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Publication Open Access Implementing biosecurity in live plant trade networks : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2022) Marshall, MadelineNew Zealand faces unique challenges with regards to invasive species due to a high number of endemic species and correspondingly high risk for the decline of indigenous species as a result of invasive introductions. Many of these introductions have been facilitated by human mediated transport, which promotes long range movement of plants and associated pests and pathogens. The transportation of these invasive species to new environments can negatively affect native plants, crops, and industries reliant on plant production. In particular, live plant trade networks represent effective mediums to disseminate invasive species such as pathogens, pests, and weeds. The movement of live plants through professional nurseries and private retailers in New Zealand is yet to be fully investigated. Performing an assessment of contact structures derived from live plant trades can be used to prevent the introduction and spread of invasive species, thereby safeguarding both businesses and the environment. Network analysis provides suitable tools to study live plant trade systems, such as the bilateral plant nursery network, as well as the itinerary online sales network. Fundamental characteristics related to geographic distribution of plant sales (such as location of origin and destination) and key metrics related to plant product movement within live plant trade networks need to be examined in order to better understand the nature of this structure. This thesis addresses gaps in knowledge related to live plant trade in New Zealand by generating networks that characterise human-mediated movement of horticultural products. Subsequently, developing network models of such systems was used to determine their vulnerability to invasive species acquisition and spread. This was accomplished via the assessment of three live plant trade systems of particular relevance to New Zealand biosecurity. These studies thusly characterise the forestry nursery transport network, the initial incursion of the invasive plant pathogen myrtle rust (Austropuccinia psidii) into New Zealand, and plant sales facilitated by the New Zealand-based online retailer Trade Me. Firstly, assessment of the forestry nursery transport network described the movement of product from seed orchards to nurseries to plantation forests and the biosecurity protocols in place at forestry nurseries. This study identifies seed orchards as the point of production most likely to facilitate widespread dispersal of a pathogen through the industry. The second study system, assessment of the initial incursion of myrtle rust into New Zealand, characterises the sale of nursery plants from myrtle rust positive nurseries during the first three months of the incursion. These networks identified a lack of comprehensive record keeping at ornamental nurseries as a risk for future invasions that are facilitated by contaminated nursery stock. Additionally, assessment of all myrtle rust positive locations during the first two years of the incursion identified delimiting surveys as a highly successful surveillance tool that would benefit from more research into optimisation of the survey radius depending on the nature of the invasive. The third and final study system, which characterised plant sales facilitated by Trade Me, employed the networking of plant sales based on their subcategorisation on the Trade Me site (into one of nine subcategories chosen by Trade Me) as well as the suburb of residence for both the seller and buyer of a product. Additionally, an assessment of the most common taxa sold on the site was conducted. The information derived from this study can be adopted for immediate use in biosecurity responses in the event of an introduction of an unwanted pest or pathogen vectored on ornamental plants, as well as identify the plant product classes at highest risk for long-distance dispersal.Publication Open Access Seed treatment options for New Zealand carrot production : A thesis submitted in partial fulfilment of the requirements for the Degree of Master at Lincoln University(Lincoln University, 2023) Spencer, EdwinThe New Zealand carrot industry currently uses fungicide seed coatings, rather than using some of the biological options available for disease control. The industry standard seed treatment has been in use since at least 2008. This research had the aim of comparing the current seed treatment with a pre-commercial biological (Trichoderma) seed treatment under a variety of conditions to determine the best approach. Data were gathered to show the effects of the various seed treatments on the carrots’ emergence, harvest weights, disease severity, and storage ability. A total of four experiments were conducted, two in the field and two in the glasshouse. A further experiment assessed the effects of all the pesticides applied to the crop or seed on Trichoderma conidia germination. A field trial was established in a commercial crop at Waiuku with five different seed treatments, including the combination of chemical and biological seed treatments. Unfortunately, due to covid restrictions, no data could be gathered until final carrot harvest, and harvested carrots were used in a cool store based storage trial. The Trichoderma alone treatment significantly increased yield over the industry standard seed treatment but there was no difference in storage performance among the treatments. A second field trial at Lincoln compared between chemical and Trichoderma seed treatments and untreated seed. These carrots were grown at a site known to contain soil-borne pathogens, and the crop received no pesticide applications. The aim was to investigate whether Trichoderma could provide long term disease control and increase marketable carrot yield. The carrots were also ground stored for a month after harvest to further test any long term disease suppression. However no significant differences were recorded among the treatments for any of the parameters measured. The glasshouse trials used soil from major carrot growing areas of New Zealand and looked at