Celeste Linde

New species of Tulasnella associated with terrestrial orchids in Australia

Publisher: Springer Science and Business Media LLC

Date: 10-03-2017

DOI: 10.5598/IMAFUNGUS.2017.08.01.03

Himalayan-Tibetan Plateau Uplift Drives Divergence of Polyploid Poppies: Meconopsis Viguier (Papaveraceae)

Publisher: Public Library of Science (PLoS)

Date: 16-06-2014

DOI: 10.1371/JOURNAL.PONE.0099177

Seven new Serendipita species associated with Australian terrestrial orchids

Publisher: Informa UK Limited

Date: 02-08-2021

DOI: 10.1080/00275514.2021.1919848

Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini

Publisher: Wiley

Date: 06-2008

DOI: 10.1111/J.1365-294X.2008.03843.X

Cryptostylis species (Orchidaceae) from a broad geographic and habitat range associate with a phylogenetically narrow lineage of Tulasnellaceae fungi

Publisher: Elsevier BV

Date: 08-2022

DOI: 10.1016/J.FUNBIO.2022.06.001

Abstract: While many Australian terrestrial orchids have highly specialized mycorrhizal associations, we tested the hypothesis that the geographically widespread orchid genus Cryptostylis associates with a ersity of fungal species. Using fungal isolation and molecular approaches, we investigated the mycorrhizal associations of five Australian Cryptostylis species (27 sites s led) and included limited s ling from three Asiatic Cryptostylis species (two sites). Like related orchid genera, Tulasnellaceae formed the main fungal associations of the Cryptostylis species we s led, although some ectomycorrhizal, ericoid and saprotrophic fungi were detected infrequently. Each species of Australian Cryptostylis associated with three to seven Tulasnella Operational Taxonomic Units (OTUs), except for C. hunteriana where only one Tulasnella OTU was detected. In total, eleven Tulasnella OTUs associated with Australian Cryptostylis. The Asiatic Cryptostylis associated with four different Tulasnella OTUs belonging to the same lineage as the Australian species. While five Tulasnella OTUs (T. australiensis, T. prima, T. warcupii, T. densa, and T. punctata) were used by multiple species of Australian Cryptostylis, the most commonly used OTU differed between orchid species. The association with different Tulasnella fungi by Cryptostylis species co-occurring at the same site suggests that in any given environmental condition, Cryptostylis species may intrinsically favour different fungal OTUs.

Congruent species delineation of Tulasnella using multiple loci and methods

Publisher: Wiley

Date: 13-09-2013

DOI: 10.1111/NPH.12492

Invaded range of the blackberry pathogen Phragmidium violaceum in the Pacific Northwest of the USA and the search for its provenance

Publisher: Springer Science and Business Media LLC

Date: 17-02-2013

DOI: 10.1007/S10530-013-0413-3

Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini

Publisher: Oxford University Press (OUP)

Date: 24-07-2009

DOI: 10.1093/MOLBEV/MSP166

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population

Publisher: Frontiers Media SA

Date: 16-06-2017

DOI: 10.3389/FPLS.2017.01029

New species ofTulasnellaassociated with Australian terrestrial orchids in the subtribes Megastylidinae and Thelymitrinae

Publisher: Informa UK Limited

Date: 04-03-2022

DOI: 10.1080/00275514.2021.2019547

Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity

Publisher: Elsevier BV

Date: 04-2017

DOI: 10.1016/J.FUNECO.2016.11.009

THE HOST BIAS OF THREE EPIPHYTIC AERIDINAE ORCHID SPECIES IS REFLECTED, BUT NOT EXPLAINED, BY MYCORRHIZAL FUNGAL ASSOCIATIONS

