• Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.)

      Kehlmaier, C; Graciá, E; Campbell, P; Hofmeyr, MD; SCHWEIGER, S; Martínez-Silvestre, A; Joyce, W; Fritz, U (Springer Science and Business Media LLC, 2019-11-25)
      The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage that diverged as early as the late Eocene. Diversification of Cylindraspis commenced in the mid-Oligocene, long before the formation of the Mascarene Islands. This rejects any notion suggesting that the group either arrived from nearby or distant continents over the course of the last millions of years or had even been translocated to the islands by humans. Instead, Cylindraspis likely originated on now submerged islands of the Réunion Hotspot and utilized these to island hop to reach the Mascarenes. The final diversification took place both before and after the arrival on the Mascarenes. With Cylindraspis a deeply divergent clade of tortoises became extinct that evolved long before the dodo or the Rodrigues solitaire, two other charismatic species of the lost Mascarene fauna.
    • The utility of micro-computed tomography for the non-destructive study of eye microstructure in snails

      Sumner-Rooney, L; Kenny, Nathan; Ahmed, F; Williams, ST (Springer Science and Business Media LLC, 2019-10-28)
      Molluscan eyes exhibit an enormous range of morphological variation, ranging from tiny pigment-cup eyes in limpets, compound eyes in ark clams and pinhole eyes in Nautilus, through to concave mirror eyes in scallops and the large camera-type eyes of the more derived cephalopods. Here we assess the potential of non-destructive micro-computed tomography (µ-CT) for investigating the anatomy of molluscan eyes in three species of the family Solariellidae, a group of small, deep-sea gastropods. We compare our results directly with those from traditional histological methods applied to the same specimens, and show not only that eye microstructure can be visualised in sufficient detail for meaningful comparison even in very small animals, but also that μ-CT can provide additional insight into gross neuroanatomy without damaging rare and precious specimens. Data from μ-CT scans also show that neurological innervation of eyes is reduced in dark-adapted snails when compared with the innervation of cephalic tentacles, which are involved in mechanoreception and possibly chemoreception. Molecular tests also show that the use of µ-CT and phosphotungstic acid stain do not prevent successful downstream DNA extraction, PCR amplification or sequencing. The use of µ-CT methods is therefore highly recommended for the investigation of difficult-to-collect or unique specimens.
    • 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
    • Designation of a new family group name, Tonzidae fam. nov., for the genus Tonza (Lepidoptera, Yponomeutoidea), based on immature stages of Tonza citrorrhoa

      Kobayashi, S; Matsuoka, H; Kimura, M; Sohn, J-C; Yoshiyasu, Y; Lees, David (European Journal of Taxonomy, 2018-06-12)
      The systematic position of Tonza Walker, 1864 is re-evaluated, based on the characteristics of immature stages and DNA barcodes. Larvae and pupae of Tonza citrorrhoa Meyrick, 1905 are described and illustrated for the first time. Larvae of this species form a loose web among the leaves and branches of the host plant, Putranjiva matsumurae Koidz. (Putranjivaceae Endl.). The immature stages of Tonza exhibit four unique apomorphies including: in the larva, the prolegs on A5 and A6 absent, and the seta L2 on the A1–A8 very small; in the pupa, four minute knobs are positioned in the middle portion on abdominal segments V and VI; while its caudal processes possess a W-shaped spine with numerous minute spines. These characteristics clearly distinguish Tonza from other yponomeutoid families and hence, we propose a new family group name, Tonzidae Kobayashi & Sohn fam. nov., for the genus Tonza. Existing DNA barcode data suggest a relationship with Glyphipterigidae Stainton, 1854. The family level status of Tonzidae fam. nov. provides a hypothesis that needs to be tested with larger molecular data.
    • Molecular characterization and distribution of Schistosoma cercariae collected from naturally infected bulinid snails in northern and central Côte d’Ivoire

