Andrew Mitchell

Biology
PhD
27.73

Publications

  • Andrew Mitchell
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    ABSTRACT: Natural history museums are vastly under-utilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicons (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard compliant data was recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for field work and identification, “collecting in collections” is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 02/2015; DOI:10.1111/1755-0998.12380 · 5.63 Impact Factor
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    ABSTRACT: Light trap surveillance across northern Australia and Papua New Guinea (PNG) has detected the presence of several Oriental species of Culicoides not previously reported from those countries and which appear to have arrived in recent times. Detections of C. nudipalpis Delfinado in Western Australia, C. flavipunctatus Kitaoka and C. palpifer Das Gupta and Ghosh in the Northern Territory and of C. flavipunctatus, C. fulvus Sen and Das Gupta and C. orientalis Macfie in Queensland (Qld) provide evidence of multiple pathways for incursions of biting midges into northern Australia. Of these, only C. fulvus appears to have established. Additionally, three species, C. fulvus, C. wadai Kitaoka and C. brevipalpis Delfinado, are newly reported from PNG and all appear to be well established. The arrival in PNG of C. fulvus and C. brevipalpis, both not previously reported from Qld, suggests that pathways exist for the entry of Oriental insects into New Guinea directly from Asia, rather than via Australia. Molecular analyses using DNA barcodes (partial mitochondrial cytochrome oxidase subunit one sequences) confirmed morphological identification of specimens and additionally provided strong evidence relating to the source of these incursions. At least two of these species are vectors of important livestock viruses and are likely to impact on the epidemiology of these viruses as they continue to disperse.
    Austral Entomology 01/2015; DOI:10.1111/aen.12131 · 0.80 Impact Factor
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    ABSTRACT: The monophyly of the Imicola complex, a natural species complex within subgenus C. subgen. Avaritia Fox of the biting midge genus Culicoides Latreille, is supported using morphological and molecular analyses. A diagnosis for the group along with comparative redescriptions of the male and female of the species represented in Australasia, C. brevitarsis Ki-effer and C. nudipalpis Delfinado and a description of C. asiatica Bellis sp. nov., are presented together with keys for their specific determination and molecular support for their status.
    Zootaxa 03/2014; 3768:401-427. DOI:10.11646/zootaxa.3768.4.1 · 1.06 Impact Factor
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    ABSTRACT: The Immaculatus Group of Culicoides encompassing four species from Australia, New Caledonia, Fiji, Solomon Islands, New Guinea and the Malay archipelago is revised. A diagnosis for the group, descriptions of males and females of C. shivasi sp. n. and C. collessi sp. n., a description of the male of C. immaculatus Lee & Reye, a redescription of the female of C. immaculatus and a diagnosis of C. agas Wirth & Hubert together with keys for their specific determination are pre-sented. Specific separation of the morphologically similar C. shivasi and C. immaculatus is supported by DNA barcodes (mitochondrial cytochrome oxidase I or COI) and nuclear carbomoylphosphate synthetase (CAD) sequence data.
