Optimization of primer-specific filter metrics for the assessment of mitochondrial DNA sequence data

Filter metrics are used as a quick assessment of sequence trace files in order to sort data into different categories (i.e. high quality, review, and low quality) without human intervention. The filter metrics consist of two numerical parameters for sequence quality assessment: trace score (TS) and contiguous read length (CRL). Primer-specific settings for the TS and CRL were established using a calibration dataset of 2817 traces and validated using a concordance dataset of 5617 traces. Prior to optimization, 57% of the traces required manual review before import into a sequence analysis program, whereas after optimization only 28% of the traces required manual review. After optimization of primer-specific filter metrics for mitochondrial DNA sequence data, an overall reduction of review of trace files translates into increased throughput of data analysis and decreased time required for manual review.     

A Suite of Dermestid Beetle Traces on Dinosaur Bone from the Upper Jurassic Morrison Formation,Wyoming, USA

Most studies of insect traces on fossil bone deal with one or two trace morphs found on isolated bone fragments, making it difficult to identify the trace-maker and its behavior. We report the discovery of a suite of insect traces on an articulated Camptosaurus dinosaur skeleton that permits the identification of the trace-maker and interpretations of its behavior. The traces include mandible marks, pits, and shallow bores on cortical bone, and deep, meandering furrows and tunnels (borings) on articular surfaces. The interiors of bones are intensely mined, and the cavities and borings are filled with fine bone fragments (insect frass). The distinctive mandible marks consist of opposing sets of parallel grooves, indicating the maker had two apical teeth set on symmetrical mandibles and that all of the traces were made by a single taxon. Comparison of the fossils with the mandible morphology and bone traces of extant insects indicates dermestid beetles made the traces. Based on extant dermestid behavior, soft tissues were likely absent and the bones were lipid-laden when the traces were made. Examination of more than 5,000 bones from the Morrison and Cedar Mountain formations shows insect traces on bone are common but overlooked and that many bones are substantially damaged by insect mining. The key to the recognition of these important yet subtle traces is a search model and an intense, oblique light source.     

The development of Archaeopteris: new evolutionary characters from the structural analysis of an Early Famennian trunk from southeast Morocco

A 5 m long trunk of a young Archaeopteris/Callixylon erianum tree from the Late Devonian of Morocco shows new branching patterns for early lignophytes. This progymnosperm tree produces a helical pattern of traces that we infer belonged to reduced, short-lived, primary (apical) branches (type A) as well as two types of adventitious traces (types B and H). We infer that type-B traces supplied branches that initiate close to the site of attachment on the trunk of some, but not all type-A branches in an irregular but nonrandom pattern. Unlike ephemeral type-A branches, those of type B persist and become long-lived, potentially permanent units of the architecture of Archaeopteris trees. Type-H adventitious traces are also short-lived and occur singly or in serial groups, but differ from traces of either type A or B branches by lacking differentiation into a readily identifiable organ category. We interpret type-H traces as supplying latent primordia that could develop into either adventitious roots or shoots depending on extrinsic factors. Our new data suggest that Archaeopteris had a wide range of branch primordium amplitude. Type-B branches compare with axillary lateral branch buds of some Early Carboniferous spermatophytes (Calamopitys) and are a major developmental departure from the strictly apical, pseudomonopodial shoot branching of older aneurophyte progymnosperms. Type-H traces suggest that Archaeopteris trees had some potential for formation of adventitious roots or shoots in response to environmental factors, such as partial burial by overbank sedimentation. Collectively, these novel methods of tree branching may partly explain the extraordinary success and worldwide dominance of Archaeopteris forests on fluvially dominated, Late Devonian floodplains.     