Publisher: Wiley

Date: 04-2013

DOI: 10.3732/AJB.1200411

Abstract: The three co-occurring epiphytic orchid species, Sarcochilus hillii, Plectorrhiza tridentata, and Sarcochilus parviflorus vary in host specificity all are found predominantly on the tree Backhousia myrtifolia but some also associate with a broad range of species. Despite this specialization, no fitness advantage has been detected for adult orchid plants growing on the preferred host. Therefore, we predicted that the host specialization of these orchid species is a consequence of a bias toward particular orchid mycorrhizal fungi, which are in turn biased toward particular woody plant species. To test this hypothesis, we s led representatives of each orchid species on B. myrtifolia and other host species across sites. Rhizoctonia-like fungi were isolated from orchid roots and identified using molecular markers. Three groups of fungi were identified, and the orchid species varied in their specificity for these. All fungal groups were found on the host B. myrtifolia yet at all sites, only one orchid species, S. hillii, associated with all three groups. Our results demonstrate that these orchid species did vary in their mycorrhizal specificity however, the distribution of their mycorrhizal associates did not directly explain their host associations. Rather, we propose that the mycorrhizal relationship of these orchid species is complex and have suggested future avenues of research.

Asymbiotic germination of Prasophyllum (Orchidaceae) requires low mineral concentration

Publisher: CSIRO Publishing

Date: 13-03-2023

DOI: 10.1071/BT22116

Abstract: Context Asymbiotic germination is used for propagation of orchids and to assess seed viability. However, asymbiotic germination media remain undeveloped for Prasophyllum (Orchidaceae), a genus with 39 threatened species in southern Australia. Aims To develop asymbiotic germination and replate media for Prasophyllum, and determine whether survival of asymbiotically grown seedlings under nursery conditions is enhanced through the addition of a mycorrhizal fungus to potting media. Methods Using Prasophyllum frenchii as a model, we tested 81 asymbiotic germination medium combinations. The three best-performing media were then compared against four untested commercial media, with and without added coconut water and/or banana. The best-performing medium was trialled on 18 additional Prasophyllum species. Twenty-four replate media were then tested for their ability to support seedling development. We measured the survival of seedlings under nursery conditions with and without the addition of mycorrhizal Ceratobasidium fungus to potting media. Key results Low concentrations of minerals, auxins and cytokinins were necessary for asymbiotic germination of P. frenchii, although germination was highest overall on the commercial medium W9.5 with 5% coconut water. The most effective replate medium was W9 with 5% banana. However, survival of seedlings was 1.7%, 2 years after transferral to potting media in the nursery, regardless of the addition or absence of a mycorrhizal fungus. Conclusions Asymbiotic media can effectively germinate Prasophyllum seed, although deflasked seedlings have low survival rates. Implications Our media are broadly applicable to assess seed viability in Prasophyllum. However, poor survival of asymbiotically grown seedlings contrasts with recently published evidence of high seedling survival using symbiotic propagation methods, indicating that plants should be propagated symbiotically for conservation programs.

Evolutionary relationships among pollinators and repeated pollinator sharing in sexually deceptive orchids

Publisher: Wiley

Date: 17-07-2017

DOI: 10.1111/JEB.13125

Abstract: The mechanism of pollinator attraction is predicted to strongly influence both plant ersification and the extent of pollinator sharing between species. Sexually deceptive orchids rely on mimicry of species-specific sex pheromones to attract their insect pollinators. Given that sex pheromones tend to be conserved among related species, we predicted that in sexually deceptive orchids, (i) pollinator sharing is rare, (ii) closely related orchids use closely related pollinators and (iii) there is strong bias in the wasp lineages exploited by orchids. We focused on species that are pollinated by sexual deception of thynnine wasps in the distantly related genera Caladenia and Drakaea, including new field observations for 45 species of Caladenia. Specialization was extreme with most orchids using a single pollinator species. Unexpectedly, seven cases of pollinator sharing were found, including two between Caladenia and Drakaea, which exhibit strikingly different floral morphology. Phylogenetic analysis of pollinators using four nuclear sequence loci demonstrated that although orchids within major clades primarily use closely related pollinator species, up to 17% of orchids within these clades are pollinated by a member of a phylogenetically distant wasp genus. Further, compared to the total ersity of thynnine wasps within the study region, orchids show a strong bias towards exploiting certain genera. Although these patterns may arise through conservatism in the chemical classes used in sex pheromones, apparent switches between wasp clades suggest unexpected flexibility in floral semiochemical production. Alternatively, wasp sex pheromones within lineages may exhibit greater chemical ersity than currently appreciated.