how chemicals and Trichoderma could help reduce the impact of the pathogens present compared to untreated seed. Additional data related to growth promotion such as foliage, taproot, and fine root weight were also recorded. Both trials tended to show that both the Trichoderma and chemical seed treatment had comparable performance in emergence and disease control and that this exceeded that of untreated seed. No growth promotion effects were recorded based on the dry weights of the foliage, taproots, or fine roots. To test Trichoderma conidia germination in the presence of pesticides, conidia were incubated at 25°C in the presence of pesticides at label rate concentrations. Glyphosate, difenoconazole, and mancozeb completely inhibited conidia germination but the seed treatment fungicides did not. Overall the results suggest that, under the conditions used, a Trichoderma seed treatment had a similar performance to the commonly used fungicide seed treatment. There was no best seed treatment in this study, but more options have been identified. The results in glasshouse conditions were not replicated in the field. The results also suggest that this strain of Trichoderma did not provide long term disease control, or promote carrot growth. The compatibility results showed that these strains of Trichoderma are sensitive to some pesticides but they are pesticides that are unlikely to come into direct contact with the conidia. The seed treatment fungicides did not affect conidial germination.Publication Open Access Preadaptation, hybridisation, and breeding system shape the invasion of three Rumex species in New Zealand : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2022) Savinen, Sandra ElisabetResearch has previously shown that Rumex (Polygonaceae) species introduced to New Zealand have multiple potential drivers behind their success, such as phenotypic plasticity, enemy release, and niche shift. However, it is not known whether these changes were caused by post-introduction evolution, or what other drivers could explain the success of these agricultural weeds. I combined demo-genetic traits and processes to assess how hybridisation and introgression, genetic differentiation, and breeding system contribute to the invasiveness of three introduced Rumex species. I compared plants from the species’ native (Europe, mainly the UK) and introduced (New Zealand) range and assessed whether the success is more likely due to prior adaptation or post-introduction evolution. Ploidy is associated with increased invasiveness, and if a species has multiple geo-cytotypes, higher ploidies are often found within the introduced range. Similarly, self-compatibility can help introduced populations to counter mate limitation and mixed mating can introduce new alleles to populations. I found no differences in genome sizes or chromosome numbers between plants from the two ranges using flow cytometry and manual chromosome counts. In addition, a comparison between bagged and unbagged Rumex conglomeratus plants showed no consequences from selfing, indicating mixed mating strategies. Surprisingly, the overall seed viability was lower for provenances from the introduced range compared to the native range. Hybridisation and introgression can increase genetic variation and help with adaptation to new environments. In a field survey, hybrid plants were found in New Zealand. However, the majority were likely first-generation hybrids, making introgression an unlikely driver behind the invasiveness. In addition, the parent species co-occurrence was lower in New Zealand compared to the UK. Lastly, genetic differentiation can indicate the origin of the introduction, as well as how likely a post-introduction evolution is a driver behind the invasiveness. A minimal differentiation was revealed by genotyping-by-sequencing both within but also between the native and introduced ranges. The population genetic analyses suggest that the UK is a likely origin for these species but admixture from elsewhere was also found. This would have likely helped the introduced populations to maintain comparable level of genetic variation to the native populations. As limited differences were found between the native and introduced populations, the investigated traits and processes are unlikely to explain the invasiveness in New Zealand. Rather, the success of these species is likely caused by prior adaptation. In addition, as these species are primarily agricultural weeds within both provenances, anthropogenically induced adaptation to invade is likely the main driver behind the success of these species. This method of adaptation, likely coupled with jack-of-all-trades genotypes, have allowed the species to thrive in manmade habitats, all around the globe. Thus, similar weeds within these habitats need to be carefully monitored to prevent further invasions in the future.Publication Open Access Purification of high-molecular-weight antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates(Multidisciplinary Digital Publishing Institute (MDPI), 2022-10) Babar, TK; Glare, Travis; Hampton, John; Hurst, MRH; Narciso, JO; Beattie, ABrevibacillus laterosporus (Bl) is a Gram-positive and spore-forming bacterium belonging to the Brevibacillus brevis phylogenetic cluster. Globally, insect pathogenic strains of the bacterium have been isolated, characterised, and some activities have been patented. Two isolates, Bl 1821L and Bl 1951, exhibiting pathogenicity against the diamondback moth and mosquitoes, are under development as a biopesticide in New Zealand. However, due to the suspected activity of putative antibacterial proteins (ABPs), the endemic isolates often grow erratically. Various purification methods, including size exclusion chromatography, sucrose density gradient centrifugation, polyethylene glycol precipitation, and ammonium sulphate precipitation employed in this study, enabled the isolation of two putative antibacterial proteins of ∼30 and ∼48 kD from Bl 1821L and one putative antibacterial protein of ∼30 kD from Bl 1951. Purification of the uninduced cultures of Bl 1821L and Bl 1951 also yielded protein bands of ∼30 and ∼48 kD on SDS-PAGE, which indicated their spontaneous induction. A disc diffusion assay was used to determine