Sero‐taxonomy of skeletal macromolecules in living Terebratulid brachiopods

Antibodies prepared against macromolecules isolated from the shells of three living brachiopod genera have proved to be of considerable taxonomic significance, in that the pattern of cross‐reactivity of all three antisera consistently points to a new interpretation for the evolution of the largest extant brachiopod order, the Terebratulida. This new molecular evidence actually complements rather than contradicts the existing morphology‐based taxonomy, since detailed systematic investigation of the taxa in question has already demonstrated subtle but significant morphological differences in the major taxonomic characters which appear to reflect this new interpretation.

As fragments of skeletal macromolecules, including antigenic determinants, are known to survive for many millions of years within the protected micro‐environments provided by enclosing biominerals, these results suggest that such molecular fossils could well provide important insights on at least the high‐level taxonomic relationships of fossil organisms.     

Oldest known Eucalyptus macrofossils are from South America

The evolutionary history of Eucalyptus and the eucalypts, the larger clade of seven genera including Eucalyptus that today have a natural distribution almost exclusively in Australasia, is poorly documented from the fossil record. Little physical evidence exists bearing on the ancient geographical distributions or morphologies of plants within the clade. Herein, we introduce fossil material of Eucalyptus from the early Eocene (ca. 51.9 Ma) Laguna del Hunco paleoflora of Chubut Province, Argentina; specimens include multiple leaves, infructescences, and dispersed capsules, several flower buds, and a single flower. Morphological similarities that relate the fossils to extant eucalypts include leaf shape, venation, and epidermal oil glands; infructescence structure; valvate capsulate fruits; and operculate flower buds. The presence of a staminophore scar on the fruits links them to Eucalyptus, and the presence of a transverse scar on the flower buds indicates a relationship to Eucalyptus subgenus Symphyomyrtus. Phylogenetic analyses of morphological data alone and combined with aligned sequence data from a prior study including 16 extant eucalypts, one outgroup, and a terminal representing the fossils indicate that the fossils are nested within Eucalyptus. These are the only illustrated Eucalyptus fossils that are definitively Eocene in age, and the only conclusively identified extant or fossil eucalypts naturally occurring outside of Australasia and adjacent Mindanao. Thus, these fossils indicate that the evolution of the eucalypt group is not constrained to a single region. Moreover, they strengthen the taxonomic connections between the Laguna del Hunco paleoflora and extant subtropical and tropical Australasia, one of the three major ecologic-geographic elements of the Laguna del Hunco paleoflora. The age and affinities of the fossils also indicate that Eucalyptus subgenus Symphyomyrtus is older than previously supposed. Paleoecological data indicate that the Patagonian Eucalyptus dominated volcanically disturbed areas adjacent to standing rainforest surrounding an Eocene caldera lake.     

Fossil Araceae from a Paleocene neotropical rainforest in Colombia

Both the fossil record and molecular data support a long evolutionary history for the Araceae. Although the family is diverse in tropical America today, most araceous fossils, however, have been recorded from middle and high latitudes. Here, we report fossil leaves of Araceae from the middle-late Paleocene of northern Colombia, and review fossil araceous pollen grains from the same interval. Two of the fossil leaf species are placed in the new fossil morphogenus Petrocardium Herrera, Jaramillo, Dilcher, Wing et Gomez-N gen. nov.; these fossils are very similar in leaf morphology to extant Anthurium; however, their relationship to the genus is still unresolved. A third fossil leaf type from Cerrejón is recognized as a species of the extant genus Montrichardia, the first fossil record for this genus. These fossils inhabited a coastal rainforest ～60-58 million years ago with broadly similar habitat preferences to modern Araceae.     

Screening of random peptide library of hemagglutinin from pandemic 2009 A(H1N1) influenza virus reveals unexpected antigenically important regions

The antigenic structure of the membrane protein hemagglutinin (HA) from the 2009 A(H1N1) influenza virus was dissected with a high-throughput screening method using complex antisera. The approach involves generating yeast cell libraries displaying a pool of random peptides of controllable lengths on the cell surface, followed by one round of fluorescence-activated cell sorting (FACS) against antisera from mouse, goat and human, respectively. The amino acid residue frequency appearing in the antigenic peptides at both the primary sequence and structural level was determined and used to identify "hot spots" or antigenically important regions. Unexpectedly, different antigenic structures were seen for different antisera. Moreover, five antigenic regions were identified, of which all but one are located in the conserved HA stem region that is responsible for membrane fusion. Our findings are corroborated by several recent studies on cross-neutralizing H1 subtype antibodies that recognize the HA stem region. The antigenic peptides identified may provide clues for creating peptide vaccines with better accessibility to memory B cells and better induction of cross-neutralizing antibodies than the whole HA protein. The scheme used in this study enables a direct mapping of the antigenic regions of viral proteins recognized by antisera, and may be useful for dissecting the antigenic structures of other viral proteins.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