    Zootaxa 06/2013; 3680(1):15-37. DOI:10.11646/zootaxa.3680.1.4 · 1.06 Impact Factor
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    ABSTRACT: The hemipteran suborder Auchenorrhyncha comprises a rich assemblage of plant feeding species, many of which are widespread in distribution and act as vectors of viral and fungal diseases affecting plants. Species level identifications in this group generally are possible only by examination of male specimens; prior DNA barcode analyses of a limited range of Auchenorrhyncha indicate that this approach may provide an expedient means to identify species within this diverse group. In this study we explored the utility of DNA barcoding for identification of a wider range of Auchenorrhyncha species than has been examined previously. Diverse fulgoroid (planthopper) and membracoid (leafhopper and allies) Auchenorrhyncha were sampled from Barrow Island, Western Australia, and identified to the least inclusive taxonomic units using morphology. DNA barcodes from 546 adult specimens were obtained and analysed using a General mixed Yule – Coalescent (GMYC) modelling approach to genetically delimit putative species, as a comparison to the morphospecies identifications. Additional DNA barcodes (N = 106) were obtained from nymphs and these were compared to adult DNA barcodes to identify species present among immature specimens. Among adult specimens, 73 species were congruently delimited by morphology and genetic analyses when modelled using a single threshold GMYC. Congruence between morphological and molecular species assignments was greatly reduced when the Yule – Coalescent transition was allowed to vary across genetic lineages. In a separate DNA barcode analysis of all specimens using neighbour joining distance metrics, nymphs and physically degraded specimens were in most cases genetically linked to adult conspecifics. Ten genetic clades detected among the nymphs were not observed among adults and did not match pre-existing sequence accessions in GenBank or DNA barcode records in BOLD. Of the 73 adult Auchenorrhyncha species congruently identified by DNA barcoding and morphology, most were Cicadellidae (N = 53 morphospecies), the remaining 20 morphospecies were sparsely representative of ten other families. Formal identifications to species level were available for only 36% of these 73 morphospecies, owing mainly to an absence of diagnostic male specimens within many of the delimited species. Indeterminate species detected among adults and nymphs are designated with interim species codes. The work presented here demonstrates that DNA barcoding is likely to be a powerful investigative tool for identifying and understanding species limits in the Auchenorrhyncha, particularly if it is used within an integrative taxonomic framework.
    Records of the Australian Museum Supplement 01/2013; 83:253-285.
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    ABSTRACT: Thanks to the recent development of integrative approaches that combine dated phylogenies with models of biogeographic evolution, it is becoming more feasible to assess the roles of dispersal and vicariance in creating complex patterns of geographical distribution. However, the historical biogeography of taxa with good dispersal abilities, like birds or flying insects, still remains largely unknown because of the lack of complete phylogenies accompanied by robust estimates of divergence times. In this study, we investigate the evolution and historical biogeography of the globally distributed pest genus Spodoptera (Lepidoptera: Noctuidae) using complete taxon sampling and an extensive set of analyses. Through the analysis of a combined morphological and molecular dataset, we provide the first robust phylogenetic framework for this widespread and economically important group of moths. Historical biogeography approaches indicate that dispersal events have been the driving force in the biogeographic history of the group. One of the most interesting findings of this study is the probable occurrence of two symmetric long-distance dispersal events between the Afrotropical and the Neotropical region, which appear to have occurred in the late Miocene. Even more remarkably, our dated phylogenies reveal that the diversification of the clade that includes specialist grass feeders has followed closely the expansion of grasslands in the Miocene, similar to the adaptive radiation of specialist grazing mammals during the same period.
    Molecular Phylogenetics and Evolution 08/2012; 65(3):855-70. DOI:10.1016/j.ympev.2012.08.006 · 4.02 Impact Factor
  • Andrew Austin, Andrew Mitchell
    Invertebrate Systematics 01/2012; 26(6):iii. DOI:10.1071/ISv26n6_PR · 1.59 Impact Factor
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    ABSTRACT: Abstract An examination of the five described species of the New Guinean genus Zophiuma Fennah (Hemiptera: Fulgoromorpha: Lophopidae), has confirmed that Zophiuma guineae (Lallemand) is a new synonym of Zophiuma pupillata (Stål) and that Zophiuma lobulata Ghauri is a new synonym of Zophiuma butawengi (Heller). The third species of the genus, Zophiuma doreyensis Distant, is known only from the male holotype. The morphology of the male genitalia and mitochondrial cytochrome oxidase subunit I (COI) gene sequences were used to compare Z. pupillata and Z. butawengi. Both the male genitalia and the COI sequences showed clear cut differences between the two species with little intraspecific variation in comparison to interspecific variation. Sequence data demonstrated that males collected with the distinctively coloured Z. pupillata females are the males of that species. Male genitalia of Z. pupillata are described and illustrated for the first time and a key for the discrimination of the three species of the genus is provided.