the antagonistic activities of the putative ABPs. Subsequent transmission electron microscope (TEM) examination of a purified putative antibacterial protein-containing solution showed the presence of encapsulin (∼30 kD) and polysheath (∼48 kD)-like structures. Although only the ∼30 kD protein was purified from Bl 1951, both structures were seen in this strain under TEM. Furthermore, while assessing the antibacterial activity of some fractions of Bl 1951 against Bl 1821L in the size exclusion chromatography method, the population of Bl 1821L persister cells was noted. Overall, this work added a wealth of knowledge about the purification of the high-molecular-weight (HMW) proteins (bacteriocins) of Gram-positive bacteria including Bl.Publication Open Access Purification of high molecular-weight antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates(MDPI, 2022-08-29) Babar, TK; Glare, Travis; Hampton, John; Hurst, MRH; Narciso, JO; Beattie, ABrevibacillus laterosporus (Bl) is a Gram-positive and spore-forming bacterium belonging to the Brevibacillus brevis phylogenetic cluster. Globally, insect pathogenic strains of the bacterium have been isolated, characterised, and some activities patented. Two isolates, Bl 1821L and Bl 1951, exhibiting pathogenicity against the diamondback moth and mosquitoes, are under development as a biopesticide in New Zealand. However, due to the suspected activity of putative antibacterial proteins (ABPs), the endemic isolates often grow erratically. Various purification methods including size exclusion chromatography, sucrose density gradient centrifugation, polyethylene glycol precipitation, and ammonium sulphate precipitation employed in this study enabled the isolation of two putative antibacterial proteins of ~30 kD and ~48 kD from Bl 1821L and one putative antibacterial protein of ~30 kD from Bl 1951. Purification of the uninduced cultures of Bl 1821L and Bl 1951 also yielded the protein bands of ~30 kD and ~48 kD on SDS-PAGE which indicated their spontaneous induction. Disc diffusion assay was used to determine the antagonistic activities of the putative ABPs. Subsequent transmission electron microscope (TEM) examination of purified putative antibacterial protein-containing solution showed the presence of encapsulin (~30 kD) and polysheath (~48 kD) like structures. Although only the ~30 kD protein was purified from Bl 1951, both structures were seen in this strain under TEM. Furthermore, while assessing the antibacterial activity of some fractions of Bl 1951 against Bl 1821L in size exclusion chromatography method, population of Bl 1821L persister cells was noted. Overall, this work added a wealth of knowledge for the purification of the HMW proteins (bacteriocins) of the Gram-positive bacteria including Bl.Publication Open Access Isolation, purification, and characterisation of a phage tail-like bacteriocin from the insect pathogenic bacterium Brevibacillus laterosporus(Multidisciplinary Digital Publishing Institute (MDPI), 2022-08) Babar, TK; Glare, Travis; Hampton, John; Hurst, MRH; Narciso, JOThe Gram-positive and spore-forming bacterium Brevibacillus laterosporus (Bl) belongs to the Brevibacillus brevis phylogenetic cluster. Isolates of the species have demonstrated pesticidal potency against a wide range of invertebrate pests and plant diseases. Two New Zealand isolates, Bl 1821L and Bl 1951, are under development as biopesticides for control of diamondback moth and other pests. However, due to the often-restricted growth of these endemic isolates, production can be an issue. Based on the previous work, it was hypothesised that the putative phages might be involved. During investigations of the cause of the disrupted growth, electron micrographs of crude lysate of Bl 1821L showed the presence of phages’ tail-like structures. A soft agar overlay method with PEG 8000 precipitation was used to differentiate between the antagonistic activity of the putative phage and phage tail-like structures (bacteriocins). Assay tests authenticated the absence of putative phage activity. Using the same method, broad-spectrum antibacterial activity of Bl 1821L lysate against several Gram-positive bacteria was found. SDS-PAGE of sucrose density gradient purified and 10 kD MWCO concentrated lysate showed a prominent protein band of ∼48 kD, and transmission electron microscopy revealed the presence of polysheath-like structures. N-terminal sequencing of the ∼48 kD protein mapped to a gene with weak predicted amino acid homology to a Bacillus PBSX phage-like element xkdK, the translated product of which shared >90% amino acid similarity to the phage tail-sheath protein of another Bl published genome, LMG15441. Bioinformatic analysis also identified an xkdK homolog in the Bl 1951 genome. However, genome comparison of the region around the xkdK gene between Bl 1821L and Bl 1951 found differences including two glycine rich protein encoding genes which contain imperfect repeats (1700 bp) in Bl 1951, while a putative phage region resides in the analogous Bl 1821L region. Although comparative analysis of the genomic organisation of Bl 1821L and Bl 1951 PBSX-like region with the defective phages PBSX, PBSZ, and PBP 180 of Bacillus subtilis isolates 168 and W23, and Bacillus phage PBP180 revealed low amino acids similarity, the genes encode similar functional proteins in similar arrangements, including phage tail-sheath (XkdK), tail (XkdO), holin (XhlB), and N-acetylmuramoyl-L-alanine (XlyA). AMPA analysis identified a bactericidal stretch of 13 amino acids in the ∼48 kD sequenced protein of Bl 1821L. Antagonistic activity of the purified ∼48 kD phage tail-like protein in the assays differed remarkably from the crude lysate by causing a decrease of 34.2% in the number of viable cells of Bl 1951, 18 h after treatment as compared to the control. Overall, the identified inducible phage tail-like particle is likely to have implications for the in vitro growth of the insect pathogenic isolate Bl 1821L.Publication Open Access Global assessment of three Rumex species reveals inconsistent climatic niche shifts across multiple introduced ranges(Springer Nature, 2022-08-16) Carlin, TF; Bufford, Jennifer; Hulme, Philip; Godsoe, WilliamClimatic niche shifts occur when