the fruit of Lauraceae species during its reproductive and post‐reproductive seasons. To understand and advance appropriate conservation measures, this study identified the bellbird's foraging challenges in its search for a temporally and spatially fluctuating resource. Although there are at least 96 species of Lauraceae found in the five life zones of Monteverde, the distinct distributions of tree species both among and within life zones require the bellbirds to track seasonal fruiting across the various zones. In this 6‐year study, we monitored the fruiting of tree species and bellbird abundance in 24 study plots within its post‐reproductive life zone, the Premontane Wet forest, to identify preferred bellbird food resources and how the fruiting of these species drives the spatial distribution of the bellbird. Our research revealed phenological patterns of annual, biennial, and triennial fruiting with high levels of fruiting synchrony within several identified key fruit species. Of critical conservation importance is that no single species of Lauraceae produced a consistent food supply for bellbirds each year. Therefore, even within life zones, the bellbird's survival depends on its mobility to search for and obtain fruit, as well as the availability of fruits of multiple tree species. The conservation implications include focused attention on multiple core areas within given life zones, protection of existing forest and remnant trees, and forest restoration with plantings of multiple tree species. We suspect that other tropical frugivorous species face similar conservation challenges.     

Craniometric variation of some Mediterranean and Atlantic populations of Stenella coeruleoalba (Mammalia,Delphinidae): A three‐dimensional geometric morphometric analysis

The variability of cranial features of Atlantic and Mediterranean samples of Stenella coeruleoalba was examined using a three‐dimensional geometric morphometric approach. Data were collected on 79 skulls from the upper and middle Mediterranean Sea, the Atlantic French coasts, and Scotland. Three‐dimensional x, y, and z coordinates of 27 landmarks were recorded on each left half skull using a Microscribe 3‐D digitizer. All configurations were rotated, centered, and scaled, and residuals from the mean configuration were analyzed through multivariate analyses of variance. Mahalanobis distances among populations were used to evaluate phenetic relationships. Consensus configurations were compared to visualize shape differences among samples. Analyses revealed significant differences among populations, a clear distinction of the Scottish coasts dolphins from the other samples, and a closer relationship of the dolphins from the French coasts to the Mediterranean populations than to the Scottish one. Shape differences are mainly concentrated in the rostral and in the occipital regions of the skull. Phylogenetic and adaptive factors were invoked as possible causes of the variation patterns.     

A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher‐level classification

Pyraloidea, one of the largest superfamilies of Lepidoptera, comprise more than 15 684 described species worldwide, including important pests, biological control agents and experimental models. Understanding of pyraloid phylogeny, the basis for a predictive classification, is currently provisional. We present the most detailed molecular estimate of relationships to date across the subfamilies of Pyraloidea, and assess its concordance with previous morphology‐based hypotheses. We sequenced up to five nuclear genes, totalling 6633 bp, in each of 42 pyraloids spanning both families and 18 of the 21 subfamilies, plus up to 14 additional genes, for a total of 14 826 bp, in 21 of those pyraloids plus all 24 outgroups. Maximum likelihood analyses yield trees that, within Pyraloidea, differ little among datasets and character treatments and are strongly supported at all levels of divergence (83% of nodes with bootstrap ≥80%). Subfamily relationships within Pyralidae, all very strongly supported (>90% bootstrap), differ only slightly from a previous morphological analysis, and can be summarized as Galleriinae + Chrysauginae (Phycitinae (Pyralinae + Epipaschiinae)). The main remaining uncertainty involves Chrysauginae, of which the poorly studied Australian genera may constitute the basal elements of Galleriinae + Chrysauginae or even of Pyralidae. In Crambidae the molecular phylogeny is also strongly supported, but conflicts with most previous hypotheses. Among the newly proposed groupings are a ‘wet‐habitat clade’ comprising Acentropinae + Schoenobiinae + Midilinae, and a provisional ‘mustard oil clade’ containing Glaphyriinae, Evergestinae and Noordinae, in which the majority of described larvae feed on Brassicales. Within this clade a previous synonymy of Dichogaminae with the Glaphyriinae is supported. Evergestinae syn. n. and Noordinae syn. n. are here newly synonymized with Glaphyriinae, which appear to be paraphyletic with respect to both. Pyraustinae and Spilomelinae as sampled here are each monophyletic but form a sister group pair. Wurthiinae n. syn. , comprising the single genus Niphopyralis Hampson, which lives in ant nests, are closely related to, apparently subordinate within, and here newly synonymized with, Spilomelinae syn. n.     

