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Coleoptera: Nitidulidae) of the South Pacific

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Molecular systematics and colour variation of Carpophilus species (Coleoptera: Nitidulidae) of the South Pacific A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science at Lincoln University by Samuel David James Brown Lincoln University 2009 ii iii And every creature which is in heaven, and on the earth, and under the earth, and under the sea, and all that are in them, heard I saying \Blessing, and honour and glory, and power, be unto him that sitteth upon the throne, and unto the Lamb for ever and ever." Revelation 5:13 iv Addendum Subsequent to the submission of this thesis, Carpophilus sp. 1 was identi- fied by A. G. Kirejtshuk as C. robustus Murray. This species was originally described by Murray(1864) as a variety of C. vittiger, but has been rein- stated as a full species and will be described fully in an upcoming revision by Kirejtshuk. v Abstract of a thesis submitted in partial fulfilment of the requirements of the Degree of Master of Science. Molecular systematics of Carpophilus species (Coleoptera: Nitidulidae) of the South Pacific by S. D. J. Brown The sap beetle genus Carpophilus Stephens (Coleoptera: Nitidulidae) is a large genus consisting of over 200 species and are found worldwide. Several species are important pests of crops and stored products, and are frequently intercepted as part of biosecurity operations. The genus is poorly known taxonomically, and there are several species groups that are challenging to identify by morphological methods. In particular, two species found across the Pacific, C. maculatus Murray and C. oculatus Murray are frequently confused with each other. These two species are similar in size and colour, but differ primarily by the shape of the colour pattern on their elytra. How- ever, this colour pattern is highly variable within both species, leading to ambiguity in the indentification of these species. Within C. oculatus, three subspecies have been described based on differences in the male genitalia and pronotal punctation: C. o. oculatus and C. o. gilloglyi Dobson are dis- tributed widely across the Pacific, while C. o. cheesmani Dobson is known only from Vanuatu. A search of literature records and specimen collections revealed 32 species of Carpophilus recorded from the Pacific region. In addition there remain several unidentified specimens representing at least four species, two of which will be described subsequent to this research. A number of species recorded in the literature may have been misidentified, and these require further field vii viii ABSTRACT collections and inspection of museum specimens to confirm their presence in the Pacific. To test the validity of the subspecies of C. oculatus, and its distinctive- ness from C. maculatus, a phylogeny of available specimens of Carpophilus was inferred from one mitochondrial gene (cytochrome c oxidase subunit I (COI)), and two nuclear genes (28S ribsomal RNA (28S) and the internal transcribed spacer 2 (ITS2)). These data show large genetic distances be- tween the three subspecies of C. oculatus of 7{12%. Given these distances are similar to those between other species in the genus, this indicates these subspecies may be elevated to full species. The data also consistently sup- port a monophyletic relationship between C. o. oculatus and C. o. gilloglyi. Nuclear genes also support C. o. cheesmani as part of a clade with the other subspecies, but these relationships are unresolved in COI. Carpophilus maculatus was not supported as being the sister taxon of the C. o. oculatus and C. o. gilloglyi clade. Other relationships within Carpophilus were un- resolved, possibly due to a combination of incomplete taxon sampling, and saturation of substitutions within the COI gene. Phylogeographic analysis of specimens collected from several localities within the range of C. oculatus showed that, with only one exception, there were no shared haplotypes between archipelagoes. This result suggests it may be possible to determine the provenence of intercepted specimens, pro- viding further information regarding potential invasion pathways. A degree of geographic structuring was also present within C. o. gilloglyi, being sep- arated into a western clade found in Fiji and Rotuma and an eastern clade distributed from the Kermadec Islands and Tonga to French Polynesia. This separation was most profound in COI data, with a mean pairwise distance between the clades of 7%. ITS2 data also demonstrates a degree of differ- entiation between the two clades, based on differences in the insertions and deletions between the clades. The variability in the shape and colour of the elytral pattern of C. oc- ulatus was also investigated. Colour was quantified using a method based on Red-Green-Blue (RGB) colour values derived from digital photographs, while an outline analysis of the elytral pattern was conducted using elliptic Fourier analysis (EFA). Principal Components Analysis of the RGB values and EFA coefficients showed no clear separation between subspecies, nor were any trends correlated with host fruit or collection localities. ix Variation at all levels and all measures studied in this thesis show that this geographic region and this genus of beetles offer intruiging insights into speciation, biogeography and biological invasions. There is much scope for further research on the causes and consequences of this variation and the lives of these interesting insects. Keywords: Carpophilus oculatus, taxonomy, systematics, COI, 28S, ITS2, phylogeography, elliptic Fourier analysis, colour quantification. Acknowledgements I am extremely grateful to a huge number of people for their guidance, help, assistance, and