Invasion history of Lycium ferocissimum in Australia: The impact of admixture on genetic diversity and differentiation

Aim

We investigated the invasion history of Lycium ferocissimum, a spine-covered shrub native to South Africa that was introduced to Australia in the mid-1800s, and has since developed into a damaging invasive plant of undisturbed landscapes and pastures. In addition to identifying the provenance of the Australian plants, we tested for evidence of admixture, and contrasted genetic diversity and structuring across the native and introduced ranges.

Location

Samples were collected across South Africa (24 localities) and Australia (26 localities).

Methods

We used genotyping-by-sequencing (3117 SNPs across 381 individuals) to assess population genetic structuring in L. ferocissimum across Australia and South Africa. Coalescent analyses were used to explicitly test contrasting invasion scenarios.

Results

Clear geographic genetic structuring was detected across South Africa, with distinct clusters in the Eastern and Western Cape provinces. The L. ferocissimum plants in Australia form their own genetic cluster, with a similar level of genetic diversity as plants in South Africa. Coalescent analyses demonstrated that the lineage in Australia was formed by admixture between Eastern Cape and Western Cape plants, with most of the genetic material from the Australian lineage originating from the Western Cape. Our analyses suggest that L. ferocissimum plants were originally introduced to South Australia, though it is unclear whether admixture occurred before or after its introduction to Australia. We detected little evidence of geographic genetic structure across Australia, although many of the populations were genetically distinct from one another.

Main Conclusions

Our results illustrate how admixture can result in genetically diverse and distinct invasive populations. The complex invasion history of L. ferocissimum in Australia poses particular challenges for biological control. We suggest potential biological control agents should be screened against admixed plants (in addition to plants from the Eastern and Western Cape) to test whether they provide effective control of the genetically distinct invasive lineage.     

A new species of gall midge (Diptera: Cecidomyiidae) damaging flower buds of goji berry Lycium barbarum (Solanaceae)

Larvae of a previously undescribed gall midge species have been feeding within malformed flower buds of goji berry Lycium barbarum L. (Solanaceae) in China, preventing fruit development and causing damage to the fruit industry. The new species is named Gephyraulus lycantha Jiao & Kolesik, its morphology is described, the COI mitochondrial gene segment is sequenced, and the biology is outlined. In order to taxonomically accommodate the new gall midge, the scope of the genus Gephyraulus is broadened and now encompasses also species that lack dorso-apical sensoria on the female cercus.LSID: urn:lsid:zoobank.org:pub:17B243CF-5235-405B-AA60-8E872C848367.     

Lycium amarum sp. nov. (Solanaceae) from Xizang,supported from morphological characters and phylogenetic analysis

Lycium amarum sp. nov. L. Q. Huang is described based on its general morphology and pollen micromorphology, which were compared with closely related Lycium species. The phylogenetic relationships among the new species and closely related Lycium species belonging to the tribe Lycieae were investigated based on the DNA sequence data of the granule‐bound starch synthase (GBSSI) gene. Morphologically, L. amarum is similar to L. chinense Mill. sharing lanceolate or linear‐oblanceolate leaves, three‐lobed calyx, villous ring slightly above the filament base, and adjacent corolla tube, however, L. amarum may be diagnosed by its prominent tubercles at the base of spines, thinly leathery leaves, and a two‐tine crack on the tip of calyx lobes. According to our results, the new species is close to L. barbarum L., L. chinense, L. dasystemum Pojark, and L. yunnanense Kuang & Lu.     

Presence of pathogenic cryptococci on trees situated in two recreational areas in South Africa

Knowledge of the environmental prevalence of members of the Cryptococcus neoformans/Cryptococcus gattii species complex is important, since cryptococcal infection is acquired from the environment. We determined whether trees located in two South African recreational areas harboured pathogenic cryptococci and compared the isolates to clinical isolates obtained from Western Cape hospitals with molecular typing techniques. The majority of isolates originating from trees in a public park in Cape Town (PPCT) were C. gattii sensu stricto, followed by C. neoformans sensu stricto genotype AFLP1/VNI. The PPCT trees might be a source of infection, since all genotype AFLP1/VNI isolates from these trees and one clinical isolate belonged to the same sequence type (ST), i.e. ST23. Recombination and basidiospore production might be occurring in PPCT trees that contained C. gattii s.s. isolates belonging to both mating types. The presence of C. gattii s.s. in PPCT trees might therefore pose a risk to human health.     