Continental-scale distribution and diversity of Ceratobasidium orchid mycorrhizal fungi in Australia

Publisher: Oxford University Press (OUP)

Date: 02-06-2021

DOI: 10.1093/AOB/MCAB067

Abstract: Mycorrhizal fungi are a critical component of the ecological niche of most plants and can potentially constrain their geographical range. Unlike other types of mycorrhizal fungi, the distributions of orchid mycorrhizal fungi (OMF) at large spatial scales are not well understood. Here, we investigate the distribution and ersity of Ceratobasidium OMF in orchids and soils across the Australian continent. We s led 217 Ceratobasidium isolates from 111 orchid species across southern Australia and combined these with 311 Ceratobasidium sequences from GenBank. To estimate the taxonomic ersity of Ceratobasidium associating with orchids, phylogenetic analysis of the ITS sequence locus was undertaken. Sequence data from the continent-wide Australian Microbiome Initiative were used to determine the geographical range of operational taxonomic units (OTUs) detected in orchids, with the distribution and climatic correlates of the two most frequently detected OTUs modelled using MaxEnt. We identified 23 Ceratobasidium OTUs associating with Australian orchids, primarily from the orchid genera Pterostylis, Prasophyllum, Rhizanthella and Sarcochilus. OTUs isolated from orchids were closely related to, but distinct from, known pathogenic fungi. Data from soils and orchids revealed that ten of these OTUs occur on both east and west sides of the continent, while 13 OTUs were recorded at three locations or fewer. MaxEnt models suggested that the distributions of two widespread OTUs are correlated with temperature and soil moisture of the wettest quarter and far exceeded the distributions of their host orchid species. Ceratobasidium OMF with cross-continental distributions are common in Australian soils and frequently have geographical ranges that exceed that of their host orchid species, suggesting these fungi are not limiting the distributions of their host orchids at large spatial scales. Most OTUs were distributed within southern Australia, although several OTUs had distributions extending into central and northern parts of the continent, illustrating their tolerance of an extraordinarily wide range of environmental conditions.

Ceratobasidium orchid mycorrhizal fungi reveal intraspecific variation and interaction with different nutrient media in symbiotic germination of Prasophyllum (Orchidaceae)

Publisher: Springer Science and Business Media LLC

Date: 07-2022

DOI: 10.1007/S13199-022-00874-9

Abstract: Understanding how nutrient requirements of orchid mycorrhizal fungi (OMF) affect symbiotic germination is essential for the ex situ conservation of threatened orchids and their mycorrhizal symbioses. Yet the influence of isolate-level variation in OMF nutrient preferences on orchid germination is unknown. We tested germination of Prasophyllum frenchii (Orchidaceae) on 15 different media of varying carbon and macronutrient compositions with three Ceratobasidium isolates of the same operational taxonomic unit (OTU) as determined with internal transcribed spacer locus sequencing. There was a significant interaction between media and fungal isolate on percentage germination, with each isolate recording its highest percentage germination on different nutrient media (Isolate 9.3: 5.2 ± 1.4% on MOM–S Isolate 8.2: 5.4 ± 1.1% on MOM + S Isolate 4.3: 2.2 ± 0.5% on 1.25 g/L wheat bran agar). Across all isolates, germination (percentage germination 0) occurred more frequently on wheat bran agar media (39.7% of plates) than on oatmeal agar media (6.0% of plates). There was also an effect of media type on aerial hyphal growth behaviour of the OMF isolate. All isolates supported growth through to adult flowering plants. We demonstrated that symbiotic germination of Prasophyllum is affected by media composition. Further, percentage germination and aerial hyphal growth behaviour differed significantly among OMF isolates of the same OTU. This illustrates that a ersity of functionally significant fungal strains occurs within a single OTU, a previously unknown aspect of OMF research with important ecological and conservation implications.

