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Supplementary material 6 from: Hannunen S, Tuomola J (2020) Assessing the probability of freedom from pine wood nematode based on 19 years of surveys. NeoBiota 58: 75-106. https://doi.org/10.3897/neobiota.58.38313
Probability_of_freedom_function.R
Supplementary material 1 from: Hannunen S, Tuomola J (2020) Assessing the probability of freedom from pine wood nematode based on 19 years of surveys. NeoBiota 58: 75-106. https://doi.org/10.3897/neobiota.58.38313
readme.txt
Supplementary material 2 from: Hannunen S, Tuomola J (2020) Assessing the probability of freedom from pine wood nematode based on 19 years of surveys. NeoBiota 58: 75-106. https://doi.org/10.3897/neobiota.58.38313
Sensitivity.R
Data on the Finnish pine wood nematode surveys 2000-2018
<p>These files contain the data needed for assessing the confidence in pest freedom gained in the Finnish pine wood nematode (PWN) surveys in 2000-2018 using the FinnSURV-Assess PWN application.</p> <p>The contents of the files are the following:</p> <ul> <li>1.1_N_inspected_sites_wood_FI.csv: The number of inspected sites in the wood sampling component of the survey</li> <li>1.2_N_inspected_sites_Monochamus_FI.csv: The number of inspected sites in the <em>Monochamus</em> trapping component of the survey</li> <li>1.2_n_samples_per_inspected_site_Monochamus_FI.csv: The number of samples per inspected site in the <em>Monochamus</em> trapping component of the survey</li> <li>1.3_Area_with_host_plants_FI.csv: The area covered with PWN host plants within the area for which the results of the surveys will be generalized, km<sup>2</sup></li> <li>1.4_Area_of_entry_sites_FI.csv: The area of sites in with elevated probability of PWN introduction, i.e. harbors, industrial areas and landfills, km<sup>2</sup></li> </ul> <p>In all the files, the first row has the names of the regions included and the first column has the years considered, and the data in the table is arranged accordingly.</p>
Translocation experiment reveals capacity for mountain pine beetle persistence under climate warming
<p>Predicting species response to climate change is a central challenge in ecology, particularly for species that inhabit large geographic areas. The mountain pine beetle (MPB) is a significant tree mortality agent in western North America with a distribution limited by climate. Recent warming has caused large-scale MPB population outbreaks within its historical distribution, in addition to migration northward in western Canada. The relative roles of genetic and environmental sources of variation governing MPB capacity to persist-in-place in a changing climate, and the migratory potential at its southern range edge in the United States, have not been investigated. We reciprocally translocated MPB populations taken from the core and southern edge of their range, and simultaneously translocated both populations to a warmer, low-elevation site near the southern range boundary where MPB activity has historically been absent despite suitable hosts. We found genetic variability and extensive plasticity in multiple fitness traits that would allow both populations to persist in a warming climate that resembles the thermal regime of our low-elevation site. We demonstrate, for the first time, that supercooling points in MPBs are influenced both by genetic and environmental factors. Both populations reproduced with seasonally appropriate univoltine generation times at all translocated sites, and bivoltinism was not observed. The highest reproductive success occurred at the warmest, out-of-range low-elevation site, suggesting that southward migration may not be temperature-limited.</p>
Figure 2 from: Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A (2020) Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys 73: 87-108. https://doi.org/10.3897/mycokeys.73.53028
Figure 2 Morphological differences between Caliciopsis moriondi and C. pineaA–CCaliciopsis moriondi: A four-week-old colonies grown at 20 °C on MEA B, C ascomata growing from a canker of Pinus radiataD–FCaliciopsis pinea: D four-week-old colonies grown at 20 °C on MEA E, F ascomata growing from a canker of P. radiata.
Supplementary material 1 from: Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A (2020) Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys 73: 87-108. https://doi.org/10.3897/mycokeys.73.53028
Figure S1. One of the most parsimonious trees from EF1-α sequence datasets
Figure 1 from: Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A (2020) Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys 73: 87-108. https://doi.org/10.3897/mycokeys.73.53028
Figure 1 Caliciopsis moriondi structures A cankers on a Pinus radiata trunk B–D ascomata growing from a canker B image of C. pinea ascigerous columns from an archive of 1970 (provided by Prof. Paolo Capretti) E–G asci H ascospores I ascigerous, terminal portion L four weeks colony grown at 20 °C on MEA. Scale bars: 2.5 µm (F–H), 5 µm (I).
