An annotated check list of Ramularia species in Australia

An annotated check list of Ramularia species in Australia, based on re-examinations of collections deposited at BRIP, DAR and VPRI, is presented. Twenty-eight species are reported in Australia, most of them on introduced host plants. The new species Cladosporium myrtacearum, Ramularia craspediicola and R. muehlenbeckiae are described. Collections of Cladosporium uredinicola, Neoramularia karelii, Passalora perfoliati and Pseudocercospora pongamiae-pinnatae, previously deposited in Australian herbaria under 'Ramularia sp.', are newly recognised for Australia.

A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia.

Mastreviruses (family Geminiviridae) that infect monocotyledonous plants occur throughout the temperate and tropical regions of Asia, Africa, Europe and Australia. Despite the identification of a very diverse array of mastrevirus species whose members infect African monocots, few such species have been discovered in other parts of the world. For example, the sequence of only a single monocot-infecting mastrevirus, Chloris striate mosaic virus (CSMV), has been reported so far from Australia, even though earlier biological and serological studies suggested that other distinct mastreviruses were present. Here, we have obtained the complete nucleotide sequence of a virus from the grass Digitaria didactyla originating from Australia. Analysis of the sequence shows the virus to be a typical mastrevirus, with four open reading frames, two in each orientation, separated by two non-coding intergenic regions. Although it showed the highest levels of sequence identity to CSMV (68.7%), their sequences are sufficiently diverse for the virus to be considered a member of a new species in the genus Mastrevirus, based on the present species demarcation criteria. We propose that the name first used during the 1980s be used for this species, Digitaria didactyla striate mosaic virus (DDSMV).

Species within Mycosphaerellaceae and Teratosphaeriaceae from eucalypts in eastern Australia

Twenty eight species within Mycosphaerellaceae and Teratosphaeriaceae (includes Mycosphaerella, Teratosphaeria, Pseudocercospora and Sonderhenia) are reported from Eucalyptus and Corymbia in New South Wales and Queensland, Australia, based on field surveys and examination of herbarium specimens and published reports. Teratosphaeria cryptica was the most commonly recorded species, with the widest host range and distribution, followed by Mycosphaerella marksii. Six new species are described: T. keanei, T. coolabuniensis, T. crispata, M. medusae, M. nootherensis and T. praelongispora. New or interesting records for known species are reported, including new records for Australia (T. pluritubularis and T. verrucosiafricana) and new records for Queensland (T. excentrica, T. multiseptata, T. nubilosa, T. suberosa and Ps. pseudoeucalyptorum).

Descriptions and keys to fungus-feeding Australian species in 5 genera of thrips

Fifty species in five genera of fungus feeding thrips, collected in part by Bush Blitz, are described. Details of 35 new species are combined with species previously named but not recognisable from literature, and illustrated identification keys to all species published. All specimens are data-based. These thrips are important ecologically, being associated with nutrient recycling from dead plants, and as food for various birds, lizards and frogs.

Appressoria in Mycoleptodiscus species

Appressoria formed by germinating conidia of Mycoleptodiscus species in vitro were examined as a possible source of taxonomic information. There were large differences in morphology between appressoria formed by the 12 taxa examined, and it is suggested that characteristics of the appressorium, such as size, shape, curvature, septation and germ pore size, provide additional differentiating criteria which are of use in the taxonomy of the genus. Three new species of Mycoleptodiscus are described, M. coloratus, M. geniculatus, and M. variabilis.

The Colletotrichum boninense species complex

Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequence data indicated that C. boninense represents a species complex. A multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) of 86 strains previously identified as C. boninense and other related strains revealed 18 clades. These clades are recognised here as separate species, including C. boninense s. str., C. hippeastri, C. karstii and 12 previously undescribed species, C. annellatum, C. beeveri, C. brassicicola, C. brasiliense, C. colombiense, C. constrictum, C. cymbidiicola, C. dacrycarpi, C. novae-zelandiae, C. oncidii, C. parsonsiae and C. torulosum. Seven of the new species are only known from New Zealand, perhaps reflecting a sampling bias. The new combination C. phyllanthi was made, and C. dracaenae Petch was epitypified and the name replaced with C. petchii. Typical for species of the C. boninense species complex are the conidiogenous cells with rather prominent periclinal thickening that also sometimes extend to form a new conidiogenous locus or annellations as well as conidia that have a prominent basal scar. Many species in the C. boninense complex form teleomorphs in culture. TAXONOMIC NOVELTIES: New combination - Colletotrichum phyllanthi (H. Surendranath Pai) Damm, P.F. Cannon & Crous. Name replacement - C. petchii Damm, P.F. Cannon & Crous. New species - C. annellatum Damm, P.F. Cannon & Crous, C. beeveri Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. brassicicola Damm, P.F. Cannon & Crous, C. brasiliense Damm, P.F. Cannon, Crous & Massola, C. colombiense Damm, P.F. Cannon, Crous, C. constrictum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. cymbidiicola Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. dacrycarpi Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. novae-zelandiae Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. oncidii Damm, P.F. Cannon & Crous, C. parsonsiae Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. torulosum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir. Typifications: Epitypifications - C. dracaenae Petch.