Lichen Bioerosion on Fossil Vertebrates from the Cenozoic of Patagonia and Antarctica

Different traces occur on fossil bones and teeth coming from the Early Miocene Gaiman Formation (Patagonia, Argentina). Most traces were attributed to the action of terrestrial and marine predators and scavengers. However, other traces on bones and teeth from this unit and one tooth from the Eocene La Meseta Formation (Antarctica) are attributed to chemical corrosion by lichens in recent times, that is, in a very late diagenetic time. The living lichens and calcium oxalate deposits occurring on the traces and their particular pattern indicates that they were not produced by vegetal roots. The lichens include reproductive structures which allowed a proper determination. A kind of corrosion pattern (Type 1) on bones and teeth from Patagonia is associated to Sarcogyne orbicularis Körber, Verrucaria sp. Schrad, and Buellia aff. punctiformis (Hoff.) Massal. The lichen Aspicilia aff. aquatica produced rounded holes on an Antarctic tooth (Type 2). On the same tooth, the epilithic lichen Caloplaca sp. Th. Fries did not leave any kind of mark on the enameloid.     

Maternal manipulation of hatching asynchrony limits sibling cannibalism in the predatory mite Phytoseiulus persimilis

1. Sibling cannibalism is a common phenomenon in the animal kingdom but entails a high risk of direct and inclusive fitness loss for the mother and her offspring. Therefore, mechanisms limiting sibling cannibalism are expected to be selected for. One way of maternal manipulation of sibling cannibalism is to influence hatching asynchrony between nearby laid eggs. This has rarely been tested experimentally. 2. We examined the ability of ovipositing females of the cannibalistic predatory mite Phytoseiulus persimilis to influence the occurrence of sibling cannibalism among offspring by manipulating hatching asynchrony of nearby laid eggs. 3. In the first experiment, we assessed the occurrence of sibling cannibalism in relation to the hatching interval (24 h and 48 h) between nearby laid eggs. In the second experiment, we tested whether ovipositing females discriminate sites containing young (24-h old) and old (48-h old) eggs, fresh and old traces (metabolic waste products and possibly pheromones) left by the same female (24 h and 48 h ago), or young eggs plus fresh female traces and old eggs plus old female traces. Both experiments were conducted with and without prey. 4. Without prey, siblings were more likely to cannibalize each other if the hatching interval between nearby laid eggs was short (24 h). Cannibalism occurred less often when senior siblings (protonymphs) experienced a delay in the opportunity to cannibalize junior siblings (larvae). 5. Independent of prey availability, females preferentially added new eggs to sites containing old eggs plus old female traces but did neither distinguish between young and old eggs presented without own traces nor between fresh and old traces presented without eggs. 6. We discuss cue perception and use by P. persimilis females and contrast the outcome of our experiments and theoretical predictions of sibling cannibalism. We conclude that P. persimilis mothers increase hatching asynchrony of nearby laid eggs to prevent sibling cannibalism on the last produced offspring. Such a behaviour may be considered a simple form of maternal care increasing the survival prospects of offspring.     

Sampling Solution Traces for the Problem of Sorting Permutations by Signed Reversals

ABSTRACT: BACKGROUND: Traditional algorithms to solve the problem of sorting by signed reversals output just one optimal solution while the space of all optimal solutions can be huge. A so-called trace represents a group of solutions which share the same set of reversals that must be applied to sort the original permutation following a partial ordering. By using traces, we therefore can represent the set of optimal solutions in a more compact way. Algorithms for enumerating the complete set of traces of solutions were developed. However, due to their exponential complexity, their practical use is limited to small permutations. A partial enumeration of traces is a sampling of the complete set of traces and can be an alternative for the study of distinct evolutionary scenarios of big permutations. Ideally, the sampling should be done uniformly from the space of all optimal solutions. This is however conjectured to be #P-complete. RESULTS: We propose and evaluate three algorithms for producing a sampling of the complete set of traces that instead can be shown in practice to preserve some of the characteristics of the space of all solutions. The first algorithm (RA) performs the construction of traces through a random selection of reversals on the list of optimal 1-sequences. The second algorithm (DFALT) consists in a slight modification of an algorithm that performs the complete enumeration of traces. Finally, the third algorithm (SWA) is based on a sliding window strategy to improve the enumeration of traces. All proposed algorithms were able to enumerate traces for permutations with up to 200 elements. CONCLUSIONS: We analysed the distribution of the enumerated traces with respect to their height and average reversal length. Various works indicate that the reversal length can be an important aspect in genome rearrangements. The algorithms RA and SWA show a tendency to lose traces with high average reversal length. Such traces are however rare, and qualitatively our results show that, for testable-sized permutations, the algorithms DFALT and SWA produce distributions which approximate the reversal length distributions observed with a complete enumeration of the set of traces.     

