Identification,expression, and molecular evolution of microRNAs in the “living fossil” Triops cancriformis (tadpole shrimp)

MicroRNAs have been identified and analyzed in various model species, but an investigation of miRNAs in nonmodel species is required for a more complete understanding of miRNA evolution. In this study, we investigated the miRNAs of the nonmodel species Triops cancriformis (tadpole shrimp), a “living fossil,” whose morphological form has not changed in almost 200 million years. Dramatic ontogenetic changes occur during its development. To clarify the evolution of miRNAs, we comparatively analyzed its miRNAs and the components of its RNAi machinery. We used deep sequencing to analyze small RNA libraries from the six different developmental stages of T. cancriformis (egg, first–fourth instars, and adult), and also analyzed its genomic DNA with deep sequencing. We identified 180 miRNAs (87 conserved miRNAs and 93 novel candidate miRNAs), and deduced the components of its RNAi machinery: the DICER1, AGO1–3, PIWI, and AUB proteins. A comparative miRNA analysis of T. cancriformis and Drosophila melanogaster showed inconsistencies in the expression patterns of four conserved miRNAs. This suggests that although the miRNA sequences of the two species are very similar, their roles differ across the species. An miRNA conservation analysis revealed that most of the conserved T. cancriformis miRNAs share sequence similarities with those of arthropods, although T. cancriformis is called a “living fossil.” However, we found that let-7 and DICER1 of T. cancriformis are more similar to those of the vertebrates than to those of the arthropods. These results suggest that miRNA systems of T. cancriformis have evolved in a unique fashion.     

Extraordinary fossils reveal the nature of Cambrian life: a commentary on Whittington (1975) ‘The enigmatic animal Opabinia regalis,Middle Cambrian,Burgess Shale,British Columbia’

Harry Whittington''s 1975 monograph on Opabinia was the first to highlight how some of the Burgess Shale animals differ markedly from those that populate today''s oceans. Categorized by Stephen J. Gould as a ‘weird wonder’ (Wonderful life, 1989) Opabinia, together with other unusual Burgess Shale fossils, stimulated ongoing debates about the early evolution of the major animal groups and the nature of the Cambrian explosion. The subsequent discovery of a number of other exceptionally preserved fossil faunas of Cambrian and early Ordovician age has significantly augmented the information available on this critical interval in the history of life. Although Opabinia initially defied assignment to any group of modern animals, it is now interpreted as lying below anomalocaridids on the stem leading to the living arthropods. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.     

Two new species of the genus Anisomysis (Anisomysis) (Crustacea,Mysida, Mysidae) from coral reef waters in Thailand

Two new species of Anisomysis Hansen, 1910 (Mysida, Mysidae), Anisomysis (Anisomysis) spinaintus sp. n. and Anisomysis (Anisomysis) phuketensis sp. n., from coral-reef waters in Thailand are described. Anisomysis (Anisomysis) spinaintus, collected in the Chaolao Beach, Chanthaburi Province, is distinguished from the closely allied species Anisomysis (Anisomysis) incisa Tattersall, 1936, and Anisomysis (Anisomysis) hawaiiensis Murano, 1995, by the presence of 6–9 spines on the apical cleft of telson, which are absent in the latter two allied species. The new species can also be distinguished from Anisomysis (Anisomysis) aikawai Ii, 1964, by the presence of a deep telson cleft and a large number of spines on the lateral margin of telson. Anisomysis (Anisomysis) phuketensis sp. n., collected in Ko Lon, Phuket, is distinguished from the allied species Anisomysis (Anisomysis) robustispina Panampunnayil, 1984, by having a short telson and a pair of long spines on the apical part of the telson. Keys to the subgenera and species of Anisomysis, including the two new species, are presented.     

Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress

The bacterium Wolbachia (order Rickettsiales), representing perhaps the most abundant vertically transmitted microbe worldwide, infects arthropods and filarial nematodes. In arthropods, Wolbachia can induce reproductive alterations and interfere with the transmission of several arthropod-borne pathogens. In addition, Wolbachia is an obligate mutualist of the filarial parasites that cause lymphatic filariasis and onchocerciasis in the tropics. Targeting Wolbachia with tetracycline antibiotics leads to sterilisation and ultimately death of adult filariae. However, several weeks of treatment are required, restricting the implementation of this control strategy. To date, the response of Wolbachia to stress has not been investigated, and almost nothing is known about global regulation of gene expression in this organism. We exposed an arthropod Wolbachia strain to doxycycline in vitro, and analysed differential expression by directional RNA-seq and label-free, quantitative proteomics. We found that Wolbachia responded not only by modulating expression of the translation machinery, but also by upregulating nucleotide synthesis and energy metabolism, while downregulating outer membrane proteins. Moreover, Wolbachia increased the expression of a key component of the twin-arginine translocase (tatA) and a phosphate ABC transporter ATPase (PstB); the latter is associated with decreased susceptibility to antimicrobials in free-living bacteria. Finally, the downregulation of 6S RNA during translational inhibition suggests that this small RNA is involved in growth rate control. Despite its highly reduced genome, Wolbachia shows a surprising ability to regulate gene expression during exposure to a potent stressor. Our findings have general relevance for the chemotherapy of obligate intracellular bacteria and the mechanistic basis of persistence in the Rickettsiales.     

The incidence of bacterial endosymbionts in terrestrial arthropods

Intracellular endosymbiotic bacteria are found in many terrestrial arthropods and have a profound influence on host biology. A basic question about these symbionts is why they infect the hosts that they do, but estimating symbiont incidence (the proportion of potential host species that are actually infected) is complicated by dynamic or low prevalence infections. We develop a maximum-likelihood approach to estimating incidence, and testing hypotheses about its variation. We apply our method to a database of screens for bacterial symbionts, containing more than 3600 distinct arthropod species and more than 150 000 individual arthropods. After accounting for sampling bias, we estimate that 52% (CIs: 48–57) of arthropod species are infected with Wolbachia, 24% (CIs: 20–42) with Rickettsia and 13% (CIs: 13–55) with Cardinium. We then show that these differences stem from the significantly reduced incidence of Rickettsia and Cardinium in most hexapod orders, which might be explained by evolutionary differences in the arthropod immune response. Finally, we test the prediction that symbiont incidence should be higher in speciose host clades. But while some groups do show a trend for more infection in species-rich families, the correlations are generally weak and inconsistent. These results argue against a major role for parasitic symbionts in driving arthropod diversification.     

Detection and characterization of Wolbachia infection in silkworm

Wolbachia naturally infects a wide variety of arthropods, where it plays important roles in host reproduction. It was previously reported that Wolbachia did not infect silkworm. By means of PCR and sequencing we found in this study that Wolbachia is indeed present in silkworm. Phylogenetic analysis indicates that Wolbachia infection in silkworm may have occurred via transfer from parasitic wasps. Furthermore, Southern blotting results suggest a lateral transfer of the wsp gene into the genomes of some wild silkworms. By antibiotic treatments, we found that tetracycline and ciprofloxacin can eliminate Wolbachia in the silkworm and Wolbachia is important to ovary development of silkworm. These results provide clues towards a more comprehensive understanding of the interaction between Wolbachia and silkworm and possibly other lepidopteran insects.     

Chimpanzee fauna isotopes provide new interpretations of fossil ape and hominin ecologies

Carbon and oxygen stable isotopes within modern and fossil tooth enamel record the aspects of an animal''s diet and habitat use. This investigation reports the first isotopic analyses of enamel from a large chimpanzee community and associated fauna, thus providing a means of comparing fossil ape and early hominin palaeoecologies with those of a modern ape. Within Kibale National Park forest, oxygen isotopes differentiate primate niches, allowing for the first isotopic reconstructions of degree of frugivory versus folivory as well as use of arboreal versus terrestrial resources. In a comparison of modern and fossil community isotopic profiles, results indicate that Sivapithecus, a Miocene ape from Pakistan, fed in the forest canopy, as do chimpanzees, but inhabited a forest with less continuous canopy or fed more on leaves. Ardipithecus, an early hominin from Ethiopia, fed both arboreally and terrestrially in a more open habitat than inhabited by chimpanzees.     