species occupy different climates in the introduced range than in their native range. Climatic niche shifts are known to occur across a range of taxa, however we do not currently understand whether climatic niche shifts can consistently be predicted across multiple introduced ranges. Using three congeneric weed species, we investigate whether climatic niche shifts in one introduced range are consistent in other ranges where the species has been introduced. We compared the climatic conditions occupied by Rumex conglomeratus, R. crispus, and R. obtusifolius between their native range (Eurasia) and three different introduced ranges (North America, Australia, New Zealand). We considered metrics of niche overlap, expansion, unfilling, pioneering, and similarity to determine whether climatic niche shifts were consistent across ranges and congeners. We found that the presence and direction of climatic niche shifts was inconsistent between introduced ranges for each species. Within an introduced range, however, niche shifts were qualitatively similar among species. North America and New Zealand experienced diverging niche expansion into drier and wetter climates respectively, whilst the niche was conserved in Australia. This work highlights how unique characteristics of an introduced range and local introduction history can drive different niche shifts, and that comparisons between only the native and one introduced range may misrepresent a species’ capacity for niche shifts. However, predictions of climatic niche shifts could be improved by comparing related species in the introduced range rather than relying on the occupied environments of the native range.Publication Open Access Multi-scenario species distribution modeling(MDPI, 2019-03) Senay, SD; Worner, SPCorrelative species distribution models (SDMs) are increasingly being used to predict suitable insect habitats. There is also much criticism of prediction discrepancies among different SDMs for the same species and the lack of effective communication about SDM prediction uncertainty. In this paper, we undertook a factorial study to investigate the effects of various modeling components (species-training-datasets, predictor variables, dimension-reduction methods, and model types) on the accuracy of SDM predictions, with the aim of identifying sources of discrepancy and uncertainty. We found that model type was the major factor causing variation in species-distribution predictions among the various modeling components tested. We also found that different combinations of modeling components could significantly increase or decrease the performance of a model. This result indicated the importance of keeping modeling components constant for comparing a given SDM result. With all modeling components, constant, machine-learning models seem to outperform other model types. We also found that, on average, the Hierarchical Non-Linear Principal Components Analysis dimension-reduction method improved model performance more than other methods tested. We also found that the widely used confusion-matrix-based model-performance indices such as the area under the receiving operating characteristic curve (AUC), sensitivity, and Kappa do not necessarily help select the best model from a set of models if variation in performance is not large. To conclude, model result discrepancies do not necessarily suggest lack of robustness in correlative modeling as they can also occur due to inappropriate selection of modeling components. In addition, more research on model performance evaluation is required for developing robust and sensitive model evaluation methods. Undertaking multi-scenario species-distribution modeling, where possible, is likely to mitigate errors arising from inappropriate modeling components selection, and provide end users with better information on the resulting model prediction uncertainty.Publication Open Access Quantifying the risk of non‐native conifer establishment across heterogeneous landscapes(Wiley on behalf of British Ecological Society, 2022-06) Wyse, Sarah; Etherington, TR; Hulme, Philip1. Pines (genus Pinus) are cultivated extensively for forestry purposes, particularly in regions that are outside the genus' native range. The most common forestry species are also typically those most likely to escape cultivation and spread rapidly, and thus pines constitute a substantial weed problem in many regions. However, there is limited knowledge of the factors underlying the spread of pines from plantations. Assessments across heterogeneous landscapes are required to provide rigorous data to support management tools and policies aiming to protect vulnerable ecosystems from pine invasions. 2. We examined the spread of Pinus radiata from forestry plantations over a ~9,000 km² landscape on Banks Peninsula, New Zealand. We used ground-based surveys from a set of viewpoints to determine tree locations, coupled with geographical information system (GIS) viewsheds to define the area surveyed. We used boosted regression trees to build a habitat model for P. radiata establishment on Banks Peninsula. 3. We surveyed an area approximately 107 km², recording 470 naturally established P. radiata individuals. Our habitat models suggested that proximity to the nearest plantation forest was the most important variable predicting P. radiata establishment, with individuals most likely to establish within 150 m of a plantation. Individuals were also most likely to establish in early successional shrub communities, proximate to roads, and on steeper topography. Highly grazed habitats were least vulnerable to P. radiata establishment. 4. The slope and aspect of the source plantation influenced the distances from the plantation at which P. radiata individuals were recorded, with individuals recorded furthest away likely to have originated from plantations that were south-facing or on steeper slopes, and therefore most exposed to strong winds. 