    Australian Journal of Entomology 02/2011; 50(1). DOI:10.1111/j.1440-6055.2010.00791.x · 0.80 Impact Factor
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    Andrew Mitchell
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    ABSTRACT: DNA barcoding is all too often derided by taxonomists with little understanding of how far this emerging subdiscipline of systematics has progressed since it was proposed by Hebert et al. (2003). A prime example is Ebach's factually incorrect and misleading recent correspondence (Ebach 2011). Ebach and I agree on one point: indeed many readers of Zootaxa would have cringed as they read his letter, though perhaps the cause was a tasteless joke. For brevity I will address only three key points he raised about the uses for DNA barcoding. First, bird strike is no laughing matter as the 155 people who survived US Airways Flight 1549 ditching into the Hudson River in January 2009 will attest. Jokes about "pâté [de] foie turbine" do not do justice to the gravity of the subject. Subsequent DNA barcoding analysis of bird remains identified the culprits as Canada Goose (Branta canadensis Linnaeus, 1758) (Marra et al. 2009). Fortunately aviation authorities recognize the importance of bird species identification following bird strike as it allows them to tailor risk management measures to particular species, and they are funding ongoing research in this area. Second, the recent literature contains many examples of taxonomists having embraced DNA barcoding to assist with their research. Ebach's claim that none would be interested is patently untrue. Recent examples include taxonomic papers on oomycetes (Bala et al. 2010), limpets (Johnson et al., 2008), collembolans (Porco et al. 2010), caddisflies (Pauls et al. 2010) and moths (Hausmann et al. 2010). In addition, taxonomists are using barcoding to associate adult and immature life stages in such disparate taxa as fish (Baldwin et al. 2009), frogs (Hiobiarilanto et al. 2010) and insects (Stur & Ekrem 2010). Third, Ebach uses the term "parataxonomy" as a slight on molecular systematists who might not have the same in-depth knowledge of morphology and biology as a taxonomic specialist. I take issue not with this insult but with the implication that we should not trust identifications made by such "non-experts". Consider the multi-billion dollar industry of medical pathology. A technician working in a commercial pathology lab is not a bacterial systematist so why do people trust diagnoses emerging from their laboratories? It is because they are following molecular biological and biochemical protocols for species diagnosis that have been developed by microbiologists, rigorously tested for their specificity and sensitivity and have withstood thorough peer-review. The parallels with DNA barcoders are self-evident. If the molecular systematists (Ebach's "parataxonomists") cranking out barcode sequences do not have the required specialist taxonomic knowledge they collaborate with taxonomists who do. Bear in mind that the DNA barcode is not just a sequence but also comprises, among other things, a voucher specimen with its corresponding collection information and a species determination. As with any taxonomic study the species determination is a hypothesis proposed by a named individual (so that people can gauge for themselves the degree of certainty of the identification) and this can be tested by subsequent researchers through further study of the voucher specimen. The same criteria that apply to a good morphological taxonomic study apply also to barcoding: have sufficient numbers of specimens been sampled, have closely related species been examined to determine the species-specificity of diagnostic character states, and so on. Thus the implication that DNA barcoding is somehow methodologically inferior to morphology-based taxonomy is based largely on ignorance. A related point often raised by the anti-barcoding lobby, is that barcoding is "not science". It is instructive here to distinguish between the initial process of building and validating a DNA barcode reference library and the subsequent technical process of performing routine identifications. Taxonomic expertise is crucial for the former, and as every researcher who has ever been involved in a DNA barcoding project knows it often comprises multiple iterations of morphology-based and molecular-based investigations to establish where species boundaries lie; this is the scientific part. Subsequently only generic technical skills are needed for running diagnostics tests; this is the technical "not science" part. The elephant in the room here is that once a thorough DNA barcode database has been built and validated,
    Zootaxa 01/2011; 2772:67-68. · 1.06 Impact Factor
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    ABSTRACT: Finschhafen disorder (FD) affects coconut and oil palms in Papua New Guinea (PNG). It is characterised by yellow-bronzing of fronds which begins at the tips and progresses towards the petiole. Although the planthopper Zophiuma lobulata (Hemiptera: Lophopidae) has been posited as a cause of FD, the basis of the relationship has not been established. Studies conducted previously on FD predate the availability of DNA-based techniques to test for the involvement of plant pathogens such as phytoplasmas that cause yellows-type diseases in many plant taxa and are transmitted by the order of insects to which Z. lobulata belongs. In this study, polymerase chain reaction (PCR) assays found no evidence of phytoplasmas or bacteria-like organisms (BLOs) in tissues of coconut and oil palm symptomatic for FD and from Z. lobulata feeding on these plants. Further studies involved releasing Z. lobulata adults and nymphs onto caged, potted coconut and oil palms and onto palm fronds enclosed in mesh sleeves. In both experiments, chlorotic symptoms on the palms were observed in the presence of Z. lobulata. Insect-free control palms did not exhibit chlorotic symptoms of FD. In the frond sleeve experiment, only the fronds where Z. lobulata fed developed chlorosis indicating that the disorder is not systemic. Unlike most yellows-type diseases associated with Hemiptera, this study indicates that FD is because of a direct feeding effect on palms by Z. lobulata rather than transmission of a pathogen.