Figure 5 from: Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A (2020) Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys 73: 87-108. https://doi.org/10.3897/mycokeys.73.53028
Figure 5 Polymorphic nucleotides from aligned sequence data of ITS, EF1-α and Bt1 loci showing the variation between isolates of Caliciopsis pinea from US and isolates of C. moriondi from the US and EU. Different colours demark variation in bases found in the sequences. Variation type is reported in the bottom part: "Sb" is the abbreviation for base's substitution; "In" is the abbreviation for base's insertion. Fix polymorphisms are signalled with "/". Sequences US232b, US67 and IT1 are respectively marked with *1, *2, *3 as representative for the following groups of sequences not reported in the figure: *1 (US151, US199, US238, US240, US232b); *2 (US52, US100, US81, US110, US149, US161, US163, US167, US172, US206, US220, US225a, US230d, US234a, US252); *3 (IT2, IT4, IT5, IT6, IT7, IT9, IT11, IT13, IT14, IT15, IT20, IT22, US66, US65)
Figure 4 from: Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A (2020) Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys 73: 87-108. https://doi.org/10.3897/mycokeys.73.53028
Figure 4 One of the most parsimonious trees of aligned ITS dataset (length = 168, CI = 0.721154, RI = 0.922043, RC = 0.762881, HI = 0.664935). The MP and Bayesian posterior probability are indicated next to the branches.
Supplementary material 2 from: Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A (2020) Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys 73: 87-108. https://doi.org/10.3897/mycokeys.73.53028
Figure S2. One of the most parsimonious trees from Bt1 sequence datasets
Figure 3 from: Migliorini D, Luchi N, Pepori AL, Pecori F, Aglietti C, Maccioni F, Munck I, Wyka S, Broders K, Wingfield MJ, Santini A (2020) Caliciopsis moriondi, a new species for a fungus long confused with the pine pathogen C. pinea. MycoKeys 73: 87-108. https://doi.org/10.3897/mycokeys.73.53028
Figure 3 One of the most parsimonious trees (length = 137) from the combined sequence datasets of the ITS rDNA, Bt1 and EF1-α loci is shown (CI = 0.9444, RI = 0.99633, RC = 0.98178, HI = 0.94098). MP bootstraps and Bayesian posterior probabilities are indicated alongside the branches. C. pseudotsugae and C. orientalisEF1-α were selected as outgroup taxa.
From refugia to contact: pine processionary moth hybrid zone in a complex biogeographic setting
<p class="MsoCommentText">Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyse their co-occurrence and hybridisation patterns in this biogeographical context.</p> <p class="MsoCommentText">We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals.</p> <p class="MsoCommentText">We confirmed the parapatric distribution of <i>Thaumetopoea</i><i> pityocampa </i>(Lepidoptera: Notodontidae) in the west and <i>T. wilkinsoni </i>in the east and identified a narrow contact zone. We identified several glacial refugia of <i>T. wilkinsoni</i> in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, <i>T. pityocampa</i> crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in north-western Turkey, but we did not identify any F<sub>1</sub> individuals. The identified hybrid zone was mostly bimodal.</p> <p>The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. <i>Thaumetopoea pityocampa</i> and <i>T. wilkinsoni</i> survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of<i> T. wilkinsoni</i> constrained <i>T. pityocampa</i> to the western Turkish shore. Additionally, we found evidence of recurrent introgression by <i>T. wilkinsoni</i> males in several <i>T. pityocampa</i> populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.</p>
Data from: Cross-species transferability of SSR loci developed from transcriptome sequencing in lodgepole pine
With the advent of next generation sequencing technologies, transcriptome level sequence collections are arising as prominent resources for the discovery of gene-based molecular markers. In a previous study more than 15 000 simple sequence repeats (SSRs) in expressed sequence tag (EST) sequences resulting from 454 pyrosequencing of Pinus contorta cDNA were identified. From these we developed PCR primers for approximately 4000 candidate SSRs. Here, we tested 184 of these SSRs for successful amplification across P. contorta and eight other pine species and examined patterns of polymorphism and allelic variability for a subset of these SSRs. Cross-species transferability was high, with high percentages of loci producing PCR products in all species tested. In addition, 50% of the loci we screened across panels of individuals from three of these species were polymorphic and allelically diverse. We examined levels of diversity in a subset of these SSRs by collecting genotypic data across several populations of Pinus ponderosa in northern Wyoming. Our results indicate the utility of mining pyrosequenced EST collections for gene-based SSRs and provide a source of molecular markers that should bolster evolutionary genetic investigations across the genus Pinus.
Data from: Novel interactions between non-native mammals and fungi facilitate establishment of invasive pines
1. The role of novel ecological interactions between mammals, fungi and plants in invaded ecosystems remains unresolved, but may play a key role in the widespread successful invasion of pines and their ectomycorrhizal fungal associates, even where mammal faunas originate from different continents to trees and fungi as in New Zealand. 2. We examine the role of novel mammal associations in dispersal of ectomycorrhizal fungal inoculum of North American pines (Pinus contorta, Pseudotsuga menziesii), and native beech trees (Lophozonia menziesii) using faecal analyses, video monitoring and a bioassay experiment. 3. Both European red deer (Cervus elaphus) and Australian brushtail possum (Trichosurus vulpecula) pellets contained spores and DNA from a range of native and non-native ectomycorrhizal fungi. 4. Faecal pellets from both animals resulted in ectomycorrhizal infection of pine seedlings with fungal genera Rhizopogon and Suillus, but not with native fungi or the invasive fungus Amanita muscaria, despite video and DNA evidence of consumption of these fungi. 5. Native L. menziesii seedlings never developed any ectomycorrhizal infection from faecal pellet inoculation. 6. Synthesis. Our results show that introduced mammals from Australia and Europe facilitate the co-invasion of invasive North American trees and Northern Hemisphere fungi in New Zealand, while we find no evidence that introduced mammals benefit native trees or fungi. This novel tripartite 'invasional meltdown', comprising taxa from three kingdoms and three continents, highlights unforeseen consequences of global biotic homogenization.