5. Synthesis and applications. Our findings on distances from plantations at which individuals established, vulnerable habitats, and the interactions we detected among our predictor variables, can be extended to aid management of non-native conifer plantings elsewhere in the Southern Hemisphere. These data can be used to contribute to improvements of decision support systems that assess likely spread risk from non-native conifer plantings. Such tools can reduce the likelihood of future pine establishment, potentially preventing biological invasions.Publication Open Access Assessment of seed production potential of Teosinte (Euchlaena mexicana) under varying agronomic management practices in the central region of Nepal : A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2021) Sanjyal, SunitaTeosinte (Euchlaena mexicana) is a popular summer herbage crop in Nepal. While it has good seed production potential, the management for seed production is unknown. A two year study was undertaken in order to investigate teosinte seed yield and seed quality for different sowing dates, seed sowing rates and cutting management in the Terai region of Nepal. A seed development, a genotypic diversity and an economic study were also conducted. There were four different sowing dates (30 March, 30 April, 30 May and 30 June), four seed rates (20, 40, 60 and 80 kgha-1) and three cutting management treatments (uncut, once cut and twice cut) arranged in a spilt split plot design. The only certified variety of teosinte in Nepal, Sirsa was used for the study. Herbage yield of teosinte was affected by sowing date, seed rate and cutting management. Maximum herbage yield (HY) and dry matter yield (DMY) from a teosinte crop grown for seed production was obtained from the 30 April sowing together with the 60 kgha-1 seed rate and two cuts. There was a positive correlation of plant height, tiller number, leaf number and leaf area index (LAI) with DMY. The effect of the environment on both teosinte herbage and seed yield was studied. Higher herbage and seed yield were produced from early sown teosinte because the longer growing season allowed the accumulation of higher growing degree days (GDD). Five critical growth stages of teosinte were identified. The temperature and GDD requirements for each growth stage were 26.1○C (135○C days), 26.0○C (2189○C days), 24.1○C (2442○C days), 20.4○C (3049○C days) and 17.2○C (3150○C days) for emergence stage (GS1), vegetative stage (GS2), flowering stage (GS3), seed development stage (GS4) and seed maturity stage (GS5) respectively. Maximum seed yield (kgha-1) was obtained from the two earlier sowings (30 March and 30 April) in both years because early sown plants were taller, and had higher LAI and more tillers and cobs per plant, ears per cob and seeds per ear than later sown plants. In 2017, there was a non-insignificant effect of seed rate on seed yield because of natural thinning of plants due to heavy rainfall and wind which caused lodging in the early vegetative stage, but in 2018 the two lower seed rates (20 and 40 kgha-1) produced the highest seed yield. For cutting management, seed yield was higher for uncut plants in both years. Seed quality was tested for seeds harvested from different sowing dates, seed rates, cutting management and cob position on the plant. Over the two seasons of trials, seed harvested from the 30 March sowing at the two lower seed rates (20 and 40 kgha-1) and uncut plants resulted in higher germination percentage and thousand seed weight (TSW) in both years. There was a significant negative correlation between the sowing dates and germination percentage and a negative correlation between sowing dates and TSW because germination percentage and TSW were reduced with each delay in sowing. There was a positive correlation between TSW and germination percentage for different sowing dates for all cobs in 2017 (R2 = 0.77) (P>0.05) and 2018 (R2 = 0.80) (P>0.05). Seed quality was also affected by the cob position on the plant. When seeds were hand harvested separately from top, middle and bottom positioned cobs, higher quality seeds (germination percentage and TSW) were obtained from seed harvested from the top positioned cobs. Teosinte seeds physiological maturity (PM) was attained at 59 days after anthesis. Harvesting teosinte seeds from the top and middle positioned cobs on the plant recovered 78% of the total seed yield, while that from the middle and the bottom positioned cobs recovered 57% of the total seed yield. Therefore harvesting mature seeds from the top and middle positioned cobs is recommended to minimize loss of quality seed from shattering which would occur if harvesting was delayed until seeds from the bottom cobs were mature. A diversity study of teosinte was conducted for 18 teosinte accessions, 17 from CYMMIT Mexico and Sirsa, to identify if any of the introduced accessions could perform better than Sirsa in terms of herbage yield, seed yield and time to seed maturation. Out of 17 accessions, accessions 5, 7 and 12 out yielded Sirsa in terms of herbage yield, seed yield and were earlier to maturity. This preliminary result suggest a possible source of material for developing new teosinte varieties in Nepal better suited for farmer’s needs, particularly to reduce the length of time required to grow a seed crop. A separate study was conducted on seven seed lots of teosinte collected from different regions of Nepal. Hier¬archical cluster analysis based using morphological charecteristics gave two distinct clusters; cluster I (Makwanpur) from the midhills and cluster II (Sarlahi, Mohattari, Bara, Chitwan, Gaughat and Tikapur) from across the southern Terai. These two clusters suggest an agro ecological differentiation for teosinte genotypes grown in Nepal. An economic analysis conducted based on the total costs and income from the different management in this research study showed that the highest gross margin was obtained from the March and the April sowings at the 20-60 kgha-1 seed rates and none or one cuts. Taking one herbage cut was not detrimental to a farmer’s gross margin for seed production.Publication Open Access Global guidelines for the sustainable use of non-native trees to prevent tree invasions and mitigate their negative impacts(Pensoft Publishers, 2020) Brundu, G; Pauchard, A; Pyšek, P; Pergl, J; Bindewald, AM; Brunori, A; Canavan, S; Campagnaro, T; Celesti-Grapow, L; de Sá Dechoum, M; Dufour-Dror, J-M; Essl, F; Flory, SL; Genovesi, P; Guarino, F; Guangzhe, L; Hulme, Philip; Jäger, H; Kettle, CJ; Krumm, F; Langdon, B; Lapin, K; Lozano, V; Le