A new gall midge of the genus Dentifibula (Diptera: Cecidomyiidae), a predator of the scale insect Aulacaspis australis feeding on mangrove Bruguiera gymnorrhiza

Dentifibula nigroapicalisKolesik sp. nov., a new species of gall midge, is described whose larvae were found preying on the mangrove scale insect Aulacaspis australisBrimblecombe (Hemiptera: Coccoidea: Diaspididae). The mangrove scale was feeding on leaves of the mangrove Bruguiera gymnorrhiza (Rhizophoraceae) in Queensland. The new species is the first DentifibulaFelt known from Australia. © 2013 Australian Entomological Society.

Phyllosticta species on orchids (Orchidaceae), introducing Phyllosticta speewahensis sp. nov. (Phyllostictaceae, Ascomycota) from northern Australia

Several species of Phyllosticta (syn. Guignardia) have been described from orchids worldwide. A new species, Phyllosticta speewahensis, is proposed for a specimen isolated from leaf spots on a hybrid Vanda orchid in northern Queensland, Australia. Phylogenetic analysis of the nrDNA internal transcribed spacer region (ITS) and partial translation elongation factor 1-alpha (TEF1) gene sequences showed that P. speewahensis is most closely related to P. hostae. The likelihood that orchids harbour further cryptic species of endophytic and pathogenic Phyllosticta species is discussed.

Fungus-feeding phlaeothripine Thysanoptera in the genus Holothrips from Australia and New Caledonia, with a structurally similar new genus, Holoengythrips

Ten species of Holothrips, including seven new species, are recognized from Australia, with one further new species from New Caledonia. A new genus, Holoengythrips, is described from Australia, with nine new species that look similar to Holothrips species in having elongate maxillary stylets that are close together medially for the full length of the head. In contrast to species of Holothrips, the species of Holoengythrips are strongly sexually dimorphic, with antennal segment VIII separated from VII and the maxillary stylets more slender, and the males have a pore plate on the eighth sternite. Holoengythrips is therefore considered to be more closely related to Hoplandrothrips.

Responses of fruit flies (Tephritidae: Dacinae) to novel male attractants in north Queensland, Australia, and improved lures for some pest species

Male fruit fly attractants, cue-lure and methyl eugenol (ME), have been successfully used for the last 50 years in the monitoring and control of Dacini fruit flies (Bactrocera and Dacus species). However, over 50% of Dacini are non-responsive to either lure, including some pest species. A new lure, zingerone, has been found to weakly attract cue- and ME-responsive species in Malaysia. In Australia it attracted a weakly cue-responsive minor pest Bactrocera jarvisi (Tryon) and three non-responsive' species. Similar compounds were tested in Queensland and attracted cue- and ME-responsive species and two non-responsive' species. In this study, 14 novel compounds, including raspberry ketone formate (RKF) (Melolure) and zingerone, were field tested in comparison with cue-lure and ME at 17 sites in north Queensland. The most attractive novel lures were isoeugenol, methyl-isoeugenol, dihydroeugenol and zingerone. Several non-responsive' species responded to the new lures: Bactrocera halfordiae (Tryon), a species of some market access concern, was most attracted to isoeugenol; B.barringtoniae (Tryon), B.bidentata (May) and B.murrayi (Perkins) responded to isoeugenol, methyl-isoeugenol and dihydroeugenol; two new species of Dacus responded to zingerone. Bactrocera kraussi (Hardy), a cue-responsive minor pest in north Queensland, was significantly more attracted to isoeugenol than cue-lure. The cue-responsive D.absonifacies (May) and D.secamoneaeDrew were significantly more attracted to zingerone than cue-lure. Bactrocera yorkensisDrew & Hancock, a ME-responsive species was significantly more attracted to isoeugenol, methyl-isoeugenol and dihydroeugenol than ME. The preferential response to RKF or cue-lure was species specific. Six species were significantly more attracted to RKF, including the pests B.tryoni (Froggatt), B.frauenfeldi (Schiner) and minor pest B.bryoniae (Tryon); eight species were significantly more attracted to cue-lure including the pest B.neohumeralis (Hardy). These findings have significance in the search for optimal male lures for pest species elsewhere in the world.

