• Phylogenomics of non-model ciliates based on transcriptomic analyses

      Chen, X; Zhao, X; Liu, X; Warren, A; Zhao, F; Miao, M (2015-05)
    • Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

      Hamilton, CA; St Laurent, RA; Dexter, K; Kitching, I; Breinholt, JW; Zwick, A; Timmermans, MJTN; Barber, JR; Kawahara, AY (BioMed Central, 2019-09-18)
      Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. Results: The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). Conclusions: Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
    • Phylogeny and Historical Biogeography of Asian Pterourus Butterflies (Lepidoptera: Papilionidae): A Case of Intercontinental Dispersal from North America to East Asia

      Wu, L-W; Yen, S-H; Lees, David; Lu, C-C; Yang, P-S; Hsu, Y-F; Boykin, LM (2015-10-20)
      The phylogenetic status of the well-known Asian butterflies often known as Agehana (a species group, often treated as a genus or a subgenus, within Papilio sensu lato) has long remained unresolved. Only two species are included, and one of them especially, Papilio maraho, is not only rare but near-threatened, being monophagous on its vulnerable hostplant, Sassafras randaiense (Lauraceae). Although the natural history and population conservation of “Agehana” has received much attention, the biogeographic origin of this group still remains enigmatic. To clarify these two questions, a total of 86 species representatives within Papilionidae were sampled, and four genes (concatenated length 3842 bp) were used to reconstruct their phylogenetic relationships and historical scenarios. Surprisingly, “Agehana” fell within the American Papilio subgenus Pterourus and not as previously suggested, phylogenetically close to the Asian Papilio subgenus Chilasa. We therefore formally synonymize Agehana with Pterourus. Dating and biogeographic analysis allow us to infer an intercontinental dispersal of an American ancestor of Asian Pterourus in the early Miocene, which was coincident with historical paleo-land bridge connections, resulting in the present “East Asia-America” disjunction distribution. We emphasize that species exchange between East Asia and America seems to be a quite frequent occurrence in butterflies during the Oligocene to Miocene climatic optima.
    • Pigmented microbial eukaryotes fuel the deep sea carbon pool in the tropical Western Pacific Ocean

      Xu, D; Sun, P; Zhang, Y; Li, R; Huang, B; Jiao, N; Warren, A; Wang, L (2018-08-29)
    • Pigs vs people: the use of pigs as analogues for humans in forensic entomology and taphonomy research

      Matuszewski, S; Hall, MJR; Moreau, G; Schoenly, KG; Tarone, AM; Villet, MH (Springer Science and Business Media LLC, 2019-06-17)
      Most studies of decomposition in forensic entomology and taphonomy have used non-human cadavers. Following the recommendation of using domestic pig cadavers as analogues for humans in forensic entomology in the 1980s, pigs became the most frequently used model cadavers in forensic sciences. They have shaped our understanding of how large vertebrate cadavers decompose in, for example, various environments, seasons and after various ante- or postmortem cadaver modifications. They have also been used to demonstrate the feasibility of several new or well-established forensic techniques. The advent of outdoor human taphonomy facilities enabled experimental comparisons of decomposition between pig and human cadavers. Recent comparisons challenged the pig-as-analogue claim in entomology and taphonomy research. In this review, we discuss in a broad methodological context the advantages and disadvantages of pig and human cadavers for forensic research and rebut the critique of pigs as analogues for humans. We conclude that experiments using human cadaver analogues (i.e. pig carcasses) are easier to replicate and more practical for controlling confounding factors than studies based solely on humans and, therefore, are likely to remain our primary epistemic source of forensic knowledge for the immediate future. We supplement these considerations with new guidelines for model cadaver choice in forensic science research.
    • The planthopper genus Spartidelphax, a new segregate of Nearctic Delphacodes (Hemiptera, Delphacidae)