Roux, JJ; Novoa, A; Nuñez, MA; Porté, AJ; Silva, JS; Schaffner, U; Sitzia, T; Tanner, R; Tshidada, N; Vítková, M; Westergren, M; Wilson, JRU; Richardson, DMSustainably managed non-native trees deliver economic and societal benefits with limited risk of spread to adjoining areas. However, some plantations have launched invasions that cause substantial damage to biodiversity and ecosystem services, while others pose substantial threats of causing such impacts. The challenge is to maximise the benefits of non-native trees, while minimising negative impacts and preserving future benefits and options. A workshop was held in 2019 to develop global guidelines for the sustainable use of non-native trees, using the Council of Europe – Bern Convention Code of Conduct on Invasive Alien Trees as a starting point. The global guidelines consist of eight recommendations: 1) Use native trees, or non-invasive non-native trees, in preference to invasive non-native trees; 2) Be aware of and comply with international, national, and regional regulations concerning non-native trees; 3) Be aware of the risk of invasion and consider global change trends; 4) Design and adopt tailored practices for plantation site selection and silvicultural management; 5) Promote and implement early detection and rapid response programmes; 6) Design and adopt tailored practices for invasive non-native tree control, habitat restoration, and for dealing with highly modified ecosystems; 7) Engage with stakeholders on the risks posed by invasive non-native trees, the impacts caused, and the options for management; and 8) Develop and support global networks, collaborative research, and information sharing on native and non-native trees. The global guidelines are a first step towards building global consensus on the precautions that should be taken when introducing and planting non-native trees. They are voluntary and are intended to complement statutory requirements under international and national legislation. The application of the global guidelines and the achievement of their goals will help to conserve forest biodiversity, ensure sustainable forestry, and contribute to the achievement of several Sustainable Development Goals of the United Nations linked with forest biodiversity.Publication Open Access Projecting the continental accumulation of alien species through to 2050(Wiley, 2021-03) Seebens, H; Bacher, S; Blackburn, TM; Capinha, C; Dawson, W; Dullinger, S; Genovesi, P; Hulme, PE; van Kleunen, M; Kühn, I; Jeschke, JM; Lenzner, B; Liebhold, AM; Pattison, Z; Pergl, J; Pyšek, P; Winter, M; Essl, FBiological invasions have steadily increased over recent centuries. However, we still lack a clear expectation about future trends in alien species numbers. In particular, we do not know whether alien species will continue to accumulate in regional floras and faunas, or whether the pace of accumulation will decrease due to the depletion of native source pools. Here, we apply a new model to simulate future numbers of alien species based on estimated sizes of source pools and dynamics of historical invasions, assuming a continuation of processes in the future as observed in the past (a business-as-usual scenario). We first validated performance of different model versions by conducting a back-casting approach, therefore fitting the model to alien species numbers until 1950 and validating predictions on trends from 1950 to 2005. In a second step, we selected the best performing model that provided the most robust predictions to project trajectories of alien species numbers until 2050. Altogether, this resulted in 3,790 stochastic simulation runs for 38 taxon–continent combinations. We provide the first quantitative projections of future trajectories of alien species numbers for seven major taxonomic groups in eight continents, accounting for variation in sampling intensity and uncertainty in projections. Overall, established alien species numbers per continent were predicted to increase from 2005 to 2050 by 36%. Particularly, strong increases were projected for Europe in absolute (+2,543 ± 237 alien species) and relative terms, followed by Temperate Asia (+1,597 ± 197), Northern America (1,484 ± 74) and Southern America (1,391 ± 258). Among individual taxonomic groups, especially strong increases were projected for invertebrates globally. Declining (but still positive) rates were projected only for Australasia. Our projections provide a first baseline for the assessment of future developments of biological invasions, which will help to inform policies to contain the spread of alien species.Publication Open Access Combining laser rangefinder and viewshed technologies to improve ground surveys of invasive tree distributions(John Wiley & Sons Ltd on behalf of British Ecological Society, 2022-03) Wyse, Sarah; Hulme, Philip; Etherington, TR1. Quantifying the spatial extent, location and habitat associations of invasive tree species is critical to predict their future spread and prioritise areas for management. Species–environment relationship analyses are useful tools for understanding and predicting the potential geographical distribution of these species; however, such tools require rigorous and extensive data about species presence and, crucially, the area surveyed. 2. Here, we describe a method for performing ground-based visual surveys of invasive trees from a set of viewpoints that utilises laser rangefinder and global navigation satellite system (GNSS) technology to detect tree locations. We then highlight the novel use of geographical information system (GIS) viewsheds as a tool to define the area surveyed. 