The fossil record and taphonomy of butterflies and moths (Insecta,Lepidoptera): implications for evolutionary diversity and divergence-time estimates

Background

It is conventionally accepted that the lepidopteran fossil record is significantly incomplete when compared to the fossil records of other, very diverse, extant insect orders. Such an assumption, however, has been based on cumulative diversity data rather than using alternative statistical approaches from actual specimen counts.

Results

We reviewed documented specimens of the lepidopteran fossil record, currently consisting of 4,593 known specimens that are comprised of 4,262 body fossils and 331 trace fossils. The temporal distribution of the lepidopteran fossil record shows significant bias towards the late Paleocene to middle Eocene time interval. Lepidopteran fossils also record major shifts in preservational style and number of represented localities at the Mesozoic stage and Cenozoic epoch level of temporal resolution. Only 985 of the total known fossil specimens (21.4%) were assigned to 23 of the 40 extant lepidopteran superfamilies. Absolute numbers and proportions of preservation types for identified fossils varied significantly across superfamilies. The secular increase of lepidopteran family-level diversity through geologic time significantly deviates from the general pattern of other hyperdiverse, ordinal-level lineages.

Conclusion

Our statistical analyses of the lepidopteran fossil record show extreme biases in preservation type, age, and taxonomic composition. We highlight the scarcity of identified lepidopteran fossils and provide a correspondence between the latest lepidopteran divergence-time estimates and relevant fossil occurrences at the superfamily level. These findings provide caution in interpreting the lepidopteran fossil record through the modeling of evolutionary diversification and in determination of divergence time estimates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0290-8) contains supplementary material, which is available to authorized users.     

The impact of the Pull of the Recent on extant elasmobranchs

Modern elasmobranchs have a long evolutionary history and an abundant fossil record that consists mainly of teeth. Many fossil taxa have living representatives. However, the representation of extant taxa in the fossil record is unknown. To begin to understand the geological history of extant elasmobranchs, we here assess the quality of their fossil record. We do so by assessing the Pull of the Recent (POR). The POR can bias the fossil record because the rather complete record of living taxa allows palaeontologists to identify fossil members of the modern clades and to bridge time bins where fossils are absent. We assessed the impact of the POR by quantifying the proportion of extant elasmobranchs that have a fossil record, but do not occur in the last 5 million years (Pliocene and Pleistocene). We found that the POR does not affect orders and families, but it does affect 24% of elasmobranch genera. Within the different elasmobranch orders, the Lamniformes display the most complete generic fossil record, with no impact of the POR. Although modest, the impact of the POR in extant elasmobranch genera is higher than that found in other taxa. Overall, the geological history of elasmobranchs contradicts the usual assumption that the fossil record becomes worse backwards in time. This is the case across geographical regions and tooth size, further suggesting that sampling intensity and outcrop availability might explain the POR effect on sharks and rays.     

Early Oligocene Callitris and Fitzroya (Cupressaceae) from Tasmania

This paper documents Early Oligocene fossilized foliage and ovulate cones from Lea River, Tasmania and identifies them as belonging to two extant southern hemisphere Cupressaceae genera, Callitris and Fitzroya. Most importantly, it sheds some light on evolutionary trends within Callitris, a genus with numerous extant Australian species and two extant New Caledonian species. Callitris has a very poor fossil record and, because of the present absence of a molecular data set that includes all species, its phylogeny remains somewhat ambiguous. Although Fitzroya foliage has previously been described from a number of Tasmanian sites, this is the first recording of fertile material. The ovulate cones of the Callitris and Fitzroya macrofossils are characterized by bract-scale complexes in two whorls of three and are subtended by scale-like leaves in whorls of three. The fossilized foliage specimens consist of scale-like leaves in whorls of three. These morphological characteristics are only exhibited by three extant southern hemisphere cupressaceous genera, Callitris, Actinostrobus, and Fitzroya. The assignment of the fossils to extinct Callitris and Fitzroya species is made by comparisons with species from these three extant genera. Although much of the Lea River flora are wet rainforest taxa, the Callitris fossils have characteristics of both wet- and dry-adapted extant species.     