      Tian-Bi, Y-NT; Webster, BL; Konan, CK; Allan, F; Diakité, NR; Ouattara, M; Salia, D; Koné, A; Kakou, AK; Rabone, M; et al. (Springer Nature, 2019-03-19)
      Accurate identification of schistosome species infecting intermediate host snails is important for understanding parasite transmission, schistosomiasis control and elimination. Cercariae emerging from infected snails cannot be precisely identified morphologically to the species level. We used molecular tools to clarify the distribution of the Schistosoma haematobium group species infecting bulinid snails in a large part of Côte d’Ivoire and confirmed the presence of interspecific hybrid schistosomes. Methods Between June 2016 and March 2017, Bulinus snails were sampled in 164 human-water contact sites from 22 villages of the northern and central parts of Côte d’Ivoire. Multi-locus genetic analysis (mitochondrial cox1 and nuclear ITS) was performed on individual schistosome cercariae shed from snails, in the morning and in the afternoon, for species and hybrid identification. Results Overall, 1923 Bulinus truncatus, 255 Bulinus globosus and 1424 Bulinus forskalii were obtained. Among 2417 Bulinus screened, 25 specimens (18 B. truncatus and seven B. globosus) shed schistosomes, with up to 14% infection prevalence per site and time point. Globally, infection rates per time point ranged between 0.6 and 4%. Schistosoma bovis, S. haematobium and S. bovis × S. haematobium hybrids infected 0.5%, 0.2% and 0.4% of the snails screened, respectively. Schistosoma bovis and hybrids were more prevalent in B. truncatus, whereas S. haematobium and hybrid infections were more prevalent in B. globosus. Schistosoma bovis-infected Bulinus were predominantly found in northern sites, while S. haematobium and hybrid infected snails were mainly found in central parts of Côte d’Ivoire. Conclusions The data highlight the necessity of using molecular tools to identify and understand which schistosome species are transmitted by specific intermediate host snails. The study deepens our understanding of the epidemiology and transmission dynamics of S. haematobium and S. bovis in Côte d’Ivoire and provides the first conclusive evidence for the transmission of S. haematobium × S. bovis hybrids in this West African country. Trial registration ISRCTN, ISRCTN10926858. Registered 21 December 2016; retrospectively registered (see: http://www.isrctn.com/ISRCTN10926858)
    • Sex biases in bird and mammal natural history collections.

      Cooper, N; Bond, AL; Davis, JL; Portela Miguez, R; Tomsett, L; Helgen, Kristofer (Royal Society, 2019-10-23)
      Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.
    • Combining simulation modeling and stable isotope analyses to reconstruct the last known movements of one of Nature’s giants

      Trueman, C; Jackson, A; Chadwick, K; Coombs, Ellen J; Feyrer, L; Magozzi, S; Sabin, R; Cooper, N (PeerJ Inc., 2019-10-18)
      The spatial ecology of rare, migratory oceanic animals is difficult to study directly. Where incremental tissues are available, their chemical composition can provide valuable indirect observations of movement and diet. Interpreting the chemical record in incremental tissues can be highly uncertain, however, as multiple mechanisms interact to produce the observed data. Simulation modeling is one approach for considering alternative hypotheses in ecology and can be used to consider the relative likelihood of obtaining an observed record under different combinations of ecological and environmental processes. Here we show how a simulation modeling approach can help to infer movement behaviour based on stable carbon isotope profiles measured in incremental baleen tissues of a blue whale (Balaenoptera musculus). The life history of this particular specimen, which stranded in 1891 in the UK, was selected as a case study due to its cultural significance as part of a permanent display at the Natural History Museum, London. We specifically tested whether measured variations in stable isotope compositions across the analysed baleen plate were more consistent with residency or latitudinal migrations. The measured isotopic record was most closely reproduced with a period of residency in sub-tropical waters for at least a full year followed by three repeated annual migrations between sub-tropical and high latitude regions. The latitudinal migration cycle was interrupted in the year prior to stranding, potentially implying pregnancy and weaning, but isotopic data alone cannot test this hypothesis. Simulation methods can help reveal movement information coded in the biochemical compositions of incremental tissues such as those archived in historic collections, and provides context and inferences that are useful for retrospective studies of animal movement, especially where other sources of individual movement data are sparse or challenging to validate.
    • Cryptic diversity of limestone karst inhabiting land snails (Cyclophorus spp.) in northern Vietnam, their evolutionary history and the description of four new species