New species, reports, observations and taxonomical changes of southern African rust fungi (Uredinales)

This work presents research on the diversity of the southern African rust mycobiota (Uredinales). It describes new species, lists new reports and adds new information on several rust fungi. Puccinia cornurediata, Puccinia dioscoreae-mundtii, Puccinia horti-kirstenboschi, Puccinia othonnoides, Puccinia rapipes, Puccinia subindumentana, Uredo otholobii and Uromyces lotononidicola are described as new; Puccinia verwoerdiana is assigned to Puccinia lycii as a synonym, and Uredo lotononi to U. lotononidicola. Comprehensive accounts and keys are presented for Puccinia species on Lycium (Solanaceae), Helichrysum and Othonna (Asteraceae). Puccinia butleri and Uromyces bidenticola are new reports for South Africa, and Puccinia spinulosa is new for Namibia. So far, the latter species has only been known from Madagascar, and P. butleri from the Indian subcontinent. Taxonomical novelties are P. cornurediata R. Berndt; P. dioscoreae-mundtii R. Berndt, A.R. Wood & E. Uhlmann; P. horti-kirstenboschi R. Berndt & E. Uhlmann; P. othonnoides R. Berndt, A.R. Wood & E. Uhlmann; P. rapipes R. Berndt & E. Uhlmann; P. subindumentana R. Berndt; U. otholobii R. Berndt, A.R. Wood & E. Uhlmann and U. lotononidicola R. Berndt     

Pythium intermedium,a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems

Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.     

Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences

Lycium comprises approximately 70 species and is disjunctly distributed in temperate to subtropical regions in South America, North America, southern Africa, Eurasia, and Australia. Among them, only Lycium sandwicense A. Gray sporadically occurs widely on oceanic islands in the Pacific Ocean. To investigate phylogenetic and biogeographic relationships of the genus with emphasis on L. sandwicense, the coding region of matK, the two intergenic spacers trnT (UGU)-trnL (UAA) and trnL (UAA)-trnF (GAA), and the trnL (UAA) intron of chloroplast DNA (cpDNA) were sequenced. A strict consensus tree resulting from the phylogenetic analysis indicates the following: (1) New World species comprise a potentially paraphyletic assemblage; (2) southern African, Australian, and Eurasian species together are monophyletic; (3) southern African species are a paraphyletic assemblage; and (4) L. sandwicense is in a clade with certain New World species. The estimated biogeographic events based on the cpDNA analysis indicate that (1) Lycium originated in the New World, (2) all southern African, Australian, and Eurasian species have a common ancestor from the New World, (3) Australian and Eurasian species originated once from a southern African progenitor, and (4) L. sandwicense differentiated from the New World species.     

Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of Lycium chinense: A Traditional Chinese Medicinal Plant

Although Lycium chinense (goji berry) is an important traditional Chinese medicinal plant, little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species. To elucidate small RNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5’-RACE experiments. A total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (7 known and 5 novel) were fruit-specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that “metabolic pathways” is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit molecular biology. This study is the first, to detect known and novel miRNAs, and their potential targets, of L. chinense. The data and findings that are presented here might be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.     

Hemiuridae (Digenea) from marine fishes of the southern Indian Ocean: Genus Lecithochirium Lühe, 1901 (Lecithochiriinae)

The genus Lecithochirium is briefly discussed and a provisional key to species groups is presented. The following species are described, figured and/or recorded from regions of the southern Indian Ocean: Lecithochirium genypteri from Xiphiurus capensis, Cape Province; L. magnus from Gymnothorax woodwardi and G. javanicus, Western Australia; L. parafusiforme n. sp. from G. flavimarginatus, Natal (type-host and locality) and G. woodwardi, Western Australia; L. macrorchis from G. woodwardi; Leithochirium sp. (ghanense-group?) from Platycephalus bassensis, South Australia; L. kawakawa from Euthynnus affinis and Chrysoblephus anglicus, Natal; Lecithochirium sp. (synodi-group?) from Saurida undosquamis, Natal; L. gymnapisti n. sp. from Gymnapistes marmoratus, Western Australia; L. jaffense from Trachichthodes gerrardi, South Australia and Blennioclinus brachycephalus, Cape Province; Lecithochirium sp. (group unknown) from Alectis ciliaris, Natal.     