3. Using the invasive conifer, Pinus radiata, as our target, we undertook a ground-truthing exercise for 50 trees established in the wild to assess the accuracy of the method and determine the suitable spatial resolution for GIS data that would be used in subsequent species–environment relationship analyses. For these trees, location error was positively related to distance from the tree to the viewpoint. The calculated locations for all trees within 600 m of the observer were within 25 m of the location as determined by the GNSS unit, with a median location error of 4 m. These results indicate that data of a resolution suitable for mapping invasive trees can be efficiently collected over large areas. We also outline suggestions and instructions for computing the viewsheds to determine the surveyed area. 4. This approach allows for efficient collection of accurate data on the occurrence of non-native trees and the land area surveyed. These data can underpin species–environment relationship analyses that then form the basis of risk maps for areas prone to future invasion. Given the speed and accuracy with which data can be obtained using this method, and the use of standard and easily accessible field equipment and GIS software, we recommend this approach to other spatial and invasion ecologists.Publication Open Access A molecular approach to study Hymenoptera diets using wasp nests(Pensoft Publishers, 2020) Lefort, M-C; Beggs, JR; Glare, Travis; Saunders, TE; Doyle, EJ; Boyer, SThe study of animal diets has benefited from the rise of high-throughput DNA sequencing applied to stomach content or faecal samples. The latter can be fresh samples used to describe recent meals or older samples, which can provide information about past feeding activities. For most invertebrates, however, it is difficult to access ‘historical’ samples, due to the small size of the animals and the absence of permanent defecation sites. Therefore, sampling must be repeated to account for seasonal variation and to capture the overall diet of a species. This study develops a method to describe the overall diet of nest-building Hymenoptera, based on a single sampling event, by analysing prey DNA from faeces accumulated in brood cells. We collected 48 nests from two species of introduced paper wasps (Polistes chinensis Fabricius and P. humilis Fabricius) in the urban and peri-urban areas of Auckland, New Zealand and selected two samples per nest. One from brood cells in the outer layer of the nest to represent the most recent diet and one from brood cells in an inner layer to represent older diet. Diet differed between species, although both fed mainly on Thysanoptera, Lepidoptera and Acariformes. Prey taxa identified to species level included both agricultural pests and native species. Prey communities consumed were significantly different between inner and outer nest samples, suggesting seasonal variation in prey availability and/or a diversification of the wasps’ diet as the colony grows. We also show for the first time potential predation of marine organisms by Polistes wasps. Our study provides field evidence that Polistes wasps feed on agricultural pests, supporting the hypothesis that some social wasp species could have a suppressing effect on agricultural pests. The proposed methodology is readily applicable to other nest-building Hymenoptera and has the potential to provide comprehensive knowledge about their diet with minimum sampling effort. Such knowledge is essential to measure the ecological impact of invasive Vespidae and support the conservation of native invertebrate biodiversity.Publication Open Access The Epidemiological Framework for Biological Invasions (EFBI): An interdisciplinary foundation for the assessment of biosecurity threats(Pensoft Publishers, 2020-10-15) Hulme, Philip; Baker, R; Freckleton, R; Hails, RS; Hartley, M; Harwood, J; Marion, G; Smith, GC; Williamson, MEmerging microparasite (e.g. viruses, bacteria, protozoa and fungi) epidemics and the introduction of non-native pests and weeds are major biosecurity threats worldwide. The likelihood of these threats is often estimated from probabilities of their entry, establishment, spread and ease of prevention. If ecosystems are considered equivalent to hosts, then compartment disease models should provide a useful framework for understanding the processes that underpin non-native species invasions. To enable greater cross-fertilisation between these two disciplines, the Epidemiological Framework for Biological Invasions (EFBI) is developed that classifies ecosystems in relation to their invasion status: Susceptible, Exposed, Infectious and Resistant. These states are linked by transitions relating to transmission, latency and recovery. This viewpoint differs markedly from the species-centric approaches often applied to non-native species. It allows generalisations from epidemiology, such as the force of infection, the basic reproductive ratio R0, super-spreaders, herd immunity, cordon sanitaire and ring vaccination, to be discussed in the novel context of non-native species and helps identify important gaps in the study of biological invasions. The EFBI approach highlights several limitations inherent in current approaches to the study of biological invasions including: (i) the variance in non-native abundance across ecosystems is rarely reported; (ii) field data rarely (if ever) distinguish source from sink ecosystems; (iii) estimates of the susceptibility of ecosystems to invasion seldom account for differences in exposure to non-native species; and (iv) assessments of ecosystem susceptibility often confuse the processes that underpin patterns of spread within -and between- ecosystems. Using the invasion of lakes as a model, the EFBI approach is shown to present a new biosecurity perspective that takes account of ecosystem status and complements demographic models to deliver clearer insights into the dynamics of biological invasions at the landscape scale. It will help to identify whether management of the susceptibility of ecosystems, of the number of vectors, or of the diversity of pathways (for movement between ecosystems) is the best way of limiting or reversing the population growth of a non-native species. The framework can be adapted to incorporate increasing levels of complexity and realism and to provide insights into how to monitor, map and manage biological invasions more effectively.Publication Open Access Prospects for regenerative agriculture in Chile(Universidad Austral de Chile, 2019-08-30) Wratten, Stephen; Shields, Morgan; González-Chang, MA global perspective, why we need a greener agriculture? “I am a photosynthesis manager and an ecosystem service provider”. This profound statement was made by a Swedish farmer some years ago (Wratten, 2018). Few farmers describe their occupation in this way. However, there