Long-term logging residue loadings affect tree growth but not soil nutrients in lodgepole pine forests
<p>Both above- and below-ground characteristics are affected by logging residue loadings. Long-term monitoring of tree growth and soil nutrients was conducted. We found that tree growth but not soil nutrients were affected. There were dynamic relationships between tree growth and logging residue loadings.</p>
Data from: Parasites structuring ecological communities: the mistletoe footprint in Mediterranean pine forests
1. The capacity of parasitic plants in structuring natural communities is increasingly recognized. These plants can affect the structure, composition and productivity of plant communities by modifying the competitive balance between hosts and non-host species and by altering the quantity and quality of resources entering the soil. Despite the progress made in this field, there is still a lack of integrative studies showing the structuring capacity of parasitic plants in forest ecosystems, where their effect may be less detectable due to the long lifespan of the system. 2. In this study we evaluate the long-term impact of Viscum album subsp. austriacum on the woody-plant community of a Mediterranean pineland. This mistletoe remains several years on the same host, exerting long-lasting, spatially concentrated effects on community and ecosystem characteristics. Mistletoe concentrates zoochorous seeds and induces changes in the soil fertility and light availability beneath the canopy of parasitized trees, which have the potential to facilitate zoochorous-plant colonization, recruitment, and growth at the same time as it weakens the host. Here, we analyse whether mistletoe-driven changes could result in a nucleus of zoochorous woody plants nourished by the abundant organic detritus accumulated under the host. We also analyse whether mistletoe effects can expand after host death. 3. We selected unparasitized, parasitized, and dead parasitized Pinus nigra trees, in which we studied the joint effect of mistletoe-mediated changes in soil nutrient and light availability, with the seed rain, seed predation, seedling establishment, plant recruitment, and plant growth. Light- and soil-nutrient resources were greater under parasitized trees, and intensified after host death. The seed rain was maximum under parasitized trees, where seedling recruitment proved more likely. Sapling density, richness, and growth increased with the development of parasitism. 4. Our findings show that Viscum album exerts a strong and lasting impact on the structure and dynamics of Mediterranean pinelands, with parasitized trees acting as centres for the establishment and growth of colonizing fleshy-fruited woody species, which, over the long term, promote vegetation shifts by limiting dominant pine trees and facilitating less represented fleshy-fruited shrubs.
Data from: The critical role of local refugia in postglacial colonization of Chinese pine: joint inferences from DNA analyses, pollen records, and species distribution modeling
The importance of long-distance migration from low to high latitudes relative to local spread from northern refugia after the Last Glacial Maximum (LGM) remains a focus of debate for many temperate tree species. We assessed the dynamics of Chinese pine (Pinus tabulaeformis), a widespread species endemic to northern China, since the LGM by integrating cytoplasmic DNA data, mapped pollen records and ecological niche modeling. Genetic variation among 544 individuals from 50 populations spanning the entire natural species range revealed eight genetic clusters with distinct geographic distribution, indicating glacial lineages likely originating from multiple local microrefugia. Palynological evidence suggested that the northernmost part of the natural distribution originated from local postglacial spread. Niche modeling indicated high probability of the species being present in the area of the Loess Plateau and coastal areas north of the Yangtze River during the LGM. The three lines of evidence jointly suggest that the species persisted through the last glaciation in the mountains surrounding the Loess Plateau of northern China and that the current distribution of the species originated primarily from the spread of local refugial populations, instead of long-distance migration. These results cast doubt on the notion that Chinese pine migrated from areas south of the Yangtze River and underscore the importance of northern refugia.
Data from: Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)
Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life-history strategies as they influence the effective population size (Ne). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of Ne. An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among plant species. Here, we have estimated the distribution of deleterious fitness effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α) for 11 species of soft pines (subgenus Strobus) using DNA sequence data from 167 orthologous nuclear gene fragments. Most newly arising nonsynonymous mutations were inferred to be so strongly deleterious that they would rarely become fixed. Little evidence for long-term adaptive evolution was detected, as all 11 estimates for α were not significantly different from zero. Nucleotide diversity at synonymous sites, moreover, was strongly correlated with attributes of the DFE across species, thus illustrating a strong consistency with the expectations from the Nearly Neutral Theory of molecular evolution. Application of these patterns to genome-wide expectations for these species, however, was difficult as the loci chosen for analysis were a biased set of conserved loci which greatly influenced estimates of the DFE and α. This implies that genome-wide parameter estimates will need truly genome-wide data, so that many of existing patterns documented previously for forest trees (e.g. little evidence for signature of selection) may need revision.
Data from: Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae)
Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.
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