Mapping antibody binding sites on cytochrome c with synthetic peptides: Are results representative of the antigenic structure of proteins?

Crystallographic work on antigen-antibody complexes has revealed that extensive surface areas of proteins may interact with antibodies. On the other hand, most experimental approaches to locate and define antigenic determinants of protein antigens rely on the linear sequence of the polypeptide chain. Hence the question arises whether mapping of antibody binding sites by analysis of the reactivity of anti-protein antibodies with synthetic peptides can provide a representative picture of the antigenic structure of a protein antigen. We have addressed this question using yeast iso-1 cytochrome c as a protein antigen against which antisera were raised in rabbits. The reaction of the antisera with 103 synthetic hexapeptides covering the entire sequence of cytochrome c was tested by the pepscan procedure in which peptides are coupled to polyethylene rods and tested by ELISA. For the assay, anti-cytochrome c antibodies were fractionated by affinity chromatography on native yeast iso-1 cytochrome c and on apo-cytochrome c; the latter is a random coil. It was found that only antibodies retained by the apo-cytochrome c affinity column react with synthetic peptides. These antibodies comprise a small fraction, probably less than 2%, of all cytochrome c-specific antibodies. The majority of antigenic determinants, which seem to consist of strongly conformation-dependent topographic epitopes, could not be uncovered by the peptide approach. Epitope mapping with short peptides seems of limited usefulness in the case of small, globular, and conformationally stable proteins like cytochrome c.     

Macromolecules in brachiopod shells: characterization and diagenesis

An immunological investigation was conducted of soluble intra-crystalline macromolecules isolated from living and fossil brachiopod shells, which had previously been used for an immunologically based study of phylogeny (serotaxonomy). The soluble intra-crystalline macromolecules comprised 0.03% by weight of the extant shell material. Bulk analysis and gel electrophoresis indicated that the organic material is predominantly glycoprotein, and contains up to 30% by weight carbohydrate. Treatment of the macromolecules with periodate and proteinase K revealed that antibodies were raised predominantly against the carbohydrate moieties. Using a specially adapted dot blot immunobinding assay (DIBA) the decay in immunological signal over geological time was determined. Pleistocene shells have lost between 99 and 99.9% of immunological reactivity, and original antigenic determinants form a declining proportion of total organic matter. It is suggested that condensation reactions between amino acids and sugars account for the rapid destruction of determinants; this has important implications for the direction of future studies on fossil macromolecules. □ Serotaxonomy, biomolecular palaeontology, glycoproteins, melanoidins, brachiopods.     

Immunoabsorption of membrane-specific antibodies for determination of exposed and hidden proteins in human erythrocyte membranes.

Human erythrocyte membrane proteins solubilized with the non-ionic detergent Berol EMU-043 have been characterized by crossed immunoelectrophoresis with rabbit antibodies raised against the membrane material. Three out of sixteen membrane-specific immunoprecipitates disappeared when the antisera were first absorbed with intact erythrocytes. This finding indicates that three antigens are exposed on the outside of the erythrocyte membrane. One of these antigens showed acetylcholinesterase activity, and another was the major glycoprotein (glycophorin) as shown by crossed-line immunoelectrophoresis. No antigenic determinants of the latter protein were detected within the membrane or on its inner surface. In crossed immunoelectrophoresis with antisera after absorption with washed, non-sealed membranes only one precipitate remained. This precipitate corresponded to albumin. Accordingly, several proteins seem to have antigenic determinants exposed on the inside of the membrane.     

Immunoabsorption of membrane-specific antibodies for determination of exposed and hidden proteins in human erythrocyte membranes

Human erythrocyte membrane proteins solubilized with the non-ionic detergent Berol EMU-043 have been characterized by crossed immunoelectrophoresis with rabbit antibodies raised against the membrane material. Three out of sixteen membrane-specific immunoprecipitates disappeared when the antisera were first absorbed with intact erythrocytes. This finding indicates that three antigens are exposed on the outside of the erythrocyte membrane. One of these antigens showed acetylcholinesterase activity, and another was the major glycoprotein (glycophorin) as shown by crossed-line immunoelectrophoresis. No antigenic determinants of the latter protein were detected within the membrane or on its inner surface.In crossed immunoelectrophoresis with antisera after absorption with washed, non-sealed membranes only one precipitate remained. This precipitate corresponded to albumin. Accordingly, several proteins seem to have antigenic determinants exposed on the inside of the membrane.     