friendship throughout this project. First, I would like to thank my supervisory team of Dr Karen Armstrong, Dr Rob Cruickshank, Dr Rich Leschen and Mr John Marris for guidance through the duration of this project. Ronald Dobson (Glasgow) very gener- ously provided data on Pacific Carpophilus specimens he had accumulated over the years, and gave advice on dissection protocols and identification. Dr Curtis Ewing (UC Berkeley, California) provided advice on molecular meth- ods, material from Rapa and allowed me use of his unpublished Carpophilus sequences to get me started. This study could not have been possible if it were not for the over- whelming willingness of a number of people to assist me with collecting Carpophilus from throughout the Pacific. My thanks go to Kiteni Kurika (NARI, Papua New Guinea), Kuatemane Tuapola (Ministry of Agriculture, Samoa), Christian Mille (IAC, New Caledonia), Sada Nand Lal (SPC, Fiji), Maja Poeschko (Ministry of Agriculture, Cook Islands), Nick Porch (ANU, Canberra, Australia) and Katharina P¨otz. Museum specimens were generously loaned by James Hogan (Oxford University Museum of Natural History, UK), Shepherd Myers (Bishop Mu- seum, Hawaii), Geoff Monteith (Queensland Museum, Australia), Geoff Hancock (Hunterian Museum, UK), Olwyn Green (MAF Biosecurity, New Zealand) and Hilda Waqa (University of the South Pacific, Fiji). In Tahiti I was most warmly and generously hosted by Dominique Eyrin. Rudolph Putoa ( D´epartement de la Recherche Agronomique) and his team showed me around the island and found fruit for me to fossick through. The Gump Research Station on Moorea put me up for a couple of nights in their excellent facilities and Jean-Lu^ıctook me around the island. In Vanuatu, Linette Berukilukilu and Timothy Tumukon (Vanuatu Quar- antine and Inspection Service, Port Vila) took a lot of time out of their busy schedules to show me around Efate and Santo. David Hollander assisted with taking photos of specimens. Julien Claude generously allowed use of his R functions. The Lincoln Spatial Ecology Group provided support for GIS and multivariate statistics. Maps (Figs x xi 2.1& 4.1) were modified from the publicly available Oceania regional map published by the CIA world factbook. I gratefully acknowledge the financial assistance that the C. Alma Baker Trust and Freemasons Postgraduate Scholarship have given me. The Royal Society of New Zealand (Canterbury branch) also provided a travel grant to get to Brisbane for the 8th Invertebrate Biodiversity and Conservation Conference. The staff and students of Lincoln University have also been a tremendous help. In particular I would like to thank Pierre Hohmann for reviewing my translation of C. littoralis, Peter Holder and Rupert Collins for entertaining times in the office and Rupert for being my fellow taxonomy geek. Friends and family. I would like to thank Marcus for being my sparring partner in a very enjoyable bisemester pool competition. The scores will not be divulged here . To Dalin, my beautiful fianc´ee, thank you so much for your love and support. It's been a privilege getting to know you these two years past. Finally, I would like to acknowledge Jesus Christ, my Saviour and Lord. However you made this world and its amazing diversity, it is a privelige indeed to be able to discover more about these creatures that reflect your beauty, love and generosity. Contents Addendumv Abstract vii Acknowledgementsx Contents xii List of Figures xv List of Tables xix Abbreviations xxi 1 Introduction1 1.1 Carpophilus overview and importance.............1 1.2 Taxonomy and classification...................3 1.3 Philosophy of species and subspecies..............7 1.4 Aims and objectives.......................9 2 Carpophilus checklist 11 2.1 Introduction............................ 11 2.2 Methods.............................. 12 2.2.1 Data collection.....................
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    A Microsatellite-Based Identification Tool Used to Confirm Vector Association in a Fungal Tree Pathogen

    Australasian Plant Pathology (2018) 47:63–69 https://doi.org/10.1007/s13313-017-0535-7 ORIGINAL PAPER A microsatellite-based identification tool used to confirm vector association in a fungal tree pathogen D. H. Lee1 & J. Roux2 & B. D. Wingfield3 & M. J. Wingfield1 Received: 28 July 2017 /Accepted: 5 December 2017 /Published online: 18 January 2018 # Australasian Plant Pathology Society Inc. 2017 Abstract Many fungi live in close association with insects, and some are specifically vectored by them. One of the best examples is found in the so-called Ophiostomatoid fungi, including species of Ceratocystis and other genera in the Ceratocystidaceae. Our under- standing of vectorship in these fungi is based predominantly on either their frequency of isolation from insects or the success with which these fungi are isolated from their insect vectors. The fact that Ceratocystis species mostly have casual as opposed to highly specific relationships with their insect vectors makes it difficult to prove insect vector relations. In order to provide unambiguous support for Ceratocystis species being vectored by insects, we interrogated whether genotypes of the tree pathogen, Ceratocystis albifundus, would be shared between isolates retrieved from either infected trees or nitidulid beetles. Ceratocystis albifundus isolates were collected from nitidulid beetles and from naturally occurring wounds on trees in the Kruger National Park (KNP) in South Africa. The genotypes of these isolates were then determined using eight microsatellite markers, and they were compared using a haploid network analyses. A high frequency of Multi-Locus Haplotypes (MLHs) derived from nitidulid beetles was found to be shared with those from wounded trees across the KNP.