Mutations as molecular tools : The metabolic-rate dependent molecular clock and DNA barcoding of allied species

Mutation and recombination are the fundamental processes leading to genetic variation in natural populations. This variation forms the raw material for evolution through natural selection and drift. Therefore, studying mutation rates may reveal information about evolutionary histories as well as phylogenetic interrelationships of organisms. In this thesis two molecular tools, DNA barcoding and the molecular clock were examined. In the first part, the efficiency of mutations to delineate closely related species was tested and the implications for conservation practices were assessed. The second part investigated the proposition that a constant mutation rate exists within invertebrates, in form of a metabolic-rate dependent molecular clock, which can be applied to accurately date speciation events. DNA barcoding aspires to be an efficient technique to not only distinguish between species but also reveal population-level variation solely relying on mutations found on a short stretch of a single gene. In this thesis barcoding was applied to discriminate between Hylochares populations from Russian Karelia and new Hylochares findings from the greater Helsinki region in Finland. Although barcoding failed to delineate the two reproductively isolated groups, their distinct morphological features and differing life-history traits led to their classification as two closely related, although separate species. The lack of genetic differentiation appears to be due to a recent divergence event not yet reflected in the beetles molecular make-up. Thus, the Russian Hylochares was described as a new species. The Finnish species, previously considered as locally extinct, was recognized as endangered. Even if, due to their identical genetic make-up, the populations had been regarded as conspecific, conservation strategies based on prior knowledge from Russia would not have guaranteed the survival of the Finnish beetle. Therefore, new conservation actions based on detailed studies of the biology and life-history of the Finnish Hylochares were conducted to protect this endemic rarity in Finland. The idea behind the strict molecular clock is that mutation rates are constant over evolutionary time and may thus be used to infer species divergence dates. However, one of the most recent theories argues that a strict clock does not tick per unit of time but that it has a constant substitution rate per unit of mass-specific metabolic energy. Therefore, according to this hypothesis, molecular clocks have to be recalibrated taking body size and temperature into account. This thesis tested the temperature effect on mutation rates in equally sized invertebrates. For the first dataset (family Eucnemidae, Coleoptera) the phylogenetic interrelationships and evolutionary history of the genus Arrhipis had to be inferred before the influence of temperature on substitution rates could be studied. Further, a second, larger invertebrate dataset (family Syrphidae, Diptera) was employed. Several methodological approaches, a number of genes and multiple molecular clock models revealed that there was no consistent relationship between temperature and mutation rate for the taxa under study. Thus, the body size effect, observed in vertebrates but controversial for invertebrates, rather than temperature may be the underlying driving force behind the metabolic-rate dependent molecular clock. Therefore, the metabolic-rate dependent molecular clock does not hold for the here studied invertebrate groups. This thesis emphasizes that molecular techniques relying on mutation rates have to be applied with caution. Whereas they may work satisfactorily under certain conditions for specific taxa, they may fail for others. The molecular clock as well as DNA barcoding should incorporate all the information and data available to obtain comprehensive estimations of the existing biodiversity and its evolutionary history.

Taxonomy and phylogeny of the manna lichens and allied species (Megasporaceae)