Specific mycorrhizal associations involving the same fungal taxa in common and threatened Caladenia (Orchidaceae): implications for conservation

Publisher: Oxford University Press (OUP)

Date: 18-08-2020

DOI: 10.1093/AOB/MCAA116

Abstract: In orchid conservation, quantifying the specificity of mycorrhizal associations, and establishing which orchid species use the same fungal taxa, is important for sourcing suitable fungi for symbiotic propagation and selecting sites for conservation translocation. For Caladenia subgenus Calonema (Orchidaceae), which contains 58 threatened species, we ask the following questions. (1) How many taxa of Serendipita mycorrhizal fungi do threatened species of Caladenia associate with? (2) Do threatened Caladenia share orchid mycorrhizal fungi with common Caladenia? (3) How geographically widespread are mycorrhizal fungi associated with Caladenia? Fungi were isolated from 127 Caladenia species followed by DNA sequencing of the internal transcibed spacer (ITS) sequence locus. We used a 4.1–6 % sequence ergence cut-off range to delimit Serendipita operational taxonomic units (OTUs). We conducted trials testing the ability of fungal isolates to support germination and plant growth. A total of 597 Serendipita isolates from Caladenia, collected from across the Australian continent, were used to estimate the geographic range of OTUs. Across the genus, Caladenia associated with ten OTUs of Serendipita (Serendipitaceae) mycorrhizal fungi. Specificity was high, with 19 of the 23 threatened Caladenia species s led in detail associating solely with OTU A, which supported plants from germination to adulthood. The majority of populations of Caladenia associated with one OTU per site. Fungal sharing was extensive, with 62 of the 79 Caladenia s led in subgenus Calonema associating with OTU A. Most Serendipita OTUs were geographically widespread. Mycorrhizal fungi can be isolated from related common species to propagate threatened Caladenia. Because of high specificity of most Caladenia species, only small numbers of OTUs typically need to be considered for conservation translocation. When selecting translocation sites, the geographic range of the fungi is not a limiting factor, and using related Caladenia species to infer the presence of suitable fungal OTUs may be feasible.

Fungal Planet description sheets: 1112–1181

Publisher: Naturalis Biodiversity Center

Date: 31-12-2020

DOI: 10.3767/PERSOONIA.2020.45.10

Abstract: Novel species of fungi described in this study include those from various countries as follows: Australia , Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi , Lophotrichus medusoides from stem tissue of Citrus garrawayi , Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.)and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida , Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus , Veloboletus limbatus (incl. Veloboletus gen. nov.)onsoil. Austria , Cortinarius glaucoelotus onsoil. Bulgaria , Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada , Cantharellus betularum among leaf litter of Betula , Penicillium saanichii from house dust. Chile , Circinella l ensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum . China, Colletotrichum cycadis on leaves of Cycas revoluta . Croatia , Phialocephala melitaea on fallen branch of Pinus halepensis . Czech Republic , Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic , Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France , Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans , Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana , Hypoxylon hepaticolor on dead corticated branch. Great Britain , Inocybe ionolepis on soil. India , Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora . Iran , Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis . Italy , Penicillium vallebormidaense from compost. Namibia , Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis . Pakistan , Russula shawarensis from soil on forest floor. Russia , Cyberlindnera dauci from Daucus carota . South Africa , Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum , Endoconidioma euphorbiae on leaves of Euphorbia mauritanica , Eucasphaeria proteae on leaves of Protea neriifolia , Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima , Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii , Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum , Neometulocladosporiella seifertii on leaves of Combretum caffrum , Paramyrothecium pituitipietianum on stems of Grielum humifusum , Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius , Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii . Sweden , Coprinopsis rubra on cow dung, Elaphomyces nemoreus fromdeciduouswoodlands. Spain , Polyscytalum pini-canariensis on needles of Pinus canariensis , Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber . Thailand , Tolypocladium flavonigrum on Elaphomyces sp. USA , Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus , Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides , Pseudogymnoascus palmeri fromcavesediment. Vietnam , Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.