    Annals of Applied Biology 12/2010; 158(1):139 - 148. DOI:10.1111/j.1744-7348.2010.00450.x · 1.96 Impact Factor
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    ABSTRACT: Detecting and controlling the movements of invasive species, such as insect pests, relies upon rapid and accurate species identification in order to initiate containment procedures by the appropriate authorities. Many species in the tussock moth genus Lymantria are significant forestry pests, including the gypsy moth Lymantria dispar L., and consequently have been a focus for the development of molecular diagnostic tools to assist in identifying species and source populations. In this study we expand the taxonomic and geographic coverage of the DNA barcode reference library, and further test the utility of this diagnostic method, both for species/subspecies assignment and for determination of geographic provenance of populations. Cytochrome oxidase I (COI) barcodes were obtained from 518 individuals and 36 species of Lymantria, including sequences assembled and generated from previous studies, vouchered material in public collections, and intercepted specimens obtained from surveillance programs in Canada. A maximum likelihood tree was constructed, revealing high bootstrap support for 90% of species clusters. Bayesian species assignment was also tested, and resulted in correct assignment to species and subspecies in all instances. The performance of barcoding was also compared against the commonly employed NB restriction digest system (also based on COI); while the latter is informative for discriminating gypsy moth subspecies, COI barcode sequences provide greater resolution and generality by encompassing a greater number of haplotypes across all Lymantria species, none shared between species. This study demonstrates the efficacy of DNA barcodes for diagnosing species of Lymantria and reinforces the view that the approach is an under-utilized resource with substantial potential for biosecurity and surveillance. Biomonitoring agencies currently employing the NB restriction digest system would gather more information by transitioning to the use of DNA barcoding, a change which could be made relatively seamlessly as the same gene region underlies both protocols.
    PLoS ONE 12/2010; 5(12):e14280. DOI:10.1371/journal.pone.0014280 · 3.53 Impact Factor
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    ABSTRACT: Novel investigations into sugarcane stem borers, their distribution and their natural enemies, were conducted in small-scale farmers' fields and indigenous host plants growing in wetlands and irrigation channels in three regions of Ethiopia. Sugarcane, in most parts of the country, was infested with two Busseola species, identified as Busseola phaia and B. fusca. The incidence of infested sugarcane stalks by these ranged between 2 and 50% in individual fields. The incidence of Chilo partellus infested sugarcane stalks was high but this species was restricted to fewer areas in the Oromia and Amhara regions. Sesamia calamistis was recorded in two of the 54 sugarcane farms visited and in the sedge, Cyperus papyrus, growing on the edge of Lake Tana. Eldana saccharina, which is the most important pest of sugarcane in other parts of Africa, was recovered only from indigenous sedges (Cyperus spp.) growing in watering channels and large water bodies. Busseola phaia has not previously been reported from Ethiopia, and ours is the first report of this species attacking sugarcane in Africa. Seven species of parasitoid wasp were recorded from all of the stem borers found: the tachinids Linnaemya sp., Schembria eldanae and Actia sp., the braconids Dolichogenidea sp. and Cotesia flavipes, an unidentified scelionid, and a solitary parasitoid of unknown taxon. Two fungal pathogens (Entomophthora sp. and Beauveria bassiana) and a bacterial disease (Bacillus thuringiensis) were also recorded.