      von Oheimb, Katharina C. M.; von Oheimb, Parm Viktor; Hirano, T; Do, TV; Ablett, J; Luong, HV; Pham, SV; Naggs, F (Public Library of Science (PLoS), 2019-10-23)
      Limestone karsts can form terrestrial habitat islands for calcium-dependent organisms. In Vietnam, many karst habitats are threatened, while their rich biodiversity is still far from being thoroughly explored. Given that conservation of karst biota strongly relies on correct species identification, the presence of undetected cryptic species can pose severe problems. The present study focuses on cryptic diversity among karst-inhabiting land snails of the genus Cyclophorus in northern Vietnam, where specimens with a similar shell morphology have been reported from various regions. In order to examine the diversity and evolutionary history of this “widespread morphotype”, we generated a Bayesian phylogeny based on DNA sequence data. Automatic Barcode Gap Discovery (ABGD) and the Bayesian implementation of the Poisson tree processes model (bPTP) contributed to species delimitation and analyses of shell shape and size aided the morphological characterisation of individual species. We found that the examined specimens of the widespread morphotype did not form a single monophyletic group in the phylogeny but clustered into several different clades. We delimited nine different species that develop the widespread morphotype and described four of them as new. Processes of convergent evolution were probably involved in the origin of the delimited species, while their generally allopatric distribution could result from interspecific competition. Our findings indicate ongoing processes of speciation and a potential case of morphological character displacement. The high degree of morphological overlap found among the species underlines the importance of DNA sequence data for species delimitation and description in the genus Cyclophorus. Given the findings of the present study and the high potential that as yet undiscovered cryptic taxa have also evolved in other groups of karst-inhabiting organisms, we argue for a systematic and efficient detection and description of Vietnam’s karst biodiversity to provide a solid basis for future conservation planning.
    • Novel molecular approach to define pest species status and tritrophic interactions from historical Bemisia specimens

      Tay, WT; Elfekih, S; Polaszek, Andrew; Court, LN; Evans, GA; Gordon, KHJ; De Barro, PJ (Nature Research, 2017-03-27)
      Museum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri Lankan Bemisia emiliae cotype puparium, and of a 1942 Japanese Bemisia puparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects including B. tabaci pest species complex. Bemisia emiliae’s draft mitogenome showed a high degree of homology with published B. tabaci mitogenomes, and exhibited 98–100% partial mitochondrial DNA Cytochrome Oxidase I (mtCOI) gene identity with the B. tabaci species known as Asia II-7. The partial mtCOI gene of the Japanese specimen shared 99% sequence identity with the Bemisia ‘JpL’ genetic group. Metagenomic analysis identified bacterial sequences in both Bemisia specimens, while hymenopteran sequences were also identified in the Japanese Bemisia puparium, including complete mtCOI and rRNA genes, and various partial mtDNA genes. At 88–90% mtCOI sequence identity to Aphelinidae wasps, we concluded that the 1942 Bemisia nymph was parasitized by an Eretmocerus parasitoid wasp. Our approach enables the characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng gDNA, and to infer historical tritrophic relationships in Bemisia whiteflies.
    • Reduction of eyes in last-instar beetle larvae: a special observation in Trictenotomidae, based on Trictenotoma formosana Kriesche, 1919

