• Taxonomy and phylogeny of mud owls (Annelida: Sternaspidae), including a new synonymy and new records from the Southern Ocean, North East Atlantic Ocean and Pacific Ocean: challenges in morphological delimitation

      Drennan, R; Wiklund, H; Rouse, GW; Georgieva, MN; Wu, X; Kobayashi, G; Yoshino, K; Glover, AG (Springer Science and Business Media LLC, 2019-09-04)
      Species delimitation in sternaspid polychaetes is currently based on the morphology of a limited suite of characters, namely characters of the ventro-caudal shield—a unique feature of the family. Sternaspid species description has increased rapidly in recent years; however, the validity of the shield as a diagnostic character has not been assessed through molecular means. This study performs the largest molecular taxonomy of Sternaspidae to date, using the nuclear gene 18S, and the mitochondrial genes 16S and cytochrome oxidase subunit I (COI) to assess phylogenetic relationships within the family, to reassess the placement of Sternaspidae within the wider polychaete tree and to investigate the effectiveness of the shield as a diagnostic morphological character. This study includes many new records and reports Sternaspis affinis Stimpson, 1864 from USA Pacific coastline and genetic connectivity between specimens identified as Sternaspis cf. annenkovae Salazar-Vallejo & Buzhinskaja, 2013 from off southeastern Australia and specimens identified as Sternaspis cf. williamsae Salazar-Vallejo & Buzhinskaja, 2013 from the northwestern Pacific. In addition, we investigate material identified as Sternaspis cf. scutata (Ranzani, 1817) in the English Channel and compare with S. scutata through both molecular and morphological means. We further perform a detailed morphological and molecular investigation of new sternaspid material collected from the Southern Ocean and Antarctic Peninsula and regard Sternaspis monroi Salazar-Vallejo, 2014 syn. n. as a junior synonym of Sternaspis sendalli Salazar-Vallejo, 2014, two species recently described from the region, raising questions concerning the validity of current morphological delimitation.
    • Taxonomy based on science is necessary for global conservation

      Thomson, SA; Pyle, RL; Ahyong, ST; Alonso-Zarazaga, M; Ammirati, S; Araya, JF; Todd, JA; Barclay, Maxwell V.L.; Michel, Ellinor; Nikolaeva, Svetlana; et al. (2018-03-14)
    • Telenomus remus, a Candidate Parasitoid for the Biological Control of Spodoptera frugiperda in Africa, is already Present on the Continent

      Kenis, M; du Plessis, H; Van den Berg, J; Ba, MN; Goergen, G; Kwadjo, KE; Baoua, I; Tefera, T; Buddie, A; Cafa, G; et al. (MDPI, 2019-03-29)
      The fall armyworm, Spodoptera frugiperda, a moth originating from tropical and subtropical America, has recently become a serious pest of cereals in sub-Saharan Africa. Biological control offers an economically and environmentally safer alternative to synthetic insecticides that are being used for the management of this pest. Consequently, various biological control options are being considered, including the introduction of Telenomus remus, the main egg parasitoid of S. frugiperda in the Americas, where it is already used in augmentative biological control programmes. During surveys in South, West, and East Africa, parasitized egg masses of S. frugiperda were collected, and the emerged parasitoids were identified through morphological observations and molecular analyses as T. remus. The presence of T. remus in Africa in at least five countries provides a great opportunity to develop augmentative biological control methods and register the parasitoid against S. frugiperda. Surveys should be carried out throughout Africa to assess the present distribution of T. remus on the continent, and the parasitoid could be re-distributed in the regions where it is absent, following national and international regulations. Classical biological control should focus on the importation of larval parasitoids from the Americas.
    • Tetracapsuloides bryosalmonae abundance in river water

      Fontes, I; Hartikainen, H; Holland, JW; Secombes, CJ; Okamura, B (2017-04-20)
    • Time for a rethink: time sub-sampling methods in disparity-through-time analyses

      Guillerme, T; Cooper, N; Smith, A (The Palaeontological Association, 2018-04-22)
      Disparity‐through‐time analyses can be used to determine how morphological diversity changes in response to mass extinctions, or to investigate the drivers of morphological change. These analyses are routinely applied to palaeobiological datasets, yet, although there is much discussion about how to best calculate disparity, there has been little consideration of how taxa should be sub‐sampled through time. Standard practice is to group taxa into discrete time bins, often based on stratigraphic periods. However, this can introduce biases when bins are of unequal size, and implicitly assumes a punctuated model of evolution. In addition, many time bins may have few or no taxa, meaning that disparity cannot be calculated for the bin and making it harder to complete downstream analyses. Here we describe a different method to complement the disparity‐through‐time tool‐kit: time‐slicing. This method uses a time‐calibrated phylogenetic tree to sample disparity‐through‐time at any fixed point in time rather than binning taxa. It uses all available data (tips, nodes and branches) to increase the power of the analyses, specifies the implied model of evolution (punctuated or gradual), and is implemented in R. We test the time‐slicing method on four example datasets and compare its performance in common disparity‐through‐time analyses. We find that the way we time sub‐sample taxa can change our interpretations of the results of disparity‐through‐time analyses. We advise using multiple methods for time sub‐sampling taxa, rather than just time binning, to gain a better understanding disparity‐through‐time.
    • The timescale of early land plant evolution