A universal and reliable assay for molecular sex identification of three‐spined sticklebacks (Gasterosteus aculeatus)

In heterogametic species, biological differences between the two sexes are ubiquitous, and hence, errors in sex identification can be a significant source of noise and bias in studies where sex‐related sources of variation are of interest or need to be controlled for. We developed and validated a universal multimarker assay for reliable sex identification of three‐spined sticklebacks (Gasterosteus aculeatus). The assay makes use of genotype scores from three sex‐linked loci and utilizes Bayesian probabilistic inference to identify sex of the genotyped individuals. The results, validated with 286 phenotypically sexed individuals from six populations of sticklebacks representing all major genetic lineages (cf. Pacific, Atlantic and Japan Sea), indicate that in contrast to commonly used single‐marker‐based sex identification assays, the developed multimarker assay should be 100% accurate. As the markers in the assay can be scored from agarose gels, it provides a quick and cost‐efficient tool for universal sex identification of three‐spined sticklebacks. The general principle of combining information from multiple markers to improve the reliability of sex identification is transferable and can be utilized to develop and validate similar assays for other species.     

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.     

Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three‐dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms

Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody–peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248–1257. © 2017 Wiley Periodicals, Inc.     

A high‐density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour

High‐density SNP microarrays (“SNP chips”) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high‐density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per‐SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.     

Three‐dimensional reconstruction of the stomatostylet and anterior epidermis in the nematode Aphelenchus avenae (Nematoda: Aphelenchidae) with implications for the evolution of plant parasitism

A three‐dimensional model of the stomatostylet and associated structures has been reconstructed from serial thin sections of Aphelenchus avenae, a representative of Tylenchomorpha, a group including most plant parasitic nematodes. The reconstruction is compared with previous work on bacteriovorous cephalobids and rhabditids to better understand the evolution of the stylet and its associated cells. Two arcade syncytia (“guide ring”) line the stylet shaft, supporting the hypothesis that the stylet shaft and cone (into which the shaft extends and which is not lined by syncytia) are homologous with the gymnostom of cephalobids, the sister taxon of tylenchids. Epidermal syncytia, HypA, HypB, HypC, and HypE, line the cephalic framework, vestibule, and vestibule extension, congruent with the hypothesis that these components are homologous with the cephalobid cheilostom. Relative to outgroups, HypC is expanded in A. avenae, enclosing sensilla that fill most of the cephalic framework. The homolog of syncytium HypD in the cephalobid Acrobeles complexus is not observed in A. avenae. Arcade syncytia are reduced compared with those of cephalobids. Stylet protractor muscles in A. avenae are homologous with the most anterior set of radial muscles of cephalobids. Observations to date test and verify our previous hypotheses of homology of the stomatostylet with respect to the stoma of bacteriovorous outgroups. Reconstruction of the stegostom and pharynx will provide further tests of homology and evolution of feeding structure adaptations for plant parasitism. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.     

A nearly complete skeleton of an early juvenile diplodocid (Dinosauria: Sauropoda) from the Lower Morrison Formation (Late Jurassic) of north central Wyoming and its implications for early ontogeny and pneumaticity in sauropods

A nearly complete skeleton of a juvenile sauropod from the Lower Morrison Formation (Late Jurassic, Kimmeridgian) of the Howe Ranch in Bighorn County, Wyoming is described. The specimen consists of articulated mid-cervical to mid-caudal vertebrae and most appendicular bones, but cranial and mandibular elements are missing. The shoulder height is approximately 67 cm, and the total body length is estimated to be less than 200 cm. Besides the body size, the following morphological features indicate that this specimen is an early juvenile; (1) unfused centra and neural arches in presacral, sacral and first to ninth caudal vertebrae, (2) unfused coracoid and scapula, (3) open coracoid foramen, and (4) relatively smooth articular surfaces on the limb, wrist, and ankle bones. A large scapula, short neck and tail and elongate forelimb bones relative to overall body size demonstrate relative growth. A thin-section of the mid-shaft of a femur shows a lack of annual growth lines, indicating an early juvenile individual possibly younger than a few years old. Pneumatic structures in the vertebral column of the specimen SMA 0009 show that pneumatisation of the postcranial skeleton had already started in this individual, giving new insights in the early ontogenetic development of vertebral pneumaticity in sauropods.