      Telnov, D; Hu, F-S; Pollock, DA; Lin, Z-R (2019-10-03)
      Recently, Lin & Hu (2018, 2019) unraveled the biology of Trictenotoma formosana Kriesche, 1919. For the first time since Gahan (1908) there is fresh immature stages material available for Trictenotomidae.
    • Synopsis of the pelidnotine scarabs (Coleoptera, Scarabaeidae, Rutelinae, Rutelini) and annotated catalog of the species and subspecies

      Moore, MR; Jameson, ML; Garner, BH; Audibert, C; Smith, ABT; Seidel, M (Pensoft, 2017-04-06)
      The pelidnotine scarabs (Scarabaeidae: Rutelinae: Rutelini) are a speciose, paraphyletic assemblage of beetles that includes spectacular metallic species (“jewel scarabs”) as well as species that are ecologically important as herbivores, pollinators, and bioindicators. These beetles suffer from a complicated nomenclatural history, due primarily to 20th century taxonomic and nomenclatural errors. We review the taxonomic history of the pelidnotine scarabs, present a provisional key to genera with overviews of all genera, and synthesize a catalog of all taxa with synonyms, distributional data, type specimen information, and 107 images of exemplar species. As a result of our research, the pelidnotine leaf chafers (a paraphyletic group) include 27 (26 extant and 1 extinct) genera and 420 valid species and subspecies (419 extant and 1 extinct). Our research makes biodiversity research on this group tractable and accessible, thus setting the stage for future studies that address evolutionary and ecological trends. Based on our research, 1 new species is described, 1 new generic synonym and 12 new species synonyms are proposed, 11 new lectotypes and 1 new neotype are designated, many new or revised nomenclatural combinations, and many unavailable names are presented.
    • Extensive sampling and thorough taxonomic assessment of Afrotropical Rhyssinae (Hymenoptera, Ichneumonidae) reveals two new species and demonstrates the limitations of previous sampling efforts

      Hopkins, T; Roininen, H; van Noort, S; Broad, G; Kaunisto, K; Sääksjärvi, IE (Pensoft Publishers, 2019-10-07)
      Tropical forest invertebrates, such as the parasitoid wasp family Ichneumonidae, are poorly known. This work reports some of the first results of an extensive survey implemented in Kibale National Park, Uganda. A total of 456 individuals was caught of the subfamily Rhyssinae Morley, 1913, which in the Afrotropical region was previously known from only 30 specimens. Here, the six species found at the site are described and the Afrotropical Rhyssinae are reviewed. Two new species, Epirhyssa johanna Hopkins, sp. nov. and E. quagga sp. nov., are described and a key, diagnostic characters, and descriptions for all 13 known Afrotropical species are provided, including the first description of the male of Epirhyssa overlaeti Seyrig, 1937. Epirhyssa gavinbroadi Rousse & van Noort, 2014, syn. nov. is proposed to be a synonym of E. uelensis Benoit, 1951. Extensive sampling with Malaise traps gave an unprecedented sample size, and the method is recommended for other poorly known tropical areas.
    • 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.
    • International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017.

      Turland, NJ; Wiersema, JH; Barrie, FR; Greuter, W; Hawksworth, DL; Herendeen, PS; Knapp, S; Kusber, W-H; Li, D-Z; Marhold, K; et al. (Koeltz Botanical BooksGlahutten, Germany, 2018-06-26)
      The rules that govern the scientific naming of algae, fungi, and plants are revised at the Nomenclature Section of an International Botanical Congress (IBC). This edition of the International Code of Nomenclature for algae, fungi, and plants embodies the decisions of the XIX IBC, which took place in Shenzhen, China in July, 2017. This Shenzhen Code supersedes the Melbourne Code (McNeill & al. in Regnum Veg. 154. 2012), published six years ago after the XVIII IBC in Melbourne, Australia, and like its five predecessors, it is written entirely in (British) English. The Melbourne Code was translated into Chinese, French, Italian, Japanese, Korean, Portuguese, Spanish, and Turkish; it is anticipated that the Shenzhen Code, too, will become available in several languages. In questions about the meaning of provisions in translated editions of this Code, the English edition is definitive.
    • Nomenclatural notes on Anthicidae and Pyrochroidae (Coleoptera). 6