      Morris, JL; Puttick, MN; Clark, JW; Edwards, D; Kenrick, P; Pressel, S; Wellman, CH; Yang, Z; Schneider, H; Donoghue, PCJ (National Academy of Sciences of the United States of America, 2018-03-06)
      Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth’s System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte−tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian–Early Ordovician, origin.
    • Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A Transcriptomic case study in the Demosponge Halisarca caerulea

      Kenny, NJ; de Goeij, JM; de Bakker, DM; Whalen, CG; Berezikov, E; Riesgo, A (Elsevier, 2018-02)
      Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study. Less well-documented for their regenerative abilities are sponges. This is surprising, as they are both one of the earliest-branching extant metazoan phyla on Earth, and are rapidly able to respond to injury. Their sessile lifestyle, lack of an external protective layer, inability to respond to predation and filter-feeding strategy all mean that regeneration is often required. In particular the demosponge genus Halisarca has been noted for its fast cell turnover and ability to quickly adjust its cell kinetic properties to repair damage through regeneration. However, while the rate and structure of regeneration in sponges has begun to be investigated, the molecular mechanisms behind this ability are yet to be catalogued. Here we describe the assembly of a reference transcriptome for Halisarca caerulea, along with additional transcriptomes noting response to injury before, shortly following (2 h post-), and 12 h after trauma. RNAseq reads were assembled using Trinity, annotated, and samples compared, to allow initial insight into the transcriptomic basis of sponge regenerative processes. These resources are deep, with our reference assembly containing > 92.6% of the BUSCO Metazoa set of genes, and well-assembled (N50s of 836, 957, 1688 and 2032 for untreated, 2 h, 12 h and reference transcriptomes respectively), and therefore represent excellent qualitative resources as a bedrock for future study. The generation of transcriptomic resources from sponges before and following deliberate damage has allowed us to study particular pathways within this species responsible for repairing damage. We note particularly the involvement of the Wnt cascades in this process in this species, and detail the contents of this cascade, along with cell cycle, extracellular matrix and apoptosis-linked genes in this work. This resource represents an initial starting point for the continued development of this knowledge, given H. caerulea's ability to regenerate and position as an outgroup for comparing the process of regeneration across metazoan lineages. With this resource in place, we can begin to infer the regenerative capacity of the common ancestor of all extant animal life, and unravel the elements of regeneration in an often-overlooked clade.
    • Trace element concentrations in feathers of seven petrels (Pterodroma spp.)

      Philpot, SM; Lavers, JL; Nugegoda, D; Gilmour, ME; Hutton, I; Bond, A (Springer (part of Springer Nature), 2019-02-07)
      Gadfly petrels (Pterodroma spp.) are one of the most threatened and poorly studied seabird groups, and as marine predators, are exposed to biomagnified and bioaccumulated chemical pollutants from their prey.We quantified trace element concentrations in breast feathers of seven petrel species that breed in the southern hemisphere to quantify current concentrations. Selenium (Se) concentrations were significantly lower in chicks than adults; this was not observed for zinc (Zn) or lead (Pb). Overall, the species examined here exhibited similar concentrations of Se, with Pb and Zn concentrations more variable among species. The mean Se concentration in adult birds exceeded those thought to be potentially deleterious, and three species had concentrations that were above the assumed threshold for Pb toxicity. Further investigation of potentially toxic trace elements in gadfly petrels is warranted.
    • Training needs and recommendations for Citizen Science participants, facilitators and designers

      Lorke, Julia; Golumbic, YN; Ramjan, C; Atias, O (COST Action 15212, 2019-11-15)
      In this report, we aimed to systematise and elaborate on the ideas discussed during the COST Action WG2 workshop “Systematic review on training requirements and recommendations for Citizen Science” that took place in Riga on 12-13th November 2018. Building on the input from the workshop participants’ broad range of different perspectives and expertise in citizen science and education, we compiled a list of training needs for project participants, project facilitators and project designers in citizen science and categorised them into core, operational and engagement needs. Based on our experience we discussed challenges that may need to be considered when designing training in citizen science. We then addressed the needs by formulating recommendations and pointing out available resources that have been proven to be useful in our own citizen science research and practice. While we acknowledge that these training needs and training recommendations may not be complete, we believe that our approach from needs to recommendations can act as a helpful working model when designing training and the list of resources provides a starting point to delve deeper into the topic and good training examples to build on. We invite the community to provide further insights into training needs and recommendations and to contribute further resources to the list
    • Transgressive phenotypes and generalist pollination in the floral evolution of Nicotiana polyploids