is a major body of work giving substantial evidence that current high-input farming (Figure 1) has no future without changes to its approach (Pretty et al., 2018). One reason for this view is that agriculture is one of the main causes of climate disturbance, largely driven by changes in land-use practices (Bennetzen et al., 2016). The main consequence has been biodiversity loss (Sala et al., 2000). A very worrying example of this is that human activities have made 60% of mammal, bird, fish and reptile species extinct since 1970, as consumption of food and resources by the global human population has de-stabilised the ‘web of life’ (Carrington and Watts, 2018). In more scientific language, we are losing ecosystem functions provided by nature at an alarming rate and with that, ecosystem (nature’s) services are declining rapidly. Examples are declines in pollination, predation of pests and soil services. The seriousness of these losses was recently reported by workers at the University of Sheffield, UK, who predicted that Britain has only 100 harvests remaining before that country’s soils are no longer suitable for growing crops (Dunnett, 2014).Publication Open Access Tolerance of Trichoderma isolates to forestry agrichemicals(2021-01) Whelan, HelenTwo Trichoderma isolate mixtures PR6 and PR3a show promise to enhance tree growth and suppress foliar disease in New Zealand’s most important forest species, radiata pine. Availability of one or both mixtures may lead to increased productivity, sustainability, and economic gain in the New Zealand forest industry. The successful integration of these biocontrol organisms into radiata pine production systems requires knowledge of their compatibility with commonly used pesticides and other products. The sensitivity of the eight isolates that comprise the PR6 and PR3a mixtures was determined in the presence of fifty-one agrichemicals (14 fungicides, 2 fumigants, 14 herbicides, 6 insecticides, 4 fertilisers, 5 adjuvants, 2 adherents, 3 biostimulants and 1 bird repellent) commonly used in New Zealand forestry. Sensitivity of these isolates to agrichemicals was determined by in-vitro laboratory studies (spore germination, colony mycelial growth and sporulation) and in-vivo greenhouse studies using containerised radiata pine seedlings. Agrichemicals had a range of effects on isolate development in laboratory studies (Table 1). However, the sensitivity of Trichoderma PR6 established in radiata pine roots, to the single application of agrichemicals at recommended rates, was minimal or nil (Table 1). In some experiments, root colonisation in seedlings was enhanced in the first month of growth when resident competitive fungal species may have been suppressed allowing the applied Trichoderma to dominate.Publication Open Access Bioprotection for foliar diseases and disorders of radiata pine: Project overview May 2020 to December 2021(2022-01) Whelan, HelenFoliar diseases and disorders are the most significant cause of economic loss for the New Zealand Forestry industry. To alleviate losses caused by existing diseases and to reduce potential impacts of biosecurity threats, ongoing work is being conducted to establish a long-term symbiotic relationship between Pinus radiata (radiata pine) and other forestry tree species, and a beneficial microbe, Trichoderma. Trichoderma fungi can induce a broad-spectrum activity response from their host plants, enhancing the speed and strength of the plant’s response to diseases. Trichoderma has also been shown to stimulate growth of plants. The products of this research project will be Trichoderma inoculated forestry tree species, with enhanced growth and improved foliar health, potential protection against biosecurity incursions, as well as reduced chemical application in nurseries and plantations.Publication Embargo Implementing the transparency and openness promotion guidelines for data and code to support computational reproducibility within the New Zealand Journal of Ecology(New Zealand Ecological Society, 2022) Etherington, T; Brock, J; Perry, G; Wyse, SarahThe New Zealand Journal of Ecology has chosen to implement Level 1 of the data and code TOP Guidelines as of January 2022; 46(1). The Level 1 requirements are that while there are no expectations to share data or code, authors will be required to be clear about the situation. Simply stating if data or code are openly available or not can be extremely helpful, as attempting to ascertain this fact directly from the authors can be difficult and time-consuming, given the rate at which corresponding author emails cease to function. By implementing this policy, the New Zealand Journal of Ecology aligns itself not only with other major journals in the field, but also the expectations of our community of authors who are already making their data and code openly available. While this new policy does not expect or require any data or code sharing, we wish to encourage the sharing of data and code, so that the New Zealand Journal of Ecology will be supporting scientific reproducibility and benefitting our authors.Publication Open Access Invasion science in South Africa: The definitive collection(Academy of Science of South Africa, 2021-01-29) Hulme, PhilipBiological invasions by alien pests, weeds and pathogens are a global phenomenon, with increasing impacts on the environment, economy and human health. Traditionally, the poster children of the impacts of biological invasions have been oceanic islands such as Hawai’i and New Zealand, with continental areas being viewed as less prone to the ravages of invasive alien species. Yet this perspective is rapidly changing as continental areas begin to address the threat of biological invasions. For over a decade, the DSI-NRF Centre of Excellence for Invasion Biology (CIB) in South Africa has played a leading role in this changing perspective through outstanding research to reduce the rates and biodiversity impacts of biological invasions by furthering scientific understanding and predictive capability. Now, the major advances in current understanding of biological invasions delivered by the many researchers affiliated to the CIB have been captured in an encyclopaedic volume entitled Biological Invasions in South Africa.