Transmission of Pandora neoaphidis in the presence of co-occurring arthropods

Transmission of the entomopathogenic fungus Pandora neoaphidis to the nettle aphid Microlophium carnosum was assessed in the presence of arthropods that co-exist with the fungus within the habitat but do not compete for aphid hosts. The presence of a parasitoid significantly enhanced transmission, and transmission rates were similar for both enemy and non-enemy parasitoids. Although herbivory of nettle leaves by Peacock butterfly (Inchis io) caterpillars indirectly reduced the number of M. carnosum by >30% due to a reduction in leaf area for feeding, the addition of I. io significantly increased transmission of P. neoaphidis in the remaining aphids. It is likely that enhanced transmission in the presence of A. rhopalosiphii and I. io is due to disturbance and subsequent movement of the aphid, resulting in contact with conidia deposited on the leaf surface. The presence and impact of co-occurring arthropods should be taken into consideration when assessing the transmission of fungal entomopathogens.     

Arthropod visual predators in the early pelagic ecosystem: evidence from the Burgess Shale and Chengjiang biotas

Exceptional fossil specimens with preserved soft parts from the Maotianshan Shale (ca 520 Myr ago) and the Burgess Shale (505 Myr ago) biotas indicate that the worldwide distributed bivalved arthropod Isoxys was probably a non-benthic visual predator. New lines of evidence come from the functional morphology of its powerful prehensile frontal appendages that, combined with large spherical eyes, are thought to have played a key role in the recognition and capture of swimming or epibenthic prey. The swimming and steering of this arthropod was achieved by the beating of multiple setose exopods and a flap-like telson. The appendage morphology of Isoxys indicates possible phylogenetical relationships with the megacheirans, a widespread group of assumed predator arthropods characterized by a pre-oral ‘great appendage’. Evidence from functional morphology and taphonomy suggests that Isoxys was able to migrate through the water column and was possibly exploiting hyperbenthic niches for food. Although certainly not unique, the case of Isoxys supports the idea that off-bottom animal interactions such as predation, associated with complex feeding strategies and behaviours (e.g. vertical migration and hunting) were established by the Early Cambrian. It also suggests that a prototype of a pelagic food chain had already started to build-up at least in the lower levels of the water column.     

Phage loss and the breakdown of a defensive symbiosis in aphids

Terrestrial arthropods are often infected with heritable bacterial symbionts, which may themselves be infected by bacteriophages. However, what role, if any, bacteriophages play in the regulation and maintenance of insect–bacteria symbioses is largely unknown. Infection of the aphid Acyrthosiphon pisum by the bacterial symbiont Hamiltonella defensa confers protection against parasitoid wasps, but only when H. defensa is itself infected by the phage A. pisum secondary endosymbiont (APSE). Here, we use a controlled genetic background and correlation-based assays to show that loss of APSE is associated with up to sevenfold increases in the intra-aphid abundance of H. defensa. APSE loss is also associated with severe deleterious effects on aphid fitness: aphids infected with H. defensa lacking APSE have a significantly delayed onset of reproduction, lower weight at adulthood and half as many total offspring as aphids infected with phage-harbouring H. defensa, indicating that phage loss can rapidly lead to the breakdown of the defensive symbiosis. Our results overall indicate that bacteriophages play critical roles in both aphid defence and the maintenance of heritable symbiosis.     