Defence gene expression profiling to Ascochyta rabiei aggressiveness in chickpea

Publisher: Springer Science and Business Media LLC

Date: 15-04-2016

DOI: 10.1007/S00122-016-2706-2

Abstract: Significant differences in defence pathway-related gene expression were observed among chickpea cultivars following A. rabiei infection. Differential gene expression is indicative of erse resistances, a theoretical tool for selective breeding. A high number of Ascochyta rabiei pathotypes infecting chickpea in Australia has severely h ered efforts towards breeding for sustained quantitative resistance in chickpea. Breeding for sustained resistance will be aided by detailed knowledge of defence responses to isolates with different aggressiveness. As an initial step, the conserved and differential expressions of a suit of previously characterised genes known to be involved in fungal defence mechanisms were assessed among resistant and susceptible host genotypes following inoculation with high or low aggressive A. rabiei isolates. Using quantitative Real-Time PCR (qRT-PCR), 15 defence-related genes, normalised with two reference genes, were temporally differentially expressed (P < 0.005) as early as 2 h post inoculation of Genesis090 (resistant) or Kaniva (susceptible). The highly aggressive isolate, 09KAL09, induced vastly different expression profiles of eight key defence-related genes among resistant and susceptible genotypes. Six of these same genes were differentially expressed among ten host genotypes, inclusive of the best resistance sources within the Australian chickpea breeding program, indicating potential use for discrimination and selection of resistance "type" in future breeding pursuits.

Co‐infection patterns and geographic distribution of a complex pathosystem targeted by pathogen‐resistant plants

Publisher: Wiley

Date: 2012

DOI: 10.1890/11-0341.1

Abstract: Increasingly, pathogen-resistant (PR) plants are being developed to reduce the agricultural impacts of disease. However PR plants also have the potential to result in increased invasiveness of nontarget host populations and so pose a potential threat to nontarget ecosystems. In this paper we use a new framework to investigate geographical variation in the potential risk associated with unintended release of genetically modified alfalfa mosaic virus (AMV)-resistant Trifolium repens (white clover) into nontarget host populations containing AMV, clover yellow vein virus (ClYVV), and white clover mosaic virus (WCIMV) in southeastern Australia. Surveys of 213 sites in 37 habitat types over a 300 000-km2 study region showed that T. repens is a significant weed of many high-conservation-value habitats in southeastern Australia and that AMV, ClYVV, and WClMV occur in 15-97% of nontarget host populations. However, T. repens abundance varied with site disturbance, habitat conservation value, and proximity to cropping, and all viral pathogens had distinct geographic distributions and infection patterns. Virus species frequently co-infected host plants and displayed nonindependent distributions within host populations, although co-infection patterns varied across the study region. Our results clearly illustrate the complexity of conducting environmental risk assessments that involve geographically widespread, invasive pasture species and demonstrate the general need for targeted, habitat- and pathosystem-specific studies prior to the process of tiered risk assessment.

