• The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis

      Mwinyi, A; Bailly, X; Bourlat, SJ; Jondelius, U; Littlewood, T; Podsiadlowski, L (Springer Science and Business Media LLC, 2010-10-13)
      Background Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria". Results We describe the first complete mitochondrial genome sequence of a member of the Acoela, Symsagittifera roscoffensis. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of Xenoturbella bocki as sister group to or part of the deuterostomes was also unstable. Conclusions Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.
    • Phylogenetic relationships within Dicrocoeliidae (Platyhelminthes: Digenea) from birds from the Czech Republic using partial 28S rDNA sequences

      Aldhoun, J; Elmahy, R; Littlewood, T (Springerlink, 2018-09-05)
      Partial (D1-D3) 28S rRNA gene sequences from 16 isolates of digenean parasites of the family Dicrocoeliidae recovered from 16 bird species from the Czech Republic were used for phylogenetic reconstruction. Comparison with sequences available from GenBank suggests that the genus Brachylecithum is paraphyletic, requiring further validation and possible systematic revision. Although partial 28S rDNA is relatively conserved, analyses suggest that the following taxa are synonymous: Lutztrema attenuatum = L. monenteron = L. microstomum, Brachylecithum lobatum = B. glareoli. Zonorchis petiolatus is reassigned back to the genus Lyperosomum with L. collurionis as a junior synonym. The study revealed how complicated the systematics of the family Dicrocoeliidae is currently. The morphology of the group is variable, and the current distinguishing characters at species and even generic level are not sufficiently distinctive; it is difficult to identify the specimens correctly and identification of GenBank isolates is not reliable. Extensive sampling of isolates for both molecular and morphological studies is necessary to resolve the relationships within the family.
    • Phylogenetically Widespread Polyembryony in Cyclostome Bryozoans and the Protracted Asynchronous Release of Clonal Brood-Mates

      Jenkins, HL; Waeschenbach, A; Okamura, B; Hughes, RN; Bishop, JDD; Hejnol, A (2017-01-17)
    • The Phylogenetics and Biogeography of the Central Asian Hawkmoths, Hyles hippophaes and H. chamyla: Can Mitogenomics and Machine Learning Bring Clarity?

      Patzold, Franziska; Marabuto, Eduardo; Daneck, Hana; O’Neill, Mark A; Kitching, I; Hundsdoerfer, Anna K (MDPI AG, 2021-05-17)
      The western Palaearctic species of the hawkmoth genus Hyles (Lepidoptera: Sphingidae) have long been the subject of molecular phylogenetic research. However, much less attention has been paid to the taxa inhabiting the central and eastern Palaearctic, particularly Central Asia, where almost 50% of the species diversity of the genus occurs. Yet, many taxonomic conundrums hinder a proper assessment of the true diversity in these moths. One still unresolved group of species includes Hyles hippophaes and Hyles chamyla. Despite a largely overlapping morphology and ecology, a plethora of infraspecific taxa display some unique divergent characters over a wide geographical area. In this study, we undertook a taxonomic assessment of each population and resolved this species complex using an integrative approach. A combination of new computational techniques (DAISY-II) in comparative morphology and recent advances in DNA extraction methods and sequencing of museum specimens (WISC) alongside more traditional genetic approaches allowed testing of the three main phenotypes—bienerti, chamyla and apocyni—in terms of their morphological, mitochondrial and biogeographical integrity, and to elucidate their evolutionary relationships. Our results support the existence of two closely related species, Hyles chamyla and H. hippophaes, but the former species H. apocyni (here discussed as the ecological form apocyni of H. chamyla) is best regarded as a hybrid between H. chamyla and H. h. bienerti. The results indicate that the evolutionary relationship between H. chamyla and H. hippophaes is one of admixture in the context of ongoing ecological differentiation, which has led to shared morphological characters and a blurring of the species boundaries. These results clarify the evolutionary relationships of this species complex and open future research lines, including the analysis of nuclear markers and denser sampling, particularly of H. hippophaes and H. vespertilio in western Europe.
    • 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.
    • Phylogeny of Lithobiidae Newport, 1844, with emphasis on the megadiverse genus Lithobius Leach, 1814 (Myriapoda, Chilopoda)