A new species of Leptobacillim,L. symbioticum,isolated from mites and sori of soybean rust

A verticillium-like fungus forming a whitish colony and mainly solitary phialides that produced fusiform to cylindrical conidia in chains was isolated from uredinia of Phakopsora pachyrhizi, a causal agent of soybean rust. In addition, two similar looking isolates were obtained from Prostigmata mites. Our taxonomic study based on morphology and phylogenetic analysis using ITS rDNA and LSU rDNA D1/D2 region sequences revealed that the three isolates were the same species and assigned to the genus Leptobacillium. These isolates represent a new species, morphologically and phylogenetically distinguished from the type species, L. leptobactrum, and we propose L. symbioticum sp. nov. In addition, Simplicillium chinense and S. coffeanum are assigned to the genus Leptobacillium.     

Non-detection of mycoviruses in amphibian chytrid fungus (Batrachochytrium dendrobatidis) from Australia

Mycoviruses may influence the pathogenicity of disease-causing fungi. Although mycoviruses have been found in some chytrid fungi, limited testing has not detected them in Batrachochytrium dendrobatidis (Bd), the cause of the devastating amphibian disease, chytridiomycosis. Here we conducted a survey for mycovirus presence in 38 Bd isolates from Australia (n = 31), Brazil (n = 5) and South Korea (n = 2) with a combination of modern high-throughput sequencing and conventional dsRNA cellulose chromatography. Mycoviruses were not detected in any isolates. This result was unexpected, given the long evolutionary history of Bd, as well as the high prevalence of mycoviruses in related fungal species. Given our widespread sampling in Australia and the limited number of Bd introductions, we suggest that mycoviruses are uncommon or absent from Australian Bd. Testing more isolates from regions where Bd originated, as well as regions with high diversity or low fungal virulence may identify mycoviruses that could aid in disease control.     

Genetic differentiation in Pyrenophora teres populations measured with AFLP markers

The genetic structure and occurrence of mating types and forms of Pyrenophora teres, the causal agent of net blotch on barley, was studied among 278 isolates collected from the northern hemisphere and from Australia. Genetic differentiation was high (F_CT 0.238, P = 0.002) between P. teres f. teres (PTT) isolates originating from Northern Europe, North America, Russia and Australia. The P. teres population in Australia was clearly divided into two subgroups (F_CT 0.793, P < 0.001) according to the form identity: PTT and P. teres f. maculata (PTM), with the PTT samples showing a greater degree of differentiation (F_ST 0.573, P < 0.001) among Australian states than the PTM samples (F_CT 0.219, P < 0.001). No differentiation was found among locations within Australian states. Both mating types (MAT1 and MAT2) were equally common (1:1) in several locations in Australia and in Finland. The only exception was Krasnodar, Russia, where only MAT2 was identified. Our results show that the prevalence of sexual reproduction, occurrence of forms of P. teres, and genetic differentiation between geographical regions are highly variable. The paper discusses the various effects and outcomes of population selection in Australia and in the northern barley growing regions.     

Genetic diversity and specialisation of Eudarluca caricis on some graminaceous Puccinia species

Eudarluca caricis is a common hyperparasite of rusts. A total of 100 cultures were isolated from six Puccinia species or forms growing on 10 species of British grasses at two sites approximately 3 km apart. 82 isolates collected in 2005 were partially sequenced at the ITS locus, and amplified fragment length polymorphism profiles generated for 86 isolates from 2005 and 12 from 2007. Partial ITS sequences of most isolates grouped closely, in a clade with previously reported graminaceous Puccinia isolates and a number of Melampsora isolates. A second clade was very distinct and contained mostly isolates from Puccinia poarum on Poa trivialis. All isolates had distinct AFLP haplotypes. The P. poarum isolates were very distinct from isolates collected from other rusts at the same site. Isolates from P. brachypodii f. sp. arrhenatheri growing on Arrhenatherum elatius in 2005 and 2007 at the same location were distinct (P < 0.001). Isolates from each rust or grass in one year and site were more similar than expected from overall variation between isolates (P < 0.001). Isolates from P. coronata on different grasses clustered together (with isolates from P. brachypodii f. sp. poae-nemoralis), suggesting partial host rust specialisation in E. caricis.     