Genetic homogeneity of a recently introduced pathogen of chickpea, Ascochyta rabiei, to Australia

Publisher: Springer Science and Business Media LLC

Date: 11-07-2015

DOI: 10.1007/S10530-014-0752-8

Specialized ecological interactions and plant species rarity: The role of pollinators and mycorrhizal fungi across multiple spatial scales

Publisher: Elsevier BV

Date: 2014

DOI: 10.1016/J.BIOCON.2013.11.027

A tangled tale of two teal: population history of the grey Anas gracilis and chestnut teal A. castanea of Australia

Publisher: Wiley

Date: 07-2009

DOI: 10.1111/J.1600-048X.2008.04652.X

A Global Perspective on the Population Structure and Reproductive System of Phyllosticta citricarpa

Publisher: Scientific Societies

Date: 06-2017

DOI: 10.1094/PHYTO-08-16-0292-R

Abstract: The citrus pathogen Phyllosticta citricarpa was first described 117 years ago in Australia subsequently, from the summer rainfall citrus-growing regions in China, Africa, and South America and, recently, the United States. Limited information is available on the pathogen’s population structure, mode of reproduction, and introduction pathways, which were investigated by genotyping 383 isolates representing 12 populations from South Africa, the United States, Australia, China, and Brazil. Populations were genotyped using seven published and eight newly developed polymorphic simple-sequence repeat markers. The Chinese and Australian populations had the highest genetic ersities, whereas populations from Brazil, the United States, and South Africa exhibited characteristics of founder populations. The U.S. population was clonal. Based on principal coordinate and minimum spanning network analyses, the Chinese populations were distinct from the other populations. Population differentiation and clustering analyses revealed high connectivity and possibly linked introduction pathways between South Africa, Australia, and Brazil. With the exception of the clonal U.S. populations that only contained one mating type, all the other populations contained both mating types in a ratio that did not deviate significantly from 1:1. Although most populations exhibited sexual reproduction, linkage disequilibrium analyses indicated that asexual reproduction is important in the pathogen’s life cycle.

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids

Publisher: Wiley

Date: 16-02-2021

DOI: 10.1111/1755-0998.13327

Abstract: With over 25,000 species, the drivers of ersity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative de novo and reference‐guided assembly, before target sequence extraction, annotation and alignment, and application of a homology‐aware k ‐ mer block phylogenomic approach, prior to maximum likelihood and coalescence‐based phylogenetic inference. Our evaluation considered 87 taxa in two test data sets: 67 s les spanning the tribe, and 72 s les involving 24 closely related Caladenia species. The tiered design achieved high target loci recovery ( %), with the median number of recovered loci in Sets 1–5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous k ‐mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customized multitiered sequence capture strategy, in combination with promising yet underutilized phylogenomic approaches, will be effective for groups where interspecific ergence is recent, but information on deeper phylogenetic relationships is also required.

New species of Tulasnella associated with Australian terrestrial orchids in the Cryptostylidinae and Drakaeinae

Publisher: Informa UK Limited

Date: 04-11-2021

DOI: 10.1080/00275514.2020.1813473

Further evidence for sexual reproduction in Rhynchosporium secalis based on distribution and frequency of mating-type alleles

Publisher: Elsevier BV

Date: 11-2003

DOI: 10.1016/S1087-1845(03)00110-5

Abstract: Rhynchosporium secalis, the causal agent of scald on barley, is thought to be exclusively asexual because no teleomorph has been found. Partial sequences of the HMG-box and alpha-domain of Rhynchosporium secalis isolates were identified and used to develop a PCR assay for the mating-type locus. PCR lification of only one of these two domains was possible in each strain, suggesting that R. secalis has a MAT organization that is similar to other known heterothallic fungi. A multiplex PCR with primers lifying either a MAT1-1- or MAT1-2-specific licon was used to determine the distribution of mating types in several R. secalis populations. In total, 1101 isolates from Australia, Switzerland, Ethiopia, Scandinavia, California, and South Africa were included in the analysis. Mating types occurred in equal frequencies for most of these populations, suggesting frequency-dependent selection consistent with sexual reproduction. In addition, both mating types were frequently found occupying the same lesion or leaf, providing opportunities for isolates of opposite mating type to interact and reproduce sexually. We propose that R. secalis should be considered a sexual pathogen, although the sexual cycle may occur infrequently in some populations.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2010–30 November 2010

Publisher: Wiley

Date: 21-01-2011

DOI: 10.1111/J.1755-0998.2010.02970.X

Abstract: This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross-tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.