      Bartlett, C; Webb, M (2014-11-10)
      The new genus Spartidelphax is described to house three species removed from the polyphyletic genus Delphacodes. The members of Spartidelphax are coastal species native to eastern North America, and probably feed exclusively on cordgrass (Poaceae, Spartina Schreb.). The taxonomy and nomenclature of the included species (viz. S. detectus, S. luteivittus, and S. penedetectus) are reviewed. Spartidelphax luteivittus is a nomen dubium, whose type material is inadequate to provide diagnostic features contrasting with S. detectus and S. penedetectus. Diagnoses and a key are provided for the remaining Spartidelphax.
    • Plastic debris increases circadian temperature extremes in beach sediments

      Lavers, Jennifer L; Rivers-Auty, Jack; Bond, AL (Elsevier BV, 2021-05-17)
      Plastic pollution is the focus of substantial scientific and public interest, leading many to believe the issue is well documented and managed, with effective mitigation in place. However, many aspects are poorly understood, including fundamental questions relating to the scope and severity of impacts (e.g., demographic consequences at the population level). Plastics accumulate in significant quantities on beaches globally, yet the consequences for these terrestrial environments are largely unknown. Using real world, in situ measurements of circadian thermal fluctuations of beach sediment on Henderson Island and Cocos (Keeling) Islands, we demonstrate that plastics increase circadian temperature extremes. Particular plastic levels were associated with increases in daily maximum temperatures of 2.45 °C and decreases of daily minimum by − 1.50 °C at 5 cm depth below the accumulated plastic. Mass of surface plastic was high on both islands (Henderson: 571 ± 197 g/m2; Cocos: 3164 ± 1989 g/m2), but did not affect thermal conductivity, specific heat capacity, thermal diffusivity, or moisture content of beach sediments. Therefore, we suggest plastic effects sediment temperatures by altering thermal inputs and outputs (e.g., infrared radiation absorption). The resulting circadian temperature fluctuations have potentially significant implications for terrestrial ectotherms, many of which have narrow thermal tolerance limits and are functionally important in beach habitats.
    • Plastics in regurgitated Flesh-footed Shearwater (Ardenna carneipes) boluses as a monitoring tool

      Bond, AL; Hutton, Ian; Lavers, Jennifer L (Elsevier BV, 2021-04-30)
      Plastic production and pollution of the environment with plastic items is rising rapidly and outpacing current mitigation measures. Success of mitigation actions can only be determined if progress can be measured reliably through incorporation of specific, measurable targets. Here we evaluate temporal changes in the amount and composition of plastic in boluses from Flesh-footed Shearwaters during 2002-2020 and assess their suitability for measuring progress against national and international commitments to reduce plastic pollution. Plastic in the shearwater boluses showed a generally decreasing pattern from 2002 to 2015 and increasing again to 2020. The colour and type of plastics in boluses was comparable to items recovered from live and necropsied birds, but a much smaller sample size (~35 boluses/year) was required to detect changes in plastic number and mass over time. We therefore suggest shearwater boluses are a low-effort, high-statistical power monitoring tool for quantifying progress against environmental policies in Australia.
    • A Polychaete’s Powerful Punch: Venom Gland Transcriptomics of Glycera Reveals a Complex Cocktail of Toxin Homologs

      von Reumont, BM; Campbell, LI; Richter, S; Hering, L; Sykes, D; Hetmank, J; Jenner, RA; Bleidorn, C (2014-09)
    • Pooling as a strategy for the timely diagnosis of soil-transmitted helminths in stool: value and reproducibility