Pigment Diversity in Freshwater Phytoplankton. I. A Comparison of Spectrophotometric and Paper Chromatographic Methods

Spectrophotometric and paper chromatographic analyses of the pigments in the phytoplankton were made from early spring till the end of summer in two small Dutch freshwater lakes. It was found that pigment diversity cannot be adequately estimated by MARGALEF'S pigment ratio nor by polychromatic spectrophotometric methods. The pigments detected with the paper chromatographic method were: chlorophyll-a, chlorophyll-b, chlorophyll-c, phaeophytin-a (traces), phaeophorbide-a, Mg-containing chlorophyll-derivatives, carotene, lutein, violaxanthin, neoxanthin (traces), fucoxanthin, diadinoxanthin, diatoxanthin (traces), peridinin and keto-carotenoids (traces). It is suggested to distinguish between a richness-component and an evenness-component of pigment diversity.     

Echinoid bioerosion from the Pliocene of NE Spain

In the present study a series of rasping traces onshells and limestone pebbles from the Pliocene of l'Empordà (Catalunya, NE Spain) are described. The traces have been attributed to the ichnospecies Gnathichnus pentaxBromley, 1975. This type of rasping traces is produced today by regular echinoids. Comparison with the traces produced by P. lividus (Lmk) of the Catalan coast confirms its origin.     

Double rotation of the opening (closing) elytra in beetles (Coleoptera)

Transient movements of the elytra (opening and closing) were filmed in beetles tethered from below. A total of 39 specimens of 18 species representing 11 families were examined. Bright markers glued to the elytra were traced frame by frame. Body-fixed 3D traces of apical and shoulder markers were reconstructed. Shapes of traces reflected different steps of elytral movement and different types of flight. Flat circular arcs were fitted to scattered traces using the least square method. The rotation axis of the apical marker was always directed at the contralateral side. The trace of the shoulder marker was, as a rule, non-parallel to the apical trace. Usually, the shoulder marker on the costal edge of the elytron uniformly supinated in the course of adduction of the apical marker. Traces of opening and closing coincided, hence the double rotation of the elytron had one degree of freedom. The elytron to body articulation in beetles is, presumably, a spherical mechanism with two separate but linked drives for a broad swing during opening (closing).     

Crocodile swim tracks from the latest Cretaceous of Europe

Recently discovered evidence of tracks in the continental beds of the Late Cretaceous Tremp Formation in the southern Pyrenees (NE Iberian Peninsula) has been identified as scratch marks made by buoyant crocodiles. The tracks are preserved in two distinct environments and substrates (marly limestones originating in a littoral mud flat and fine‐grained sandstones deposited in fluvial settings). Most of the crocodylian traces are ascribed to ichnogenus Characichnos, whereas a single plantigrade pes track is assigned to ichnogenus cf. Crocodylopodus. The crocodylian swim traces (Characichnos ichnofacies) found in the early and late Maastrichtian co‐occur with Brontopodus ichnofacies attributable to terrestrial tetrapods (titanosaur sauropods, cf. Brontopodus ichnogenus; and hadrosaurid ornithopods, Hadrosauropodus ichnogenus). Analysis of the tracks allows the interpretation of palaeoenvironmental settings and track production. Thus, in lagoonal environments, swim tracks of crocodylians were produced during the rise of the water level in successive tide cycles; in fluvial settings, the swim traces of crocodylians were produced within the channel at the low‐water stage. To date, there are no reports of Late Cretaceous crocodylian tracks in Europe, and the studied evidence represents the first and youngest track record of the group in the latest part of the Cretaceous (C29r) in this continent and probably in the world.     