Matching symbiotic associations of an endangered orchid to habitat to improve conservation outcomes

Publisher: Oxford University Press (OUP)

Date: 12-06-2018

DOI: 10.1093/AOB/MCY094

Not an ancient relic: the endemicLivistonapalms of arid central Australia could have been introduced by humans

Publisher: The Royal Society

Date: 07-03-2012

DOI: 10.1098/RSPB.2012.0103

Abstract: Livistona mariae is an endemic palm localized in arid central Australia. This species is separated by about 1000 km from its congener L. rigida , which grows distantly in the Roper River and Nicholson–Gregory River catchments in northern Australia. Such an isolated distribution of L. mariae has been assumed to have resulted from contraction of ancestral populations as Australia aridified from the Mid-Miocene ( ca 15 Ma). To test this hypothesis at the population level, we examined the genetic relationships among 14 populations of L. mariae and L. rigida using eight nuclear microsatellite loci. Our population tree and Bayesian clustering revealed that these populations comprised two genetically distinct groups that did not correspond to the current classification at species rank, and L. mariae showed closest affinity with L. rigida from Roper River. Furthermore, coalescent ergence-time estimations suggested that the disjunction between the northern populations (within L. rigida ) could have originated by intermittent colonization along an ancient river that has been drowned repeatedly by marine transgression. During that time, L. mariae populations could have been established by opportunistic immigrants from Roper River about 15 000 years ago, concurrently with the settlement of indigenous Australians in central Australia, who are thus plausible vectors. Thus, our results rule out the ancient relic hypothesis for the origin of L. mariae .

Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia

Publisher: The Royal Society

Date: 22-12-2013

DOI: 10.1098/RSPB.2013.2182

Abstract: Climate and fire are the key environmental factors that shape the distribution and demography of plant populations in Australia. Because of limited palaeoecological records in this arid continent, however, it is unclear as to which factor impacted vegetation more strongly, and what were the roles of fire regime changes owing to human activity and megafaunal extinction (since ca 50 kya). To address these questions, we analysed historical genetic, demographic and distributional changes in a widespread conifer species complex that paradoxically grows in fire-prone regions, yet is very sensitive to fire. Genetic demographic analysis showed that the arid populations experienced strong bottlenecks, consistent with range contractions during the Last Glacial Maximum ( ca 20 kya) predicted by species distribution models. In southern temperate regions, the population sizes were estimated to have been mostly stable, followed by some expansion coinciding with climate amelioration at the end of the last glacial period. By contrast, in the flammable tropical savannahs, where fire risk is the highest, demographic analysis failed to detect significant population bottlenecks. Collectively, these results suggest that the impact of climate change overwhelmed any modifications to fire regimes by Aboriginal landscape burning and megafaunal extinction, a finding that probably also applies to other fire-prone vegetation across Australia.

Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids

Publisher: Wiley

Date: 30-10-2023

DOI: 10.1111/JEB.14107

Abstract: The study of congruency between phylogenies of interacting species can provide a powerful approach for understanding the evolutionary history of symbiotic associations. Orchid mycorrhizal fungi can survive independently of orchids making cospeciation unlikely, leading us to predict that any congruence would arise from host‐switches to closely related fungal species. The Australasian orchid subtribe Drakaeinae is an iconic group of sexually deceptive orchids that consists of approximately 66 species. In this study, we investigated the evolutionary relationships between representatives of all six Drakaeinae orchid genera (39 species) and their mycorrhizal fungi. We used an exome capture dataset to generate the first well‐resolved phylogeny of the Drakaeinae genera. A total of 10 closely related Tulasnella Operational Taxonomic Units (OTUs) and previously described species were associated with the Drakaeinae orchids. Three of them were shared among orchid genera, with each genus associating with 1–6 Tulasnella lineages. Cophylogenetic analyses show Drakaeinae orchids and their Tulasnella associates exhibit significant congruence ( p 0.001) in the topology of their phylogenetic trees. An event‐based method also revealed significant congruence in Drakaeinae– Tulasnella relationships, with duplications (35), losses (25), and failure to erge (9) the most frequent events, with minimal evidence for cospeciation (1) and host‐switches (2). The high number of duplications suggests that the orchids speciate independently from the fungi, and the fungal species association of the ancestral orchid species is typically maintained in the daughter species. For the Drakaeinae– Tulasnella interaction, a pattern of phylogenetic niche conservatism rather than coevolution likely explains the observed phylogenetic congruency in orchid and fungal phylogenies. Given that many orchid genera are characterized by sharing of fungal species between closely related orchid species, we predict that these findings may apply to a wide range of orchid lineages.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2011–31 March 2011

Publisher: Wiley

Date: 31-05-2011

DOI: 10.1111/J.1755-0998.2011.03028.X

Abstract: This article documents the addition of 111 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser oxyrinchus desotoi, Anopheles nuneztovari sensu lato, Asellus aquaticus, Calopteryx splendens, Calopteryx virgo, Centaurea aspera, Centaurea seridis, Chilina dombeyana, Proctoeces cf. lintoni and Pyrenophora teres f. teres.

Continent-wide distribution in mycorrhizal fungi: implications for the biogeography of specialized orchids

Publisher: Oxford University Press (OUP)

Date: 22-06-2015

DOI: 10.1093/AOB/MCV084

Linked machine learning classifiers improve species classification of fungi when using error-prone long-reads on extended metabarcodes

Publisher: Cold Spring Harbor Laboratory

Date: 05-2021

DOI: 10.1101/2021.05.01.442223

Abstract: The increased usage of error-prone long-read sequencing for metabarcoding of fungi has not been matched with adequate public databases and concomitant analysis approaches. We address this gap and present a proof-of-concept study for classifying fungal taxa using linked machine learning classifiers. We demonstrate the capability of linked machine learning classifiers to accurately classify species and strains using real-world and simulated fungal ribosomal DNA datasets, including plant and human pathogens. We benchmark our new approach in comparison to current alignment and k-mer based methods based on synthetic mock communities. We also assess real world applications of species identification in complex unlabelled datasets. Our machine learning approach assigned in idual nanopore long-read licon sequences to fungal species with high recall rates and low false positive rates. Importantly, our approach successfully distinguished between closely-related species and strains when in idual read errors were higher than the genetic distance between in idual taxa, which the alignment and k-mer methods could not do. The machine learning approach showed an ability to identify key species with high recall rates, even in complex s les of unknown species composition. A proof of concept machine learning approach using a tree-descent approach on a decision tree of classifiers can identify known taxa with high accuracy, and precisely detect known target species from complex s les with high recall rates. We propose this approach is suitable for detecting the known knowns of pathogens or invasive species in any environment of mostly unknown composition, including agriculture and wild ecosystems.

Linkage Projects - Grant ID: LP0990385

Start Date: 12-2009

End Date: 12-2013

Amount: $90,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP110100408

Start Date: 11-2011

End Date: 12-2015

Amount: $460,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP150102762

Start Date: 06-2015

End Date: 06-2021

Amount: $644,800.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0668487

Start Date: 2006

End Date: 12-2007

Amount: $553,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0989338

Start Date: 05-2009

End Date: 05-2013

Amount: $760,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989589

Start Date: 2009

End Date: 06-2009

Amount: $550,000.00

Funder: Australian Research Council

Industrial Transformation Training Centres - Grant ID: IC230100027

Start Date: 2023

End Date: 12-2027

Amount: $5,000,000.00

Funder: Australian Research Council