    International Journal of Pest Management 07/2010; 56(3):233-241. DOI:10.1080/09670870903470223 · 0.75 Impact Factor
  • Andrew Mitchell, Craig Maddox
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    ABSTRACT: Bark beetles are emerging as pests of macadamias, both in the native range of macadamias in Australia and worldwide wherever macadamias are cultivated. Multiple species have been detected on macadamias in Australia; however, little has been known about the identity of the species involved, other than that some belong to the genera Hypothenemus Westwood (1836) and Cryphalus Erichson (1836). Hypothenemus is a large and cosmopolitan genus, which contains two exotic species that are regulated pests for Australia: the tropical nut borer, Hypothenemus obscurus (Fabricius), is a pest of macadamias and Brazil nuts in the Americas and the Pacific, and the coffee berry borer, Hypothenemus hampei (Ferrari), is a pest of coffee found in coffee-growing areas worldwide, but not in Australia. It is essential that biosecurity authorities have reliable species diagnostic tools available in order to detect incursions of these species in Australia. However, the taxonomic literature on the relevant species is scattered and sparse, and the lack of molecular diagnostic methods means that identification of eggs and larvae has been impossible to date because the immature life stages are morphologically homogeneous. This study fills some crucial gaps in our ability to identify these species, developing diagnostic methods for the major pest species on macadamia in Australia, and for key exotic species, including both regulated pests. An integrative taxonomic approach was used incorporating both traditional morphological taxonomy and DNA barcode data in an iterative process to both identify beetles and develop robust diagnostics for them. DNA barcodes provide unambiguous discrimination of all species examined in this study, albeit a limited sample, and have the advantage that they can be used to identify all life stages of the species.
    Australian Journal of Entomology 04/2010; 49(2):104 - 113. DOI:10.1111/j.1440-6055.2010.00746.x · 0.80 Impact Factor
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    ABSTRACT: The African sugarcane stalk borer, Eldona saccharina Walker (Lepidoptera: Pyralidae), is widely distributed throughout sub-Saharan Africa and is an important insect pest of maize and sugarcane. The insect shows significant variation in behaviour, host plant and natural enemy guild in different regions. Several attempts to redistribute the natural enemies of E. saccharina from West Africa to South Africa were unsuccessful. The significant behavioural, host plant and natural enemy variations as well as failures of biocontrol attempts evoked a hypothesis of genetic diversification. To evaluate this hypothesis a molecular analysis was conducted on geographically isolated populations of E. saccharina from East, North, South and West Africa, using the cytochrome c oxidase subunit I (COI) region of the mitochondrial genome. The results revealed that E. saccharina populations are separated into four major units corresponding to the West Africa, Rift Valley, South/East Africa and southern African populations. Mitochondrial DNA divergence among the four populations ranged from 1% to 4.98%. To examine the impact of the observed genetic variation on the fertility of inter-population crosses, a mating experiment was conducted between the Rift valley and South African population to produce an F1 generation, and these were backcrossed with the South African parent population. Fertility of eggs produced by the F1/parent population cross was significantly reduced when compared to fertility of the "true" South African line, and the F1/F1 cross. The contributions of the observed genetic differences and inter population incompatibility for the failure of previous biocontrol attempts are discussed and recommendations on future biocontrol practices are given.
    Communications in agricultural and applied biological sciences 01/2010; 75(3):423-31.
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    ABSTRACT: Palm production faces serious challenges ranging from diseases to damage by insect pests, all of which may reduce productivity by as much as 30%. A number of disorders of unknown aetiology but associated with insects are now recognised. Management practices that ensure the sustainability of palm production systems require a sound understanding of the interactions between biological systems and palms. This paper discusses insect pests that attack palms, pathogens the insects vector as well as other disorders that are associated with these pests. We re-examine the disease aetiologies and procedures that have been used to understand causality. Pest management approaches such as cultural and biological control are discussed.