Ancient fig wasps indicate at least 34 Myr of stasis in their mutualism with fig trees

Fig wasps and fig trees are mutually dependent, with each of the 800 or so species of fig trees (Ficus, Moraceae) typically pollinated by a single species of fig wasp (Hymenoptera: Agaonidae). Molecular evidence suggests that the relationship existed over 65 Ma, during the Cretaceous. Here, we record the discovery of the oldest known fossil fig wasps, from England, dated at 34 Ma. They possess pollen pockets that contain fossil Ficus pollen. The length of their ovipositors indicates that their host trees had a dioecious breeding system. Confocal microscopy and scanning electron microscopy reveal that the fossil female fig wasps, and more recent species from Miocene Dominican amber, display the same suite of anatomical characters associated with fig entry and pollen-carrying as modern species. The pollen is also typical of modern Ficus. No innovations in the relationship are discernible for the last tens of millions of years.     

The anamorphic genus Monotosporella (Ascomycota) from Eocene amber and from modern Agathis resin

The anamorphic fungal genus Monotosporella (Ascomycota, Sordariomycetes) has been reco-vered from a piece of Early Eocene Indian amber, as well as from the surface of extant resin flows in New Caledonia. The fossil fungus was obtained from the Tarkeshwar Lignite Mine of Gujarat State, western India, and was part of the biota of an early tropical angiosperm rainforest. The amber inclusion represents the second fossil record of Sordariomycetes, as well as the first fossil of its particular order (either Savoryellales or Chaetosphaeriales). The fossil fungus is distinguished from extant representatives by possessing both short conidiophores and small two-septate pyriform conidia, and is described as Monotosporella doerfeltii sp. nov. Inside the amber, the anamorph is attached to its substrate, which is likely the degraded thallus of a cladoniform lichen. The extant New Caledonian species is assigned to Monotosporella setosa. It was found growing on semi-solidified resin flows of Agathis ovata (Araucariaceae), and is the first record of Monotosporella from modern resin substrates.     

A report on biocompounds from palm fossil of India

The occurrence of a large number of fossil woods having resemblance in anatomical features with the modern palm genus, Phoenix L in Deccan Intertrappean fossil flora of Maastrichtian-Danian age (i. e. Late Cretaceous and Earliest Tertiary (65-67 my)) indicates the most primitive record of date palm. Present discovery of biocompounds from fossil wood of Phoenix collected from Deccan Intertrappean having affinity with the biocompounds known from modern plant further exemplify the earliest documentation of Phoenix in Indian peninsula.     

The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration

The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA^His differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.     

Molecular phylogenetic evidence supports a new family of octocorals and a new genus of Alcyoniidae (Octocorallia,Alcyonacea)

Molecular phylogenetic evidence indicates that the octocoral family Alcyoniidae is highly polyphyletic, with genera distributed across Octocorallia in more than 10 separate clades. Most alcyoniid taxa belong to the large and poorly resolved Holaxonia–Alcyoniina clade of octocorals, but members of at least four genera of Alcyoniidae fall outside of that group. As a first step towards revision of the family, we describe a new genus, Parasphaerasclera gen. n., and family, Parasphaerascleridae fam. n., of Alcyonacea to accommodate species of Eleutherobia Pütter, 1900 and Alcyonium Linnaeus, 1758 that have digitiform to digitate or lobate growth forms, completely lack sclerites in the polyps, and have radiates or spheroidal sclerites in the colony surface and interior. Parasphaerascleridae fam. n. constitutes a well-supported clade that is phylogenetically distinct from all other octocoral taxa. We also describe a new genus of Alcyoniidae, Sphaerasclera gen. n., for a species of Eleutherobia with a unique capitate growth form. Sphaerasclera gen. n. is a member of the Anthomastus–Corallium clade of octocorals, but is morphologically and genetically distinct from Anthomastus Verrill, 1878 and Paraminabea Williams & Alderslade, 1999, two similar but dimorphic genera of Alcyoniidae that are its sister taxa. In addition, we have re-assigned two species of Eleutherobia that have clavate to capitate growth forms, polyp sclerites arranged to form a collaret and points, and spindles in the colony interior to Alcyonium, a move that is supported by both morphological and molecular phylogenetic evidence.     