Amphibian swimming traces from the Lower Permian of southern New Mexico

Fossilised traces of swimming amphibians, assigned to Batrachichnus delicatulus and Serpentichnus robledoensis igen. et isp. nov., are described from the Lower Permian of the Robledo Mountains, southern New Mexico. The B. delicatulus specimen is interpreted as a trackway of a small 'amphibian' (temnospondyl, nectridean, microsaur or juvenile embolomere) swimming straight ahead. S. robledoensis consists of repeated pes imprints separated by discontinuous, L-shaped imprints (body traces). It is interpreted as a trackway of an 'amphibian' swimming in a similar manner to the motion of a side-winding snake. The producer of S. robledoensis is more distinctive than in B. delicatulus , and is suggestive of the lysorophian Brachydectes . This is the first locomotory trace to be assigned to this 'amphibian' group.     

Enigmatic ichnites in the middle triassic of Southern Spain

In southern Spain, within the Chiclana de Segura Formation of red detrital fades, enigmatic structures were found whose origins are discussed here. Each structure is composed of the union of elongated traces, two laterals and a shorter central one. All are concave epireliefs at the top of a sandstone bed whose age is assumed to be Ladinian (Triassic). The sediments formed within a fluvial environment. We describe these imprints, their structures and measurements, and discuss their orientations and associations. The traces probably have an organic origin, and are most likely tracks made by a vertebrate, possibly an archosaur, although no osseous remains have been found to confirm this interpretation.     

Bite traces on dicynodont bones and the early evolution of large terrestrial predators

Nied?wiedzki, G., Gorzelak, P. & Sulej, T. 2010: Bite traces on dicynodont bones and the early evolution of large terrestrial predators. Lethaia, Vol. 44, pp. 87–92. Dicynodont (Synapsida: Anomodontia) bones from the Late Triassic (late Norian/early Rhaetian) of Poland yield characteristic tooth marks that can be attributed to three ichnotaxa (Linichnus serratus, Knethichnus parallelum and Nihilichnus nihilicus). The general shape and dimension of these traces perfectly match the dental morphology of a co‐occurring carnivorous dinosaur. It is therefore concluded that early carnivorous dinosaurs were feeding on dicynodonts. This discovery constitutes one of the oldest evidence of dinosaur predator–prey interaction. It is suggested that an evolutionary increase in the size of dicynodonts across the Late Triassic may have been driven by selection pressure to reach a size refuge from early dinosaur predators. □Bite traces, dicynodonts, dinosaurs, predation, Triassic.     

ANATOMY OF THE GYNOECIUM IN TWO SPECIES OF BAKERIDESIA (MALVACEAE)

Structure of the gynoecium is described in two species of Bakeridesia, subgenus Bakeridesia (Malvaceae, tribe Malveae). The dorsal wall of each carpel bears a winglike projection with a marginal pair of pubescent, bluntly dentate wings. The projection arises as a single, solid ridge of tissue after the ovules are initiated and after the ventral carpellary margins are fused with the receptacle. Two multiseriate layers of fiber-sclereids line each locule and continue into the winglike projection where they are separated by parenchyma. Gynoecial vascularization is described in detail. The richly vascularized carpels are supplied by five traces: a median dorsal trace, which bifurcates into two dorsal bundles; two lateral traces; and two ventral traces. Adjacent ventral traces, lateral traces, and septal bundles are fused—i.e., they are held in common by neighboring carpels. The presence of lateral carpellary traces may be a primitive character in the tribe Malveae.     

Review of Dinosaur Tail Traces

Since 1858, when Hitchcock first recorded dinosaur tail traces from the Jurassic of Massachusetts, USA, a number of dinosaur tail traces have been reported. Although considered rare, at least 38 records of dinosaur tail traces have previously been reported in the literature. These occurrences are herein reviewed in order to understand their geographic and stratigraphic distribution, types of tail trace makers, and characteristics of dinosaur tail traces. Several terms for dinosaur tail traces have been employed and they are divided into tail impressions (TIs) for resting traces, and tail drag impressions (TDIs) for locomotion traces. Possible criteria for distinguishing, measuring and comparing TIs and TDIs are suggested. In addition, herringbone structures, one of the characteristic features of tail traces associated with ornithopod and theropod tracks, are discussed. Estimated speeds of tail trace makers are shown to be rather low. Finally, the abundance of tail traces associated with bipedal, rather than quadrupedal, dinosaurs is considered a reflection of behavior.     