Cambrian anemones with preserved soft tissue from the Chengjiang biota, China

The group Cnidaria includes 'jellyfish', soft-bodied anemone and anemone-like forms and calcified corals. These diploblastic organisms have a fossil record extending back to the earliest metazoans of the Neoproterozoic; however certain cnidarians of the subclass Zoantharia, characterized by soft-bodied anemone-like forms, are absent or poorly represented in the fossil record. Despite the paucity of fossils, it is thought that calcification by soft anemone-like animals was responsible for producing the skeleton that allowed the preservation of the first corals. We report discovery of an abundant assemblage of in situ soft-bodied polyps with tissues. They are preserved in exquisite detail and come from the well-known Lower Cambrian Chengjiang biota of Yunnan, China. The soft-bodied polyps display a simple anatomy that is comparable to some extant anemones of the order Actinaria. The new fossils are assigned to Archisaccophyllia kunmingensis n. gen. et n. sp. Their simple and conservative form suggests that these fossils may represent some kind of ancestral rootstock. The preserved life assemblage provides a unique snapshot of Lower Cambrian anemone life and provides clues for relationships with extant actiniarians as well as calcified corals.     

A reappraisal of the Palaeopantopoda with description of a species from the Jurassic

The Devonian fossil Palaeoisopus appears, in the light of recent evidence from newly found specimens, to be much nearer extant pycnogonids than previously surmised. The fossil record of the Pycnogonida is extended to the Jurassic on the basis of a long overlooked Solenhofen example. Most of the specimens ascribed to the common Solenhofen Phalangites cannot be pycnogonids, but it is possible that we are dealing with a complex of superficially similar fossils. A revision of the classification of the fossil pycnogonids (Order Palaeopantopoda) is suggested in the light of this new material.     

Use of synthetic peptides to map the antigenic determinants of glycoprotein D of herpes simplex virus.

The predictive algorithm Surfaceplot (J.M.R. Parker, D. Guo, and R.S. Hodges, Biochemistry 25:5425-5432, 1986) was used to examine glycoprotein D of herpes simplex virus type 1 (HSV-1) for amino acid residues with a high probability of being exposed on the molecular surface. Based on these data, 11 different peptides corresponding to 10-residue segments in the primary sequence of glycoprotein D and one 20-residue segment were synthesized, conjugated to carrier proteins, and used to generate specific antisera in rabbits. Two synthetic peptides predicted not to be on the surface of glycoprotein D were included as negative controls. The polyclonal antisera against individual synthetic peptide conjugates were in turn evaluated for their ability to recognize both isolated glycoprotein D and intact HSV-1 virions in an enzyme-linked immunosorbent assay. Based on Surfaceplot predictions, eight linear antigenic sites on glycoprotein D were thereby defined from the 12 antipeptide antisera prepared. Four of these sites contained epitopes to which complement-independent neutralizing antibodies could be generated. The latter sites corresponded to sequences 12 to 21, 267 to 276, 288 to 297, and 314 to 323 of the mature protein. An additional peptide sequence, 2 to 21, was found to generate antisera which had potent virus-neutralizing capacity in the presence of complement. Identification of a neutralizing epitope in the sequence 314 to 323 makes it likely that the membrane-spanning region of glycoprotein D is within the subsequent sequence, 323 to 339. Antipeptide antisera prepared in this study from 12 synthetic peptides contained 13 surface sites predicted by Surfaceplot, of which 7 were not predicted by the parameters of Hopp and Woods (Proc. Natl. Acad. Sci. USA 78:3824-3828, 1981). Of these seven sites not predicted by the Hopp and Woods plot, all generated antipeptide antibodies that bound to HSV-1 virions and three of these seven sites generated neutralizing antibodies. In total, 8 of 12 synthetic peptides containing surface regions produced antipeptide antibodies that bound to HSV-1 virions and 5 of these generated neutralizing antibodies. These results suggest the advantages of Surfaceplot in mapping antigenic determinants in proteins.     