Phylogeny of early Australopithecus: new fossil evidence from the Woranso-Mille (central Afar,Ethiopia)

The earliest evidence of Australopithecus goes back to ca 4.2 Ma with the first recorded appearance of Australopithecus ‘anamensis’ at Kanapoi, Kenya. Australopithecus afarensis is well documented between 3.6 and 3.0 Ma mainly from deposits at Laetoli (Tanzania) and Hadar (Ethiopia). The phylogenetic relationship of these two ‘species’ is hypothesized as ancestor–descendant. However, the lack of fossil evidence from the time between 3.6 and 3.9 Ma has been one of its weakest points. Recent fieldwork in the Woranso-Mille study area in the Afar region of Ethiopia has yielded fossil hominids dated between 3.6 and 3.8 Ma. These new fossils play a significant role in testing the proposed relationship between Au. anamensis and Au. afarensis. The Woranso-Mille hominids (3.6–3.8 Ma) show a mosaic of primitive, predominantly Au. anamensis-like, and some derived (Au. afarensis-like) dentognathic features. Furthermore, they show that, as currently known, there are no discrete and functionally significant anatomical differences between Au. anamensis and Au. afarensis. Based on the currently available evidence, it appears that there is no compelling evidence to falsify the hypothesis of ‘chronospecies pair’ or ancestor–descendant relationship between Au. anamensis and Au. afarensis. Most importantly, however, the temporally and morphologically intermediate Woranso-Mille hominids indicate that the species names Au. afarensis and Au. anamensis do not refer to two real species, but rather to earlier and later representatives of a single phyletically evolving lineage. However, if retaining these two names is necessary for communication purposes, the Woranso-Mille hominids are best referred to as Au. anamensis based on new dentognathic evidence.     

Palaeomagnetic analysis of the Sterkfontein palaeocave deposits: implications for the age of the hominin fossils and stone tool industries

Palaeomagnetic analysis was conducted on speleothems from Members 1-5 at Sterkfontein Cave, South Africa. Palaeomagnetic analysis of siltstone and speleothem from the bulk of Member 4 indicate a reversed magnetic polarity that dates the deposits and its Australopithecus africanus fossils to between 2.58 and ∼2.16 Ma. Further confirmation of this age comes in the form of two short normal polarity events correlated to the Rèunion (∼2.16 Ma) and Huckleberry Ridge (∼2.05 Ma) events in speleothem capping the bulk of Member 4 and coeval with deposition of the final phase of Member 4, including A. africanus fossil Sts 5. At ∼2.16-2.05 Ma, Sts 5 is the youngest representative of A. africanus yet discovered. Palaeomagnetic analysis of the Silberberg Grotto deposits identifies a single short geomagnetic field event in flowstone overlying the StW 573 Australopithecus fossil, which is suggested to represent the Rèunion event at ∼2.16 Ma. This further supports the uranium lead age estimates of 2.3-2.2 Ma for the StW 573 fossil. Based on a reversed polarity for the deposits below the skeleton it cannot be older than 2.58 Ma. If StW 573 is considered to be a second species of Australopithecus then this indicates that two species of Australopithecus are present at Sterkfontein between 2.6 and 2.0 Ma. All of the Member 5 deposits date to less than 1.8 Ma based on a comparison of palaeomagnetic, faunal, and electron spin resonance age estimates. The StW 53 fossil bearing infill (M5A) is intermediate in age between Member 4 and the rest of Member 5 (B-C) at around 1.78-1.49 Ma. The rest of Member 5 (B-C) containing Oldowan and Acheulian stone tools and Homo and Paranthropus fossils was deposited gradually between 1.40 and 1.07 Ma, much younger than previously suggested.