The specimen exhibits a number of diplodocid features (e.g., very elongate slender scapular blade with a gradually dorsoventrally expanded distal end, a total of nine dorsal vertebrae, presence of the posterior centroparapophyseal lamina in the posterior dorsal vertebrae). Although a few diplodocid taxa, Diplodocus, cf. Apatosaurus, and cf. Barosaurus, are known from several fossil sites near the Howe Ranch, identification of this specimen, even at a generic level, is difficult due to a large degree of ontogenetic variation.     

A new phylogenetic test for comparing multiple high‐dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae)

The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best‐fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high‐dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development‐informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best‐fit modularity hypothesis. Furthermore, we show that bioluminescent lateral photophores evolve at a similar rate as, and are strongly integrated with, body shape in lanternfishes. These results suggest that overlapping life‐history constraints on development and movement define axes of body shape evolution in lanternfishes, and that the positions of their lateral photophore complexes are likely a passive outcome of the interaction of these ecological pressures.     

A new longirostrine dyrosaurid (Crocodylomorpha,Mesoeucrocodylia) from the Paleocene of north‐eastern Colombia: biogeographic and behavioural implications for New‐World Dyrosauridae

Abstract: Fossils of dyrosaurid crocodyliforms are limited in South America, with only three previously diagnosed taxa including the short‐snouted Cerrejonisuchus improcerus from the Paleocene Cerrejón Formation of north‐eastern Colombia. Here we describe a second dyrosaurid from the Cerrejón Formation, Acherontisuchus guajiraensis gen. et sp. nov., based on three partial mandibles, maxillary fragments, teeth, and referred postcrania. The mandible has a reduced seventh alveolus and laterally depressed retroarticular process, both diagnostic characteristics of Dyrosauridae. Acherontisuchus guajiraensis is distinct among known dyrosaurids in having a unique combination of craniomandibular characteristics, and postcranial morphology that suggests it may have occupied a more placid, fluvial habitat than most known Old‐World dyrosaurids. Results from a cladistic analysis of Dyrosauridae, using 82 primarily cranial and mandibular characters, support an unresolved relationship between A. guajiraensis and a combination of New‐ and Old‐World dyrosaurids including Hyposaurus rogersii, Congosaurus bequaerti, Atlantosuchus coupatezi, Guarinisuchus munizi, Rhabdognathus keiniensis and Rhabdognathus aslerensis. Our results are consistent with an African origin for Dyrosauridae with multiple dispersals into the New World during the Late Cretaceous and a transition from marine habitats in ancestral taxa to more fluvial habitats in more derived taxa.     

A new fluorescent chemosensor for cadmium(II) based on a pyrene‐appended piperidone derivative and its β‐cyclodextrin complex

We report, in this article, a piperidin‐4‐one derivative carrying pyrenyl fluorescent reporter groups which acts as a Cd²⁺ ion sensor. The compound is synthesized and characterized using IR and NMR spectral techniques. The compound forms an inclusion complex with β‐cyclodextrin. It selectively binds to Cd²⁺ ions in water and aqueous β‐cyclodextrin media. The stoichiometry of the host–guest complex of the compound with β‐cyclodextrin is 1:2. The ligand–metal ion binding stoichiometry is 1:1 both in water and in β‐cyclodextrin. The linear concentration range of detection of the metal ion is reported. Cyclodextrin complex formation does not affect the metal ion selectivity of the compound.     

The detection of sex‐linked heteroplasmy in Pseudocardium sachalinense (Bivalvia: Mactridae) and its implications for the distribution of doubly uniparental inheritance of mitochondrial DNA

Although mitochondrial inheritance in metazoans is typically strictly maternal, doubly uniparental inheritance (DUI) is probably the major exception to this widespread rule. DUI has been found in many species of bivalve molluscs, belonging to several different families. Based on current understanding, the detection of DUI generally relies on the detection of two distinct mitochondrial DNA lineages: a female‐transmitted one, that dominates somatic tissues in males and females and eggs, and a male‐transmitted one, that dominates the male germline and sperm. When a new species with DUI is identified, novel data are available to make a better inference on the evolution of this phenomenon within the Bivalvia. In this study, mitochondrial heteroplasmy in Pseudocardium sachalinense (Schrenck, 1862) is described. This species belongs to the family of Mactridae, in which DUI has not been previously demonstrated: this finding allowed to upgrade the present knowledge about the distribution of DUI.     