      McCarthy, EW; Chase, MW; Knapp, S; Litt, A; Leitch, AR; Le Comber, SC (2016-08-08)
    • Transition in sexual system and sex chromosome evolution in the tadpole shrimp Triops cancriformis

      Mathers, TC; Hammond, RL; Jenner, RA; Haenfling, B; Atkins, J; Gomez, A (2015-07)
    • Traumatic myiasis in farmed animals caused by Wohlfahrtia magnifica in southern Italy (Diptera: Sarcophagidae)

      Bonacci, T; Curia, G; Leoncini, R; Whitmore, D (PAGEpress, 2017-06-30)
      Ten herds of sheep and goats (455 heads) were inspected for the presence of traumatic myiasis between May and September 2013 in the province of Cosenza, Calabria, southern Italy. Nine cases were discovered in sheep, goats and a sheepdog. Infested body sites included external genitalia, wounds (sheep and sheepdog) and hooves (goats). Larvae were removed from the infested body areas and reared to adult stage in the laboratory. Both the larvae and the adults were identified as belonging to the Mediterranean screwworm fly Wohlfahrtia magnifica (Schiner, 1862) (Diptera: Sarcophagidae), an obligatory parasite of humans and warm-blooded vertebrates. To our knowledge, these are the first cases of wohlfahrtiosis in sheep and goats to be reported from Calabria. The infested animals were living outdoors in spring and summer, and enclosed in sheds during the autumn and winter months. Observed effects of the myiases included severely impeded walking and tissue damage. Wohlfahrtiosis can cause significant economic loss to farmers. Data about the local distribution, seasonality and types of infestation caused by W. magnifica are useful to farmers and vets to improve control systems, in Calabria as elsewhere within the distributional range of the species.
    • Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species

      Plese, Bruna; Rossi, Maria Eleonora; Kenny, Nathan James; Taboada, Sergi; Koutsouveli, Vasiliki; Riesgo, Ana (Wiley, 2019-05-09)
      Mitochondrial resources are of known utility to many fields of phylogenetic, population and molecular biology. Their combination of faster and slower‐evolving regions and high copy number enables them to be used in many situations where other loci are unsuitable, with degraded samples and after recent speciation events.The advent of next‐generation sequencing technologies (and notably the Illumina platform) has led to an explosion in the number of samples that can be studied at transcriptomic level, at relatively low cost. Here we describe a robust pipeline for the recovery of mitochondrial genomes from these RNA‐sequencing resources. This pipeline can be used on sequencing of a variety of depths, and reliably recovers the protein coding and ribosomal gene complements of mitochondria from almost any transcriptomic sequencing experiment. The complete sequence of the mitochondrial genome can also be recovered when sequencing is performed in sufficient depth. We show the efficacy of our pipeline using data from eight nonmodel invertebrates of six disparate phyla. Interestingly, among our poriferan data, where microbiological symbionts are known empirically to make mitochondrial assembly difficult, this pipeline proved especially useful. Our pipeline will allow the recovery of mitochondrial data from a variety of previously sequenced samples, and add an additional angle of enquiry to future RNA‐sequencing efforts, simplifying the process of mitochondrial genome assembly for even the most recalcitrant clades and adding these data to the scientific record for a range of future uses.
    • Two European Cornus L. feeding leafmining moths, Antispila petryi Martini, 1899, sp. rev. and A. treitschkiella (Fischer von Röslerstamm, 1843) (Lepidoptera, Heliozelidae): an unjustified synonymy and overlooked range expansion

      van Nieukerken, EVN; Lees, DC; Doorenweerd, C; Koster, SJC; Bryner, R; Schreurs, A; Timmermans, MJTN; Sattler, K (Pensoft Publishers, 2018-01-26)
      Antispila treitschkiella (Fischer von Röslerstamm, 1843) and A. petryi Martini, 1899, sp. rev. were regarded as synonymous since 1978, but are shown to be two clearly separated species with different hostplants, life histories, DNA barcodes and morphology. Antispila treitschkiella feeds on Cornus mas L., is bivoltine, and has, by following its ornamentally planted host, greatly expanded its range in north-western Europe. In contrast A. petryi feeds on the widespread native C. sanguinea L., is univoltine, and is one of only two Antispila species previously resident in the British Isles, the Netherlands and northern Europe. Consequently, the increase in abundance of A. treitschkiella in the Netherlands since the early 1990s and in Great Britain in recent years must be regarded as part of a recent expansion into north-western Europe, whereas the native A. petryi is hardly expanding and less abundant. In Britain, detailed surveys of parks and living collections confirmed the monophagy of these two species. A search of British herbarium samples provided no evidence for an earlier date of establishment. Information on recognition of all stages, including DNA barcodes, and distribution is provided, and these two species are compared with the third European Cornus L. leafminer, A. metallella (Denis & Schiffermüller, 1775).