Fossilized spermatozoa preserved in a 50-Myr-old annelid cocoon from Antarctica

The origin and evolution of clitellate annelids—earthworms, leeches and their relatives—is poorly understood, partly because body fossils of these delicate organisms are exceedingly rare. The distinctive egg cases (cocoons) of Clitellata, however, are relatively common in the fossil record, although their potential for phylogenetic studies has remained largely unexplored. Here, we report the remarkable discovery of fossilized spermatozoa preserved within the secreted wall layers of a 50-Myr-old clitellate cocoon from Antarctica, representing the oldest fossil animal sperm yet known. Sperm characters are highly informative for the classification of extant Annelida. The Antarctic fossil spermatozoa have several features that point to affinities with the peculiar, leech-like ‘crayfish worms'' (Branchiobdellida). We anticipate that systematic surveys of cocoon fossils coupled with advances in non-destructive analytical methods may open a new window into the evolution of minute, soft-bodied life forms that are otherwise only rarely observed in the fossil record.     

Remarkably preserved annelid worms from the La Meseta Formation (Eocene), Seymour Island, Antarctica

Abstract: Worm tubes, which exhibit the replaced tube-lining membrane, have been collected from the lowermost Lower Eocene Acantilados Allomember of the La Meseta Formation, Seymour Island, Antarctica. The discovery represents the oldest examples of preservation of the tube-lining membrane of tube-dwelling Polychaeta in the fossil record. A new genus and species, Caprascolex antarcticus , are described. The specimens are preserved as thin coatings of amorphous iron oxide on the inner surface of the moulds interpreted to be the replaced tube-lining membrane. Examination of the rarely described tube-lining mucosoid membrane in extant polychaetes shows that the fossils are nearly identical in morphology and scale to extant forms. These fossils record in remarkable detail the morphology of the tube-lining membrane, which appears to be composed of growth bands formed as the worm constructed the tube. The tube-lining is believed to have been originally preserved as pyrite, with subsequent oxidation to iron oxide. The tube-lining membrane of worm tubes possibly is known from only one other fossil occurrence.     

Immunogenicity of synthetic peptides derived from Plasmodium falciparum proteins

To obtain antibodies suitable to be used in an antigen-capture assay, we have identified, synthesized, and evaluated a series of peptides from different Plasmodium falciparum excretory-secretory proteins: glutamate-rich protein (GLURP); histidine-rich protein 2; histidine-rich protein 3; Falciparum interspersed repeat antigen and, serine-rich antigen homologous. Conformational as well as antigenic predictions were performed using the ANTHEPROT package. Chemical synthesis was carried out by the multiple manual synthesis using the t-boc strategy. The peptides were used as antigens for the preparation of polyclonal antibodies in rabbits. Out of the 14 peptide constructs, eight by ELISA and, six by MABA elicited antibodies that showed correspondence between the predictive study and the immunogenicity obtained in rabbits. All antipeptide (GLURP, HRP2, and FIRA) antisera were found to bind to the corresponding synthetic sequence in an ELISA assay. The binding activity and specificity of antibodies were determined by Western blot with supernatant culture from P. falciparum. Anti-GLURP (IMT-94 and IMT-200) antisera bound to five molecules present in supernatant with molecular weight of 73, 82, 116, 124, and 128 kDa. Anti-HRP2 (IMT-192) antisera recognized a band of 58 kDa. In both cases, the specific molecules were inhibited by preincubation with the homologous peptide. Anti-HRP3, anti-FIRA neither anti-SERPH antisera showed reactivity. Anti-peptides HRP2 antibodies recognized the recombinant protein present in Parasight-F test. The same way, synthetic peptides from HRPII molecule were recognized by monoclonal antibody present in the Parasight-F assay. Our results confirm the potential value of synthetic peptides when inducing monospecific polyclonal antibodies for the development of diagnostic tests based on the capture of antigens.     

Proteaceae Leaf Fossils: Phylogeny,Diversity, Ecology and Austral Distributions

Foliar fossils of Proteaceae are reviewed, and useful specimens for interpreting evolution, and past and present distributions and environments are discussed. There are no definite Cretaceous occurrences. However, there is evidence of extant lineages dating from the Paleocene onwards, including tribe Persoonieae of subfamily Persoonioideae and each of the four tribes of subfamily Grevilleoideae. High diversity and abundance characterizes the Australian fossil record, including sclerophyllous and xeromorphic forms, but there is little evidence of the prominent extant subfamily Proteoideae. New Zealand had a much higher diversity of Proteaceae than at present, including Oligo-Miocene species of open vegetation. The South American leaf fossil record is not extensive. However, the fossil records of Embothrieae and Orites are consistent with the distributions of their extant relatives in South America and Australia being the result of vicariance. Overall, there is a need for more research on placing Proteaceae leaf fossils in a phylogenetic context.