      PAPAIAKOVOU, MARINA; Wright, J; Pilotte, N; Chooneea, D; Schär, F; Truscott, JE; Dunn, JC; Gardiner, I; Walson, JL; Williams, SA; et al. (Springer Science and Business Media LLC, 2019-09-16)
      Background The strategy of pooling stool specimens has been extensively used in the field of parasitology in order to facilitate the screening of large numbers of samples whilst minimizing the prohibitive cost of single sample analysis. The aim of this study was to develop a standardized reproducible pooling protocol for stool samples, validated between two different laboratories, without jeopardizing the sensitivity of the quantitative polymerase chain reaction (qPCR) assays employed for the detection of soil-transmitted helminths (STHs). Two distinct experimental phases were recruited. First, the sensitivity and specificity of the established protocol was assessed by real-time PCR for each one of the STHs. Secondly, agreement and reproducibility of the protocol between the two different laboratories were tested. The need for multiple stool sampling to avoid false negative results was also assessed. Finally, a cost exercise was conducted which included labour cost in low- and high-wage settings, consumable cost, prevalence of a single STH species, and a simple distribution pattern of the positive samples in pools to estimate time and money savings suggested by the strategy. Results The sensitivity of the pooling method was variable among the STH species but consistent between the two laboratories. Estimates of specificity indicate a ‘pooling approach’ can yield a low frequency of ‘missed’ infections. There were no significant differences regarding the execution of the protocol and the subsequent STH detection between the two laboratories, which suggests in most cases the protocol is reproducible by adequately trained staff. Finally, given the high degree of agreement, there appears to be little or no need for multiple sampling of either individuals or pools. Conclusions Our results suggest that the pooling protocol developed herein is a robust and efficient strategy for the detection of STHs in ‘pools-of-five’. There is notable complexity of the pool preparation to ensure even distribution of helminth DNA throughout. Therefore, at a given setting, cost of labour among other logistical and epidemiological factors, is the more concerning and determining factor when choosing pooling strategies, rather than losing sensitivity and/or specificity of the molecular assay or the method.
    • Population substructure and signals of divergent adaptive selection despite admixture in the sponge Dendrilla antarctica from shallow waters surrounding the Antarctic Peninsula

      Leiva, Carlos; Taboada, Sergi; Kenny, Nathan J.; Combosch, David; Giribet, Gonzalo; Jombart, Thibaut; Riesgo, Ana (Wiley, 2019-05-24)
      Antarctic shallow‐water invertebrates are exceptional candidates to study population genetics and evolution, because of their peculiar evolutionary history and adaptation to extreme habitats that expand and retreat with the ice sheets. Among them, sponges are one of the major components, yet population connectivity of none of their many Antarctic species has been studied. To investigate gene flow, local adaptation and resilience to near‐future changes caused by global warming, we sequenced 62 individuals of the sponge Dendrilla antarctica along the Western Antarctic Peninsula (WAP) and the South Shetlands (spanning ~900 km). We obtained information from 577 double digest restriction site‐associated DNA sequencing (ddRADseq)‐derived single nucleotide polymorphism (SNP), using RADseq techniques for the first time with shallow‐water sponges. In contrast to other studies in sponges, our 389 neutral SNPs data set showed high levels of gene flow, with a subtle substructure driven by the circulation system of the studied area. However, the 140 outlier SNPs under positive selection showed signals of population differentiation, separating the central–southern WAP from the Bransfield Strait area, indicating a divergent selection process in the study area despite panmixia. Fourteen of these outliers were annotated, being mostly involved in immune and stress responses. We suggest that the main selective pressure on D. antarctica might be the difference in the planktonic communities present in the central–southern WAP compared to the Bransfield Strait area, ultimately depending on sea‐ice control of phytoplankton blooms. Our study unveils an unexpectedly long‐distance larval dispersal exceptional in Porifera, broadening the use of genome‐wide markers within nonmodel Antarctic organisms.
    • The potential of the solitary parasitoid Microctonus brassicae for the biological control of the adult cabbage stem flea beetle, Psylliodes chrysocephala