      Telnov, Dmitry (Baltijas Koleopterologijas Instituts/Baltic Institute of Coleopterology, 2018-12-23)
      Five new combinations, three new synonyms and two new statuses for the Anthicidae are proposed. New distributional data or corrections are provided on 65 taxa of Pyrochroidae and Anthicidae. Eighteen new species and subspecies are described: Anthelephila panayensis sp. nov., Anthicus (s. str.) chitwanus sp. nov., A. (s. str.) lepcha sp. nov., A. (s. str.) vicinor sp. nov., Aulacoderus muehlei sp. nov., Clavicomus garze sp. nov., C. kham sp. nov., Cyclodinus phragmiteticola sp. nov., Macratria dotyali sp. nov., M. kopetzi sp. nov., M. leprieuri gasconica ssp. nov., Macratriomima casuarius sp. nov., M. chandleri sp. nov., Notoxus reuteri sp. nov., Rimaderus bonadonai sp. nov., R. sahyadri sp. nov., Stenidius obliquesetosus sp. nov., and Tomoderus schmidti sp. nov. Additional description is given for Anthelephila kresli Kejval, 2007 and Yunnanomonticola Telnov, 2002.
    • Descriptions of two new Australian genera of Anthicidae (Insecta: Coleoptera)

      Telnov, Dmitry (Baltijas Koleopterologijas Instituts/Baltic Institute of Coleopterology, 2018-12-23)
      Two new Australian Anthicidae genera, Australosteropes gen. nov. (Steropinae) and Sahulanthicus gen. nov. (Anthicinae: Anthicini) are described, diagnosed, and illustrated. Some critical morphological characters of these new groups and the subfamilies to which they belong are discussed. New combinations are made for the following 18 taxa: Australosteropes davidsonae (Armstrong, 1948) comb. nov. (from Macratria Newman, 1838), Sahulanthicus abundans (Lea, 1922) comb. nov., S. apicalis (King, 1869) comb. nov., S. baudinensis (Champion, 1895) comb. nov., S. brevicollis (King, 1869) comb. nov., S. cavifrons (Champion, 1895) comb. nov., S. crassipes (LaFerté-Sénectère, 1849) comb. nov., S. crassus (King, 1869) comb. nov., S. discoideus (Champion, 1895) comb. nov., S. immaculatus (King, 1869) comb. nov., S. inglorius (Lea, 1896) comb. nov., S. laticollis (MacLeay, 1872) comb. nov., S. luridus (King, 1869) comb. nov., S. monostigma (Champion, 1895) comb. nov., S. obliquefasciatus (King, 1869) comb. nov., S. permutatus (Pic, 1897) comb. nov., S. scutellatus (Lea, 1896) comb. nov. (all from Microhoria Chevrolat, 1877), and S. dilatipennis (Pic, 1900) comb. nov. (from Anthicus Paykull, 1798). Lectotype is designated for Sahulanthicus dilatipennis (Pic, 1900).
    • New, north-easternmost locality for Bembidion monticola Sturm, 1825 (Coleoptera: Carabidae) in Europe: relict of ancient distribution or a result of range expansion?

      Kovalenko, YN; Telnov, Dmitry (Entomological Society of Finland, 2018-09-17)
      A new record of a subpopulation of Bembidion monticola Sturm, 1825 from Arkhangelsk region (Northern Europe, Russia) is discussed. The locality of this record is remote, about 700 km to the east from the northernmost previously known locality of this species. Ecology and distribution of B. monticola in northern Europe are reviewed, as well as possible ways of its spread further to northeast are hypothesised.
    • A review of the Helophorus frater-praenanus group of species, with description of a new species and additional faunal records of Helophorus Fabricius from China and Bhutan (Coleoptera: Helophoridae)