A Study of Image Memory in Lower Primates

Two forms of memory are known: short-term (operative, fresh, dynamic) and long-term (stable, permanent) (1-3). The first form involves memorization for brief time intervals, short-term retention of traces that "fade out" within a few minutes. The second form of memory is engaged in prolonged retention of traces that can still be reproduced after a long lapse of time, such as several hours, days, or weeks.     

Exploring the Mechanism of General Anesthesia: Kinetic Analysis of GABAA Receptor Electrophysiology

A kinetic model of the effect of agonist and anesthetics on ligand-gated ion channels, developed in earlier work, is further refined and used to predict traces observed in fast-perfusion electrophysiological studies on recombinant GABA_A receptors under a wide range of agonist and/or anesthetic concentrations. The model incorporates only three conformational states (resting, open, and desensitized) but allows for the modulation of the conformational free energy landscape connecting these states resulting from adsorption of agonist and/or anesthetic to the bilayer in which the protein is embedded. The model is shown to reproduce the diverse and complex features of experimental traces remarkably well, including both anesthetic-induced and agonist-induced traces, as well as the modulation of agonist-induced traces by anesthetic, either coapplied or continuously present. The solutions to the kinetic equations, which give the time-dependence of each of the nine protein states (three ligation states for each of the three conformations), describe the flow of probability among these states and thus reveal the kinetic underpinnings of the traces. Many of the parameters in the model, such as the desorption rate constants of anesthetic and agonist, are directly related to model-independent experimental measurements and thus can serve as a definitive test of its validity.     

The PsbP-like protein (sll1418) of Synechocystis sp. PCC 6803 stabilises the donor side of Photosystem II

The PsbP-like protein of the cyanobacterium Synechocystis sp. PCC 6803 is a peripheral component of Photosystem II, located at the lumenal side of the thylakoid membrane. Removal of this protein leads to decreased competitive potential of a PsbP-like deletion mutant when grown in a mixture with wild-type cells. Flash-induced oxygen evolution traces of the mutant show a higher probability of misses, correlated with increased amplitudes of the S-states decay in the dark. Thermoluminescence emission traces demonstrate a changed charge recombination pattern in the mutant, the S(3)Q(B)(-) couple becoming the major species instead of the S(2)Q(B)(-). Our data suggest a possible role of the PsbP-like protein in stabilisation of the charge separation in Photosystem II of cyanobacteria through interaction with the Mn cluster.     

Dolichols of the fern Matteucia struthiopteris

Dolichols isolated from leaves of the fern Matteucia struthiopteris were present as a mixture of prenologues composed of 14 up to 20 isoprene units with Dol-16 dominating. They comprised approximately 0.004% of the fresh weight of fresh plant tissue and were accompanied by traces of polyprenols (Pren-14 up to Pren-17, Pren-16 dominating). Their structure was confirmed by electropray ionization mass spectrometry (ESI-MS). This is the first time that dolichols have been reported as dominating polyisoprenoid alcohols in plant photosynthetic tissue.     

Study of the oleanolic and ursolic acid contents of some species of the Lamiaceae

The oleanolic and ursolic acid contents from 88 taxa of Lamiaceae (19 genera, 66 species, 8 subspecies, 9 varieties and 5 hybrids) were investigated using gas chromatography. Both triterpenoid acids were present in all of the investigated taxa, but the plants belonging in the subfamily Nepetoideae produced significantly higher amounts than those in the subfamily Lamioideae. The oleanolic acid content ranged from traces to 1.840% dry weight, and that of ursolic acid from traces to 4.019% dry weight.