• 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; 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.
    • Temminck's Gallus giganteus; a gigantic obstacle to Darwin's theory of domesticated fowl origin?

      van Grouw, Hein; Dekkers, Wim (British Ornithologists' Club, 2020-09-21)
      In 1813, based on the single foot of a large chicken, Temminck named a ‘new' species of junglefowl, Gallus giganteus. He considered this ‘species’ the ancestor of several large domesticated chicken breeds and believed it was one of six wild ancestral species of domestic fowl. Temminck's hypothesis was rejected by Blyth who thought Red Junglefowl G. gallus was the sole ancestor. The arrival into Britain of several very large Asian chicken breeds in the mid-19th century led to speculation that Temminck's G. giganteus may have been their wild ancestor. Darwin, who had initially agreed with Blyth, noted several peculiarities in the Cochin, a large Asian breed, which he concluded might not have been achieved by selective breeding, and questioned whether G. giganteus was involved in their ancestry. Temminck's giant junglefowl appeared to be a significant hurdle for Darwin in his effort to prove a single ancestral origin for domestic chickens.
    • 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, Harald; 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.
    • To remain or leave: Dispersal variation and its genetic consequences in benthic freshwater invertebrates

      Ruggeri, Paolo; Pasternak, E; Okamura, B (Wiley, 2019-10-18)
      Variation in dispersal capacity may influence population genetic variation and relatedness of freshwater animals thus demonstrating how life‐history traits influence patterns and processes that in turn influence biodiversity. The majority of studies have focused on the consequences of dispersal variation in taxa inhabiting riverine systems whose dendritic nature and upstream/downstream gradients facilitate characterizing populations along networks. We undertook extensive, large‐scale investigations of the impacts of hydrological connectivity on population genetic variation in two freshwater bryozoan species whose dispersive propagules (statoblasts) are either attached to surfaces (Fredericella sultana) or are released as buoyant stages (Cristatella mucedo) and that live primarily in either lotic (F. sultana) or lentic environments (C. mucedo). Describing population genetic structure in multiple sites characterized by varying degrees of hydrological connectivity within each of three (or four) UK regions enabled us to test the following hypotheses: (1) genetic diversity and gene flow will be more influenced by hydrological connectivity in populations of C. mucedo (because F. sultana dispersal stages are retained); (2) populations of F. sultana will be characterized by greater genetic divergence than those of C. mucedo (reflecting their relative dispersal capacities); and (3) genetic variation will be greatest in F. sultana (reflecting a propensity for genetic divergence as a result of its low dispersal potential). We found that hydrological connectivity enhanced genetic diversity and gene flow among C. mucedo populations but not in F. sultana while higher overall measures of clonal diversity and greater genetic divergence characterized populations of F. sultana. We suggest that genetic divergence over time within F. sultana populations reflects a general constraint of releasing propagules that might eventually be swept to sea when taxa inhabit running waters. In contrast, taxa that primarily inhabit lakes and ponds may colonize across hydrologically connected regions, establishing genetically related populations. Our study contributes more nuanced views about drivers of population genetic structures in passively dispersing freshwater invertebrates as outlined by the Monopolization Hypothesis (Acta Oecologica, 23, 2002, 121) by highlighting how a range of demographic and evolutionary processes reflect life‐history attributes of benthic colonial invertebrates (bryozoans) and cyclically parthenogenetic zooplankton. In addition, growing evidence that genetic divergence may commonly characterize populations of diverse groups of riverine taxa suggests that organisms inhabiting lotic systems may be particularly challenged by environmental change. Such change may predispose riverine populations to extinction as a result of genetic divergence combined with limited dispersal and gene flow.
    • The Tomato (Solanum lycopersicum L., Solanaceae) and Its Botanical Relatives

      Knapp, S; Peralta, IE; Causse, M; Giovannoni, J; Bouzayen, M; Zouine, M (Springer, 2016-11-24)
      The cultivated tomato, Solanum lycopersicum L., is a member of the small section Lycopersicon along with its 12 wild relatives. An additional four species from sections Juglandifolia and Lycopersicoides are traditionally considered as tomato wild relatives. These species are all endemic to South America, but the cultivated tomato itself has achieved worldwide distribution with the help of human populations. Tomato and its wild relatives are part of a larger monophyletic group (the Potato clade) that also contains the potatoes and their wild relatives. Here we review the taxonomic and phylogenetic history, relationships and species-level taxonomy of the cultivated tomato and its wild relatives, and highlight important studies of diversity that remain to be undertaken in the group, especially in light of global environmental and climatic change.
    • The tomato genome sequence provides insights into fleshy fruit evolution

      Knapp, S; The Tomato Genome Consortium (TGC) (Springer Science and Business Media LLC, 2012-05-30)
      Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
    • 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 from three seabird species breeding in the Timor Sea

      Lavers, JL; Humphreys-Williams, Emma; Crameri, NJ; Bond, AL (Elsevier BV, 2020-01-29)
      Mobile marine predators, such as seabirds, are frequently used as broad samplers of contaminants that are widespread in the marine environment. The Timor Sea off remote Western Australia is a poorly studied, yet rapidly expanding area of offshore development. To provide much needed data on contamination in this region, we quantified trace element concentrations in breast feathers of three seabird species breeding on Bedout Island. While adult Masked Boobies Sula dactylatra exhibited some of the highest concentrations, values for all species were below toxicology thresholds for seabirds and were comparable to those reported in other closely related species. The low concentrations detected in the birds provide a valuable baseline and suggest that the local marine environment around Bedout is in relatively good condition. However, careful monitoring is warranted in light increasing anthropogenic activity in this region.
    • 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)