      ANGUS, RB; Jia, F-L; Chen, Z-N (Austrian Zoological-Botanical Society and the Vienna Coleopterists Society (Wiener Coleopterologenverein, WCV), 2014)
      The six species of the East Palaearctic Helophorus frater-praenanus group (Coleoptera: Helophoridae) are reviewed and a new species, H. aquila sp.n. is described from China (Qinghai). Habitus, head and pronotum and aedeagophores are figured for all the species and a key for their identification is given. Four further species which could be confused with the H. frater-praenanus group are discussed and illustrated. These are H. croaticus KUWERT, 1886, H. pumilio ERICHSON, 1837, H. pitcheri ANGUS, 1970 and H. shatrovskyi ANGUS, 1985. Additional faunal records of Helophorus FABRICIUS species from the Tibetan Plateau and other areas of China are given. Helophorus tuberculatus GYLLENHAL, 1808 is recorded from Bhutan for the first time
    • Recommended best practices for plastic and litter ingestion studies in marine birds: Collection, processing, and reporting

      Provencher, JF; Borrelle, SB; Bond, AL; Lavers, JL; van Franeker, JA; Kühn, S; Hammer, S; Avery-Gomm, S; Mallory, ML (Canadian Science Publishing, 2019-05-09)
      Marine plastic pollution is an environmental contaminant of significant concern. There is a lack of consistency in sample collection and processing that continues to impede meta-analyses and largescale comparisons across time and space. This is true for most taxa, including seabirds, which are the most studied megafauna group with regards to plastic ingestion research. Consequently, it is difficult to evaluate the impacts and extent of plastic contamination in seabirds fully and accurately, and to make inferences about species for which we have little or no data. We provide a synthesized set of recommendations specific for seabirds and plastic ingestion studies that include best practices in relation to sample collection, processing, and reporting, as well as highlighting some “cross-cutting” methods. We include guidance for how carcasses, regurgitations, and pellets should be handled and treated to prevent cross-contamination, and a discussion of what size class of microplastics can be assessed in each sample type. Although we focus on marine bird samples, we also include standardized techniques to remove sediment and biological material that are generalizable to other taxa. Lastly, metrics and data presentation of ingested plastics are briefly reviewed in the context of seabird studies.
    • Pushing the limits of whole genome amplification: successful sequencing of RADseq library from a single microhymenopteran (Chalcidoidea, Trichogramma)

      Cruaud, A; Groussier, G; Genson, G; Saune, L; Polaszek, A; Rasplus, J-Y (PeerJ, 2018-10-16)
      A major obstacle to high-throughput genotyping of microhymenoptera is their small size. As species are difficult to discriminate, and because complexes may exist, the sequencing of a pool of specimens is hazardous. Thus, one should be able to sequence pangenomic markers (e.g., RADtags) from a single specimen. To date, whole genome amplification (WGA) prior to library construction is still a necessity as at most 10 ng of DNA can be obtained from single specimens (sometimes less). However, this amount of DNA is not compatible with manufacturer’s requirements for commercial kits. Here we test the accuracy of the GenomiPhi kit V2 on Trichogramma wasps by comparing RAD libraries obtained from the WGA of single specimens (F0 and F1 generation, about1 ng input DNA for the WGA (0.17–2.9 ng)) and a biological amplification of genomic material (the pool of the progeny of the F1 generation). Globally, we found that 99% of the examined loci (up to 48,189 for one of the crosses, 109 bp each) were compatible with the mode of reproduction of the studied model (haplodiploidy) and Mendelian inheritance of alleles. The remaining 1% (0.01% of the analysed nucleotides) could represent WGA bias or other experimental/analytical bias. This study shows that the multiple displacement amplification method on which the GenomiPhi kit relies, could also be of great help for the high-throughput genotyping of microhymenoptera used for biological control, or other organisms from which only a very small amount of DNA can be extracted, such as human disease vectors (e.g., sandflies, fleas, ticks etc.).