      Jordan, A; Broad, G; Stigenberg, J; Hughes, J; Stone, J; Bedford, I; Penfield, S; Wells, R (Wiley, 2020-05-15)
      The cabbage stem flea beetle (CSFB), Psylliodes chrysocephala L. (Coleoptera: Chrysomelidae), is a major pest of oilseed rape, Brassica napus L. (Brassicaceae), within the UK and continental Europe. Following the withdrawal of many broad‐spectrum pesticides, most importantly neonicotinoids, and with increased incidence of pyrethroid resistance, few chemical control options remain, resulting in the need for alternative pest management strategies. We identified the parasitoid wasp Microctonus brassicae (Haeselbarth) (Hymenoptera: Braconidae) within CSFB collected from three independent sites in Norfolk, UK. Parasitism of adult CSFB was confirmed, and wasp oviposition behaviour was described. Moreover, we show that within captive colonies parasitism rates are sufficient to generate significant biological control of CSFB populations. A sequence of the M. brassicae mitochondrial cytochrome oxidase 1 (MT‐CO1) gene was generated for rapid future identification. Moroccan specimens of Microctonus aethiopoides (Loan), possessing 90% sequence similarity, were the closest identified sequenced species. This study represents the first description published in English of this parasitoid of the adult cabbage stem flea beetle.
    • Praziquantel coverage in schools and communities targeted for the elimination of urogenital schistosomiasis in Zanzibar: a cross-sectional survey

      Knopp, S; Person, B; Ame, SM; Ali, SM; Muhsin, J; Juma, S; Khamis, IS; Rabone, M; Blair, L; Fenwick, A; et al. (2016-12)
    • Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

      Wood, CL; Sokolow, SH; Jones, IJ; Chamberlin, AJ; Lafferty, KD; Kuris, AM; Jocque, M; Hopkins, S; Adams, G; Buck, JC; et al. (Proceedings of the National Academy of Sciences, 2019-10-28)
      Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships between intermediate host snails (abundance, density, and prevalence) and human urogenital schistosomiasis reinfection (prevalence and intensity in schoolchildren after drug administration). However, we also found that snail distributions were so patchy in space and time that obtaining useful data required effort that exceeds what is feasible in standard monitoring and control campaigns. Instead, we identified several environmental proxies that were more effective than snail variables for predicting human infection: the area covered by suitable snail habitat (i.e., floating, nonemergent vegetation), the percent cover by suitable snail habitat, and size of the water contact area. Unlike snail surveys, which require hundreds of person-hours per site to conduct, habitat coverage and site area can be quickly estimated with drone or satellite imagery. This, in turn, makes possible large-scale, high-resolution estimation of human urogenital schistosomiasis risk to support targeting of both mass drug administration and snail control efforts.
    • Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

      De Palma, A; Abrahamczyk, S; Aizen, MA; Albrecht, M; Basset, Y; Bates, A; Blake, RJ; Boutin, C; Bugter, R; Connop, S; et al. (2016-11)
    • Preliminary survival and movement data for a declining population of Flesh-footed Shearwater Ardenna carneipes in Western Australia provides insights into marine threats

      Lavers, J; Lisovski, S; Bond, A (Cambridge University Press, 2018-08-31)
      Seabirds face diverse threats on their breeding islands and while at sea. Human activities have been linked to the decline of seabird populations, yet over-wintering areas typically receive little or no protection. Adult survival rates, a crucial parameter for population persistence in long-lived species, tend to be spatially or temporally restricted for many seabird species, limiting our understanding of factors driving population trends at some sites. We used bio-loggers to study the migration of Western Australian Flesh-footed Shearwaters Ardenna carneipes carneipes and estimated adult survival over five years. Western Australia is home to around 35% of the world’s breeding Flesh-footed Shearwaters, a population which was up-listed to Vulnerable in 2015. During the austral winter, shearwaters migrated across the central Indian Ocean to their non-breeding grounds off western Sri Lanka. Low site fidelity on breeding islands, mortality of adult birds at sea (e.g. fisheries bycatch), and low annual breeding frequency likely contributed to the low estimated annual adult survival (2011–2015: ϕ = 0.634-0.835).
    • Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources

      Kenny, NJ; Noreña, C; Damborenea, C; Grande, C (Elsevier, 2018-02)
      For their apparent morphological simplicity, the Platyhelminthes or “flatworms” are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade. Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a “Turbellarian-like” clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.