Genetic structure of Eurasian otter (Lutra lutra,Carnivora: Mustelidae) populations from the western Baltic sea region and its implications for the recolonization of north‐western Germany

We analysed 229 Eurasian otters from eastern and north‐western Germany, Denmark and southern Sweden based on sequences of the mtDNA control region and genotypes at 12 polymorphic nuclear microsatellite loci. The main focus of the study lay on the north‐west German otters from Schleswig‐Holstein, which represent a newly established and expanding population recolonizing a formerly inhabited region, thereby closing the distributional gap between the large eastern population and the long‐isolated and genetically depleted Danish population. As found before in this species, mtDNA variability was very low but we identified a hitherto unknown haplotype in Sweden. Expected heterozygosities were between 0.46 and 0.69 and thus within the range known from the literature. There were only weak signs of a founder effect in the Schleswig‐Holstein otters with respect to allelic diversity (but not heterozygosity). Nevertheless, there was a statistically significant bottleneck signal based on deviations from mutation‐drift equilibrium in Schleswig‐Holstein. All statistical approaches (amova s, factorial correspondence analysis, assignment tests and Bayesian structure analysis) unequivocally showed that north‐western Germany has so far been predominantly recolonized by otters of east German origin, but we also found evidence of admixture through immigration from Denmark. Both the Danish and the north‐west German otter population will benefit from further exchange in the wake of the ongoing range expansion.     

A second species in the endemic New Caledonian genus Gastrolepis (Stemonuraceae) and its implications for the conservation status of high‐altitude maquis vegetation: coherent application of the IUCN Red List criteria is urgently needed in New Caledonia

A new species in the previously monotypic, endemic New Caledonian genus Gastrolepis (Stemonuraceae) is described. Gastrolepis alticola differs from G. austrocaledonica by its shorter and thicker petioles, strongly coriaceous leaves with revolute margins, shorter inflorescences, and pubescent corollas. The new species is further distinguished by its ecology, occurring only in high‐altitude maquis on two massifs in southern New Caledonia, Mt. Kouakoué and the Montagne des Sources. Gastrolepis alticola is assigned a preliminary conservation status of ‘Endangered’ using the World Conservation Union (IUCN) Red List criteria. Comparison of the IUCN threat status for the 19 species endemic to this distinctive, restricted vegetation type reveals a striking lack of consistency and underscores the need for a reassessment of the entire New Caledonian flora. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 775–783.     

Identification and analysis of residues contained on β → α loops of the dual‐substrate (βα)8 phosphoribosyl isomerase A specific for its phosphoribosyl anthranilate isomerase activity

A good model to experimentally explore evolutionary hypothesis related to enzyme function is the ancient‐like dual‐substrate (βα)₈ phosphoribosyl isomerase A (PriA), which takes part in both histidine and tryptophan biosynthesis in Streptomyces coelicolor and related organisms. In this study, we determined the Michaelis–Menten enzyme kinetics for both isomerase activities in wild‐type PriA from S. coelicolor and in selected single‐residue monofunctional mutants, identified after Escherichia coli in vivo complementation experiments. Structural and functional analyses of a hitherto unnoticed residue contained on the functionally important β → α loop 5, namely, Arg¹³⁹, which was postulated on structural grounds to be important for the dual‐substrate specificity of PriA, is presented for the first time. Indeed, enzyme kinetics analyses done on the mutant variants PriA_Ser⁸¹Thr and PriA_Arg¹³⁹Asn showed that these residues, which are contained on β → α loops and in close proximity to the N‐terminal phosphate‐binding site, are essential solely for the phosphoribosyl anthranilate isomerase activity of PriA. Moreover, analysis of the X‐ray crystallographic structure of PriA_Arg¹³⁹Asn elucidated at 1.95 Å herein strongly implicates the occurrence of conformational changes in this β → α loop as a major structural feature related to the evolution of the dual‐substrate specificity of PriA. It is suggested that PriA has evolved by tuning a fine energetic balance that allows the sufficient degree of structural flexibility needed for accommodating two topologically dissimilar substrates—within a bifunctional and thus highly constrained active site—without compromising its structural stability.