    Australian Journal of Entomology 10/2009; 48(4):328 - 342. DOI:10.1111/j.1440-6055.2009.00724.x · 0.80 Impact Factor
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    ABSTRACT: The assembly of a DNA barcode library for Australian Lepidoptera revealed that Oenochroma vinaria Guenée, 1858, as currently understood, is actually a mix of two different species. By analyzing DNA barcodes from recently collected specimens and the 150 year-old female lectotype of O. vinaria, we propose a reliable assignment of the name vinaria to one of these two species. A lectotype is designated for Monoctenia decora, a confirmed synonym of O. vinaria, and a new species, Oenochroma barcodificata sp. nov., is described. This species is only known from Tasmania and New South Wales; its biology and immature stages are described in detail.
    Zootaxa 09/2009; 2239(2239):1-21. · 1.06 Impact Factor
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    ABSTRACT: Abstract Surveys to investigate the distribution and abundance of stem borers in natural habitats were conducted in February 2006 and January–February 2007. The surveys included eastern, northern and central parts of South Africa as well as three localities in Lesotho. During the surveys, Eldana saccharina Walker was recovered from three new localities in inland South Africa and two new indigenous hosts, Phragmites australis Cav. and Panicum maximum Jacq. from Boskop in the North-West Province and Oribi Gorge in KwaZulu-Natal respectively. Populations of E. saccharina in different parts of Africa are known for their differences in larval feeding behaviours, host plant choice and natural enemies. It is important to understand the origin of the newly recovered population for prevention of incursion and efficient management in case it invades crops. Molecular analysis indicated that the populations recovered in these new locations and from the new host plants are part of the southern African population of E. saccharina. With change in climate, and disturbance in wetlands the insect is expected in the future to be more abundant and problematic in inland areas of southern Africa.
    Journal of Applied Entomology 07/2009; 133:440-455. DOI:10.1111/j.1439-0418.2009.01390.x · 1.70 Impact Factor
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    DAVID G. HERBERT, ANDREW MITCHELL
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    ABSTRACT: The land snail superfamily Orthalicoidea, although generally assumed to be of Gondwanan origin, is considered by the majority of recent authors to be absent from the African continent. However, two poorly-known African genera, Aillya and Prestonella, have historically been referred to the orthalicoid family Bulimulidae s.l. Anatomical study of Aillya has subsequently shown it to be morphologically distinct from the Bulimulidae and referable to a family of its own, outside the Orthalicoidea, but Prestonella has remained an enigmatic taxon of unknown affinity. Using molecular and morphological evidence, we demonstrate conclusively that Prestonella is indeed a member of the Bulimulidae s.l. We thus confirm that this family is represented in Africa, and that it has a classical disjunct, tri-continental southern distribution. Thus, either the origin of the family must at the least predate the separation of Africa and South America in the Mid Cretaceous (under a vicariance scenario) or there must have been subsequent dispersal between the isolated Gondwanan fragments. In view of the limited dispersal ability of terrestrial snails, we consider the former more likely. Anatomically, Prestonella exhibits many character states thought to be plesiomorphic, suggesting a relationship with the subfamily Bulimulinae. Bayesian analysis of nuclear DNA sequence data places it as sister group (posterior probability = 1.0) to an Australasian clade comprising Bothriembryon and Placostylus. However, taxon sampling within the Orthalicoidea is currently inadequate to permit meaningful resolution of subfamilial affinity using molecular data. Similarly, although those orthalicoid taxa for which molecular data are available comprise a well-supported clade, the relationships of this clade to other stylommatophoran clades remain unresolved. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 203–221.
    Biological Journal of the Linnean Society 12/2008; 96(1):203 - 221. DOI:10.1111/j.1095-8312.2008.01109.x · 2.54 Impact Factor

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