Four Tulasnella taxa associated with populations of the Australian evergreen terrestrial orchid Cryptostylis ovata

Of the more than 400 indigenous orchid species in Western Australia, Cryptostylis ovata is the only species that retains its leaves all year round. It exists as a terrestrial herb and occasionally as an epiphyte in forested areas. Like all terrestrial orchids, C. ovata plants associate with mycorrhizal fungi, but their identities have not previously been investigated. Fungi were isolated from pelotons in rhizomes collected from three southern and two northern populations of C. ovata on six occasions over two years. Phylogenetic analysis of ITS sequences temporally and spatially revealed that all the fungal isolates were of Tulasnella species of four distinct groups. One Tulasnella group was present only in the three southern orchid populations, and it closely resembled T. prima isolates previously described from Chiloglottis sp. orchids from eastern Australia. Isolates collected from plants in the two northern populations were of three undescribed Tulasnella groups. Analysis of intra-group diversity using inter-simple sequence repeat markers revealed that plants were usually colonised by a single genotype of Tulasnella at each sampling period, and this genotype usually, but not always, persisted with the host plant over both years tested.     

Comparative floral morphology in Lycieae (Solanceae)

Comparative organography (excepting carpels studied previously) and anatomy of the flower are reported for some American members of the genera of Lyciaeae:Lycium, Grabowskia, andPhrodus. Data obtained are mostly new since no comprehensive floral anatomical work has been carried out in the tribe. These results include the first report of extrafloral nectaries on the inner epidermis of the calyx inPhrodus andGrabowskia. Results are discussed and compared with previous reports for the family, older than the exclusively AmericanPhrodus andGrabowskia. Lycium shows great morphological diversity while the other two genera are less variable but have more specialized features. A key, based on floral characters, to the genera, of Lycieae and sections ofLycium is provided.     

Psychrotolerant bacteria isolated from the leaf apoplast of cold-adapted wild plants improve the cold resistance of bean (Phaseolus vulgaris L.) under low temperature

We have isolated psychrotolerant bacteria from the leaf apoplast of cold-adapted wild plants and aimed to investigate their effect on the cold resistance of bean (Phaseolus vulgaris L.). Based on the findings of 16S rRNA gene sequence analysis, 20 isolates belonging to 5 bacteria species (Pseudomonas fragi, P. chloropaphis, P. fluorescens, P. proteolytica and Brevibacterium frigoritolerans) were identified in the leaf apoplastic fluid of Draba nemorosa, Galanthus gracilis, Colchicum speciousum, Scilla siberica, Erodium cicutarium, respectively. We have determined that 6 of the 20 isolates have exhibited ACC (1-aminocyclopropane-1-carboxylate) deaminase activity and secreted different extracellular proteins under cold condition (+4 °C) compared to normal growth condition (28 °C). The six isolates were then inoculated independently of each other to the leaves of 10-day-old bean seedlings growing under normal conditions (25/22 °C, 16/8 h photoperiod), and the inoculated and uninoculated (control) seedlings were transferred to cold (9/5 °C, 16/8 h photoperiod) for 3 days. The bacterial inoculations have decreased freezing injury, ice nucleating activity and lipid peroxidation content in parallel with the decrease of reactive oxygen species level such as O₂^.- and H₂O₂ in the inoculated seedlings compared to the control. In addition, the inoculations of the isolates have stimulated the activity of apoplastic antioxidant enzymes including superoxide dismutase, catalase, peroxidase, and glutathione reductase. The results show that the inoculations improve the cold resistance of bean seedlings and the psychrotolerant bacterial isolates can be evaluated within the group of plant growth promoting bacteria (PGPB) which can increase tolerance of cold-sensitive crops.     

Variation in fruit sugar composition of Lycium barbarum L. and Lycium chinense Mill. of different regions and varieties

In this study, the contents of fructose, glucose, sucrose, Lycium barbarum polysaccharide (LBP) and total sugar were determined in the fruits of different cultivated varieties of L. barbarum and of the congeneric species Lycium chinense from different regions. The results showed that the sugar accumulated mainly in the form of hexoses (glucose & fructose). Significant correlations among metabolism-related sugars, LBP and total sugar in the fruit of Ningqi No.1 implied the important role of sugar metabolism in the syntheses of LBP and total sugar. The LBP content of Ningqi No.1 in Ningxia region was the highest among all the cultivated varieties and species. The sugar accumulation was significantly affected by ecological factors such as HCO₃⁻, Na⁺, Ca²⁺, Mg²⁺ and Cl⁻ in soil total salt, pH, soil organic matter and available nitrogen. These findings have profound implications for proper fertilization management and any attempt to grow L. barbarum in new sites.     