This dissertation is focused on the taxonomy, phylogeny, and ecology of the vagrant, erratic and allied terricolous and saxicolous species of the genera Aspicilia A. Massal. and Circinaria Link (Megasporaceae), particularly those traditionally referred to as manna lichens . The group has previously been defined on the basis of few morphological characters. The phylogeny of the family Megasporaceae is inferred from the combined dataset of nuLSU and mtSSU sequences. Five genera Aspicilia, Circinaria, Lobothallia, Megaspora, and Sagedia are recognized. Lobothallia is sister of the four other genera, while Aspicilia and Sagedia form the next clade. All these genera have small asci with eight spores. Circinaria is a sister genus of Megaspora, and these two have in common asci with (1 4) 6 8 large spores. Circinaria forms a monophyletic group and sphaerothallioid species form a monophyletic group within Circinaria. The presence of certain morphological characters such as pseudocyphellae, thickness of cortex and medulla layers, as well as ecological differences in sphaerothallioid species distinguish it from some other crustose species, especially those containing aspicilin and characterised by thin cortex and medulla layers, conidium length c. 6 12 µm and absence of pseudocyphellae. If sphaerothallioid species are accepted as a distinct genus, the rest of the Circinaria species would remain as a paraphyletic assemblage. Currently, the genus Circinaria includes all the sphaerothallioid species and its generic position is confirmed and accepted. Thus, it is proposed as a correct generic name also for the manna lichens described originally in other genera. Phylogeny at the species level was studied using nrITS sequence data. Traditionally, morphological characters have been used for the recognition of species. They were re-evaluated in the light of molecular data. Since characters such as vagrant, erratic and crustose growth forms proved to be misleading for the recognition of some species, a combination of several characters (including molecular data) is recommended. Vagrant growth form seems to have evolved several times among the distantly related lineages and even within a single population. The reasons behind the high plasticity in the external morphology of the sphaerothallioid Circinaria remain, however, unknown. Six new species are recognized: Aspicilia tibetica, Circinaria arida, C. digitata nom provis., C. gyrosa nom. provis., C. rogeri nom. provis., and C. rostamii nom. provis. Based on an analysis of nrITS dataset, three new erratic, vagrant and crustose species were also recognized, but these require additional study. The results also reveal that C. elmorei and C. hispida are not monophyletic as currently understood. In addition, 13 new combinations in the genus Circinaria are proposed.

A new cryptic rock-dwelling Hemidactylus (Squamata: Gekkonidae) from south India

A new species of gecko, Hemidactylus graniticolus sp. nov. is described from Karnataka state, south India. This large-sized (SVL to at least 110.6 mm), rupicolous gecko differs from congeners in having 16-18 longitudinal rows of fairly regularly arranged, subtrihedral, weakly keeled, striated tubercles at midbody; 9-11 and 12-13 subdigital lamellae on the first and fourth digits, respectively, of both manus and pes; tail with transverse series of four enlarged tubercles on each tail segment; 23-28 femoral pores on each side separated by 1-3 poreless scales; 12-14 supralabials and 9-11 infralabials. Molecular data support the distinctiveness of the new species and its affinities with large-bodied, tuberculate Hemidactylus spp. from India and Sri Lanka.

A new parasitic bee of the genus Braunsapis from India (Hymenoptera : Apidae : Allodapini)

A new species of allodapine bee (Apidae, Xylocopinae, Allodapini), Braunsapis bislensis, is described from southern India. To judge by its reduced mouthparts and scopa, it is a social parasite, perhaps in nests of B. puangensis (Cockerell).

Revision of the scolopendrid centipede digitipes Attems, 1930, from India (Chilopoda: Scolopendromorpha): reconciling molecular and morphological estimates of species diversity

Recent work on molecular phylogenetics of Scolopendridae from the Western Ghats, Peninsular India, has suggested the presence of six cryptic species of the otostigmine Digitipes Attems, 1930, together with three species described in previous taxonomic work by Jangi and Dass (1984). Digitipes is the correct generic attribution for a monophyletic group of Indian species, these being united with three species from tropical Africa (including the type) that share a distomedial process on the ultimate leg femur of males that is otherwise unknown in Otostigminae. Second maxillary characters previously used in the diagnosis of Digitipes are dismissed because Indian species do not possess the putatively diagnostic character states. Two new species from the Western Ghats that correspond to groupings identified based on monophyly, sequence divergence and coalescent analysis using molecular data are diagnosed based on distinct morphological characters. They are D. jangii and D. periyarensis n. spp. Three species named by Jangi and Dass (Digitipes barnabasi, D. coonoorensis and D. indicus) are revised based on new collections; D. indicus is a junior subjective synonym of Arthrorhabdus jonesii Verhoeff, 1938, the combination becoming Digitipes jonesii (Verhoeff, 1938) n. comb. The presence of Arthrorhabdus in India is accordingly refuted. Three putative species delimited by molecular and ecological data remain cryptic from the perspective of diagnostic morphological characters and are presently retained in D. barnabasi, D. jangii and D. jonesii. A molecularly-delimited species that resolved as sister group to a well-supported clade of Indian Digitipes is identified as Otostigmus ruficeps Pocock, 1890, originally described from a single specimen and revised herein. One Indian species originally assigned to Digitipes, D. gravelyi, deviates from confidently-assigned Digitipes with respect to several characters and is reassigned to Otostigmus, as O. gravelyi (Jangi and Dass, 1984) n. comb.