      Ganske, Anne‐Sarah; Vahtera, Varpu; Dányi, László; Edgecombe, GD; Akkari, Nesrine (Wiley, 2020-11-04)
      Phylogenetic analyses based on molecular and morphological data were conducted to shed light on relationships within the mostly Palaearctic/Oriental centipede family Lithobiidae, with a particular focus on the Palaearctic genus Lithobius Leach, 1814 (Lithobiidae, Lithobiomorpha), which contains >500 species and subspecies. Previous studies based on morphological data resolved Lithobius as nonmonophyletic, but molecular-based phylogenetic analyses have until now sampled few species. To elucidate species inter-relationships of the genus, test the validity of its classification into subgenera, and infer its relationships with other Lithobiidae, we obtained molecular data (nuclear markers: 18S rRNA, 28S rRNA; mitochondrial markers: 16S rRNA, COI) and 61 morphological characters for 44 species of Lithobius representing four of its eight subgenera and nine other representatives of Lithobiidae. The data were analyzed phylogenetically using maximum-likelihood, parsimony and Bayesian inference. This study suggests that (i) a close relationship between L. giganteus and the pterygotergine Disphaerobius loricatus highlighted in recent morphological analyses is also strongly supported by molecular data, and Pterygoterginae is formally synonymized with Lithobiinae; (ii) the Oriental/Australian genus Australobius is consistently resolved as sister group to all other sampled Lithobiidae by the molecular and combined data; (iii) the subfamily Ethopolyinae may be paraphyletic; (iv) the genus Lithobius is nonmonophyletic; (v) the subgenera Lithobius, Sigibius and Monotarsobius are nonmonophyletic and should not be used in future taxonomic studies; and (vi) there are instances of cryptic species and cases in which subspecies should be elevated to full species status, as identified for some European taxa within Lithobius.
    • Phylogeny of the Hawkmoth Tribe Ambulycini (Lepidoptera: Sphingidae): Mitogenomes from Museum Specimens Resolve Major Relationships

      Timmermans, Martijn; Daghmoumi, Sainab M; Glass, Deborah; Hamilton, Chris A; Kawahara, Akito Y; Kitching, Ian J (Oxford University Press (OUP), 2019-12-23)
      Abstract: Ambulycini are a cosmopolitan tribe of the moth family Sphingidae, comprised of 10 genera, 3 of which are found in tropical Asia, 4 in the Neotropics, 1 in Africa, 1 in the Middle East, and 1 restricted to the islands of New Caledonia. Recent phylogenetic analyses of the tribe have yielded conflicting results, and some have suggested a close relationship of the monobasic New Caledonian genus CompsulyxHolloway, 1979 to the Neotropical ones, despite being found on opposite sides of the Pacific Ocean. Here, we investigate relationships within the tribe using full mitochondrial genomes, mainly derived from dry-pinned museum collections material. Mitogenomic data were obtained for 19 species representing nine of the 10 Ambulycini genera. Phylogenetic trees are in agreement with a tropical Asian origin for the tribe. Furthermore, results indicate that the Neotropical genus Adhemarius Oiticica Filho, 1939 is paraphyletic and support the notion that OrectaRothschild & Jordan 1903 and TrogolegnumRothschild & Jordan, 1903 may need to be synonymized. Finally, in our analysis the Neotropical genera do not collectively form a monophyletic group, due to a clade comprising the New Caledonian genus Compsulyx and the African genus BatocnemaRothschild & Jordan, 1903 being placed as sister to the Neotropical genus ProtambulyxRothschild & Jordan, 1903. This finding implies a complex biogeographic history and suggests the evolution of the tribe involved at least two long-distance dispersal events.
    • 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.
    • Plant and fungal collections: Current status, future perspectives

      Paton, Alan; Antonelli, Alexandre; Carine, Mark; Forzza, Rafaela Campostrini; Davies, Nina; Demissew, Sebsebe; Dröge, Gabriele; Fulcher, Tim; Grall, Aurelie; Holstein, Norbert; et al. (Wiley, 2020-09-29)
      Societal Impact Statement Plant and fungal specimens provide the auditable evidence that a particular organism occurred at a particular place, and at a particular point in time, verifying past occurrence and distribution. They also document the aspects of human exploration and culture. Collectively specimens form a global asset with significant potential for new uses to help address societal and environmental challenges. Collections also serve as a platform to engage and educate a broad range of stakeholders from the academic to the public, strengthening engagement and understanding of plant and fungal diversity—the basis of life on Earth. Summary We provide a global review of the current state of plant and fungal collections including herbaria and fungaria, botanic gardens, fungal culture collections, and biobanks. The review focuses on the numbers of collections, major taxonomic group and species level coverage, geographical representation and the extent to which the data from collections are digitally accessible. We identify the major gaps in these collections and in digital data. We also consider what collection types need to be further developed to support research, such as environmental DNA and cryopreservation of desiccation-sensitive seeds. Around 31% of vascular plant species are represented in botanic gardens, and 17% of known fungal species are held in culture collections, both these living collections showing a bias toward northern temperate taxa. Only 21% of preserved collections are available via the Global Biodiversity Information Facility (GBIF) with Asia, central and north Africa and Amazonia being relatively under-represented. Supporting long-term collection facilities in biodiverse areas should be considered by governmental and international aid agencies, in addition to short-term project funding. Institutions should consider how best to speed up digitization of collections and to disseminate all data via aggregators such as GBIF, which will greatly facilitate use, research, and community curation to improve quality. There needs to be greater alignment between biodiversity informatics initiatives and standards to allow more comprehensive analysis of collections data and to facilitate linkage of extended information, facilitating broader use. Much can be achieved with greater coordination through existing initiatives and strengthening relationships with users.
    • 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.