Identification of Fungi in the Botryosphaeriaceae Family Associated with Stem Blight of Vaccinium spp. in the Southeastern United States

Stem blight is a major disease of blueberry caused by Botryosphaeriaceae fungi. Chemical and cultural management options are limited, putting emphasis on breeding efforts to identify sources of resistance. The efficacy and durability of host resistance could be impacted by the species composition of the pathogen population in a region and by the isolates employed in the screenings used to identify the resistance. Samples (365) were collected from southern highbush (SHB) and rabbiteye blueberry (REB) cultivars from 28 sites in the southeastern US (AL, FL, GA, NC, and SC). Colony morphology identified 86% of the isolates as Botryosphaeriaceae. Conidia morphology and Maximum Likelihood analysis of the Internal Transcribed Spacer rDNA regions (ITS), translation elongation factor one alpha (tef1-α), and β-tubulin were used to identify isolates at genera or species level. A PCR-restriction fragment length polymorphism (PCR-RFLP) test was used to identify isolates to genus. Neofusicoccum and Lasiodiplodia were the predominant genera. N. kwambonambiense, N. ribis, L. theobromae and L. pseudotheobromae were the most common species isolated. Phylogenies conducted with a limited number of isolates indicated non-clonal and potentially diverse populations occur on blueberry that warrant additional study. Botryosphaeria corticis, B. dothidea, and Diplodia seriata were isolated infrequently.     

Evolutionary insight into the Peripatopsis balfouri sensu lato species complex (Onychophora: Peripatopsidae) reveals novel lineages and zoogeographic patterning

Evolutionary relationships in the widely distributed velvet worm Peripatopsis balfouri sensu lato species complex were examined using DNA sequence data, gross and SEM morphology. Sequence data were generated for the COI mtDNA and the 18S rRNA loci and analysed using a Bayesian inference approach, maximum likelihood and maximum parsimony. Phylogenetic analyses of the combined DNA sequence data revealed that Peripatopsis clavigera specimens from the southern Cape (clade 1) was sister to P. balfouri sensu lato specimens from the Cederberg Mountains (clade 2). Within the main P. balfouri sensu lato species complex, three addition clades could be discerned (clades 3, 4 and 5). The obligatory troglobitic species Peripatopsis alba was equidistant between the Cape Peninsula and adjacent interior (clade 3) and the two Boland and Hottentots Holland Mountains (clades 4 and 5). On the Cape Peninsula, P. stelliporata specimens nested among the sympatric P. balfouri sensu lato specimens. The Cape Peninsula specimens were sister to specimens from Jonkershoek site 1, Kogelberg and Simonsberg. Two Boland clades were retrieved, comprising Du Toit's Kloof, Bain's Kloof and Mitchell's Pass and sister (in clade 4) to specimens from the Boland and adjacent Hottentots Holland Mountains in clade 5. These results revealed complex biogeographic patterning in the P. balfouri sensu lato species complex. The presence of sympatric, yet genetically discrete species pairs at six of the sample localities (Du Toit's Kloof, Simonsberg, Jonkershoek sites 1 and 2, Kogelberg and Landroskop) suggests that there is reproductive isolation between the lineages. Divergence time estimations suggest a Miocene/Pliocene/Pleistocene cladogenesis. A taxonomic revision of the P. balfouri sensu lato species complex was undertaken to stabilize the taxonomy. P. clavigera is monophyletic and retained for the southern Cape specimens, P. balfouri sensu stricto is now confined to the Cape Peninsula and adjacent interior, while P. stelliporata is regarded as a junior synonym of the latter taxon, P. alba is endemic to the Wynberg Cave systems on the Cape Peninsula. Three novel species (Peripatopsis cederbergiensis, sp. n., Peripatopsis bolandi sp. n. and Peripatopsis purpureus, sp. n.) are described.